0s autopkgtest [21:41:22]: starting date and time: 2024-11-23 21:41:22+0000 0s autopkgtest [21:41:22]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [21:41:22]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.cs9lcqd9/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:openmpi --apt-upgrade gromacs --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=openmpi/5.0.5-6 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-7.secgroup --name adt-plucky-amd64-gromacs-20241123-203113-juju-7f2275-prod-proposed-migration-environment-2-69eb2531-1e49-4dd4-85e1-0a930b460086 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 39s autopkgtest [21:42:01]: testbed dpkg architecture: amd64 39s autopkgtest [21:42:01]: testbed apt version: 2.9.8 39s autopkgtest [21:42:01]: @@@@@@@@@@@@@@@@@@@@ test bed setup 39s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 40s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [50.6 kB] 40s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [908 kB] 40s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.6 kB] 40s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9704 B] 40s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [39.3 kB] 40s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [83.8 kB] 40s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted i386 Packages [2408 B] 40s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [40.1 kB] 40s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [278 kB] 40s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [780 kB] 40s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [20.0 kB] 40s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [5528 B] 40s Fetched 2305 kB in 0s (8142 kB/s) 40s Reading package lists... 41s Reading package lists... 42s Building dependency tree... 42s Reading state information... 42s Calculating upgrade... 42s The following package was automatically installed and is no longer required: 42s libsgutils2-1.46-2 42s Use 'sudo apt autoremove' to remove it. 42s The following NEW packages will be installed: 42s libsgutils2-1.48 42s The following packages will be upgraded: 42s amd64-microcode bash bpftrace curl debconf debconf-i18n distro-info 42s dracut-install fwupd-signed gir1.2-girepository-2.0 gir1.2-glib-2.0 hostname 42s init init-system-helpers intel-microcode libaudit-common libaudit1 42s libcurl3t64-gnutls libcurl4t64 libgirepository-1.0-1 libglib2.0-0t64 42s libglib2.0-data liblzma5 libpam-modules libpam-modules-bin libpam-runtime 42s libpam0g libplymouth5 libselinux1 libsemanage-common libsemanage2 linux-base 42s lxd-installer openssh-client openssh-server openssh-sftp-server 42s pinentry-curses plymouth plymouth-theme-ubuntu-text python3-blinker 42s python3-debconf python3-jsonschema-specifications python3-rpds-py sg3-utils 42s sg3-utils-udev vim-common vim-tiny xxd xz-utils 42s 49 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 42s Need to get 19.8 MB of archives. 42s After this operation, 3623 kB of additional disk space will be used. 42s Get:1 http://ftpmaster.internal/ubuntu plucky/main amd64 bash amd64 5.2.32-1ubuntu2 [918 kB] 42s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 hostname amd64 3.25 [11.1 kB] 42s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 init-system-helpers all 1.67ubuntu1 [39.1 kB] 42s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit-common all 1:4.0.2-2ubuntu1 [6578 B] 42s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libaudit1 amd64 1:4.0.2-2ubuntu1 [53.9 kB] 42s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 debconf-i18n all 1.5.87ubuntu1 [204 kB] 42s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-debconf all 1.5.87ubuntu1 [4156 B] 42s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 debconf all 1.5.87ubuntu1 [124 kB] 42s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam0g amd64 1.5.3-7ubuntu4 [69.6 kB] 42s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libselinux1 amd64 3.7-3ubuntu1 [86.9 kB] 42s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-modules-bin amd64 1.5.3-7ubuntu4 [53.7 kB] 42s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-modules amd64 1.5.3-7ubuntu4 [294 kB] 42s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 init amd64 1.67ubuntu1 [6428 B] 42s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 openssh-sftp-server amd64 1:9.9p1-3ubuntu2 [41.2 kB] 42s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 openssh-server amd64 1:9.9p1-3ubuntu2 [625 kB] 42s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 openssh-client amd64 1:9.9p1-3ubuntu2 [1080 kB] 42s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libpam-runtime all 1.5.3-7ubuntu4 [40.8 kB] 42s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 liblzma5 amd64 5.6.3-1 [156 kB] 42s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage-common all 3.7-2build1 [7186 B] 42s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 libsemanage2 amd64 3.7-2build1 [105 kB] 42s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 distro-info amd64 1.12 [20.0 kB] 42s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-girepository-2.0 amd64 1.82.0-2 [25.3 kB] 42s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 gir1.2-glib-2.0 amd64 2.82.2-3 [182 kB] 42s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-0t64 amd64 2.82.2-3 [1655 kB] 42s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 libgirepository-1.0-1 amd64 1.82.0-2 [88.7 kB] 42s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 libglib2.0-data all 2.82.2-3 [51.7 kB] 42s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 vim-tiny amd64 2:9.1.0861-1ubuntu1 [1037 kB] 42s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 vim-common all 2:9.1.0861-1ubuntu1 [395 kB] 42s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 xxd amd64 2:9.1.0861-1ubuntu1 [67.8 kB] 42s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 libplymouth5 amd64 24.004.60-2ubuntu3 [145 kB] 42s Get:31 http://ftpmaster.internal/ubuntu plucky/main amd64 plymouth-theme-ubuntu-text amd64 24.004.60-2ubuntu3 [10.3 kB] 42s Get:32 http://ftpmaster.internal/ubuntu plucky/main amd64 plymouth amd64 24.004.60-2ubuntu3 [140 kB] 42s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 xz-utils amd64 5.6.3-1 [276 kB] 42s Get:34 http://ftpmaster.internal/ubuntu plucky/main amd64 bpftrace amd64 0.21.2-2ubuntu3 [1787 kB] 43s Get:35 http://ftpmaster.internal/ubuntu plucky/main amd64 curl amd64 8.9.1-2ubuntu3 [243 kB] 43s Get:36 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl4t64 amd64 8.9.1-2ubuntu3 [420 kB] 43s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 dracut-install amd64 105-2ubuntu2 [35.9 kB] 43s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 fwupd-signed amd64 1.55+1.7-1 [30.6 kB] 43s Get:39 http://ftpmaster.internal/ubuntu plucky/main amd64 libcurl3t64-gnutls amd64 8.9.1-2ubuntu3 [412 kB] 43s Get:40 http://ftpmaster.internal/ubuntu plucky/main amd64 libsgutils2-1.48 amd64 1.48-0ubuntu1 [124 kB] 43s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 linux-base all 4.10.1ubuntu1 [34.8 kB] 43s Get:42 http://ftpmaster.internal/ubuntu plucky/main amd64 lxd-installer all 10 [5264 B] 43s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 pinentry-curses amd64 1.3.1-0ubuntu2 [41.6 kB] 43s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-blinker all 1.9.0-1 [10.7 kB] 43s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-rpds-py amd64 0.21.0-2ubuntu1 [323 kB] 43s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-jsonschema-specifications all 2023.12.1-2 [9116 B] 43s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 sg3-utils amd64 1.48-0ubuntu1 [1042 kB] 43s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 sg3-utils-udev all 1.48-0ubuntu1 [6608 B] 43s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 amd64-microcode amd64 3.20240820.1ubuntu1 [187 kB] 43s Get:50 http://ftpmaster.internal/ubuntu plucky/main amd64 intel-microcode amd64 3.20241112.1ubuntu2 [7055 kB] 43s Preconfiguring packages ... 43s Fetched 19.8 MB in 0s (93.0 MB/s) 43s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75624 files and directories currently installed.) 43s Preparing to unpack .../bash_5.2.32-1ubuntu2_amd64.deb ... 43s Unpacking bash (5.2.32-1ubuntu2) over (5.2.32-1ubuntu1) ... 43s Setting up bash (5.2.32-1ubuntu2) ... 43s update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode 43s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75624 files and directories currently installed.) 43s Preparing to unpack .../hostname_3.25_amd64.deb ... 43s Unpacking hostname (3.25) over (3.23+nmu2ubuntu2) ... 43s Setting up hostname (3.25) ... 43s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75624 files and directories currently installed.) 43s Preparing to unpack .../init-system-helpers_1.67ubuntu1_all.deb ... 43s Unpacking init-system-helpers (1.67ubuntu1) over (1.66ubuntu1) ... 43s Setting up init-system-helpers (1.67ubuntu1) ... 44s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75624 files and directories currently installed.) 44s Preparing to unpack .../libaudit-common_1%3a4.0.2-2ubuntu1_all.deb ... 44s Unpacking libaudit-common (1:4.0.2-2ubuntu1) over (1:4.0.1-1ubuntu2) ... 44s Setting up libaudit-common (1:4.0.2-2ubuntu1) ... 44s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75624 files and directories currently installed.) 44s Preparing to unpack .../libaudit1_1%3a4.0.2-2ubuntu1_amd64.deb ... 44s Unpacking libaudit1:amd64 (1:4.0.2-2ubuntu1) over (1:4.0.1-1ubuntu2) ... 44s Setting up libaudit1:amd64 (1:4.0.2-2ubuntu1) ... 44s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75624 files and directories currently installed.) 44s Preparing to unpack .../debconf-i18n_1.5.87ubuntu1_all.deb ... 44s Unpacking debconf-i18n (1.5.87ubuntu1) over (1.5.86ubuntu1) ... 44s Preparing to unpack .../python3-debconf_1.5.87ubuntu1_all.deb ... 44s Unpacking python3-debconf (1.5.87ubuntu1) over (1.5.86ubuntu1) ... 44s Preparing to unpack .../debconf_1.5.87ubuntu1_all.deb ... 44s Unpacking debconf (1.5.87ubuntu1) over (1.5.86ubuntu1) ... 44s Setting up debconf (1.5.87ubuntu1) ... 44s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75624 files and directories currently installed.) 44s Preparing to unpack .../libpam0g_1.5.3-7ubuntu4_amd64.deb ... 44s Unpacking libpam0g:amd64 (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ... 44s Setting up libpam0g:amd64 (1.5.3-7ubuntu4) ... 44s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75624 files and directories currently installed.) 44s Preparing to unpack .../libselinux1_3.7-3ubuntu1_amd64.deb ... 44s Unpacking libselinux1:amd64 (3.7-3ubuntu1) over (3.5-2ubuntu5) ... 44s Setting up libselinux1:amd64 (3.7-3ubuntu1) ... 44s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75624 files and directories currently installed.) 44s Preparing to unpack .../libpam-modules-bin_1.5.3-7ubuntu4_amd64.deb ... 44s Unpacking libpam-modules-bin (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ... 45s Setting up libpam-modules-bin (1.5.3-7ubuntu4) ... 45s pam_namespace.service is a disabled or a static unit not running, not starting it. 45s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75624 files and directories currently installed.) 45s Preparing to unpack .../libpam-modules_1.5.3-7ubuntu4_amd64.deb ... 45s Unpacking libpam-modules:amd64 (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ... 45s Setting up libpam-modules:amd64 (1.5.3-7ubuntu4) ... 45s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75624 files and directories currently installed.) 45s Preparing to unpack .../init_1.67ubuntu1_amd64.deb ... 45s Unpacking init (1.67ubuntu1) over (1.66ubuntu1) ... 45s Preparing to unpack .../openssh-sftp-server_1%3a9.9p1-3ubuntu2_amd64.deb ... 45s Unpacking openssh-sftp-server (1:9.9p1-3ubuntu2) over (1:9.7p1-7ubuntu5) ... 45s Preparing to unpack .../openssh-server_1%3a9.9p1-3ubuntu2_amd64.deb ... 45s Unpacking openssh-server (1:9.9p1-3ubuntu2) over (1:9.7p1-7ubuntu5) ... 45s Preparing to unpack .../openssh-client_1%3a9.9p1-3ubuntu2_amd64.deb ... 45s Unpacking openssh-client (1:9.9p1-3ubuntu2) over (1:9.7p1-7ubuntu5) ... 45s Preparing to unpack .../libpam-runtime_1.5.3-7ubuntu4_all.deb ... 45s Unpacking libpam-runtime (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ... 45s Setting up libpam-runtime (1.5.3-7ubuntu4) ... 46s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75626 files and directories currently installed.) 46s Preparing to unpack .../liblzma5_5.6.3-1_amd64.deb ... 46s Unpacking liblzma5:amd64 (5.6.3-1) over (5.6.2-2) ... 46s Setting up liblzma5:amd64 (5.6.3-1) ... 46s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75626 files and directories currently installed.) 46s Preparing to unpack .../libsemanage-common_3.7-2build1_all.deb ... 46s Unpacking libsemanage-common (3.7-2build1) over (3.5-1build6) ... 46s Setting up libsemanage-common (3.7-2build1) ... 46s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75625 files and directories currently installed.) 46s Preparing to unpack .../libsemanage2_3.7-2build1_amd64.deb ... 46s Unpacking libsemanage2:amd64 (3.7-2build1) over (3.5-1build6) ... 46s Setting up libsemanage2:amd64 (3.7-2build1) ... 46s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75625 files and directories currently installed.) 46s Preparing to unpack .../00-distro-info_1.12_amd64.deb ... 46s Unpacking distro-info (1.12) over (1.9) ... 46s Preparing to unpack .../01-gir1.2-girepository-2.0_1.82.0-2_amd64.deb ... 46s Unpacking gir1.2-girepository-2.0:amd64 (1.82.0-2) over (1.80.1-4) ... 46s Preparing to unpack .../02-gir1.2-glib-2.0_2.82.2-3_amd64.deb ... 46s Unpacking gir1.2-glib-2.0:amd64 (2.82.2-3) over (2.82.1-0ubuntu1) ... 46s Preparing to unpack .../03-libglib2.0-0t64_2.82.2-3_amd64.deb ... 46s Unpacking libglib2.0-0t64:amd64 (2.82.2-3) over (2.82.1-0ubuntu1) ... 46s Preparing to unpack .../04-libgirepository-1.0-1_1.82.0-2_amd64.deb ... 46s Unpacking libgirepository-1.0-1:amd64 (1.82.0-2) over (1.80.1-4) ... 46s Preparing to unpack .../05-libglib2.0-data_2.82.2-3_all.deb ... 46s Unpacking libglib2.0-data (2.82.2-3) over (2.82.1-0ubuntu1) ... 46s Preparing to unpack .../06-vim-tiny_2%3a9.1.0861-1ubuntu1_amd64.deb ... 46s Unpacking vim-tiny (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ... 46s Preparing to unpack .../07-vim-common_2%3a9.1.0861-1ubuntu1_all.deb ... 46s Unpacking vim-common (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ... 46s Preparing to unpack .../08-xxd_2%3a9.1.0861-1ubuntu1_amd64.deb ... 46s Unpacking xxd (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ... 46s Preparing to unpack .../09-libplymouth5_24.004.60-2ubuntu3_amd64.deb ... 46s Unpacking libplymouth5:amd64 (24.004.60-2ubuntu3) over (24.004.60-1ubuntu11) ... 46s Preparing to unpack .../10-plymouth-theme-ubuntu-text_24.004.60-2ubuntu3_amd64.deb ... 46s Unpacking plymouth-theme-ubuntu-text (24.004.60-2ubuntu3) over (24.004.60-1ubuntu11) ... 46s Preparing to unpack .../11-plymouth_24.004.60-2ubuntu3_amd64.deb ... 46s Unpacking plymouth (24.004.60-2ubuntu3) over (24.004.60-1ubuntu11) ... 47s Preparing to unpack .../12-xz-utils_5.6.3-1_amd64.deb ... 47s Unpacking xz-utils (5.6.3-1) over (5.6.2-2) ... 47s Preparing to unpack .../13-bpftrace_0.21.2-2ubuntu3_amd64.deb ... 47s Unpacking bpftrace (0.21.2-2ubuntu3) over (0.21.2-2ubuntu2) ... 47s Preparing to unpack .../14-curl_8.9.1-2ubuntu3_amd64.deb ... 47s Unpacking curl (8.9.1-2ubuntu3) over (8.9.1-2ubuntu2) ... 47s Preparing to unpack .../15-libcurl4t64_8.9.1-2ubuntu3_amd64.deb ... 47s Unpacking libcurl4t64:amd64 (8.9.1-2ubuntu3) over (8.9.1-2ubuntu2) ... 47s Preparing to unpack .../16-dracut-install_105-2ubuntu2_amd64.deb ... 47s Unpacking dracut-install (105-2ubuntu2) over (105-1ubuntu1) ... 47s Preparing to unpack .../17-fwupd-signed_1.55+1.7-1_amd64.deb ... 47s Unpacking fwupd-signed (1.55+1.7-1) over (1.54+1.6-1build1) ... 47s Preparing to unpack .../18-libcurl3t64-gnutls_8.9.1-2ubuntu3_amd64.deb ... 47s Unpacking libcurl3t64-gnutls:amd64 (8.9.1-2ubuntu3) over (8.9.1-2ubuntu2) ... 47s Selecting previously unselected package libsgutils2-1.48:amd64. 47s Preparing to unpack .../19-libsgutils2-1.48_1.48-0ubuntu1_amd64.deb ... 47s Unpacking libsgutils2-1.48:amd64 (1.48-0ubuntu1) ... 47s Preparing to unpack .../20-linux-base_4.10.1ubuntu1_all.deb ... 47s Unpacking linux-base (4.10.1ubuntu1) over (4.5ubuntu9) ... 47s Preparing to unpack .../21-lxd-installer_10_all.deb ... 47s Unpacking lxd-installer (10) over (9) ... 47s Preparing to unpack .../22-pinentry-curses_1.3.1-0ubuntu2_amd64.deb ... 47s Unpacking pinentry-curses (1.3.1-0ubuntu2) over (1.2.1-3ubuntu5) ... 47s Preparing to unpack .../23-python3-blinker_1.9.0-1_all.deb ... 47s Unpacking python3-blinker (1.9.0-1) over (1.8.2-1) ... 47s Preparing to unpack .../24-python3-rpds-py_0.21.0-2ubuntu1_amd64.deb ... 47s Unpacking python3-rpds-py (0.21.0-2ubuntu1) over (0.20.0-0ubuntu3) ... 47s Preparing to unpack .../25-python3-jsonschema-specifications_2023.12.1-2_all.deb ... 47s Unpacking python3-jsonschema-specifications (2023.12.1-2) over (2023.12.1-1ubuntu1) ... 47s Preparing to unpack .../26-sg3-utils_1.48-0ubuntu1_amd64.deb ... 47s Unpacking sg3-utils (1.48-0ubuntu1) over (1.46-3ubuntu5) ... 47s Preparing to unpack .../27-sg3-utils-udev_1.48-0ubuntu1_all.deb ... 47s Unpacking sg3-utils-udev (1.48-0ubuntu1) over (1.46-3ubuntu5) ... 47s Preparing to unpack .../28-amd64-microcode_3.20240820.1ubuntu1_amd64.deb ... 47s Unpacking amd64-microcode (3.20240820.1ubuntu1) over (3.20240116.2+nmu1ubuntu1.1) ... 47s Preparing to unpack .../29-intel-microcode_3.20241112.1ubuntu2_amd64.deb ... 47s Unpacking intel-microcode (3.20241112.1ubuntu2) over (3.20241112.1ubuntu1) ... 48s Setting up pinentry-curses (1.3.1-0ubuntu2) ... 48s Setting up distro-info (1.12) ... 48s Setting up linux-base (4.10.1ubuntu1) ... 48s Setting up init (1.67ubuntu1) ... 48s Setting up libcurl4t64:amd64 (8.9.1-2ubuntu3) ... 48s Setting up bpftrace (0.21.2-2ubuntu3) ... 48s Setting up openssh-client (1:9.9p1-3ubuntu2) ... 48s Setting up intel-microcode (3.20241112.1ubuntu2) ... 48s intel-microcode: microcode will be updated at next boot 48s Setting up python3-debconf (1.5.87ubuntu1) ... 48s Setting up libcurl3t64-gnutls:amd64 (8.9.1-2ubuntu3) ... 48s Setting up fwupd-signed (1.55+1.7-1) ... 48s Setting up libsgutils2-1.48:amd64 (1.48-0ubuntu1) ... 48s Setting up debconf-i18n (1.5.87ubuntu1) ... 48s Setting up amd64-microcode (3.20240820.1ubuntu1) ... 48s amd64-microcode: microcode will be updated at next boot 48s Setting up xxd (2:9.1.0861-1ubuntu1) ... 48s Setting up libglib2.0-0t64:amd64 (2.82.2-3) ... 48s No schema files found: doing nothing. 48s Setting up libglib2.0-data (2.82.2-3) ... 48s Setting up vim-common (2:9.1.0861-1ubuntu1) ... 48s Setting up xz-utils (5.6.3-1) ... 48s Setting up gir1.2-glib-2.0:amd64 (2.82.2-3) ... 48s Setting up lxd-installer (10) ... 48s Setting up python3-rpds-py (0.21.0-2ubuntu1) ... 48s Setting up dracut-install (105-2ubuntu2) ... 48s Setting up libplymouth5:amd64 (24.004.60-2ubuntu3) ... 48s Setting up libgirepository-1.0-1:amd64 (1.82.0-2) ... 48s Setting up curl (8.9.1-2ubuntu3) ... 48s Setting up python3-jsonschema-specifications (2023.12.1-2) ... 48s Setting up sg3-utils (1.48-0ubuntu1) ... 48s Setting up python3-blinker (1.9.0-1) ... 49s Setting up openssh-sftp-server (1:9.9p1-3ubuntu2) ... 49s Setting up openssh-server (1:9.9p1-3ubuntu2) ... 49s Installing new version of config file /etc/ssh/moduli ... 49s Replacing config file /etc/ssh/sshd_config with new version 50s Setting up plymouth (24.004.60-2ubuntu3) ... 50s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 50s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 59s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 59s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 59s Setting up vim-tiny (2:9.1.0861-1ubuntu1) ... 59s Setting up sg3-utils-udev (1.48-0ubuntu1) ... 59s update-initramfs: deferring update (trigger activated) 59s Setting up plymouth-theme-ubuntu-text (24.004.60-2ubuntu3) ... 59s update-initramfs: deferring update (trigger activated) 59s Setting up gir1.2-girepository-2.0:amd64 (1.82.0-2) ... 59s Processing triggers for install-info (7.1.1-1) ... 60s Processing triggers for initramfs-tools (0.142ubuntu35) ... 60s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 60s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 68s Processing triggers for libc-bin (2.40-1ubuntu3) ... 68s Processing triggers for ufw (0.36.2-8) ... 68s Processing triggers for man-db (2.13.0-1) ... 69s Processing triggers for debianutils (5.21) ... 70s Reading package lists... 70s Building dependency tree... 70s Reading state information... 70s The following packages will be REMOVED: 70s libsgutils2-1.46-2* 71s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 71s After this operation, 294 kB disk space will be freed. 71s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75656 files and directories currently installed.) 71s Removing libsgutils2-1.46-2:amd64 (1.46-3ubuntu5) ... 71s Processing triggers for libc-bin (2.40-1ubuntu3) ... 71s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 71s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 71s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 71s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 72s Reading package lists... 72s Reading package lists... 73s Building dependency tree... 73s Reading state information... 73s Calculating upgrade... 73s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 73s Reading package lists... 73s Building dependency tree... 73s Reading state information... 74s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s autopkgtest [21:42:36]: rebooting testbed after setup commands that affected boot 77s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 88s autopkgtest [21:42:50]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 89s autopkgtest [21:42:51]: @@@@@@@@@@@@@@@@@@@@ apt-source gromacs 92s Get:1 http://ftpmaster.internal/ubuntu plucky/universe gromacs 2024.2-1 (dsc) [3648 B] 92s Get:2 http://ftpmaster.internal/ubuntu plucky/universe gromacs 2024.2-1 (tar) [48.1 MB] 92s Get:3 http://ftpmaster.internal/ubuntu plucky/universe gromacs 2024.2-1 (tar) [42.4 MB] 92s Get:4 http://ftpmaster.internal/ubuntu plucky/universe gromacs 2024.2-1 (diff) [37.8 kB] 92s gpgv: Signature made Sat May 11 22:19:23 2024 UTC 92s gpgv: using RSA key 843E5FA61E6063389876D2E5EE4AFD69EC65108F 92s gpgv: issuer "nbreen@debian.org" 92s gpgv: Can't check signature: No public key 92s dpkg-source: warning: cannot verify inline signature for ./gromacs_2024.2-1.dsc: no acceptable signature found 94s autopkgtest [21:42:56]: testing package gromacs version 2024.2-1 95s autopkgtest [21:42:57]: build not needed 97s autopkgtest [21:42:59]: test gromacs-regressiontests: preparing testbed 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 97s Starting pkgProblemResolver with broken count: 0 97s Starting 2 pkgProblemResolver with broken count: 0 97s Done 98s The following additional packages will be installed: 98s build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu cpp-x86-64-linux-gnu 98s fonts-mathjax g++ g++-14 g++-14-x86-64-linux-gnu g++-x86-64-linux-gnu gcc 98s gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu gromacs gromacs-data 98s isa-support libamd-comgr2 libamdhip64-5 libasan8 libblas3 libcc1-0 98s libdrm-amdgpu1 libevent-pthreads-2.1-7t64 libfabric1 libfftw3-bin 98s libfftw3-dev libfftw3-double3 libfftw3-long3 libfftw3-quad3 libfftw3-single3 98s libgcc-14-dev libgfortran5 libgomp1 libgromacs-dev libgromacs9 98s libhsa-runtime64-1 libhsakmt1 libhwasan0 libhwloc-plugins libhwloc15 98s libibmad5 libibumad3 libisl23 libitm1 libjs-mathjax liblapack3 libllvm17t64 98s liblsan0 libmpc3 libmunge2 libmuparser2v5 libnblib-gmx-dev libnblib-gmx0 98s libopenmpi3t64 libpciaccess0 libpmix2t64 libpsm-infinipath1 libpsm2-2 98s libquadmath0 librdmacm1t64 libstdc++-14-dev libtsan2 libubsan1 libucx0 98s libxnvctrl0 mpi-default-bin ocl-icd-libopencl1 openmpi-bin openmpi-common 98s sse4.2-support 98s Suggested packages: 98s cpp-doc gcc-14-locales cpp-14-doc g++-multilib g++-14-multilib gcc-14-doc 98s gcc-multilib manpages-dev autoconf automake libtool flex bison gdb gcc-doc 98s gcc-14-multilib gdb-x86-64-linux-gnu pymol libfftw3-doc mpi-default-dev 98s zlib1g-dev libhwloc-contrib-plugins fonts-mathjax-extras fonts-stix 98s libjs-mathjax-doc libstdc++-14-doc opencl-icd gfortran | fortran-compiler 98s The following NEW packages will be installed: 98s autopkgtest-satdep build-essential cpp cpp-14 cpp-14-x86-64-linux-gnu 98s cpp-x86-64-linux-gnu fonts-mathjax g++ g++-14 g++-14-x86-64-linux-gnu 98s g++-x86-64-linux-gnu gcc gcc-14 gcc-14-x86-64-linux-gnu gcc-x86-64-linux-gnu 98s gromacs gromacs-data isa-support libamd-comgr2 libamdhip64-5 libasan8 98s libblas3 libcc1-0 libdrm-amdgpu1 libevent-pthreads-2.1-7t64 libfabric1 98s libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-long3 libfftw3-quad3 98s libfftw3-single3 libgcc-14-dev libgfortran5 libgomp1 libgromacs-dev 98s libgromacs9 libhsa-runtime64-1 libhsakmt1 libhwasan0 libhwloc-plugins 98s libhwloc15 libibmad5 libibumad3 libisl23 libitm1 libjs-mathjax liblapack3 98s libllvm17t64 liblsan0 libmpc3 libmunge2 libmuparser2v5 libnblib-gmx-dev 98s libnblib-gmx0 libopenmpi3t64 libpciaccess0 libpmix2t64 libpsm-infinipath1 98s libpsm2-2 libquadmath0 librdmacm1t64 libstdc++-14-dev libtsan2 libubsan1 98s libucx0 libxnvctrl0 mpi-default-bin ocl-icd-libopencl1 openmpi-bin 98s openmpi-common sse4.2-support 98s 0 upgraded, 72 newly installed, 0 to remove and 0 not upgraded. 98s Need to get 213 MB/213 MB of archives. 98s After this operation, 935 MB of additional disk space will be used. 98s Get:1 /tmp/autopkgtest.TiJpdO/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [764 B] 98s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 isa-support amd64 26 [16.3 kB] 98s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 sse4.2-support amd64 26 [3454 B] 98s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libisl23 amd64 0.27-1 [685 kB] 98s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libmpc3 amd64 1.3.1-1build2 [55.3 kB] 98s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [11.9 MB] 98s Get:7 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-14 amd64 14.2.0-8ubuntu1 [1030 B] 98s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [5452 B] 98s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 cpp amd64 4:14.1.0-2ubuntu1 [22.4 kB] 98s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 libcc1-0 amd64 14.2.0-8ubuntu1 [47.6 kB] 98s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-8ubuntu1 [148 kB] 98s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 libitm1 amd64 14.2.0-8ubuntu1 [29.1 kB] 98s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 libasan8 amd64 14.2.0-8ubuntu1 [2998 kB] 98s Get:14 http://ftpmaster.internal/ubuntu plucky/main amd64 liblsan0 amd64 14.2.0-8ubuntu1 [1317 kB] 98s Get:15 http://ftpmaster.internal/ubuntu plucky/main amd64 libtsan2 amd64 14.2.0-8ubuntu1 [2732 kB] 98s Get:16 http://ftpmaster.internal/ubuntu plucky/main amd64 libubsan1 amd64 14.2.0-8ubuntu1 [1177 kB] 98s Get:17 http://ftpmaster.internal/ubuntu plucky/main amd64 libhwasan0 amd64 14.2.0-8ubuntu1 [1634 kB] 98s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 libquadmath0 amd64 14.2.0-8ubuntu1 [153 kB] 98s Get:19 http://ftpmaster.internal/ubuntu plucky/main amd64 libgcc-14-dev amd64 14.2.0-8ubuntu1 [2814 kB] 98s Get:20 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [23.3 MB] 98s Get:21 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-14 amd64 14.2.0-8ubuntu1 [528 kB] 98s Get:22 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [1214 B] 98s Get:23 http://ftpmaster.internal/ubuntu plucky/main amd64 gcc amd64 4:14.1.0-2ubuntu1 [5000 B] 98s Get:24 http://ftpmaster.internal/ubuntu plucky/main amd64 libstdc++-14-dev amd64 14.2.0-8ubuntu1 [2504 kB] 98s Get:25 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-8ubuntu1 [13.3 MB] 98s Get:26 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-14 amd64 14.2.0-8ubuntu1 [19.9 kB] 98s Get:27 http://ftpmaster.internal/ubuntu plucky/main amd64 g++-x86-64-linux-gnu amd64 4:14.1.0-2ubuntu1 [966 B] 98s Get:28 http://ftpmaster.internal/ubuntu plucky/main amd64 g++ amd64 4:14.1.0-2ubuntu1 [1100 B] 98s Get:29 http://ftpmaster.internal/ubuntu plucky/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 98s Get:30 http://ftpmaster.internal/ubuntu plucky/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 98s Get:31 http://ftpmaster.internal/ubuntu plucky/universe amd64 libllvm17t64 amd64 1:17.0.6-18 [26.0 MB] 99s Get:32 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3build2 [14.4 MB] 99s Get:33 http://ftpmaster.internal/ubuntu plucky/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [21.7 kB] 99s Get:34 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsakmt1 amd64 5.7.0-1build1 [62.9 kB] 99s Get:35 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhsa-runtime64-1 amd64 5.7.1-2build1 [491 kB] 99s Get:36 http://ftpmaster.internal/ubuntu plucky/universe amd64 libamdhip64-5 amd64 5.7.1-5 [9643 kB] 99s Get:37 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-4 [332 kB] 99s Get:38 http://ftpmaster.internal/ubuntu plucky/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [7966 B] 99s Get:39 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3build1 [178 kB] 99s Get:40 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpsm2-2 amd64 11.2.185-2.1 [193 kB] 99s Get:41 http://ftpmaster.internal/ubuntu plucky/main amd64 librdmacm1t64 amd64 52.0-2ubuntu1 [70.8 kB] 99s Get:42 http://ftpmaster.internal/ubuntu plucky/universe amd64 libfabric1 amd64 1.17.0-3ubuntu1 [658 kB] 99s Get:43 http://ftpmaster.internal/ubuntu plucky/main amd64 libfftw3-double3 amd64 3.3.10-1ubuntu4 [839 kB] 99s Get:44 http://ftpmaster.internal/ubuntu plucky/main amd64 libfftw3-long3 amd64 3.3.10-1ubuntu4 [378 kB] 99s Get:45 http://ftpmaster.internal/ubuntu plucky/main amd64 libfftw3-quad3 amd64 3.3.10-1ubuntu4 [669 kB] 99s Get:46 http://ftpmaster.internal/ubuntu plucky/main amd64 libfftw3-single3 amd64 3.3.10-1ubuntu4 [871 kB] 99s Get:47 http://ftpmaster.internal/ubuntu plucky/main amd64 libfftw3-bin amd64 3.3.10-1ubuntu4 [39.2 kB] 99s Get:48 http://ftpmaster.internal/ubuntu plucky/main amd64 libfftw3-dev amd64 3.3.10-1ubuntu4 [2345 kB] 99s Get:49 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 99s Get:50 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc15 amd64 2.11.2-1 [193 kB] 99s Get:51 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-4 [3177 kB] 99s Get:52 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmuparser2v5 amd64 2.3.4-1 [137 kB] 99s Get:53 http://ftpmaster.internal/ubuntu plucky/universe amd64 libmunge2 amd64 0.5.15-4build1 [14.7 kB] 99s Get:54 http://ftpmaster.internal/ubuntu plucky/main amd64 libpciaccess0 amd64 0.17-3build1 [18.6 kB] 99s Get:55 http://ftpmaster.internal/ubuntu plucky/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu4 [12.6 kB] 99s Get:56 http://ftpmaster.internal/ubuntu plucky/universe amd64 ocl-icd-libopencl1 amd64 2.3.2-1build1 [38.5 kB] 99s Get:57 http://ftpmaster.internal/ubuntu plucky/universe amd64 libhwloc-plugins amd64 2.11.2-1 [16.0 kB] 99s Get:58 http://ftpmaster.internal/ubuntu plucky/universe amd64 libpmix2t64 amd64 5.0.3-2 [697 kB] 99s Get:59 http://ftpmaster.internal/ubuntu plucky/main amd64 libibumad3 amd64 52.0-2ubuntu1 [29.0 kB] 99s Get:60 http://ftpmaster.internal/ubuntu plucky/main amd64 libibmad5 amd64 52.0-2ubuntu1 [42.6 kB] 99s Get:61 http://ftpmaster.internal/ubuntu plucky/universe amd64 libucx0 amd64 1.17.0+ds-3build1 [1162 kB] 99s Get:62 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 libopenmpi3t64 amd64 5.0.5-6 [2093 kB] 99s Get:63 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgromacs9 amd64 2024.2-1 [32.3 MB] 100s Get:64 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnblib-gmx0 amd64 2024.2-1 [332 kB] 100s Get:65 http://ftpmaster.internal/ubuntu plucky/universe amd64 libnblib-gmx-dev amd64 2024.2-1 [26.2 kB] 100s Get:66 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 openmpi-common all 5.0.5-6 [95.6 kB] 100s Get:67 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 openmpi-bin amd64 5.0.5-6 [169 kB] 100s Get:68 http://ftpmaster.internal/ubuntu plucky/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 100s Get:69 http://ftpmaster.internal/ubuntu plucky/universe amd64 gromacs-data all 2024.2-1 [41.0 MB] 100s Get:70 http://ftpmaster.internal/ubuntu plucky/universe amd64 gromacs amd64 2024.2-1 [57.3 kB] 100s Get:71 http://ftpmaster.internal/ubuntu plucky/universe amd64 libgromacs-dev amd64 2024.2-1 [168 kB] 100s Get:72 http://ftpmaster.internal/ubuntu plucky/universe amd64 mpi-default-bin amd64 1.17 [2296 B] 101s Preconfiguring packages ... 101s Fetched 213 MB in 2s (87.3 MB/s) 101s Selecting previously unselected package isa-support:amd64. 101s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75651 files and directories currently installed.) 101s Preparing to unpack .../isa-support_26_amd64.deb ... 101s Unpacking isa-support:amd64 (26) ... 101s Setting up isa-support:amd64 (26) ... 101s Selecting previously unselected package sse4.2-support. 101s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 75678 files and directories currently installed.) 101s Preparing to unpack .../00-sse4.2-support_26_amd64.deb ... 101s Unpacking sse4.2-support (26) ... 101s Selecting previously unselected package libisl23:amd64. 101s Preparing to unpack .../01-libisl23_0.27-1_amd64.deb ... 101s Unpacking libisl23:amd64 (0.27-1) ... 101s Selecting previously unselected package libmpc3:amd64. 101s Preparing to unpack .../02-libmpc3_1.3.1-1build2_amd64.deb ... 101s Unpacking libmpc3:amd64 (1.3.1-1build2) ... 101s Selecting previously unselected package cpp-14-x86-64-linux-gnu. 101s Preparing to unpack .../03-cpp-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 101s Unpacking cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 101s Selecting previously unselected package cpp-14. 102s Preparing to unpack .../04-cpp-14_14.2.0-8ubuntu1_amd64.deb ... 102s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 102s Selecting previously unselected package cpp-x86-64-linux-gnu. 102s Preparing to unpack .../05-cpp-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 102s Unpacking cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 102s Selecting previously unselected package cpp. 102s Preparing to unpack .../06-cpp_4%3a14.1.0-2ubuntu1_amd64.deb ... 102s Unpacking cpp (4:14.1.0-2ubuntu1) ... 102s Selecting previously unselected package libcc1-0:amd64. 102s Preparing to unpack .../07-libcc1-0_14.2.0-8ubuntu1_amd64.deb ... 102s Unpacking libcc1-0:amd64 (14.2.0-8ubuntu1) ... 102s Selecting previously unselected package libgomp1:amd64. 102s Preparing to unpack .../08-libgomp1_14.2.0-8ubuntu1_amd64.deb ... 102s Unpacking libgomp1:amd64 (14.2.0-8ubuntu1) ... 102s Selecting previously unselected package libitm1:amd64. 102s Preparing to unpack .../09-libitm1_14.2.0-8ubuntu1_amd64.deb ... 102s Unpacking libitm1:amd64 (14.2.0-8ubuntu1) ... 102s Selecting previously unselected package libasan8:amd64. 102s Preparing to unpack .../10-libasan8_14.2.0-8ubuntu1_amd64.deb ... 102s Unpacking libasan8:amd64 (14.2.0-8ubuntu1) ... 102s Selecting previously unselected package liblsan0:amd64. 102s Preparing to unpack .../11-liblsan0_14.2.0-8ubuntu1_amd64.deb ... 102s Unpacking liblsan0:amd64 (14.2.0-8ubuntu1) ... 102s Selecting previously unselected package libtsan2:amd64. 102s Preparing to unpack .../12-libtsan2_14.2.0-8ubuntu1_amd64.deb ... 102s Unpacking libtsan2:amd64 (14.2.0-8ubuntu1) ... 102s Selecting previously unselected package libubsan1:amd64. 102s Preparing to unpack .../13-libubsan1_14.2.0-8ubuntu1_amd64.deb ... 102s Unpacking libubsan1:amd64 (14.2.0-8ubuntu1) ... 102s Selecting previously unselected package libhwasan0:amd64. 102s Preparing to unpack .../14-libhwasan0_14.2.0-8ubuntu1_amd64.deb ... 102s Unpacking libhwasan0:amd64 (14.2.0-8ubuntu1) ... 102s Selecting previously unselected package libquadmath0:amd64. 102s Preparing to unpack .../15-libquadmath0_14.2.0-8ubuntu1_amd64.deb ... 102s Unpacking libquadmath0:amd64 (14.2.0-8ubuntu1) ... 102s Selecting previously unselected package libgcc-14-dev:amd64. 102s Preparing to unpack .../16-libgcc-14-dev_14.2.0-8ubuntu1_amd64.deb ... 102s Unpacking libgcc-14-dev:amd64 (14.2.0-8ubuntu1) ... 102s Selecting previously unselected package gcc-14-x86-64-linux-gnu. 102s Preparing to unpack .../17-gcc-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 102s Unpacking gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 102s Selecting previously unselected package gcc-14. 102s Preparing to unpack .../18-gcc-14_14.2.0-8ubuntu1_amd64.deb ... 102s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 102s Selecting previously unselected package gcc-x86-64-linux-gnu. 102s Preparing to unpack .../19-gcc-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 102s Unpacking gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 102s Selecting previously unselected package gcc. 102s Preparing to unpack .../20-gcc_4%3a14.1.0-2ubuntu1_amd64.deb ... 102s Unpacking gcc (4:14.1.0-2ubuntu1) ... 103s Selecting previously unselected package libstdc++-14-dev:amd64. 103s Preparing to unpack .../21-libstdc++-14-dev_14.2.0-8ubuntu1_amd64.deb ... 103s Unpacking libstdc++-14-dev:amd64 (14.2.0-8ubuntu1) ... 103s Selecting previously unselected package g++-14-x86-64-linux-gnu. 103s Preparing to unpack .../22-g++-14-x86-64-linux-gnu_14.2.0-8ubuntu1_amd64.deb ... 103s Unpacking g++-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 103s Selecting previously unselected package g++-14. 103s Preparing to unpack .../23-g++-14_14.2.0-8ubuntu1_amd64.deb ... 103s Unpacking g++-14 (14.2.0-8ubuntu1) ... 103s Selecting previously unselected package g++-x86-64-linux-gnu. 103s Preparing to unpack .../24-g++-x86-64-linux-gnu_4%3a14.1.0-2ubuntu1_amd64.deb ... 103s Unpacking g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 103s Selecting previously unselected package g++. 103s Preparing to unpack .../25-g++_4%3a14.1.0-2ubuntu1_amd64.deb ... 103s Unpacking g++ (4:14.1.0-2ubuntu1) ... 103s Selecting previously unselected package build-essential. 103s Preparing to unpack .../26-build-essential_12.10ubuntu1_amd64.deb ... 103s Unpacking build-essential (12.10ubuntu1) ... 103s Selecting previously unselected package fonts-mathjax. 103s Preparing to unpack .../27-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 103s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 103s Selecting previously unselected package libllvm17t64:amd64. 103s Preparing to unpack .../28-libllvm17t64_1%3a17.0.6-18_amd64.deb ... 103s Unpacking libllvm17t64:amd64 (1:17.0.6-18) ... 104s Selecting previously unselected package libamd-comgr2:amd64. 104s Preparing to unpack .../29-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_amd64.deb ... 104s Unpacking libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 104s Selecting previously unselected package libdrm-amdgpu1:amd64. 104s Preparing to unpack .../30-libdrm-amdgpu1_2.4.123-1_amd64.deb ... 104s Unpacking libdrm-amdgpu1:amd64 (2.4.123-1) ... 104s Selecting previously unselected package libhsakmt1:amd64. 104s Preparing to unpack .../31-libhsakmt1_5.7.0-1build1_amd64.deb ... 104s Unpacking libhsakmt1:amd64 (5.7.0-1build1) ... 104s Selecting previously unselected package libhsa-runtime64-1. 104s Preparing to unpack .../32-libhsa-runtime64-1_5.7.1-2build1_amd64.deb ... 104s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 104s Selecting previously unselected package libamdhip64-5. 104s Preparing to unpack .../33-libamdhip64-5_5.7.1-5_amd64.deb ... 104s Unpacking libamdhip64-5 (5.7.1-5) ... 104s Selecting previously unselected package libblas3:amd64. 104s Preparing to unpack .../34-libblas3_3.12.0-4_amd64.deb ... 104s Unpacking libblas3:amd64 (3.12.0-4) ... 104s Selecting previously unselected package libevent-pthreads-2.1-7t64:amd64. 104s Preparing to unpack .../35-libevent-pthreads-2.1-7t64_2.1.12-stable-10_amd64.deb ... 104s Unpacking libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 104s Selecting previously unselected package libpsm-infinipath1. 104s Preparing to unpack .../36-libpsm-infinipath1_3.3+20.604758e7-6.3build1_amd64.deb ... 104s Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 104s Selecting previously unselected package libpsm2-2. 104s Preparing to unpack .../37-libpsm2-2_11.2.185-2.1_amd64.deb ... 104s Unpacking libpsm2-2 (11.2.185-2.1) ... 104s Selecting previously unselected package librdmacm1t64:amd64. 104s Preparing to unpack .../38-librdmacm1t64_52.0-2ubuntu1_amd64.deb ... 104s Unpacking librdmacm1t64:amd64 (52.0-2ubuntu1) ... 104s Selecting previously unselected package libfabric1:amd64. 104s Preparing to unpack .../39-libfabric1_1.17.0-3ubuntu1_amd64.deb ... 104s Unpacking libfabric1:amd64 (1.17.0-3ubuntu1) ... 105s Selecting previously unselected package libfftw3-double3:amd64. 105s Preparing to unpack .../40-libfftw3-double3_3.3.10-1ubuntu4_amd64.deb ... 105s Unpacking libfftw3-double3:amd64 (3.3.10-1ubuntu4) ... 105s Selecting previously unselected package libfftw3-long3:amd64. 105s Preparing to unpack .../41-libfftw3-long3_3.3.10-1ubuntu4_amd64.deb ... 105s Unpacking libfftw3-long3:amd64 (3.3.10-1ubuntu4) ... 105s Selecting previously unselected package libfftw3-quad3:amd64. 105s Preparing to unpack .../42-libfftw3-quad3_3.3.10-1ubuntu4_amd64.deb ... 105s Unpacking libfftw3-quad3:amd64 (3.3.10-1ubuntu4) ... 105s Selecting previously unselected package libfftw3-single3:amd64. 105s Preparing to unpack .../43-libfftw3-single3_3.3.10-1ubuntu4_amd64.deb ... 105s Unpacking libfftw3-single3:amd64 (3.3.10-1ubuntu4) ... 105s Selecting previously unselected package libfftw3-bin. 105s Preparing to unpack .../44-libfftw3-bin_3.3.10-1ubuntu4_amd64.deb ... 105s Unpacking libfftw3-bin (3.3.10-1ubuntu4) ... 105s Selecting previously unselected package libfftw3-dev:amd64. 105s Preparing to unpack .../45-libfftw3-dev_3.3.10-1ubuntu4_amd64.deb ... 105s Unpacking libfftw3-dev:amd64 (3.3.10-1ubuntu4) ... 105s Selecting previously unselected package libgfortran5:amd64. 105s Preparing to unpack .../46-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 105s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 105s Selecting previously unselected package libhwloc15:amd64. 105s Preparing to unpack .../47-libhwloc15_2.11.2-1_amd64.deb ... 105s Unpacking libhwloc15:amd64 (2.11.2-1) ... 105s Selecting previously unselected package liblapack3:amd64. 105s Preparing to unpack .../48-liblapack3_3.12.0-4_amd64.deb ... 105s Unpacking liblapack3:amd64 (3.12.0-4) ... 105s Selecting previously unselected package libmuparser2v5:amd64. 105s Preparing to unpack .../49-libmuparser2v5_2.3.4-1_amd64.deb ... 105s Unpacking libmuparser2v5:amd64 (2.3.4-1) ... 105s Selecting previously unselected package libmunge2:amd64. 105s Preparing to unpack .../50-libmunge2_0.5.15-4build1_amd64.deb ... 105s Unpacking libmunge2:amd64 (0.5.15-4build1) ... 105s Selecting previously unselected package libpciaccess0:amd64. 105s Preparing to unpack .../51-libpciaccess0_0.17-3build1_amd64.deb ... 105s Unpacking libpciaccess0:amd64 (0.17-3build1) ... 105s Selecting previously unselected package libxnvctrl0:amd64. 105s Preparing to unpack .../52-libxnvctrl0_510.47.03-0ubuntu4_amd64.deb ... 105s Unpacking libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 105s Selecting previously unselected package ocl-icd-libopencl1:amd64. 105s Preparing to unpack .../53-ocl-icd-libopencl1_2.3.2-1build1_amd64.deb ... 105s Unpacking ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 105s Selecting previously unselected package libhwloc-plugins:amd64. 105s Preparing to unpack .../54-libhwloc-plugins_2.11.2-1_amd64.deb ... 105s Unpacking libhwloc-plugins:amd64 (2.11.2-1) ... 105s Selecting previously unselected package libpmix2t64:amd64. 105s Preparing to unpack .../55-libpmix2t64_5.0.3-2_amd64.deb ... 105s Unpacking libpmix2t64:amd64 (5.0.3-2) ... 105s Selecting previously unselected package libibumad3:amd64. 105s Preparing to unpack .../56-libibumad3_52.0-2ubuntu1_amd64.deb ... 105s Unpacking libibumad3:amd64 (52.0-2ubuntu1) ... 105s Selecting previously unselected package libibmad5:amd64. 105s Preparing to unpack .../57-libibmad5_52.0-2ubuntu1_amd64.deb ... 105s Unpacking libibmad5:amd64 (52.0-2ubuntu1) ... 105s Selecting previously unselected package libucx0:amd64. 105s Preparing to unpack .../58-libucx0_1.17.0+ds-3build1_amd64.deb ... 105s Unpacking libucx0:amd64 (1.17.0+ds-3build1) ... 105s Selecting previously unselected package libopenmpi3t64:amd64. 105s Preparing to unpack .../59-libopenmpi3t64_5.0.5-6_amd64.deb ... 105s Unpacking libopenmpi3t64:amd64 (5.0.5-6) ... 105s Selecting previously unselected package libgromacs9:amd64. 105s Preparing to unpack .../60-libgromacs9_2024.2-1_amd64.deb ... 105s Unpacking libgromacs9:amd64 (2024.2-1) ... 106s Selecting previously unselected package libnblib-gmx0:amd64. 106s Preparing to unpack .../61-libnblib-gmx0_2024.2-1_amd64.deb ... 106s Unpacking libnblib-gmx0:amd64 (2024.2-1) ... 106s Selecting previously unselected package libnblib-gmx-dev. 106s Preparing to unpack .../62-libnblib-gmx-dev_2024.2-1_amd64.deb ... 106s Unpacking libnblib-gmx-dev (2024.2-1) ... 106s Selecting previously unselected package openmpi-common. 106s Preparing to unpack .../63-openmpi-common_5.0.5-6_all.deb ... 106s Unpacking openmpi-common (5.0.5-6) ... 106s Selecting previously unselected package openmpi-bin. 106s Preparing to unpack .../64-openmpi-bin_5.0.5-6_amd64.deb ... 106s Unpacking openmpi-bin (5.0.5-6) ... 106s Selecting previously unselected package libjs-mathjax. 106s Preparing to unpack .../65-libjs-mathjax_2.7.9+dfsg-1_all.deb ... 106s Unpacking libjs-mathjax (2.7.9+dfsg-1) ... 107s Selecting previously unselected package gromacs-data. 107s Preparing to unpack .../66-gromacs-data_2024.2-1_all.deb ... 107s Unpacking gromacs-data (2024.2-1) ... 111s Selecting previously unselected package gromacs. 111s Preparing to unpack .../67-gromacs_2024.2-1_amd64.deb ... 111s Unpacking gromacs (2024.2-1) ... 111s Selecting previously unselected package libgromacs-dev. 111s Preparing to unpack .../68-libgromacs-dev_2024.2-1_amd64.deb ... 111s Unpacking libgromacs-dev (2024.2-1) ... 111s Selecting previously unselected package mpi-default-bin. 111s Preparing to unpack .../69-mpi-default-bin_1.17_amd64.deb ... 111s Unpacking mpi-default-bin (1.17) ... 111s Selecting previously unselected package autopkgtest-satdep. 111s Preparing to unpack .../70-1-autopkgtest-satdep.deb ... 111s Unpacking autopkgtest-satdep (0) ... 111s Setting up libpciaccess0:amd64 (0.17-3build1) ... 111s Setting up fonts-mathjax (2.7.9+dfsg-1) ... 111s Setting up libjs-mathjax (2.7.9+dfsg-1) ... 111s Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10) ... 111s Setting up libibumad3:amd64 (52.0-2ubuntu1) ... 111s Setting up libibmad5:amd64 (52.0-2ubuntu1) ... 111s Setting up libgomp1:amd64 (14.2.0-8ubuntu1) ... 111s Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu4) ... 111s Setting up libblas3:amd64 (3.12.0-4) ... 111s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 111s Setting up libmunge2:amd64 (0.5.15-4build1) ... 111s Setting up libllvm17t64:amd64 (1:17.0.6-18) ... 111s Setting up libquadmath0:amd64 (14.2.0-8ubuntu1) ... 111s Setting up libhwloc15:amd64 (2.11.2-1) ... 111s Setting up libmpc3:amd64 (1.3.1-1build2) ... 111s Setting up libfftw3-double3:amd64 (3.3.10-1ubuntu4) ... 111s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 111s Setting up libubsan1:amd64 (14.2.0-8ubuntu1) ... 111s Setting up ocl-icd-libopencl1:amd64 (2.3.2-1build1) ... 111s Setting up libhwasan0:amd64 (14.2.0-8ubuntu1) ... 111s Setting up libasan8:amd64 (14.2.0-8ubuntu1) ... 111s Setting up sse4.2-support (26) ... 111s Setting up libpsm2-2 (11.2.185-2.1) ... 111s Setting up openmpi-common (5.0.5-6) ... 111s Setting up librdmacm1t64:amd64 (52.0-2ubuntu1) ... 111s Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3build2) ... 111s Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3build1) ... 111s update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode 111s Setting up libmuparser2v5:amd64 (2.3.4-1) ... 111s Setting up libtsan2:amd64 (14.2.0-8ubuntu1) ... 111s Setting up libisl23:amd64 (0.27-1) ... 111s Setting up libcc1-0:amd64 (14.2.0-8ubuntu1) ... 111s Setting up liblsan0:amd64 (14.2.0-8ubuntu1) ... 111s Setting up libitm1:amd64 (14.2.0-8ubuntu1) ... 111s Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ... 111s Setting up libfabric1:amd64 (1.17.0-3ubuntu1) ... 111s Setting up gromacs-data (2024.2-1) ... 111s Setting up liblapack3:amd64 (3.12.0-4) ... 111s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 111s Setting up libfftw3-single3:amd64 (3.3.10-1ubuntu4) ... 111s Setting up libfftw3-long3:amd64 (3.3.10-1ubuntu4) ... 111s Setting up libhwloc-plugins:amd64 (2.11.2-1) ... 111s Setting up libfftw3-quad3:amd64 (3.3.10-1ubuntu4) ... 111s Setting up cpp-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 111s Setting up libpmix2t64:amd64 (5.0.3-2) ... 111s Setting up cpp-14 (14.2.0-8ubuntu1) ... 111s Setting up libgcc-14-dev:amd64 (14.2.0-8ubuntu1) ... 111s Setting up libstdc++-14-dev:amd64 (14.2.0-8ubuntu1) ... 111s Setting up libhsakmt1:amd64 (5.7.0-1build1) ... 111s Setting up cpp-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 111s Setting up libfftw3-bin (3.3.10-1ubuntu4) ... 111s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 111s Setting up cpp (4:14.1.0-2ubuntu1) ... 111s Setting up gcc-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 111s Setting up libfftw3-dev:amd64 (3.3.10-1ubuntu4) ... 111s Setting up gcc-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 111s Setting up gcc-14 (14.2.0-8ubuntu1) ... 111s Setting up libamdhip64-5 (5.7.1-5) ... 111s Setting up g++-14-x86-64-linux-gnu (14.2.0-8ubuntu1) ... 111s Setting up g++-x86-64-linux-gnu (4:14.1.0-2ubuntu1) ... 111s Setting up g++-14 (14.2.0-8ubuntu1) ... 111s Setting up libucx0:amd64 (1.17.0+ds-3build1) ... 111s Setting up gcc (4:14.1.0-2ubuntu1) ... 111s Setting up libopenmpi3t64:amd64 (5.0.5-6) ... 111s Setting up g++ (4:14.1.0-2ubuntu1) ... 111s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 111s Setting up build-essential (12.10ubuntu1) ... 111s Setting up openmpi-bin (5.0.5-6) ... 111s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 111s update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist 111s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 111s Setting up libgromacs9:amd64 (2024.2-1) ... 111s Setting up mpi-default-bin (1.17) ... 111s Setting up gromacs (2024.2-1) ... 111s Setting up libgromacs-dev (2024.2-1) ... 111s Setting up libnblib-gmx0:amd64 (2024.2-1) ... 111s Setting up libnblib-gmx-dev (2024.2-1) ... 111s Setting up autopkgtest-satdep (0) ... 111s Processing triggers for man-db (2.13.0-1) ... 112s Processing triggers for libc-bin (2.40-1ubuntu3) ... 115s (Reading database ... 106160 files and directories currently installed.) 115s Removing autopkgtest-satdep (0) ... 115s autopkgtest [21:43:17]: test gromacs-regressiontests: [----------------------- 115s ======================================================== 115s Starting regression tests: basic build, single precision 115s ======================================================== 115s Testing acetonitrilRF . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/acetonitrilRF/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/acetonitrilRF/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/acetonitrilRF/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/acetonitrilRF/topol -maxwarn 10 >grompp.out 2>grompp.err 115s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/acetonitrilRF/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 115s gmx mdrun -nb cpu -notunepme >mdrun.out 2>&1 115s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/acetonitrilRF/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 116s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/acetonitrilRF/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 116s PASSED but check mdp file differences 116s Testing aminoacids . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/aminoacids/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/aminoacids/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/aminoacids/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/aminoacids/topol -maxwarn 10 >grompp.out 2>grompp.err 116s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/aminoacids/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 116s gmx mdrun -notunepme >mdrun.out 2>&1 116s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/aminoacids/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 116s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/aminoacids/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 116s PASSED but check mdp file differences 116s Testing argon . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/argon/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/argon/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/argon/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/argon/topol -maxwarn 10 >grompp.out 2>grompp.err 116s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/argon/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 116s gmx mdrun -nb cpu -notunepme >mdrun.out 2>&1 116s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/argon/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 116s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/argon/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 116s PASSED but check mdp file differences 116s Testing awh_multibias . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/index >grompp.out 2>grompp.err 116s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 116s gmx mdrun -notunepme -cpi /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/continue -noappend >mdrun.out 2>&1 116s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/reference_s.edr -e2 ener.part0002.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 116s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/reference_s.trr -f2 traj.part0002.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 116s PASSED but check mdp file differences 116s Testing awh_multidim . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim/index >grompp.out 2>grompp.err 116s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 116s gmx mdrun -notunepme >mdrun.out 2>&1 116s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 116s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 116s PASSED but check mdp file differences 116s Testing butane . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/butane/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/butane/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/butane/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/butane/topol -maxwarn 10 >grompp.out 2>grompp.err 116s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/butane/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 116s gmx mdrun -notunepme >mdrun.out 2>&1 116s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/butane/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 116s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/butane/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 116s PASSED but check mdp file differences 116s Testing cbt . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/cbt/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/cbt/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/cbt/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/cbt/topol -maxwarn 10 >grompp.out 2>grompp.err 116s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/cbt/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 116s gmx mdrun -nb cpu -notunepme >mdrun.out 2>&1 116s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/cbt/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 117s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/cbt/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 117s PASSED but check mdp file differences 117s Testing dd121 . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dd121/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dd121/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dd121/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dd121/topol -maxwarn 10 >grompp.out 2>grompp.err 117s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dd121/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 117s gmx mdrun -ntmpi 12 -notunepme >mdrun.out 2>&1 132s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dd121/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 132s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dd121/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 132s PASSED but check mdp file differences 132s Testing dec+water . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dec+water/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dec+water/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dec+water/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dec+water/topol -maxwarn 10 >grompp.out 2>grompp.err 132s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dec+water/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 132s gmx mdrun -nb cpu -notunepme >mdrun.out 2>&1 132s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dec+water/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 132s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dec+water/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 132s PASSED but check mdp file differences 132s Testing distance_restraints . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/distance_restraints/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/distance_restraints/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/distance_restraints/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/distance_restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 132s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/distance_restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 132s gmx mdrun -ntmpi 1 -notunepme >mdrun.out 2>&1 132s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/distance_restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 132s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/distance_restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 132s PASSED but check mdp file differences 132s Testing ethyleenglycol . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/ethyleenglycol/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/ethyleenglycol/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/ethyleenglycol/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/ethyleenglycol/topol -maxwarn 10 >grompp.out 2>grompp.err 132s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/ethyleenglycol/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 132s gmx mdrun -notunepme >mdrun.out 2>&1 133s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/ethyleenglycol/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 133s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/ethyleenglycol/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 133s PASSED but check mdp file differences 133s Testing field . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/field/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/field/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/field/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/field/topol -maxwarn 10 >grompp.out 2>grompp.err 133s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/field/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 133s gmx mdrun -notunepme >mdrun.out 2>&1 133s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/field/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 133s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/field/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 133s PASSED but check mdp file differences 133s Testing nacl . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nacl/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nacl/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nacl/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nacl/topol -maxwarn 10 >grompp.out 2>grompp.err 133s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nacl/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 133s gmx mdrun -notunepme >mdrun.out 2>&1 134s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nacl/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 134s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nacl/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 134s PASSED but check mdp file differences 134s Testing nbnxn-energy-groups . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-energy-groups/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-energy-groups/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-energy-groups/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-energy-groups/topol -maxwarn 10 >grompp.out 2>grompp.err 134s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-energy-groups/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 134s gmx mdrun -nb cpu -notunepme >mdrun.out 2>&1 134s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-energy-groups/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 134s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-energy-groups/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 134s PASSED but check mdp file differences 134s Testing nbnxn-free-energy . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy/topol -maxwarn 10 >grompp.out 2>grompp.err 134s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 134s gmx mdrun -notunepme >mdrun.out 2>&1 134s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 134s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 134s PASSED but check mdp file differences 134s Testing nbnxn-free-energy-vv . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy-vv/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy-vv/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy-vv/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy-vv/topol -maxwarn 10 >grompp.out 2>grompp.err 134s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy-vv/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 134s gmx mdrun -notunepme >mdrun.out 2>&1 135s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy-vv/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 135s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy-vv/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 135s PASSED but check mdp file differences 135s Testing nbnxn-ljpme-geometric . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-geometric/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-geometric/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-geometric/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-geometric/topol -maxwarn 10 >grompp.out 2>grompp.err 135s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-geometric/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 135s gmx mdrun -notunepme >mdrun.out 2>&1 135s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-geometric/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 135s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-geometric/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 135s PASSED but check mdp file differences 135s Testing nbnxn-ljpme-LB . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB/topol -maxwarn 10 >grompp.out 2>grompp.err 135s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 135s gmx mdrun -notunepme >mdrun.out 2>&1 136s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 136s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 136s PASSED but check mdp file differences 136s Testing nbnxn-ljpme-LB-geometric . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/topol -maxwarn 10 >grompp.out 2>grompp.err 136s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 136s gmx mdrun -notunepme >mdrun.out 2>&1 138s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 138s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 138s PASSED but check mdp file differences 138s Testing nbnxn-vdw-force-switch . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-force-switch/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-force-switch/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-force-switch/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-force-switch/topol -maxwarn 10 >grompp.out 2>grompp.err 138s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-force-switch/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 138s gmx mdrun -notunepme >mdrun.out 2>&1 138s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-force-switch/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 138s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-force-switch/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 138s PASSED but check mdp file differences 138s Testing nbnxn-vdw-potential-switch . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch/topol -maxwarn 10 >grompp.out 2>grompp.err 138s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 138s gmx mdrun -notunepme >mdrun.out 2>&1 138s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 138s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 138s PASSED but check mdp file differences 138s Testing nbnxn-vdw-potential-switch-argon . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/topol -maxwarn 10 >grompp.out 2>grompp.err 138s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 138s gmx mdrun -notunepme >mdrun.out 2>&1 138s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 138s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 138s PASSED but check mdp file differences 138s Testing nbnxn_pme . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme/topol -maxwarn 10 >grompp.out 2>grompp.err 138s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 138s gmx mdrun -notunepme >mdrun.out 2>&1 139s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 139s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 139s PASSED but check mdp file differences 139s Testing nbnxn_pme_order5 . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order5/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order5/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order5/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order5/topol -maxwarn 10 >grompp.out 2>grompp.err 139s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order5/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 139s gmx mdrun -notunepme >mdrun.out 2>&1 139s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order5/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 139s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order5/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 139s PASSED but check mdp file differences 139s Testing nbnxn_pme_order6 . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order6/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order6/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order6/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order6/topol -maxwarn 10 >grompp.out 2>grompp.err 139s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order6/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 139s gmx mdrun -notunepme >mdrun.out 2>&1 139s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order6/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 139s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order6/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 140s PASSED but check mdp file differences 140s Testing nbnxn_rf . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rf/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rf/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rf/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rf/topol -maxwarn 10 >grompp.out 2>grompp.err 140s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rf/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 140s gmx mdrun -notunepme >mdrun.out 2>&1 140s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rf/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 140s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rf/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 140s PASSED but check mdp file differences 140s Testing nbnxn_rzero . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rzero/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rzero/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rzero/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rzero/topol -maxwarn 10 >grompp.out 2>grompp.err 140s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rzero/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 140s gmx mdrun -notunepme >mdrun.out 2>&1 140s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rzero/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 140s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rzero/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 140s PASSED but check mdp file differences 140s Testing nbnxn_vsite . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_vsite/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_vsite/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_vsite/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_vsite/topol -maxwarn 10 >grompp.out 2>grompp.err 140s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_vsite/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 140s gmx mdrun -ntmpi 6 -notunepme >mdrun.out 2>&1 147s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_vsite/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 147s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_vsite/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 147s PASSED but check mdp file differences 147s Testing nst_mismatch . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nst_mismatch/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nst_mismatch/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nst_mismatch/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nst_mismatch/topol -maxwarn 10 >grompp.out 2>grompp.err 147s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nst_mismatch/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 147s gmx mdrun -notunepme >mdrun.out 2>&1 147s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nst_mismatch/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 147s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nst_mismatch/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 147s PASSED but check mdp file differences 147s Testing octahedron . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/octahedron/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/octahedron/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/octahedron/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/octahedron/topol -maxwarn 10 >grompp.out 2>grompp.err 147s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/octahedron/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 147s gmx mdrun -notunepme >mdrun.out 2>&1 148s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/octahedron/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 148s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/octahedron/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 148s PASSED but check mdp file differences 148s Testing orientation-restraints . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/orientation-restraints/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/orientation-restraints/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/orientation-restraints/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/orientation-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 148s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/orientation-restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 148s gmx mdrun -ntmpi 1 -notunepme >mdrun.out 2>&1 152s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/orientation-restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 152s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/orientation-restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 152s PASSED but check mdp file differences 152s Testing position-restraints . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/position-restraints/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/position-restraints/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/position-restraints/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/position-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 152s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/position-restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 152s gmx mdrun -notunepme >mdrun.out 2>&1 152s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/position-restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 152s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/position-restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 152s PASSED but check mdp file differences 152s Testing pr-vrescale . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pr-vrescale/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pr-vrescale/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pr-vrescale/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pr-vrescale/topol -maxwarn 10 >grompp.out 2>grompp.err 152s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pr-vrescale/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 152s gmx mdrun -notunepme >mdrun.out 2>&1 153s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pr-vrescale/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 153s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pr-vrescale/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 153s PASSED but check mdp file differences 153s Testing pull_constraint . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint/index >grompp.out 2>grompp.err 153s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 153s gmx mdrun -notunepme >mdrun.out 2>&1 153s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 153s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 153s PASSED but check mdp file differences 153s Testing pull_cylinder . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder/index >grompp.out 2>grompp.err 153s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 153s gmx mdrun -notunepme >mdrun.out 2>&1 153s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 153s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 153s PASSED but check mdp file differences 153s Testing pull_geometry_angle . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle/index >grompp.out 2>grompp.err 153s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 153s gmx mdrun -notunepme >mdrun.out 2>&1 154s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 154s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 154s PASSED but check mdp file differences 154s Testing pull_geometry_angle-axis . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis/index >grompp.out 2>grompp.err 154s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 154s gmx mdrun -notunepme >mdrun.out 2>&1 154s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 154s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 154s PASSED but check mdp file differences 154s Testing pull_geometry_dihedral . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral/index >grompp.out 2>grompp.err 154s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 154s gmx mdrun -notunepme >mdrun.out 2>&1 154s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 154s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 154s PASSED but check mdp file differences 154s Testing reb . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/reb/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/reb/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/reb/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/reb/topol -maxwarn 10 >grompp.out 2>grompp.err 154s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/reb/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 154s gmx mdrun -nb cpu -notunepme >mdrun.out 2>&1 155s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/reb/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 155s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/reb/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 155s PASSED but check mdp file differences 155s Testing sw . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/sw/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/sw/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/sw/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/sw/topol -maxwarn 10 >grompp.out 2>grompp.err 155s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/sw/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 155s gmx mdrun -ntmpi 1 -notunepme >mdrun.out 2>&1 155s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/sw/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 155s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/sw/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 155s PASSED but check mdp file differences 155s Testing swap_x . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x/index >grompp.out 2>grompp.err 155s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 155s gmx mdrun -notunepme >mdrun.out 2>&1 156s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 156s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 156s PASSED but check mdp file differences 156s Testing swap_y . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y/index >grompp.out 2>grompp.err 156s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 156s gmx mdrun -notunepme >mdrun.out 2>&1 157s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 157s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 157s PASSED but check mdp file differences 157s Testing swap_z . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z/index >grompp.out 2>grompp.err 158s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 158s gmx mdrun -notunepme >mdrun.out 2>&1 158s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 158s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 158s PASSED but check mdp file differences 158s Testing tip4p . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p/topol -maxwarn 10 >grompp.out 2>grompp.err 159s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 159s gmx mdrun -notunepme >mdrun.out 2>&1 159s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 159s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 159s PASSED but check mdp file differences 159s Testing tip4p_continue . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/topol -maxwarn 10 >grompp.out 2>grompp.err 159s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 159s gmx mdrun -notunepme -cpi /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/continue -noappend >mdrun.out 2>&1 159s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/reference_s.edr -e2 ener.part0002.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 159s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/reference_s.trr -f2 traj.part0002.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 159s PASSED but check mdp file differences 159s Testing tip4pflex . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4pflex/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4pflex/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4pflex/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4pflex/topol -maxwarn 10 >grompp.out 2>grompp.err 159s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4pflex/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 159s gmx mdrun -notunepme >mdrun.out 2>&1 160s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4pflex/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 160s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4pflex/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 160s PASSED but check mdp file differences 160s Testing urea . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/urea/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/urea/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/urea/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/urea/topol -maxwarn 10 >grompp.out 2>grompp.err 160s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/urea/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 160s gmx mdrun -notunepme >mdrun.out 2>&1 160s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/urea/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 160s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/urea/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 160s PASSED but check mdp file differences 160s Testing walls . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/walls/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/walls/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/walls/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/walls/topol -maxwarn 10 >grompp.out 2>grompp.err 160s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/walls/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 160s gmx mdrun -notunepme >mdrun.out 2>&1 160s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/walls/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 160s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/walls/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 160s PASSED but check mdp file differences 160s All 48 complex tests PASSED 160s Testing coulandvdwsequential_coul . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_coul/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_coul/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_coul/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_coul/topol -maxwarn 10 >grompp.out 2>grompp.err 161s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_coul/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 161s gmx mdrun -notunepme >mdrun.out 2>&1 161s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_coul/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 161s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_coul/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 161s PASSED but check mdp file differences 161s Testing coulandvdwsequential_vdw . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_vdw/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_vdw/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_vdw/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_vdw/topol -maxwarn 10 >grompp.out 2>grompp.err 161s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_vdw/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 161s gmx mdrun -notunepme >mdrun.out 2>&1 162s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_vdw/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 162s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_vdw/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 162s PASSED but check mdp file differences 162s Testing coulandvdwtogether . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwtogether/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwtogether/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwtogether/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwtogether/topol -maxwarn 10 >grompp.out 2>grompp.err 162s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwtogether/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 162s gmx mdrun -notunepme >mdrun.out 2>&1 163s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwtogether/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 163s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwtogether/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 163s PASSED but check mdp file differences 163s Testing expanded . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/expanded/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/expanded/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/expanded/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/expanded/topol -maxwarn 10 >grompp.out 2>grompp.err 163s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/expanded/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 163s gmx mdrun -notunepme >mdrun.out 2>&1 163s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/expanded/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 163s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/expanded/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 163s PASSED but check mdp file differences 163s Testing relative . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative/topol -maxwarn 10 >grompp.out 2>grompp.err 164s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 164s gmx mdrun -notunepme >mdrun.out 2>&1 165s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 165s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 165s PASSED but check mdp file differences 165s Testing relative-position-restraints . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative-position-restraints/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative-position-restraints/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative-position-restraints/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative-position-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 165s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative-position-restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 165s gmx mdrun -notunepme >mdrun.out 2>&1 166s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative-position-restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 166s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative-position-restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 166s PASSED but check mdp file differences 166s Testing restraints . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/restraints/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/restraints/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/restraints/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 167s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 167s gmx mdrun -notunepme >mdrun.out 2>&1 179s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 179s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 179s PASSED but check mdp file differences 179s Testing simtemp . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/simtemp/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/simtemp/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/simtemp/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/simtemp/topol -maxwarn 10 >grompp.out 2>grompp.err 179s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/simtemp/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 179s gmx mdrun -notunepme >mdrun.out 2>&1 179s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/simtemp/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 179s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/simtemp/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 179s PASSED but check mdp file differences 179s Testing transformAtoB . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/transformAtoB/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/transformAtoB/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/transformAtoB/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/transformAtoB/topol -maxwarn 10 >grompp.out 2>grompp.err 179s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/transformAtoB/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 179s gmx mdrun -notunepme >mdrun.out 2>&1 180s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/transformAtoB/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 180s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/transformAtoB/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 180s PASSED but check mdp file differences 180s Testing vdwalone . . . gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/vdwalone/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/vdwalone/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/vdwalone/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/vdwalone/topol -maxwarn 10 >grompp.out 2>grompp.err 180s gmx check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/vdwalone/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 180s gmx mdrun -notunepme >mdrun.out 2>&1 180s gmx check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/vdwalone/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 180s gmx check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/vdwalone/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 180s PASSED but check mdp file differences 180s All 10 freeenergy tests PASSED 180s All 0 extra tests PASSED 180s Testing linfix . . . 180s gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix/topol -maxwarn 2 >grompp.out 2>grompp.err 180s echo 0 | gmx make_edi -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix/eigenvec.trr -outfrq 1 -linfix 1 -linstep 0.0013 -o sam.edi 1>make_edi.out 2>make_edi.err 180s gmx mdrun -ei sam.edi -eo linfix.xvg >mdrun.out 2>&1 180s Comparing column #0 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix/edsam_reference.xvg and linfix.xvg ... all within tolerance of 0 180s Comparing column #1 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix/edsam_reference.xvg and linfix.xvg ... all within tolerance of 0.05 180s Comparing column #2 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix/edsam_reference.xvg and linfix.xvg ... all within tolerance of 1e-06 180s Testing linacc . . . 180s gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc/topol -maxwarn 2 >grompp.out 2>grompp.err 180s echo 0 | gmx make_edi -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc/eigenvec.trr -outfrq 2 -linacc 1 -accdir +1 -o sam.edi 1>make_edi.out 2>make_edi.err 180s gmx mdrun -ei sam.edi -eo linacc.xvg >mdrun.out 2>&1 180s Comparing column #0 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc/edsam_reference.xvg and linacc.xvg ... all within tolerance of 0 180s Comparing column #1 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc/edsam_reference.xvg and linacc.xvg ... all within tolerance of 0.005 180s Comparing column #2 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc/edsam_reference.xvg and linacc.xvg ... all within tolerance of 0.001 180s Checking monotonicity for column 2 of file linacc.xvg ... values of column 2 are increasing monotonically. 180s Testing radfix . . . 180s gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix/topol -maxwarn 2 >grompp.out 2>grompp.err 180s echo 0 | gmx make_edi -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix/eigenvec.trr -outfrq 1 -radfix 1-2 -radstep 0.002 -o sam.edi 1>make_edi.out 2>make_edi.err 180s gmx mdrun -ei sam.edi -eo radfix.xvg >mdrun.out 2>&1 180s Comparing column #0 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix/edsam_reference.xvg and radfix.xvg ... all within tolerance of 0 180s Comparing column #1 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix/edsam_reference.xvg and radfix.xvg ... all within tolerance of 0.05 180s Comparing column #4 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix/edsam_reference.xvg and radfix.xvg ... all within tolerance of 0 180s Checking radius for file radfix.xvg ... all values within tolerance of 1e-05 180s Testing radacc . . . 180s gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radacc/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radacc/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radacc/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radacc/topol -maxwarn 2 >grompp.out 2>grompp.err 180s echo 0 | gmx make_edi -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radacc/eigenvec.trr -outfrq 3 -radacc 1-2 -o sam.edi 1>make_edi.out 2>make_edi.err 180s gmx mdrun -ei sam.edi -eo radacc.xvg >mdrun.out 2>&1 180s Comparing column #0 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radacc/edsam_reference.xvg and radacc.xvg ... all within tolerance of 0 180s Comparing column #1 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radacc/edsam_reference.xvg and radacc.xvg ... all within tolerance of 0.05 180s Checking radius for file radacc.xvg ... all values within tolerance of 1e-05 180s Checking monotonicity for column 4 of file radacc.xvg ... values of column 4 are increasing monotonically. 180s Testing radcon . . . 180s gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon/topol -maxwarn 2 >grompp.out 2>grompp.err 180s echo 0 0 | gmx make_edi -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon/eigenvec.trr -outfrq 1 -radcon 1-2 -tar /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon/target.pdb -o sam.edi 1>make_edi.out 2>make_edi.err 180s gmx mdrun -ei sam.edi -eo radcon.xvg >mdrun.out 2>&1 180s Comparing column #0 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon/edsam_reference.xvg and radcon.xvg ... all within tolerance of 0 180s Comparing column #1 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon/edsam_reference.xvg and radcon.xvg ... all within tolerance of 0.05 180s Checking radius for file radcon.xvg ... all values within tolerance of 1e-05 180s Checking monotonicity for column 4 of file radcon.xvg ... values of column 4 are decreasing monotonically. 180s Testing flooding1 . . . 180s gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/topol -maxwarn 2 >grompp.out 2>grompp.err 181s gmx mdrun -ei /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/sam.edi -eo flooding1.xvg >mdrun.out 2>&1 181s Comparing column #0 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 0 181s Comparing column #1 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1e-05 181s Comparing column #2 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1e-05 181s Comparing column #3 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1 181s Comparing column #4 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1 181s Comparing column #5 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1e-05 181s Comparing column #6 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1 181s Comparing column #7 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1 181s Testing flooding2 . . . 181s gmx grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/topol -maxwarn 2 >grompp.out 2>grompp.err 181s gmx mdrun -ei /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/sam.edi -eo flooding2.xvg >mdrun.out 2>&1 182s Comparing column #0 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 0 182s Comparing column #1 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 0.05 182s Comparing column #2 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 0.025 182s Comparing column #3 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 250 182s Comparing column #4 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 1000 182s Comparing column #5 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 0.025 182s Comparing column #6 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 250 182s Comparing column #7 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 1000 182s All 7 essential dynamics tests PASSED 182s ======================================================== 182s Starting regression tests: basic build, double precision 182s ======================================================== 182s Testing acetonitrilRF . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/acetonitrilRF/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/acetonitrilRF/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/acetonitrilRF/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/acetonitrilRF/topol -maxwarn 10 >grompp.out 2>grompp.err 182s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/acetonitrilRF/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 182s gmx_d mdrun -nb cpu -notunepme >mdrun.out 2>&1 182s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/acetonitrilRF/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 182s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/acetonitrilRF/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 182s PASSED but check mdp file differences 182s Testing aminoacids . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/aminoacids/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/aminoacids/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/aminoacids/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/aminoacids/topol -maxwarn 10 >grompp.out 2>grompp.err 182s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/aminoacids/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 182s gmx_d mdrun -notunepme >mdrun.out 2>&1 183s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/aminoacids/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 183s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/aminoacids/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 183s PASSED but check mdp file differences 183s Testing argon . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/argon/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/argon/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/argon/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/argon/topol -maxwarn 10 >grompp.out 2>grompp.err 183s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/argon/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 183s gmx_d mdrun -nb cpu -notunepme >mdrun.out 2>&1 183s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/argon/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 183s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/argon/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 183s PASSED but check mdp file differences 183s Testing awh_multibias . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/index >grompp.out 2>grompp.err 183s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 183s gmx_d mdrun -notunepme -cpi /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/continue -noappend >mdrun.out 2>&1 183s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/reference_d.edr -e2 ener.part0002.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 183s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/reference_d.trr -f2 traj.part0002.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 183s PASSED but check mdp file differences 183s Testing awh_multidim . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim/index >grompp.out 2>grompp.err 183s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 183s gmx_d mdrun -notunepme >mdrun.out 2>&1 183s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 183s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 183s PASSED but check mdp file differences 183s Testing butane . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/butane/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/butane/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/butane/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/butane/topol -maxwarn 10 >grompp.out 2>grompp.err 183s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/butane/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 183s gmx_d mdrun -notunepme >mdrun.out 2>&1 183s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/butane/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 183s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/butane/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 183s PASSED but check mdp file differences 183s Testing cbt . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/cbt/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/cbt/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/cbt/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/cbt/topol -maxwarn 10 >grompp.out 2>grompp.err 183s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/cbt/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 183s gmx_d mdrun -nb cpu -notunepme >mdrun.out 2>&1 183s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/cbt/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 183s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/cbt/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 183s PASSED but check mdp file differences 183s Testing dd121 . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dd121/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dd121/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dd121/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dd121/topol -maxwarn 10 >grompp.out 2>grompp.err 183s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dd121/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 183s gmx_d mdrun -ntmpi 12 -notunepme >mdrun.out 2>&1 199s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dd121/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 199s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dd121/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 199s PASSED but check mdp file differences 199s Testing dec+water . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dec+water/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dec+water/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dec+water/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dec+water/topol -maxwarn 10 >grompp.out 2>grompp.err 199s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dec+water/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 199s gmx_d mdrun -nb cpu -notunepme >mdrun.out 2>&1 199s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dec+water/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 199s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dec+water/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 199s PASSED but check mdp file differences 199s Testing distance_restraints . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/distance_restraints/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/distance_restraints/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/distance_restraints/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/distance_restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 199s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/distance_restraints/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 199s gmx_d mdrun -ntmpi 1 -notunepme >mdrun.out 2>&1 199s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/distance_restraints/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 199s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/distance_restraints/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 199s PASSED but check mdp file differences 199s Testing ethyleenglycol . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/ethyleenglycol/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/ethyleenglycol/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/ethyleenglycol/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/ethyleenglycol/topol -maxwarn 10 >grompp.out 2>grompp.err 199s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/ethyleenglycol/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 199s gmx_d mdrun -notunepme >mdrun.out 2>&1 199s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/ethyleenglycol/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 199s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/ethyleenglycol/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 199s PASSED but check mdp file differences 199s Testing field . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/field/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/field/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/field/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/field/topol -maxwarn 10 >grompp.out 2>grompp.err 200s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/field/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 200s gmx_d mdrun -notunepme >mdrun.out 2>&1 200s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/field/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 200s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/field/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 200s PASSED but check mdp file differences 200s Testing nacl . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nacl/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nacl/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nacl/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nacl/topol -maxwarn 10 >grompp.out 2>grompp.err 200s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nacl/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 200s gmx_d mdrun -notunepme >mdrun.out 2>&1 201s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nacl/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 201s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nacl/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 201s PASSED but check mdp file differences 201s Testing nbnxn-energy-groups . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-energy-groups/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-energy-groups/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-energy-groups/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-energy-groups/topol -maxwarn 10 >grompp.out 2>grompp.err 201s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-energy-groups/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 201s gmx_d mdrun -nb cpu -notunepme >mdrun.out 2>&1 201s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-energy-groups/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 201s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-energy-groups/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 201s PASSED but check mdp file differences 201s Testing nbnxn-free-energy . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy/topol -maxwarn 10 >grompp.out 2>grompp.err 201s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 201s gmx_d mdrun -notunepme >mdrun.out 2>&1 201s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 201s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 201s PASSED but check mdp file differences 201s Testing nbnxn-free-energy-vv . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy-vv/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy-vv/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy-vv/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy-vv/topol -maxwarn 10 >grompp.out 2>grompp.err 201s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy-vv/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 201s gmx_d mdrun -notunepme >mdrun.out 2>&1 202s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy-vv/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 202s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy-vv/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 202s PASSED but check mdp file differences 202s Testing nbnxn-ljpme-geometric . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-geometric/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-geometric/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-geometric/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-geometric/topol -maxwarn 10 >grompp.out 2>grompp.err 202s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-geometric/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 202s gmx_d mdrun -notunepme >mdrun.out 2>&1 202s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-geometric/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 202s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-geometric/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 202s PASSED but check mdp file differences 202s Testing nbnxn-ljpme-LB . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB/topol -maxwarn 10 >grompp.out 2>grompp.err 202s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 202s gmx_d mdrun -notunepme >mdrun.out 2>&1 203s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 203s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 203s PASSED but check mdp file differences 203s Testing nbnxn-ljpme-LB-geometric . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/topol -maxwarn 10 >grompp.out 2>grompp.err 203s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 203s gmx_d mdrun -notunepme >mdrun.out 2>&1 204s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 204s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 204s PASSED but check mdp file differences 204s Testing nbnxn-vdw-force-switch . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-force-switch/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-force-switch/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-force-switch/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-force-switch/topol -maxwarn 10 >grompp.out 2>grompp.err 204s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-force-switch/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 204s gmx_d mdrun -notunepme >mdrun.out 2>&1 205s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-force-switch/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 205s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-force-switch/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 205s PASSED but check mdp file differences 205s Testing nbnxn-vdw-potential-switch . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch/topol -maxwarn 10 >grompp.out 2>grompp.err 205s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 205s gmx_d mdrun -notunepme >mdrun.out 2>&1 205s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 205s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 205s PASSED but check mdp file differences 205s Testing nbnxn-vdw-potential-switch-argon . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/topol -maxwarn 10 >grompp.out 2>grompp.err 205s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 205s gmx_d mdrun -notunepme >mdrun.out 2>&1 205s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 205s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 205s PASSED but check mdp file differences 205s Testing nbnxn_pme . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme/topol -maxwarn 10 >grompp.out 2>grompp.err 205s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 205s gmx_d mdrun -notunepme >mdrun.out 2>&1 206s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 206s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 206s PASSED but check mdp file differences 206s Testing nbnxn_pme_order5 . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order5/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order5/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order5/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order5/topol -maxwarn 10 >grompp.out 2>grompp.err 206s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order5/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 206s gmx_d mdrun -notunepme >mdrun.out 2>&1 206s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order5/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 206s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order5/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 206s PASSED but check mdp file differences 206s Testing nbnxn_pme_order6 . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order6/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order6/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order6/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order6/topol -maxwarn 10 >grompp.out 2>grompp.err 206s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order6/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 206s gmx_d mdrun -notunepme >mdrun.out 2>&1 206s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order6/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 206s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order6/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 206s PASSED but check mdp file differences 206s Testing nbnxn_rf . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rf/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rf/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rf/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rf/topol -maxwarn 10 >grompp.out 2>grompp.err 206s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rf/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 206s gmx_d mdrun -notunepme >mdrun.out 2>&1 207s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rf/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 207s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rf/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 207s PASSED but check mdp file differences 207s Testing nbnxn_rzero . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rzero/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rzero/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rzero/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rzero/topol -maxwarn 10 >grompp.out 2>grompp.err 207s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rzero/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 207s gmx_d mdrun -notunepme >mdrun.out 2>&1 207s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rzero/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 207s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rzero/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 207s PASSED but check mdp file differences 207s Testing nbnxn_vsite . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_vsite/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_vsite/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_vsite/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_vsite/topol -maxwarn 10 >grompp.out 2>grompp.err 207s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_vsite/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 207s gmx_d mdrun -ntmpi 6 -notunepme >mdrun.out 2>&1 213s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_vsite/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 213s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_vsite/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 213s PASSED but check mdp file differences 213s Testing nst_mismatch . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nst_mismatch/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nst_mismatch/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nst_mismatch/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nst_mismatch/topol -maxwarn 10 >grompp.out 2>grompp.err 213s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nst_mismatch/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 213s gmx_d mdrun -notunepme >mdrun.out 2>&1 213s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nst_mismatch/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 213s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nst_mismatch/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 213s PASSED but check mdp file differences 213s Testing octahedron . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/octahedron/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/octahedron/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/octahedron/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/octahedron/topol -maxwarn 10 >grompp.out 2>grompp.err 213s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/octahedron/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 213s gmx_d mdrun -notunepme >mdrun.out 2>&1 214s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/octahedron/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 214s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/octahedron/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 214s PASSED but check mdp file differences 214s Testing orientation-restraints . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/orientation-restraints/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/orientation-restraints/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/orientation-restraints/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/orientation-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 214s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/orientation-restraints/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 214s gmx_d mdrun -ntmpi 1 -notunepme >mdrun.out 2>&1 218s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/orientation-restraints/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 218s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/orientation-restraints/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 219s PASSED but check mdp file differences 219s Testing position-restraints . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/position-restraints/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/position-restraints/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/position-restraints/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/position-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 219s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/position-restraints/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 219s gmx_d mdrun -notunepme >mdrun.out 2>&1 219s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/position-restraints/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 219s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/position-restraints/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 219s PASSED but check mdp file differences 219s Testing pr-vrescale . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pr-vrescale/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pr-vrescale/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pr-vrescale/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pr-vrescale/topol -maxwarn 10 >grompp.out 2>grompp.err 219s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pr-vrescale/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 219s gmx_d mdrun -notunepme >mdrun.out 2>&1 219s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pr-vrescale/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 219s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pr-vrescale/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 219s PASSED but check mdp file differences 219s Testing pull_constraint . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint/index >grompp.out 2>grompp.err 220s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 220s gmx_d mdrun -notunepme >mdrun.out 2>&1 220s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 220s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 220s PASSED but check mdp file differences 220s Testing pull_cylinder . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder/index >grompp.out 2>grompp.err 220s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 220s gmx_d mdrun -notunepme >mdrun.out 2>&1 220s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 220s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 220s PASSED but check mdp file differences 220s Testing pull_geometry_angle . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle/index >grompp.out 2>grompp.err 220s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 220s gmx_d mdrun -notunepme >mdrun.out 2>&1 220s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 220s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 220s PASSED but check mdp file differences 220s Testing pull_geometry_angle-axis . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis/index >grompp.out 2>grompp.err 220s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 220s gmx_d mdrun -notunepme >mdrun.out 2>&1 221s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 221s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 221s PASSED but check mdp file differences 221s Testing pull_geometry_dihedral . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral/index >grompp.out 2>grompp.err 221s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 221s gmx_d mdrun -notunepme >mdrun.out 2>&1 221s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 221s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 221s PASSED but check mdp file differences 221s Testing reb . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/reb/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/reb/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/reb/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/reb/topol -maxwarn 10 >grompp.out 2>grompp.err 221s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/reb/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 221s gmx_d mdrun -nb cpu -notunepme >mdrun.out 2>&1 221s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/reb/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 221s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/reb/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 221s PASSED but check mdp file differences 221s Testing sw . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/sw/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/sw/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/sw/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/sw/topol -maxwarn 10 >grompp.out 2>grompp.err 221s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/sw/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 221s gmx_d mdrun -ntmpi 1 -notunepme >mdrun.out 2>&1 222s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/sw/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 222s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/sw/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 222s PASSED but check mdp file differences 222s Testing swap_x . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x/index >grompp.out 2>grompp.err 222s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 222s gmx_d mdrun -notunepme >mdrun.out 2>&1 223s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 223s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 223s PASSED but check mdp file differences 223s Testing swap_y . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y/index >grompp.out 2>grompp.err 223s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 223s gmx_d mdrun -notunepme >mdrun.out 2>&1 224s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 224s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 224s PASSED but check mdp file differences 224s Testing swap_z . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z/index >grompp.out 2>grompp.err 225s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 225s gmx_d mdrun -notunepme >mdrun.out 2>&1 225s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 225s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 226s PASSED but check mdp file differences 226s Testing tip4p . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p/topol -maxwarn 10 >grompp.out 2>grompp.err 226s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 226s gmx_d mdrun -notunepme >mdrun.out 2>&1 226s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 226s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 226s PASSED but check mdp file differences 226s Testing tip4p_continue . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/topol -maxwarn 10 >grompp.out 2>grompp.err 226s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 226s gmx_d mdrun -notunepme -cpi /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/continue -noappend >mdrun.out 2>&1 227s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/reference_d.edr -e2 ener.part0002.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 227s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/reference_d.trr -f2 traj.part0002.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 227s PASSED but check mdp file differences 227s Testing tip4pflex . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4pflex/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4pflex/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4pflex/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4pflex/topol -maxwarn 10 >grompp.out 2>grompp.err 227s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4pflex/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 227s gmx_d mdrun -notunepme >mdrun.out 2>&1 227s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4pflex/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 227s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4pflex/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 227s PASSED but check mdp file differences 227s Testing urea . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/urea/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/urea/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/urea/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/urea/topol -maxwarn 10 >grompp.out 2>grompp.err 227s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/urea/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 227s gmx_d mdrun -notunepme >mdrun.out 2>&1 227s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/urea/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 227s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/urea/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 227s PASSED but check mdp file differences 227s Testing walls . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/walls/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/walls/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/walls/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/walls/topol -maxwarn 10 >grompp.out 2>grompp.err 227s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/walls/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 227s gmx_d mdrun -notunepme >mdrun.out 2>&1 228s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/walls/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 228s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/walls/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 228s PASSED but check mdp file differences 228s All 48 complex tests PASSED 228s Testing coulandvdwsequential_coul . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_coul/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_coul/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_coul/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_coul/topol -maxwarn 10 >grompp.out 2>grompp.err 228s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_coul/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 228s gmx_d mdrun -notunepme >mdrun.out 2>&1 229s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_coul/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 229s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_coul/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 229s PASSED but check mdp file differences 229s Testing coulandvdwsequential_vdw . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_vdw/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_vdw/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_vdw/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_vdw/topol -maxwarn 10 >grompp.out 2>grompp.err 229s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_vdw/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 229s gmx_d mdrun -notunepme >mdrun.out 2>&1 230s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_vdw/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 230s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_vdw/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 230s PASSED but check mdp file differences 230s Testing coulandvdwtogether . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwtogether/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwtogether/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwtogether/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwtogether/topol -maxwarn 10 >grompp.out 2>grompp.err 230s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwtogether/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 230s gmx_d mdrun -notunepme >mdrun.out 2>&1 231s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwtogether/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 231s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwtogether/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 231s PASSED but check mdp file differences 231s Testing expanded . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/expanded/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/expanded/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/expanded/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/expanded/topol -maxwarn 10 >grompp.out 2>grompp.err 231s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/expanded/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 231s gmx_d mdrun -notunepme >mdrun.out 2>&1 232s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/expanded/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 232s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/expanded/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 232s PASSED but check mdp file differences 232s Testing relative . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative/topol -maxwarn 10 >grompp.out 2>grompp.err 232s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 232s gmx_d mdrun -notunepme >mdrun.out 2>&1 233s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 233s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 233s PASSED but check mdp file differences 233s Testing relative-position-restraints . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative-position-restraints/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative-position-restraints/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative-position-restraints/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative-position-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 233s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative-position-restraints/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 233s gmx_d mdrun -notunepme >mdrun.out 2>&1 234s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative-position-restraints/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 234s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative-position-restraints/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 234s PASSED but check mdp file differences 234s Testing restraints . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/restraints/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/restraints/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/restraints/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 234s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/restraints/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 234s gmx_d mdrun -notunepme >mdrun.out 2>&1 247s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/restraints/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 247s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/restraints/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 247s PASSED but check mdp file differences 247s Testing simtemp . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/simtemp/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/simtemp/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/simtemp/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/simtemp/topol -maxwarn 10 >grompp.out 2>grompp.err 248s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/simtemp/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 248s gmx_d mdrun -notunepme >mdrun.out 2>&1 248s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/simtemp/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 248s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/simtemp/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 248s PASSED but check mdp file differences 248s Testing transformAtoB . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/transformAtoB/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/transformAtoB/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/transformAtoB/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/transformAtoB/topol -maxwarn 10 >grompp.out 2>grompp.err 248s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/transformAtoB/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 248s gmx_d mdrun -notunepme >mdrun.out 2>&1 248s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/transformAtoB/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 248s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/transformAtoB/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 248s PASSED but check mdp file differences 248s Testing vdwalone . . . gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/vdwalone/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/vdwalone/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/vdwalone/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/vdwalone/topol -maxwarn 10 >grompp.out 2>grompp.err 249s gmx_d check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/vdwalone/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 249s gmx_d mdrun -notunepme >mdrun.out 2>&1 249s gmx_d check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/vdwalone/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 249s gmx_d check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/vdwalone/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 249s PASSED but check mdp file differences 249s All 10 freeenergy tests PASSED 249s All 0 extra tests PASSED 249s Testing linfix . . . 249s gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix/topol -maxwarn 2 >grompp.out 2>grompp.err 249s echo 0 | gmx_d make_edi -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix/eigenvec.trr -outfrq 1 -linfix 1 -linstep 0.0013 -o sam.edi 1>make_edi.out 2>make_edi.err 249s gmx_d mdrun -ei sam.edi -eo linfix.xvg >mdrun.out 2>&1 249s Comparing column #0 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix/edsam_reference.xvg and linfix.xvg ... all within tolerance of 0 249s Comparing column #1 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix/edsam_reference.xvg and linfix.xvg ... all within tolerance of 0.05 249s Comparing column #2 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix/edsam_reference.xvg and linfix.xvg ... all within tolerance of 1e-06 249s Testing linacc . . . 249s gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc/topol -maxwarn 2 >grompp.out 2>grompp.err 249s echo 0 | gmx_d make_edi -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc/eigenvec.trr -outfrq 2 -linacc 1 -accdir +1 -o sam.edi 1>make_edi.out 2>make_edi.err 249s gmx_d mdrun -ei sam.edi -eo linacc.xvg >mdrun.out 2>&1 249s Comparing column #0 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc/edsam_reference.xvg and linacc.xvg ... all within tolerance of 0 249s Comparing column #1 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc/edsam_reference.xvg and linacc.xvg ... all within tolerance of 0.005 249s Comparing column #2 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc/edsam_reference.xvg and linacc.xvg ... all within tolerance of 0.001 249s Checking monotonicity for column 2 of file linacc.xvg ... values of column 2 are increasing monotonically. 249s Testing radfix . . . 249s gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix/topol -maxwarn 2 >grompp.out 2>grompp.err 249s echo 0 | gmx_d make_edi -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix/eigenvec.trr -outfrq 1 -radfix 1-2 -radstep 0.002 -o sam.edi 1>make_edi.out 2>make_edi.err 249s gmx_d mdrun -ei sam.edi -eo radfix.xvg >mdrun.out 2>&1 249s Comparing column #0 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix/edsam_reference.xvg and radfix.xvg ... all within tolerance of 0 249s Comparing column #1 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix/edsam_reference.xvg and radfix.xvg ... all within tolerance of 0.05 249s Comparing column #4 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix/edsam_reference.xvg and radfix.xvg ... all within tolerance of 0 249s Checking radius for file radfix.xvg ... all values within tolerance of 1e-05 249s Testing radacc . . . 249s gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radacc/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radacc/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radacc/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radacc/topol -maxwarn 2 >grompp.out 2>grompp.err 249s echo 0 | gmx_d make_edi -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radacc/eigenvec.trr -outfrq 3 -radacc 1-2 -o sam.edi 1>make_edi.out 2>make_edi.err 249s gmx_d mdrun -ei sam.edi -eo radacc.xvg >mdrun.out 2>&1 249s Comparing column #0 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radacc/edsam_reference.xvg and radacc.xvg ... all within tolerance of 0 249s Comparing column #1 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radacc/edsam_reference.xvg and radacc.xvg ... all within tolerance of 0.05 249s Checking radius for file radacc.xvg ... all values within tolerance of 1e-05 249s Checking monotonicity for column 4 of file radacc.xvg ... values of column 4 are increasing monotonically. 249s Testing radcon . . . 249s gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon/topol -maxwarn 2 >grompp.out 2>grompp.err 249s echo 0 0 | gmx_d make_edi -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon/eigenvec.trr -outfrq 1 -radcon 1-2 -tar /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon/target.pdb -o sam.edi 1>make_edi.out 2>make_edi.err 249s gmx_d mdrun -ei sam.edi -eo radcon.xvg >mdrun.out 2>&1 249s Comparing column #0 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon/edsam_reference.xvg and radcon.xvg ... all within tolerance of 0 249s Comparing column #1 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon/edsam_reference.xvg and radcon.xvg ... all within tolerance of 0.05 249s Checking radius for file radcon.xvg ... all values within tolerance of 1e-05 249s Checking monotonicity for column 4 of file radcon.xvg ... values of column 4 are decreasing monotonically. 249s Testing flooding1 . . . 249s gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/topol -maxwarn 2 >grompp.out 2>grompp.err 250s gmx_d mdrun -ei /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/sam.edi -eo flooding1.xvg >mdrun.out 2>&1 250s Comparing column #0 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 0 250s Comparing column #1 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1e-05 250s Comparing column #2 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1e-05 250s Comparing column #3 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1 250s Comparing column #4 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1 250s Comparing column #5 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1e-05 250s Comparing column #6 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1 250s Comparing column #7 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1 250s Testing flooding2 . . . 250s gmx_d grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/topol -maxwarn 2 >grompp.out 2>grompp.err 250s gmx_d mdrun -ei /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/sam.edi -eo flooding2.xvg >mdrun.out 2>&1 251s Comparing column #0 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 0 251s Comparing column #1 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 0.05 251s Comparing column #2 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 0.025 251s Comparing column #3 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 250 251s Comparing column #4 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 1000 251s Comparing column #5 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 0.025 251s Comparing column #6 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 250 251s Comparing column #7 of .xvg files /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 1000 251s All 7 essential dynamics tests PASSED 251s ============================================================= 251s Starting regression tests: MPI build, single precision (only) 251s ============================================================= 251s Will test on 4 MPI ranks (if possible) 253s Testing acetonitrilRF . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/acetonitrilRF/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/acetonitrilRF/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/acetonitrilRF/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/acetonitrilRF/topol -maxwarn 10 >grompp.out 2>grompp.err 253s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/acetonitrilRF/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 253s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/acetonitrilRF gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1 253s 253s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/acetonitrilRF gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1' was -1 253s FAILED. Check mdrun.out, md.log file(s) in acetonitrilRF for acetonitrilRF 253s Testing aminoacids . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/aminoacids/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/aminoacids/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/aminoacids/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/aminoacids/topol -maxwarn 10 >grompp.out 2>grompp.err 254s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/aminoacids/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 254s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/aminoacids gmx_mpi mdrun -notunepme >mdrun.out 2>&1 254s 254s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/aminoacids gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 254s FAILED. Check mdrun.out, md.log file(s) in aminoacids for aminoacids 254s Testing argon . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/argon/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/argon/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/argon/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/argon/topol -maxwarn 10 >grompp.out 2>grompp.err 254s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/argon/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 255s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/argon gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1 255s 255s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/argon gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1' was -1 255s FAILED. Check mdrun.out, md.log file(s) in argon for argon 255s Testing awh_multibias . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/index >grompp.out 2>grompp.err 255s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 255s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias gmx_mpi mdrun -notunepme -cpi /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/continue -noappend >mdrun.out 2>&1 255s 255s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias gmx_mpi mdrun -notunepme -cpi /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multibias/continue -noappend >mdrun.out 2>&1' was -1 255s FAILED. Check mdrun.out, md.log file(s) in awh_multibias for awh_multibias 255s Testing awh_multidim . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim/index >grompp.out 2>grompp.err 256s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 256s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim gmx_mpi mdrun -notunepme >mdrun.out 2>&1 256s 256s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/awh_multidim gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 256s FAILED. Check mdrun.out, md.log file(s) in awh_multidim for awh_multidim 256s Testing butane . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/butane/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/butane/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/butane/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/butane/topol -maxwarn 10 >grompp.out 2>grompp.err 256s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/butane/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 256s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/butane gmx_mpi mdrun -notunepme >mdrun.out 2>&1 256s 256s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/butane gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 256s FAILED. Check mdrun.out, md.log file(s) in butane for butane 256s Testing cbt . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/cbt/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/cbt/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/cbt/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/cbt/topol -maxwarn 10 >grompp.out 2>grompp.err 257s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/cbt/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 257s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/cbt gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1 257s 257s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/cbt gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1' was -1 257s FAILED. Check mdrun.out, md.log file(s) in cbt for cbt 257s Testing dd121 . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dd121/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dd121/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dd121/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dd121/topol -maxwarn 10 >grompp.out 2>grompp.err 257s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dd121/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 258s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dd121 gmx_mpi mdrun -notunepme >mdrun.out 2>&1 258s 258s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dd121 gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 258s FAILED. Check mdrun.out, md.log file(s) in dd121 for dd121 258s Testing dec+water . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dec+water/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dec+water/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dec+water/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dec+water/topol -maxwarn 10 >grompp.out 2>grompp.err 258s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dec+water/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 258s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dec+water gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1 258s 258s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/dec+water gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1' was -1 258s FAILED. Check mdrun.out, md.log file(s) in dec+water for dec+water 258s Testing distance_restraints . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/distance_restraints/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/distance_restraints/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/distance_restraints/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/distance_restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 259s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/distance_restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 259s mpirun -np 1 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/distance_restraints gmx_mpi mdrun -notunepme >mdrun.out 2>&1 259s gmx_mpi check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/distance_restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 260s gmx_mpi check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/distance_restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 260s PASSED but check mdp file differences 260s Testing ethyleenglycol . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/ethyleenglycol/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/ethyleenglycol/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/ethyleenglycol/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/ethyleenglycol/topol -maxwarn 10 >grompp.out 2>grompp.err 260s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/ethyleenglycol/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 260s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/ethyleenglycol gmx_mpi mdrun -notunepme >mdrun.out 2>&1 260s 260s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/ethyleenglycol gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 260s FAILED. Check mdrun.out, md.log file(s) in ethyleenglycol for ethyleenglycol 260s Testing field . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/field/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/field/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/field/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/field/topol -maxwarn 10 >grompp.out 2>grompp.err 261s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/field/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 261s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/field gmx_mpi mdrun -notunepme >mdrun.out 2>&1 261s 261s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/field gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 261s FAILED. Check mdrun.out, md.log file(s) in field for field 261s Testing nacl . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nacl/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nacl/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nacl/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nacl/topol -maxwarn 10 >grompp.out 2>grompp.err 262s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nacl/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 262s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nacl gmx_mpi mdrun -notunepme >mdrun.out 2>&1 262s 262s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nacl gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 262s FAILED. Check mdrun.out, md.log file(s) in nacl for nacl 262s Testing nbnxn-energy-groups . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-energy-groups/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-energy-groups/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-energy-groups/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-energy-groups/topol -maxwarn 10 >grompp.out 2>grompp.err 262s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-energy-groups/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 263s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-energy-groups gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1 263s 263s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-energy-groups gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1' was -1 263s FAILED. Check mdrun.out, md.log file(s) in nbnxn-energy-groups for nbnxn-energy-groups 263s Testing nbnxn-free-energy . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy/topol -maxwarn 10 >grompp.out 2>grompp.err 263s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 263s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy gmx_mpi mdrun -notunepme >mdrun.out 2>&1 263s 263s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 263s FAILED. Check mdrun.out, md.log file(s) in nbnxn-free-energy for nbnxn-free-energy 263s Testing nbnxn-free-energy-vv . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy-vv/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy-vv/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy-vv/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy-vv/topol -maxwarn 10 >grompp.out 2>grompp.err 264s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy-vv/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 264s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy-vv gmx_mpi mdrun -notunepme >mdrun.out 2>&1 264s 264s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-free-energy-vv gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 264s FAILED. Check mdrun.out, md.log file(s) in nbnxn-free-energy-vv for nbnxn-free-energy-vv 264s Testing nbnxn-ljpme-geometric . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-geometric/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-geometric/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-geometric/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-geometric/topol -maxwarn 10 >grompp.out 2>grompp.err 264s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-geometric/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 265s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-geometric gmx_mpi mdrun -notunepme >mdrun.out 2>&1 265s 265s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-geometric gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 265s FAILED. Check mdrun.out, md.log file(s) in nbnxn-ljpme-geometric for nbnxn-ljpme-geometric 265s Testing nbnxn-ljpme-LB . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB/topol -maxwarn 10 >grompp.out 2>grompp.err 265s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 265s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB gmx_mpi mdrun -notunepme >mdrun.out 2>&1 265s 265s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 265s FAILED. Check mdrun.out, md.log file(s) in nbnxn-ljpme-LB for nbnxn-ljpme-LB 265s Testing nbnxn-ljpme-LB-geometric . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/topol -maxwarn 10 >grompp.out 2>grompp.err 265s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 266s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB-geometric gmx_mpi mdrun -notunepme >mdrun.out 2>&1 266s 266s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-ljpme-LB-geometric gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 266s FAILED. Check mdrun.out, md.log file(s) in nbnxn-ljpme-LB-geometric for nbnxn-ljpme-LB-geometric 266s Testing nbnxn-vdw-force-switch . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-force-switch/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-force-switch/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-force-switch/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-force-switch/topol -maxwarn 10 >grompp.out 2>grompp.err 266s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-force-switch/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 266s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-force-switch gmx_mpi mdrun -notunepme >mdrun.out 2>&1 266s 266s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-force-switch gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 266s FAILED. Check mdrun.out, md.log file(s) in nbnxn-vdw-force-switch for nbnxn-vdw-force-switch 266s Testing nbnxn-vdw-potential-switch . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch/topol -maxwarn 10 >grompp.out 2>grompp.err 267s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 267s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch gmx_mpi mdrun -notunepme >mdrun.out 2>&1 267s 267s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 267s FAILED. Check mdrun.out, md.log file(s) in nbnxn-vdw-potential-switch for nbnxn-vdw-potential-switch 267s Testing nbnxn-vdw-potential-switch-argon . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/topol -maxwarn 10 >grompp.out 2>grompp.err 267s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 268s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon gmx_mpi mdrun -notunepme >mdrun.out 2>&1 268s 268s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 268s FAILED. Check mdrun.out, md.log file(s) in nbnxn-vdw-potential-switch-argon for nbnxn-vdw-potential-switch-argon 268s Testing nbnxn_pme . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme/topol -maxwarn 10 >grompp.out 2>grompp.err 268s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 268s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme gmx_mpi mdrun -notunepme >mdrun.out 2>&1 268s 268s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 268s FAILED. Check mdrun.out, md.log file(s) in nbnxn_pme for nbnxn_pme 268s Testing nbnxn_pme_order5 . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order5/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order5/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order5/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order5/topol -maxwarn 10 >grompp.out 2>grompp.err 268s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order5/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 269s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order5 gmx_mpi mdrun -notunepme >mdrun.out 2>&1 269s 269s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order5 gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 269s FAILED. Check mdrun.out, md.log file(s) in nbnxn_pme_order5 for nbnxn_pme_order5 269s Testing nbnxn_pme_order6 . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order6/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order6/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order6/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order6/topol -maxwarn 10 >grompp.out 2>grompp.err 269s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order6/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 269s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order6 gmx_mpi mdrun -notunepme >mdrun.out 2>&1 269s 269s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_pme_order6 gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 269s FAILED. Check mdrun.out, md.log file(s) in nbnxn_pme_order6 for nbnxn_pme_order6 269s Testing nbnxn_rf . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rf/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rf/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rf/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rf/topol -maxwarn 10 >grompp.out 2>grompp.err 270s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rf/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 270s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rf gmx_mpi mdrun -notunepme >mdrun.out 2>&1 270s 270s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rf gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 270s FAILED. Check mdrun.out, md.log file(s) in nbnxn_rf for nbnxn_rf 270s Testing nbnxn_rzero . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rzero/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rzero/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rzero/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rzero/topol -maxwarn 10 >grompp.out 2>grompp.err 270s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rzero/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 271s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rzero gmx_mpi mdrun -notunepme >mdrun.out 2>&1 271s 271s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_rzero gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 271s FAILED. Check mdrun.out, md.log file(s) in nbnxn_rzero for nbnxn_rzero 271s Testing nbnxn_vsite . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_vsite/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_vsite/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_vsite/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_vsite/topol -maxwarn 10 >grompp.out 2>grompp.err 271s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_vsite/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 271s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_vsite gmx_mpi mdrun -notunepme >mdrun.out 2>&1 271s 271s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nbnxn_vsite gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 271s FAILED. Check mdrun.out, md.log file(s) in nbnxn_vsite for nbnxn_vsite 271s Testing nst_mismatch . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nst_mismatch/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nst_mismatch/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nst_mismatch/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nst_mismatch/topol -maxwarn 10 >grompp.out 2>grompp.err 272s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nst_mismatch/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 272s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nst_mismatch gmx_mpi mdrun -notunepme >mdrun.out 2>&1 272s 272s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/nst_mismatch gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 272s FAILED. Check mdrun.out, md.log file(s) in nst_mismatch for nst_mismatch 272s Testing octahedron . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/octahedron/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/octahedron/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/octahedron/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/octahedron/topol -maxwarn 10 >grompp.out 2>grompp.err 272s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/octahedron/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 273s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/octahedron gmx_mpi mdrun -notunepme >mdrun.out 2>&1 273s 273s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/octahedron gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 273s FAILED. Check mdrun.out, md.log file(s) in octahedron for octahedron 273s Testing orientation-restraints . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/orientation-restraints/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/orientation-restraints/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/orientation-restraints/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/orientation-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 273s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/orientation-restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 273s mpirun -np 1 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/orientation-restraints gmx_mpi mdrun -notunepme >mdrun.out 2>&1 278s gmx_mpi check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/orientation-restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 278s gmx_mpi check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/orientation-restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 278s PASSED but check mdp file differences 278s Testing position-restraints . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/position-restraints/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/position-restraints/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/position-restraints/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/position-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 279s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/position-restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 279s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/position-restraints gmx_mpi mdrun -notunepme >mdrun.out 2>&1 279s 279s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/position-restraints gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 279s FAILED. Check mdrun.out, md.log file(s) in position-restraints for position-restraints 279s Testing pr-vrescale . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pr-vrescale/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pr-vrescale/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pr-vrescale/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pr-vrescale/topol -maxwarn 10 >grompp.out 2>grompp.err 279s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pr-vrescale/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 280s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pr-vrescale gmx_mpi mdrun -notunepme >mdrun.out 2>&1 280s 280s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pr-vrescale gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 280s FAILED. Check mdrun.out, md.log file(s) in pr-vrescale for pr-vrescale 280s Testing pull_constraint . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint/index >grompp.out 2>grompp.err 280s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 280s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint gmx_mpi mdrun -notunepme >mdrun.out 2>&1 281s 281s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_constraint gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 281s FAILED. Check mdrun.out, md.log file(s) in pull_constraint for pull_constraint 281s Testing pull_cylinder . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder/index >grompp.out 2>grompp.err 281s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 281s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder gmx_mpi mdrun -notunepme >mdrun.out 2>&1 281s 281s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_cylinder gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 281s FAILED. Check mdrun.out, md.log file(s) in pull_cylinder for pull_cylinder 281s Testing pull_geometry_angle . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle/index >grompp.out 2>grompp.err 281s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 282s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle gmx_mpi mdrun -notunepme >mdrun.out 2>&1 282s 282s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 282s FAILED. Check mdrun.out, md.log file(s) in pull_geometry_angle for pull_geometry_angle 282s Testing pull_geometry_angle-axis . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis/index >grompp.out 2>grompp.err 282s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 282s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis gmx_mpi mdrun -notunepme >mdrun.out 2>&1 282s 282s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_angle-axis gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 282s FAILED. Check mdrun.out, md.log file(s) in pull_geometry_angle-axis for pull_geometry_angle-axis 282s Testing pull_geometry_dihedral . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral/index >grompp.out 2>grompp.err 283s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 283s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral gmx_mpi mdrun -notunepme >mdrun.out 2>&1 283s 283s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/pull_geometry_dihedral gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 283s FAILED. Check mdrun.out, md.log file(s) in pull_geometry_dihedral for pull_geometry_dihedral 283s Testing reb . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/reb/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/reb/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/reb/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/reb/topol -maxwarn 10 >grompp.out 2>grompp.err 283s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/reb/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 283s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/reb gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1 283s 283s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/reb gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1' was -1 283s FAILED. Check mdrun.out, md.log file(s) in reb for reb 283s Testing sw . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/sw/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/sw/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/sw/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/sw/topol -maxwarn 10 >grompp.out 2>grompp.err 284s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/sw/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 284s mpirun -np 1 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/sw gmx_mpi mdrun -notunepme >mdrun.out 2>&1 285s gmx_mpi check -e /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/sw/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 285s gmx_mpi check -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/sw/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 286s PASSED but check mdp file differences 286s Testing swap_x . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x/index >grompp.out 2>grompp.err 286s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 286s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x gmx_mpi mdrun -notunepme >mdrun.out 2>&1 287s 287s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_x gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 287s FAILED. Check mdrun.out, md.log file(s) in swap_x for swap_x 287s Testing swap_y . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y/index >grompp.out 2>grompp.err 287s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 287s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y gmx_mpi mdrun -notunepme >mdrun.out 2>&1 287s 287s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_y gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 287s FAILED. Check mdrun.out, md.log file(s) in swap_y for swap_y 287s Testing swap_z . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z/topol -maxwarn 10 -n /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z/index >grompp.out 2>grompp.err 288s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 288s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z gmx_mpi mdrun -notunepme >mdrun.out 2>&1 288s 288s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/swap_z gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 288s FAILED. Check mdrun.out, md.log file(s) in swap_z for swap_z 288s Testing tip4p . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p/topol -maxwarn 10 >grompp.out 2>grompp.err 289s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 289s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p gmx_mpi mdrun -notunepme >mdrun.out 2>&1 289s 289s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 289s FAILED. Check mdrun.out, md.log file(s) in tip4p for tip4p 289s Testing tip4p_continue . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/topol -maxwarn 10 >grompp.out 2>grompp.err 290s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 290s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue gmx_mpi mdrun -notunepme -cpi /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/continue -noappend >mdrun.out 2>&1 290s 290s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue gmx_mpi mdrun -notunepme -cpi /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4p_continue/continue -noappend >mdrun.out 2>&1' was -1 290s FAILED. Check mdrun.out, md.log file(s) in tip4p_continue for tip4p_continue 290s Testing tip4pflex . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4pflex/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4pflex/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4pflex/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4pflex/topol -maxwarn 10 >grompp.out 2>grompp.err 290s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4pflex/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 291s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4pflex gmx_mpi mdrun -notunepme >mdrun.out 2>&1 291s 291s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/tip4pflex gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 291s FAILED. Check mdrun.out, md.log file(s) in tip4pflex for tip4pflex 291s Testing urea . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/urea/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/urea/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/urea/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/urea/topol -maxwarn 10 >grompp.out 2>grompp.err 291s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/urea/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 291s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/urea gmx_mpi mdrun -notunepme >mdrun.out 2>&1 291s 291s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/urea gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 291s FAILED. Check mdrun.out, md.log file(s) in urea for urea 291s Testing walls . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/walls/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/walls/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/walls/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/walls/topol -maxwarn 10 >grompp.out 2>grompp.err 292s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/walls/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 292s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/walls gmx_mpi mdrun -notunepme >mdrun.out 2>&1 292s 292s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/complex/walls gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 292s FAILED. Check mdrun.out, md.log file(s) in walls for walls 292s 45 out of 48 complex tests FAILED 292s Testing coulandvdwsequential_coul . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_coul/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_coul/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_coul/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_coul/topol -maxwarn 10 >grompp.out 2>grompp.err 293s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_coul/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 293s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_coul gmx_mpi mdrun -notunepme >mdrun.out 2>&1 293s 293s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_coul gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 293s FAILED. Check mdrun.out, md.log file(s) in coulandvdwsequential_coul for coulandvdwsequential_coul 293s Testing coulandvdwsequential_vdw . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_vdw/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_vdw/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_vdw/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_vdw/topol -maxwarn 10 >grompp.out 2>grompp.err 294s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_vdw/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 294s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_vdw gmx_mpi mdrun -notunepme >mdrun.out 2>&1 294s 294s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwsequential_vdw gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 294s FAILED. Check mdrun.out, md.log file(s) in coulandvdwsequential_vdw for coulandvdwsequential_vdw 294s Testing coulandvdwtogether . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwtogether/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwtogether/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwtogether/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwtogether/topol -maxwarn 10 >grompp.out 2>grompp.err 295s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwtogether/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 295s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwtogether gmx_mpi mdrun -notunepme >mdrun.out 2>&1 295s 295s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/coulandvdwtogether gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 295s FAILED. Check mdrun.out, md.log file(s) in coulandvdwtogether for coulandvdwtogether 295s Testing expanded . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/expanded/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/expanded/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/expanded/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/expanded/topol -maxwarn 10 >grompp.out 2>grompp.err 295s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/expanded/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 295s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/expanded gmx_mpi mdrun -notunepme >mdrun.out 2>&1 295s 295s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/expanded gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 295s FAILED. Check mdrun.out, md.log file(s) in expanded for expanded 295s Testing relative . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative/topol -maxwarn 10 >grompp.out 2>grompp.err 296s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 296s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative gmx_mpi mdrun -notunepme >mdrun.out 2>&1 296s 296s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 296s FAILED. Check mdrun.out, md.log file(s) in relative for relative 296s Testing relative-position-restraints . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative-position-restraints/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative-position-restraints/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative-position-restraints/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative-position-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 296s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative-position-restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 297s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative-position-restraints gmx_mpi mdrun -notunepme >mdrun.out 2>&1 297s 297s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/relative-position-restraints gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 297s FAILED. Check mdrun.out, md.log file(s) in relative-position-restraints for relative-position-restraints 297s Testing restraints . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/restraints/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/restraints/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/restraints/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 297s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 297s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/restraints gmx_mpi mdrun -notunepme >mdrun.out 2>&1 297s 297s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/restraints gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 297s FAILED. Check mdrun.out, md.log file(s) in restraints for restraints 297s Testing simtemp . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/simtemp/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/simtemp/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/simtemp/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/simtemp/topol -maxwarn 10 >grompp.out 2>grompp.err 298s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/simtemp/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 298s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/simtemp gmx_mpi mdrun -notunepme >mdrun.out 2>&1 298s 298s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/simtemp gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 298s FAILED. Check mdrun.out, md.log file(s) in simtemp for simtemp 298s Testing transformAtoB . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/transformAtoB/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/transformAtoB/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/transformAtoB/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/transformAtoB/topol -maxwarn 10 >grompp.out 2>grompp.err 298s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/transformAtoB/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 299s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/transformAtoB gmx_mpi mdrun -notunepme >mdrun.out 2>&1 299s 299s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/transformAtoB gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 299s FAILED. Check mdrun.out, md.log file(s) in transformAtoB for transformAtoB 299s Testing vdwalone . . . gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/vdwalone/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/vdwalone/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/vdwalone/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/vdwalone/topol -maxwarn 10 >grompp.out 2>grompp.err 299s gmx_mpi check -s1 /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/vdwalone/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 299s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/vdwalone gmx_mpi mdrun -notunepme >mdrun.out 2>&1 299s 299s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/freeenergy/vdwalone gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 299s FAILED. Check mdrun.out, md.log file(s) in vdwalone for vdwalone 299s 10 out of 10 freeenergy tests FAILED 299s All 0 extra tests PASSED 299s Testing linfix . . . 299s gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix/topol -maxwarn 2 >grompp.out 2>grompp.err 300s echo 0 | gmx_mpi make_edi -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix/eigenvec.trr -outfrq 1 -linfix 1 -linstep 0.0013 -o sam.edi 1>make_edi.out 2>make_edi.err 300s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix gmx_mpi mdrun -ei sam.edi -eo linfix.xvg >mdrun.out 2>&1 300s 300s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linfix gmx_mpi mdrun -ei sam.edi -eo linfix.xvg >mdrun.out 2>&1' was -1 300s Testing linacc . . . 300s gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc/topol -maxwarn 2 >grompp.out 2>grompp.err 300s echo 0 | gmx_mpi make_edi -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc/eigenvec.trr -outfrq 2 -linacc 1 -accdir +1 -o sam.edi 1>make_edi.out 2>make_edi.err 300s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc gmx_mpi mdrun -ei sam.edi -eo linacc.xvg >mdrun.out 2>&1 300s 300s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/linacc gmx_mpi mdrun -ei sam.edi -eo linacc.xvg >mdrun.out 2>&1' was -1 300s Testing radfix . . . 300s gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix/topol -maxwarn 2 >grompp.out 2>grompp.err 301s echo 0 | gmx_mpi make_edi -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix/eigenvec.trr -outfrq 1 -radfix 1-2 -radstep 0.002 -o sam.edi 1>make_edi.out 2>make_edi.err 301s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix gmx_mpi mdrun -ei sam.edi -eo radfix.xvg >mdrun.out 2>&1 301s 301s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radfix gmx_mpi mdrun -ei sam.edi -eo radfix.xvg >mdrun.out 2>&1' was -1 301s Testing radacc . . . 301s gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radacc/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radacc/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radacc/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radacc/topol -maxwarn 2 >grompp.out 2>grompp.err 301s echo 0 | gmx_mpi make_edi -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radacc/eigenvec.trr -outfrq 3 -radacc 1-2 -o sam.edi 1>make_edi.out 2>make_edi.err 302s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radacc gmx_mpi mdrun -ei sam.edi -eo radacc.xvg >mdrun.out 2>&1 302s 302s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radacc gmx_mpi mdrun -ei sam.edi -eo radacc.xvg >mdrun.out 2>&1' was -1 302s Testing radcon . . . 302s gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon/topol -maxwarn 2 >grompp.out 2>grompp.err 302s echo 0 0 | gmx_mpi make_edi -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon/eigenvec.trr -outfrq 1 -radcon 1-2 -tar /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon/target.pdb -o sam.edi 1>make_edi.out 2>make_edi.err 302s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon gmx_mpi mdrun -ei sam.edi -eo radcon.xvg >mdrun.out 2>&1 302s 302s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/radcon gmx_mpi mdrun -ei sam.edi -eo radcon.xvg >mdrun.out 2>&1' was -1 302s Testing flooding1 . . . 302s gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/topol -maxwarn 2 >grompp.out 2>grompp.err 303s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1 gmx_mpi mdrun -ei /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/sam.edi -eo flooding1.xvg >mdrun.out 2>&1 303s 303s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1 gmx_mpi mdrun -ei /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding1/sam.edi -eo flooding1.xvg >mdrun.out 2>&1' was -1 303s Testing flooding2 . . . 303s gmx_mpi grompp -f /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/grompp.mdp -c /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/conf -r /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/conf -p /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/topol -maxwarn 2 >grompp.out 2>grompp.err 303s mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2 gmx_mpi mdrun -ei /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/sam.edi -eo flooding2.xvg >mdrun.out 2>&1 303s 303s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2 gmx_mpi mdrun -ei /tmp/autopkgtest.TiJpdO/build.vg5/src/regressiontests/essentialdynamics/flooding2/sam.edi -eo flooding2.xvg >mdrun.out 2>&1' was -1 303s Essential dynamics tests FAILED with 7 errors! 304s autopkgtest [21:46:26]: test gromacs-regressiontests: -----------------------] 304s autopkgtest [21:46:26]: test gromacs-regressiontests: - - - - - - - - - - results - - - - - - - - - - 304s gromacs-regressiontests FAIL non-zero exit status 1 304s autopkgtest [21:46:26]: @@@@@@@@@@@@@@@@@@@@ summary 304s gromacs-regressiontests FAIL non-zero exit status 1 315s virt: nova [W] Skipping flock for amd64 315s virt: Creating nova instance adt-plucky-amd64-gromacs-20241123-203113-juju-7f2275-prod-proposed-migration-environment-2-69eb2531-1e49-4dd4-85e1-0a930b460086 from image adt/ubuntu-plucky-amd64-server-20241119.img (UUID 2f2a410e-3f09-433d-912b-264888c6382a)...