0s autopkgtest [20:31:14]: starting date and time: 2024-11-23 20:31:14+0000 0s autopkgtest [20:31:14]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [20:31:14]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.lt5xtzop/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@bos03-arm64-43.secgroup --name adt-plucky-arm64-gromacs-20241123-203114-juju-7f2275-prod-proposed-migration-environment-2-005610bb-975c-42e0-87dd-328e71ec5fde --image adt/ubuntu-plucky-arm64-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/ 59s autopkgtest [20:32:13]: testbed dpkg architecture: arm64 59s autopkgtest [20:32:13]: testbed apt version: 2.9.8 59s autopkgtest [20:32:13]: @@@@@@@@@@@@@@@@@@@@ test bed setup 60s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 61s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [930 kB] 61s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [54.8 kB] 61s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9704 B] 61s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [13.6 kB] 61s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [87.1 kB] 61s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [57.8 kB] 61s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [796 kB] 61s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [19.3 kB] 61s Fetched 2043 kB in 1s (2131 kB/s) 61s Reading package lists... 64s Reading package lists... 64s Building dependency tree... 64s Reading state information... 65s Calculating upgrade... 65s The following package was automatically installed and is no longer required: 65s libsgutils2-1.46-2 65s Use 'sudo apt autoremove' to remove it. 65s The following NEW packages will be installed: 65s libsgutils2-1.48 65s The following packages will be upgraded: 65s bash bpftrace curl debconf debconf-i18n distro-info fwupd-signed 65s gir1.2-girepository-2.0 gir1.2-glib-2.0 hostname libaudit-common libaudit1 65s libcurl3t64-gnutls libcurl4t64 libgirepository-1.0-1 libglib2.0-0t64 65s libglib2.0-data libpam-modules libpam-modules-bin libpam-runtime libpam0g 65s libplymouth5 libselinux1 libsemanage-common libsemanage2 linux-base 65s lxd-installer openssh-client openssh-server openssh-sftp-server plymouth 65s plymouth-theme-ubuntu-text python3-blinker python3-dbus python3-debconf 65s python3-gi python3-jsonschema-specifications python3-rpds-py python3-yaml 65s sg3-utils sg3-utils-udev vim-common vim-tiny xxd 65s 44 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 65s Need to get 11.7 MB of archives. 65s After this operation, 2983 kB of additional disk space will be used. 65s Get:1 http://ftpmaster.internal/ubuntu plucky/main arm64 bash arm64 5.2.32-1ubuntu2 [791 kB] 66s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 hostname arm64 3.25 [11.0 kB] 66s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libaudit-common all 1:4.0.2-2ubuntu1 [6578 B] 66s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libaudit1 arm64 1:4.0.2-2ubuntu1 [54.2 kB] 66s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 debconf-i18n all 1.5.87ubuntu1 [204 kB] 66s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-debconf all 1.5.87ubuntu1 [4156 B] 66s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 debconf all 1.5.87ubuntu1 [124 kB] 66s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libpam0g arm64 1.5.3-7ubuntu4 [68.6 kB] 66s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libselinux1 arm64 3.7-3ubuntu1 [81.6 kB] 66s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libpam-modules-bin arm64 1.5.3-7ubuntu4 [50.4 kB] 66s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libpam-modules arm64 1.5.3-7ubuntu4 [285 kB] 66s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 openssh-sftp-server arm64 1:9.9p1-3ubuntu2 [36.8 kB] 66s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 openssh-server arm64 1:9.9p1-3ubuntu2 [524 kB] 66s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 openssh-client arm64 1:9.9p1-3ubuntu2 [920 kB] 66s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libpam-runtime all 1.5.3-7ubuntu4 [40.8 kB] 66s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libsemanage-common all 3.7-2build1 [7186 B] 66s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 libsemanage2 arm64 3.7-2build1 [92.2 kB] 66s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 distro-info arm64 1.12 [19.4 kB] 66s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 gir1.2-girepository-2.0 arm64 1.82.0-2 [25.2 kB] 66s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 gir1.2-glib-2.0 arm64 2.82.2-3 [182 kB] 66s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libglib2.0-0t64 arm64 2.82.2-3 [1560 kB] 66s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 libgirepository-1.0-1 arm64 1.82.0-2 [83.0 kB] 66s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 libglib2.0-data all 2.82.2-3 [51.7 kB] 66s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-dbus arm64 1.3.2-5build4 [109 kB] 66s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-gi arm64 3.50.0-3build1 [279 kB] 66s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-yaml arm64 6.0.2-1build1 [164 kB] 66s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 vim-tiny arm64 2:9.1.0861-1ubuntu1 [805 kB] 66s Get:28 http://ftpmaster.internal/ubuntu plucky/main arm64 vim-common all 2:9.1.0861-1ubuntu1 [395 kB] 66s Get:29 http://ftpmaster.internal/ubuntu plucky/main arm64 xxd arm64 2:9.1.0861-1ubuntu1 [67.3 kB] 66s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libplymouth5 arm64 24.004.60-2ubuntu3 [141 kB] 66s Get:31 http://ftpmaster.internal/ubuntu plucky/main arm64 plymouth-theme-ubuntu-text arm64 24.004.60-2ubuntu3 [9914 B] 66s Get:32 http://ftpmaster.internal/ubuntu plucky/main arm64 plymouth arm64 24.004.60-2ubuntu3 [135 kB] 66s Get:33 http://ftpmaster.internal/ubuntu plucky/main arm64 bpftrace arm64 0.21.2-2ubuntu3 [1854 kB] 66s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 curl arm64 8.9.1-2ubuntu3 [235 kB] 66s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libcurl4t64 arm64 8.9.1-2ubuntu3 [365 kB] 66s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 fwupd-signed arm64 1.55+1.7-1 [30.9 kB] 66s Get:37 http://ftpmaster.internal/ubuntu plucky/main arm64 libcurl3t64-gnutls arm64 8.9.1-2ubuntu3 [359 kB] 66s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libsgutils2-1.48 arm64 1.48-0ubuntu1 [118 kB] 66s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 linux-base all 4.10.1ubuntu1 [34.8 kB] 66s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 lxd-installer all 10 [5264 B] 66s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-blinker all 1.9.0-1 [10.7 kB] 66s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-rpds-py arm64 0.21.0-2ubuntu1 [302 kB] 66s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-jsonschema-specifications all 2023.12.1-2 [9116 B] 66s Get:44 http://ftpmaster.internal/ubuntu plucky/main arm64 sg3-utils arm64 1.48-0ubuntu1 [999 kB] 66s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 sg3-utils-udev all 1.48-0ubuntu1 [6608 B] 67s Preconfiguring packages ... 67s Fetched 11.7 MB in 1s (10.6 MB/s) 67s (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 ... 80002 files and directories currently installed.) 67s Preparing to unpack .../bash_5.2.32-1ubuntu2_arm64.deb ... 67s Unpacking bash (5.2.32-1ubuntu2) over (5.2.32-1ubuntu1) ... 68s Setting up bash (5.2.32-1ubuntu2) ... 68s 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 68s (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 ... 80002 files and directories currently installed.) 68s Preparing to unpack .../hostname_3.25_arm64.deb ... 68s Unpacking hostname (3.25) over (3.23+nmu2ubuntu2) ... 68s Setting up hostname (3.25) ... 68s (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 ... 80002 files and directories currently installed.) 68s Preparing to unpack .../libaudit-common_1%3a4.0.2-2ubuntu1_all.deb ... 68s Unpacking libaudit-common (1:4.0.2-2ubuntu1) over (1:4.0.1-1ubuntu2) ... 68s Setting up libaudit-common (1:4.0.2-2ubuntu1) ... 68s (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 ... 80002 files and directories currently installed.) 68s Preparing to unpack .../libaudit1_1%3a4.0.2-2ubuntu1_arm64.deb ... 68s Unpacking libaudit1:arm64 (1:4.0.2-2ubuntu1) over (1:4.0.1-1ubuntu2) ... 68s Setting up libaudit1:arm64 (1:4.0.2-2ubuntu1) ... 68s (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 ... 80002 files and directories currently installed.) 68s Preparing to unpack .../debconf-i18n_1.5.87ubuntu1_all.deb ... 68s Unpacking debconf-i18n (1.5.87ubuntu1) over (1.5.86ubuntu1) ... 68s Preparing to unpack .../python3-debconf_1.5.87ubuntu1_all.deb ... 68s Unpacking python3-debconf (1.5.87ubuntu1) over (1.5.86ubuntu1) ... 68s Preparing to unpack .../debconf_1.5.87ubuntu1_all.deb ... 68s Unpacking debconf (1.5.87ubuntu1) over (1.5.86ubuntu1) ... 68s Setting up debconf (1.5.87ubuntu1) ... 68s (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 ... 80002 files and directories currently installed.) 68s Preparing to unpack .../libpam0g_1.5.3-7ubuntu4_arm64.deb ... 68s Unpacking libpam0g:arm64 (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ... 69s Setting up libpam0g:arm64 (1.5.3-7ubuntu4) ... 69s (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 ... 80002 files and directories currently installed.) 69s Preparing to unpack .../libselinux1_3.7-3ubuntu1_arm64.deb ... 69s Unpacking libselinux1:arm64 (3.7-3ubuntu1) over (3.5-2ubuntu5) ... 69s Setting up libselinux1:arm64 (3.7-3ubuntu1) ... 69s (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 ... 80002 files and directories currently installed.) 69s Preparing to unpack .../libpam-modules-bin_1.5.3-7ubuntu4_arm64.deb ... 69s Unpacking libpam-modules-bin (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ... 69s Setting up libpam-modules-bin (1.5.3-7ubuntu4) ... 69s pam_namespace.service is a disabled or a static unit not running, not starting it. 69s (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 ... 80002 files and directories currently installed.) 69s Preparing to unpack .../libpam-modules_1.5.3-7ubuntu4_arm64.deb ... 69s Unpacking libpam-modules:arm64 (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ... 70s Setting up libpam-modules:arm64 (1.5.3-7ubuntu4) ... 70s (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 ... 80002 files and directories currently installed.) 70s Preparing to unpack .../openssh-sftp-server_1%3a9.9p1-3ubuntu2_arm64.deb ... 70s Unpacking openssh-sftp-server (1:9.9p1-3ubuntu2) over (1:9.7p1-7ubuntu5) ... 70s Preparing to unpack .../openssh-server_1%3a9.9p1-3ubuntu2_arm64.deb ... 70s Unpacking openssh-server (1:9.9p1-3ubuntu2) over (1:9.7p1-7ubuntu5) ... 70s Preparing to unpack .../openssh-client_1%3a9.9p1-3ubuntu2_arm64.deb ... 70s Unpacking openssh-client (1:9.9p1-3ubuntu2) over (1:9.7p1-7ubuntu5) ... 70s Preparing to unpack .../libpam-runtime_1.5.3-7ubuntu4_all.deb ... 70s Unpacking libpam-runtime (1.5.3-7ubuntu4) over (1.5.3-7ubuntu2) ... 70s Setting up libpam-runtime (1.5.3-7ubuntu4) ... 70s (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 ... 80004 files and directories currently installed.) 70s Preparing to unpack .../libsemanage-common_3.7-2build1_all.deb ... 70s Unpacking libsemanage-common (3.7-2build1) over (3.5-1build6) ... 70s Setting up libsemanage-common (3.7-2build1) ... 70s (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 ... 80003 files and directories currently installed.) 70s Preparing to unpack .../libsemanage2_3.7-2build1_arm64.deb ... 70s Unpacking libsemanage2:arm64 (3.7-2build1) over (3.5-1build6) ... 70s Setting up libsemanage2:arm64 (3.7-2build1) ... 70s (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 ... 80003 files and directories currently installed.) 70s Preparing to unpack .../00-distro-info_1.12_arm64.deb ... 70s Unpacking distro-info (1.12) over (1.9) ... 71s Preparing to unpack .../01-gir1.2-girepository-2.0_1.82.0-2_arm64.deb ... 71s Unpacking gir1.2-girepository-2.0:arm64 (1.82.0-2) over (1.80.1-4) ... 71s Preparing to unpack .../02-gir1.2-glib-2.0_2.82.2-3_arm64.deb ... 71s Unpacking gir1.2-glib-2.0:arm64 (2.82.2-3) over (2.82.1-0ubuntu1) ... 71s Preparing to unpack .../03-libglib2.0-0t64_2.82.2-3_arm64.deb ... 71s Unpacking libglib2.0-0t64:arm64 (2.82.2-3) over (2.82.1-0ubuntu1) ... 71s Preparing to unpack .../04-libgirepository-1.0-1_1.82.0-2_arm64.deb ... 71s Unpacking libgirepository-1.0-1:arm64 (1.82.0-2) over (1.80.1-4) ... 71s Preparing to unpack .../05-libglib2.0-data_2.82.2-3_all.deb ... 71s Unpacking libglib2.0-data (2.82.2-3) over (2.82.1-0ubuntu1) ... 71s Preparing to unpack .../06-python3-dbus_1.3.2-5build4_arm64.deb ... 71s Unpacking python3-dbus (1.3.2-5build4) over (1.3.2-5build3) ... 71s Preparing to unpack .../07-python3-gi_3.50.0-3build1_arm64.deb ... 71s Unpacking python3-gi (3.50.0-3build1) over (3.50.0-3) ... 71s Preparing to unpack .../08-python3-yaml_6.0.2-1build1_arm64.deb ... 71s Unpacking python3-yaml (6.0.2-1build1) over (6.0.2-1) ... 71s Preparing to unpack .../09-vim-tiny_2%3a9.1.0861-1ubuntu1_arm64.deb ... 71s Unpacking vim-tiny (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ... 71s Preparing to unpack .../10-vim-common_2%3a9.1.0861-1ubuntu1_all.deb ... 71s Unpacking vim-common (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ... 72s Preparing to unpack .../11-xxd_2%3a9.1.0861-1ubuntu1_arm64.deb ... 72s Unpacking xxd (2:9.1.0861-1ubuntu1) over (2:9.1.0777-1ubuntu1) ... 72s Preparing to unpack .../12-libplymouth5_24.004.60-2ubuntu3_arm64.deb ... 72s Unpacking libplymouth5:arm64 (24.004.60-2ubuntu3) over (24.004.60-1ubuntu11) ... 72s Preparing to unpack .../13-plymouth-theme-ubuntu-text_24.004.60-2ubuntu3_arm64.deb ... 72s Unpacking plymouth-theme-ubuntu-text (24.004.60-2ubuntu3) over (24.004.60-1ubuntu11) ... 72s Preparing to unpack .../14-plymouth_24.004.60-2ubuntu3_arm64.deb ... 72s Unpacking plymouth (24.004.60-2ubuntu3) over (24.004.60-1ubuntu11) ... 72s Preparing to unpack .../15-bpftrace_0.21.2-2ubuntu3_arm64.deb ... 72s Unpacking bpftrace (0.21.2-2ubuntu3) over (0.21.2-2ubuntu2) ... 72s Preparing to unpack .../16-curl_8.9.1-2ubuntu3_arm64.deb ... 72s Unpacking curl (8.9.1-2ubuntu3) over (8.9.1-2ubuntu2) ... 72s Preparing to unpack .../17-libcurl4t64_8.9.1-2ubuntu3_arm64.deb ... 72s Unpacking libcurl4t64:arm64 (8.9.1-2ubuntu3) over (8.9.1-2ubuntu2) ... 72s Preparing to unpack .../18-fwupd-signed_1.55+1.7-1_arm64.deb ... 72s Unpacking fwupd-signed (1.55+1.7-1) over (1.54+1.6-1build1) ... 72s Preparing to unpack .../19-libcurl3t64-gnutls_8.9.1-2ubuntu3_arm64.deb ... 72s Unpacking libcurl3t64-gnutls:arm64 (8.9.1-2ubuntu3) over (8.9.1-2ubuntu2) ... 72s Selecting previously unselected package libsgutils2-1.48:arm64. 72s Preparing to unpack .../20-libsgutils2-1.48_1.48-0ubuntu1_arm64.deb ... 72s Unpacking libsgutils2-1.48:arm64 (1.48-0ubuntu1) ... 72s Preparing to unpack .../21-linux-base_4.10.1ubuntu1_all.deb ... 72s Unpacking linux-base (4.10.1ubuntu1) over (4.5ubuntu9) ... 72s Preparing to unpack .../22-lxd-installer_10_all.deb ... 72s Unpacking lxd-installer (10) over (9) ... 72s Preparing to unpack .../23-python3-blinker_1.9.0-1_all.deb ... 72s Unpacking python3-blinker (1.9.0-1) over (1.8.2-1) ... 72s Preparing to unpack .../24-python3-rpds-py_0.21.0-2ubuntu1_arm64.deb ... 73s Unpacking python3-rpds-py (0.21.0-2ubuntu1) over (0.20.0-0ubuntu3) ... 73s Preparing to unpack .../25-python3-jsonschema-specifications_2023.12.1-2_all.deb ... 73s Unpacking python3-jsonschema-specifications (2023.12.1-2) over (2023.12.1-1ubuntu1) ... 73s Preparing to unpack .../26-sg3-utils_1.48-0ubuntu1_arm64.deb ... 73s Unpacking sg3-utils (1.48-0ubuntu1) over (1.46-3ubuntu5) ... 73s Preparing to unpack .../27-sg3-utils-udev_1.48-0ubuntu1_all.deb ... 73s Unpacking sg3-utils-udev (1.48-0ubuntu1) over (1.46-3ubuntu5) ... 73s Setting up distro-info (1.12) ... 73s Setting up linux-base (4.10.1ubuntu1) ... 73s Setting up libcurl4t64:arm64 (8.9.1-2ubuntu3) ... 73s Setting up bpftrace (0.21.2-2ubuntu3) ... 73s Setting up openssh-client (1:9.9p1-3ubuntu2) ... 73s Setting up python3-debconf (1.5.87ubuntu1) ... 73s Setting up libcurl3t64-gnutls:arm64 (8.9.1-2ubuntu3) ... 73s Setting up fwupd-signed (1.55+1.7-1) ... 73s Setting up libsgutils2-1.48:arm64 (1.48-0ubuntu1) ... 73s Setting up python3-yaml (6.0.2-1build1) ... 73s Setting up debconf-i18n (1.5.87ubuntu1) ... 73s Setting up xxd (2:9.1.0861-1ubuntu1) ... 73s Setting up libglib2.0-0t64:arm64 (2.82.2-3) ... 73s No schema files found: doing nothing. 73s Setting up libglib2.0-data (2.82.2-3) ... 73s Setting up vim-common (2:9.1.0861-1ubuntu1) ... 73s Setting up gir1.2-glib-2.0:arm64 (2.82.2-3) ... 73s Setting up lxd-installer (10) ... 74s Setting up python3-rpds-py (0.21.0-2ubuntu1) ... 74s Setting up libplymouth5:arm64 (24.004.60-2ubuntu3) ... 74s Setting up libgirepository-1.0-1:arm64 (1.82.0-2) ... 74s Setting up curl (8.9.1-2ubuntu3) ... 74s Setting up python3-jsonschema-specifications (2023.12.1-2) ... 74s Setting up sg3-utils (1.48-0ubuntu1) ... 74s Setting up python3-blinker (1.9.0-1) ... 74s Setting up openssh-sftp-server (1:9.9p1-3ubuntu2) ... 74s Setting up python3-dbus (1.3.2-5build4) ... 75s Setting up openssh-server (1:9.9p1-3ubuntu2) ... 75s Installing new version of config file /etc/ssh/moduli ... 75s Replacing config file /etc/ssh/sshd_config with new version 76s Setting up plymouth (24.004.60-2ubuntu3) ... 76s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 76s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 92s flash-kernel: deferring update (trigger activated) 92s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 92s update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults 93s Setting up vim-tiny (2:9.1.0861-1ubuntu1) ... 93s Setting up sg3-utils-udev (1.48-0ubuntu1) ... 93s update-initramfs: deferring update (trigger activated) 93s Setting up plymouth-theme-ubuntu-text (24.004.60-2ubuntu3) ... 93s update-initramfs: deferring update (trigger activated) 93s Setting up gir1.2-girepository-2.0:arm64 (1.82.0-2) ... 93s Setting up python3-gi (3.50.0-3build1) ... 93s Processing triggers for install-info (7.1.1-1) ... 93s Processing triggers for initramfs-tools (0.142ubuntu35) ... 93s update-initramfs: Generating /boot/initrd.img-6.11.0-8-generic 93s W: No lz4 in /usr/bin:/sbin:/bin, using gzip 108s System running in EFI mode, skipping. 108s Processing triggers for libc-bin (2.40-1ubuntu3) ... 108s Processing triggers for ufw (0.36.2-8) ... 108s Processing triggers for man-db (2.13.0-1) ... 109s Processing triggers for debianutils (5.21) ... 109s Processing triggers for flash-kernel (3.107ubuntu13) ... 109s System running in EFI mode, skipping. 110s Reading package lists... 110s Building dependency tree... 110s Reading state information... 110s The following packages will be REMOVED: 110s libsgutils2-1.46-2* 111s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 111s After this operation, 314 kB disk space will be freed. 111s (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 ... 80037 files and directories currently installed.) 111s Removing libsgutils2-1.46-2:arm64 (1.46-3ubuntu5) ... 111s Processing triggers for libc-bin (2.40-1ubuntu3) ... 111s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 111s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 112s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 112s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 113s Reading package lists... 113s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s Calculating upgrade... 114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 115s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s autopkgtest [20:33:09]: rebooting testbed after setup commands that affected boot 139s autopkgtest [20:33:33]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 142s autopkgtest [20:33:36]: @@@@@@@@@@@@@@@@@@@@ apt-source gromacs 150s Get:1 http://ftpmaster.internal/ubuntu plucky/universe gromacs 2024.2-1 (dsc) [3648 B] 150s Get:2 http://ftpmaster.internal/ubuntu plucky/universe gromacs 2024.2-1 (tar) [48.1 MB] 150s Get:3 http://ftpmaster.internal/ubuntu plucky/universe gromacs 2024.2-1 (tar) [42.4 MB] 150s Get:4 http://ftpmaster.internal/ubuntu plucky/universe gromacs 2024.2-1 (diff) [37.8 kB] 150s gpgv: Signature made Sat May 11 22:19:23 2024 UTC 150s gpgv: using RSA key 843E5FA61E6063389876D2E5EE4AFD69EC65108F 150s gpgv: issuer "nbreen@debian.org" 150s gpgv: Can't check signature: No public key 150s dpkg-source: warning: cannot verify inline signature for ./gromacs_2024.2-1.dsc: no acceptable signature found 152s autopkgtest [20:33:46]: testing package gromacs version 2024.2-1 154s autopkgtest [20:33:48]: build not needed 170s autopkgtest [20:34:04]: test gromacs-regressiontests: preparing testbed 171s Reading package lists... 171s Building dependency tree... 171s Reading state information... 172s Starting pkgProblemResolver with broken count: 0 172s Starting 2 pkgProblemResolver with broken count: 0 172s Done 172s The following additional packages will be installed: 172s build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu 172s fonts-mathjax g++ g++-14 g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc 172s gcc-14 gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu gromacs gromacs-data 172s libamd-comgr2 libamdhip64-5 libasan8 libblas3 libcc1-0 libdrm-amdgpu1 172s libevent-pthreads-2.1-7t64 libfabric1 libfftw3-bin libfftw3-dev 172s libfftw3-double3 libfftw3-long3 libfftw3-single3 libgcc-14-dev libgfortran5 172s libgomp1 libgromacs-dev libgromacs9 libhsa-runtime64-1 libhsakmt1 libhwasan0 172s libhwloc-plugins libhwloc15 libibmad5 libibumad3 libisl23 libitm1 172s libjs-mathjax liblapack3 libllvm17t64 liblsan0 libmpc3 libmunge2 172s libmuparser2v5 libnblib-gmx-dev libnblib-gmx0 libopenmpi3t64 libpciaccess0 172s libpmix2t64 librdmacm1t64 libstdc++-14-dev libtsan2 libubsan1 libucx0 172s libxnvctrl0 mpi-default-bin ocl-icd-libopencl1 openmpi-bin openmpi-common 172s Suggested packages: 172s cpp-doc gcc-14-locales cpp-14-doc gcc-14-doc gcc-multilib manpages-dev 172s autoconf automake libtool flex bison gdb gcc-doc gdb-aarch64-linux-gnu pymol 172s libfftw3-doc mpi-default-dev zlib1g-dev fonts-mathjax-extras fonts-stix 172s libjs-mathjax-doc libstdc++-14-doc opencl-icd gfortran | fortran-compiler 173s The following NEW packages will be installed: 173s autopkgtest-satdep build-essential cpp cpp-14 cpp-14-aarch64-linux-gnu 173s cpp-aarch64-linux-gnu fonts-mathjax g++ g++-14 g++-14-aarch64-linux-gnu 173s g++-aarch64-linux-gnu gcc gcc-14 gcc-14-aarch64-linux-gnu 173s gcc-aarch64-linux-gnu gromacs gromacs-data libamd-comgr2 libamdhip64-5 173s libasan8 libblas3 libcc1-0 libdrm-amdgpu1 libevent-pthreads-2.1-7t64 173s libfabric1 libfftw3-bin libfftw3-dev libfftw3-double3 libfftw3-long3 173s libfftw3-single3 libgcc-14-dev libgfortran5 libgomp1 libgromacs-dev 173s libgromacs9 libhsa-runtime64-1 libhsakmt1 libhwasan0 libhwloc-plugins 173s libhwloc15 libibmad5 libibumad3 libisl23 libitm1 libjs-mathjax liblapack3 173s libllvm17t64 liblsan0 libmpc3 libmunge2 libmuparser2v5 libnblib-gmx-dev 173s libnblib-gmx0 libopenmpi3t64 libpciaccess0 libpmix2t64 librdmacm1t64 173s libstdc++-14-dev libtsan2 libubsan1 libucx0 libxnvctrl0 mpi-default-bin 173s ocl-icd-libopencl1 openmpi-bin openmpi-common 173s 0 upgraded, 66 newly installed, 0 to remove and 0 not upgraded. 173s Need to get 202 MB/202 MB of archives. 173s After this operation, 886 MB of additional disk space will be used. 173s Get:1 /tmp/autopkgtest.K5CJ0h/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [768 B] 173s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libisl23 arm64 0.27-1 [676 kB] 173s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libmpc3 arm64 1.3.1-1build2 [56.8 kB] 173s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [10.6 MB] 174s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-14 arm64 14.2.0-8ubuntu1 [1028 B] 174s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [5452 B] 174s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 cpp arm64 4:14.1.0-2ubuntu1 [22.5 kB] 174s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libcc1-0 arm64 14.2.0-8ubuntu1 [49.7 kB] 174s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-8ubuntu1 [145 kB] 174s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 libitm1 arm64 14.2.0-8ubuntu1 [27.8 kB] 174s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 libasan8 arm64 14.2.0-8ubuntu1 [2893 kB] 174s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 liblsan0 arm64 14.2.0-8ubuntu1 [1283 kB] 174s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 libtsan2 arm64 14.2.0-8ubuntu1 [2686 kB] 174s Get:14 http://ftpmaster.internal/ubuntu plucky/main arm64 libubsan1 arm64 14.2.0-8ubuntu1 [1151 kB] 174s Get:15 http://ftpmaster.internal/ubuntu plucky/main arm64 libhwasan0 arm64 14.2.0-8ubuntu1 [1598 kB] 174s Get:16 http://ftpmaster.internal/ubuntu plucky/main arm64 libgcc-14-dev arm64 14.2.0-8ubuntu1 [2594 kB] 174s Get:17 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [20.9 MB] 175s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-14 arm64 14.2.0-8ubuntu1 [518 kB] 175s Get:19 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [1200 B] 175s Get:20 http://ftpmaster.internal/ubuntu plucky/main arm64 gcc arm64 4:14.1.0-2ubuntu1 [4994 B] 175s Get:21 http://ftpmaster.internal/ubuntu plucky/main arm64 libstdc++-14-dev arm64 14.2.0-8ubuntu1 [2476 kB] 175s Get:22 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-8ubuntu1 [12.1 MB] 175s Get:23 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-14 arm64 14.2.0-8ubuntu1 [19.9 kB] 175s Get:24 http://ftpmaster.internal/ubuntu plucky/main arm64 g++-aarch64-linux-gnu arm64 4:14.1.0-2ubuntu1 [958 B] 175s Get:25 http://ftpmaster.internal/ubuntu plucky/main arm64 g++ arm64 4:14.1.0-2ubuntu1 [1080 B] 175s Get:26 http://ftpmaster.internal/ubuntu plucky/main arm64 build-essential arm64 12.10ubuntu1 [4932 B] 175s Get:27 http://ftpmaster.internal/ubuntu plucky/main arm64 fonts-mathjax all 2.7.9+dfsg-1 [2208 kB] 175s Get:28 http://ftpmaster.internal/ubuntu plucky/universe arm64 libllvm17t64 arm64 1:17.0.6-18 [24.9 MB] 176s Get:29 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamd-comgr2 arm64 6.0+git20231212.4510c28+dfsg-3build2 [14.1 MB] 177s Get:30 http://ftpmaster.internal/ubuntu plucky/main arm64 libdrm-amdgpu1 arm64 2.4.123-1 [20.9 kB] 177s Get:31 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhsakmt1 arm64 5.7.0-1build1 [63.6 kB] 177s Get:32 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhsa-runtime64-1 arm64 5.7.1-2build1 [286 kB] 177s Get:33 http://ftpmaster.internal/ubuntu plucky/universe arm64 libamdhip64-5 arm64 5.7.1-5 [9704 kB] 177s Get:34 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 177s Get:35 http://ftpmaster.internal/ubuntu plucky/main arm64 libevent-pthreads-2.1-7t64 arm64 2.1.12-stable-10 [7922 B] 177s Get:36 http://ftpmaster.internal/ubuntu plucky/main arm64 librdmacm1t64 arm64 52.0-2ubuntu1 [71.5 kB] 177s Get:37 http://ftpmaster.internal/ubuntu plucky/universe arm64 libfabric1 arm64 1.17.0-3ubuntu1 [542 kB] 177s Get:38 http://ftpmaster.internal/ubuntu plucky/main arm64 libfftw3-double3 arm64 3.3.10-1ubuntu4 [392 kB] 177s Get:39 http://ftpmaster.internal/ubuntu plucky/main arm64 libfftw3-long3 arm64 3.3.10-1ubuntu4 [652 kB] 177s Get:40 http://ftpmaster.internal/ubuntu plucky/main arm64 libfftw3-single3 arm64 3.3.10-1ubuntu4 [604 kB] 177s Get:41 http://ftpmaster.internal/ubuntu plucky/main arm64 libfftw3-bin arm64 3.3.10-1ubuntu4 [33.5 kB] 177s Get:42 http://ftpmaster.internal/ubuntu plucky/main arm64 libfftw3-dev arm64 3.3.10-1ubuntu4 [1521 kB] 177s Get:43 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 177s Get:44 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhwloc15 arm64 2.11.2-1 [162 kB] 177s Get:45 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 177s Get:46 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmuparser2v5 arm64 2.3.4-1 [125 kB] 177s Get:47 http://ftpmaster.internal/ubuntu plucky/universe arm64 libmunge2 arm64 0.5.15-4build1 [14.9 kB] 177s Get:48 http://ftpmaster.internal/ubuntu plucky/main arm64 libpciaccess0 arm64 0.17-3build1 [18.9 kB] 177s Get:49 http://ftpmaster.internal/ubuntu plucky/main arm64 libxnvctrl0 arm64 510.47.03-0ubuntu4 [12.4 kB] 177s Get:50 http://ftpmaster.internal/ubuntu plucky/universe arm64 ocl-icd-libopencl1 arm64 2.3.2-1build1 [37.6 kB] 177s Get:51 http://ftpmaster.internal/ubuntu plucky/universe arm64 libhwloc-plugins arm64 2.11.2-1 [15.8 kB] 177s Get:52 http://ftpmaster.internal/ubuntu plucky/universe arm64 libpmix2t64 arm64 5.0.3-2 [662 kB] 177s Get:53 http://ftpmaster.internal/ubuntu plucky/main arm64 libibumad3 arm64 52.0-2ubuntu1 [29.3 kB] 177s Get:54 http://ftpmaster.internal/ubuntu plucky/main arm64 libibmad5 arm64 52.0-2ubuntu1 [43.1 kB] 177s Get:55 http://ftpmaster.internal/ubuntu plucky/universe arm64 libucx0 arm64 1.17.0+ds-3build1 [1093 kB] 178s Get:56 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 libopenmpi3t64 arm64 5.0.5-6 [2041 kB] 178s Get:57 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgromacs9 arm64 2024.2-1 [32.3 MB] 179s Get:58 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnblib-gmx0 arm64 2024.2-1 [307 kB] 179s Get:59 http://ftpmaster.internal/ubuntu plucky/universe arm64 libnblib-gmx-dev arm64 2024.2-1 [26.2 kB] 179s Get:60 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 openmpi-common all 5.0.5-6 [95.6 kB] 179s Get:61 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 openmpi-bin arm64 5.0.5-6 [172 kB] 179s Get:62 http://ftpmaster.internal/ubuntu plucky/main arm64 libjs-mathjax all 2.7.9+dfsg-1 [5665 kB] 180s Get:63 http://ftpmaster.internal/ubuntu plucky/universe arm64 gromacs-data all 2024.2-1 [41.0 MB] 181s Get:64 http://ftpmaster.internal/ubuntu plucky/universe arm64 gromacs arm64 2024.2-1 [58.4 kB] 181s Get:65 http://ftpmaster.internal/ubuntu plucky/universe arm64 libgromacs-dev arm64 2024.2-1 [168 kB] 181s Get:66 http://ftpmaster.internal/ubuntu plucky/universe arm64 mpi-default-bin arm64 1.17 [2296 B] 182s Fetched 202 MB in 9s (23.7 MB/s) 182s Selecting previously unselected package libisl23:arm64. 182s (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 ... 80032 files and directories currently installed.) 182s Preparing to unpack .../00-libisl23_0.27-1_arm64.deb ... 182s Unpacking libisl23:arm64 (0.27-1) ... 182s Selecting previously unselected package libmpc3:arm64. 182s Preparing to unpack .../01-libmpc3_1.3.1-1build2_arm64.deb ... 182s Unpacking libmpc3:arm64 (1.3.1-1build2) ... 182s Selecting previously unselected package cpp-14-aarch64-linux-gnu. 182s Preparing to unpack .../02-cpp-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 182s Unpacking cpp-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 182s Selecting previously unselected package cpp-14. 182s Preparing to unpack .../03-cpp-14_14.2.0-8ubuntu1_arm64.deb ... 182s Unpacking cpp-14 (14.2.0-8ubuntu1) ... 182s Selecting previously unselected package cpp-aarch64-linux-gnu. 182s Preparing to unpack .../04-cpp-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 182s Unpacking cpp-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 182s Selecting previously unselected package cpp. 182s Preparing to unpack .../05-cpp_4%3a14.1.0-2ubuntu1_arm64.deb ... 182s Unpacking cpp (4:14.1.0-2ubuntu1) ... 182s Selecting previously unselected package libcc1-0:arm64. 182s Preparing to unpack .../06-libcc1-0_14.2.0-8ubuntu1_arm64.deb ... 182s Unpacking libcc1-0:arm64 (14.2.0-8ubuntu1) ... 182s Selecting previously unselected package libgomp1:arm64. 182s Preparing to unpack .../07-libgomp1_14.2.0-8ubuntu1_arm64.deb ... 182s Unpacking libgomp1:arm64 (14.2.0-8ubuntu1) ... 182s Selecting previously unselected package libitm1:arm64. 182s Preparing to unpack .../08-libitm1_14.2.0-8ubuntu1_arm64.deb ... 182s Unpacking libitm1:arm64 (14.2.0-8ubuntu1) ... 182s Selecting previously unselected package libasan8:arm64. 182s Preparing to unpack .../09-libasan8_14.2.0-8ubuntu1_arm64.deb ... 182s Unpacking libasan8:arm64 (14.2.0-8ubuntu1) ... 183s Selecting previously unselected package liblsan0:arm64. 183s Preparing to unpack .../10-liblsan0_14.2.0-8ubuntu1_arm64.deb ... 183s Unpacking liblsan0:arm64 (14.2.0-8ubuntu1) ... 183s Selecting previously unselected package libtsan2:arm64. 183s Preparing to unpack .../11-libtsan2_14.2.0-8ubuntu1_arm64.deb ... 183s Unpacking libtsan2:arm64 (14.2.0-8ubuntu1) ... 183s Selecting previously unselected package libubsan1:arm64. 183s Preparing to unpack .../12-libubsan1_14.2.0-8ubuntu1_arm64.deb ... 183s Unpacking libubsan1:arm64 (14.2.0-8ubuntu1) ... 183s Selecting previously unselected package libhwasan0:arm64. 183s Preparing to unpack .../13-libhwasan0_14.2.0-8ubuntu1_arm64.deb ... 183s Unpacking libhwasan0:arm64 (14.2.0-8ubuntu1) ... 183s Selecting previously unselected package libgcc-14-dev:arm64. 183s Preparing to unpack .../14-libgcc-14-dev_14.2.0-8ubuntu1_arm64.deb ... 183s Unpacking libgcc-14-dev:arm64 (14.2.0-8ubuntu1) ... 183s Selecting previously unselected package gcc-14-aarch64-linux-gnu. 183s Preparing to unpack .../15-gcc-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 183s Unpacking gcc-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 184s Selecting previously unselected package gcc-14. 184s Preparing to unpack .../16-gcc-14_14.2.0-8ubuntu1_arm64.deb ... 184s Unpacking gcc-14 (14.2.0-8ubuntu1) ... 184s Selecting previously unselected package gcc-aarch64-linux-gnu. 184s Preparing to unpack .../17-gcc-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 184s Unpacking gcc-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 184s Selecting previously unselected package gcc. 184s Preparing to unpack .../18-gcc_4%3a14.1.0-2ubuntu1_arm64.deb ... 184s Unpacking gcc (4:14.1.0-2ubuntu1) ... 184s Selecting previously unselected package libstdc++-14-dev:arm64. 184s Preparing to unpack .../19-libstdc++-14-dev_14.2.0-8ubuntu1_arm64.deb ... 184s Unpacking libstdc++-14-dev:arm64 (14.2.0-8ubuntu1) ... 184s Selecting previously unselected package g++-14-aarch64-linux-gnu. 184s Preparing to unpack .../20-g++-14-aarch64-linux-gnu_14.2.0-8ubuntu1_arm64.deb ... 184s Unpacking g++-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 184s Selecting previously unselected package g++-14. 184s Preparing to unpack .../21-g++-14_14.2.0-8ubuntu1_arm64.deb ... 184s Unpacking g++-14 (14.2.0-8ubuntu1) ... 184s Selecting previously unselected package g++-aarch64-linux-gnu. 184s Preparing to unpack .../22-g++-aarch64-linux-gnu_4%3a14.1.0-2ubuntu1_arm64.deb ... 184s Unpacking g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 184s Selecting previously unselected package g++. 184s Preparing to unpack .../23-g++_4%3a14.1.0-2ubuntu1_arm64.deb ... 184s Unpacking g++ (4:14.1.0-2ubuntu1) ... 184s Selecting previously unselected package build-essential. 184s Preparing to unpack .../24-build-essential_12.10ubuntu1_arm64.deb ... 184s Unpacking build-essential (12.10ubuntu1) ... 184s Selecting previously unselected package fonts-mathjax. 184s Preparing to unpack .../25-fonts-mathjax_2.7.9+dfsg-1_all.deb ... 184s Unpacking fonts-mathjax (2.7.9+dfsg-1) ... 184s Selecting previously unselected package libllvm17t64:arm64. 184s Preparing to unpack .../26-libllvm17t64_1%3a17.0.6-18_arm64.deb ... 184s Unpacking libllvm17t64:arm64 (1:17.0.6-18) ... 185s Selecting previously unselected package libamd-comgr2:arm64. 185s Preparing to unpack .../27-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3build2_arm64.deb ... 185s Unpacking libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build2) ... 186s Selecting previously unselected package libdrm-amdgpu1:arm64. 186s Preparing to unpack .../28-libdrm-amdgpu1_2.4.123-1_arm64.deb ... 186s Unpacking libdrm-amdgpu1:arm64 (2.4.123-1) ... 186s Selecting previously unselected package libhsakmt1:arm64. 186s Preparing to unpack .../29-libhsakmt1_5.7.0-1build1_arm64.deb ... 186s Unpacking libhsakmt1:arm64 (5.7.0-1build1) ... 186s Selecting previously unselected package libhsa-runtime64-1. 186s Preparing to unpack .../30-libhsa-runtime64-1_5.7.1-2build1_arm64.deb ... 186s Unpacking libhsa-runtime64-1 (5.7.1-2build1) ... 186s Selecting previously unselected package libamdhip64-5. 186s Preparing to unpack .../31-libamdhip64-5_5.7.1-5_arm64.deb ... 186s Unpacking libamdhip64-5 (5.7.1-5) ... 186s Selecting previously unselected package libblas3:arm64. 186s Preparing to unpack .../32-libblas3_3.12.0-3build2_arm64.deb ... 186s Unpacking libblas3:arm64 (3.12.0-3build2) ... 186s Selecting previously unselected package libevent-pthreads-2.1-7t64:arm64. 186s Preparing to unpack .../33-libevent-pthreads-2.1-7t64_2.1.12-stable-10_arm64.deb 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.../38-libfftw3-single3_3.3.10-1ubuntu4_arm64.deb ... 186s Unpacking libfftw3-single3:arm64 (3.3.10-1ubuntu4) ... 186s Selecting previously unselected package libfftw3-bin. 186s Preparing to unpack .../39-libfftw3-bin_3.3.10-1ubuntu4_arm64.deb ... 186s Unpacking libfftw3-bin (3.3.10-1ubuntu4) ... 186s Selecting previously unselected package libfftw3-dev:arm64. 186s Preparing to unpack .../40-libfftw3-dev_3.3.10-1ubuntu4_arm64.deb ... 186s Unpacking libfftw3-dev:arm64 (3.3.10-1ubuntu4) ... 186s Selecting previously unselected package libgfortran5:arm64. 186s Preparing to unpack .../41-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 186s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 186s Selecting previously unselected package libhwloc15:arm64. 186s Preparing to unpack .../42-libhwloc15_2.11.2-1_arm64.deb ... 186s Unpacking libhwloc15:arm64 (2.11.2-1) ... 186s Selecting previously unselected package liblapack3:arm64. 186s Preparing to unpack .../43-liblapack3_3.12.0-3build2_arm64.deb ... 186s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 186s Selecting previously unselected package libmuparser2v5:arm64. 186s Preparing to unpack .../44-libmuparser2v5_2.3.4-1_arm64.deb ... 186s Unpacking libmuparser2v5:arm64 (2.3.4-1) ... 187s Selecting previously unselected package libmunge2:arm64. 187s Preparing to unpack .../45-libmunge2_0.5.15-4build1_arm64.deb ... 187s Unpacking libmunge2:arm64 (0.5.15-4build1) ... 187s Selecting previously unselected package libpciaccess0:arm64. 187s Preparing to unpack .../46-libpciaccess0_0.17-3build1_arm64.deb ... 187s Unpacking libpciaccess0:arm64 (0.17-3build1) ... 187s Selecting previously unselected package libxnvctrl0:arm64. 187s Preparing to unpack .../47-libxnvctrl0_510.47.03-0ubuntu4_arm64.deb ... 187s Unpacking libxnvctrl0:arm64 (510.47.03-0ubuntu4) ... 187s Selecting previously unselected package ocl-icd-libopencl1:arm64. 187s Preparing to unpack .../48-ocl-icd-libopencl1_2.3.2-1build1_arm64.deb ... 187s Unpacking ocl-icd-libopencl1:arm64 (2.3.2-1build1) ... 187s Selecting previously unselected package libhwloc-plugins:arm64. 187s Preparing to unpack .../49-libhwloc-plugins_2.11.2-1_arm64.deb ... 187s Unpacking libhwloc-plugins:arm64 (2.11.2-1) ... 187s Selecting previously unselected package libpmix2t64:arm64. 187s Preparing to unpack .../50-libpmix2t64_5.0.3-2_arm64.deb ... 187s Unpacking libpmix2t64:arm64 (5.0.3-2) ... 187s Selecting previously unselected package libibumad3:arm64. 187s Preparing to unpack .../51-libibumad3_52.0-2ubuntu1_arm64.deb ... 187s Unpacking libibumad3:arm64 (52.0-2ubuntu1) ... 187s Selecting previously unselected package libibmad5:arm64. 187s Preparing to unpack .../52-libibmad5_52.0-2ubuntu1_arm64.deb ... 187s Unpacking libibmad5:arm64 (52.0-2ubuntu1) ... 187s Selecting previously unselected package libucx0:arm64. 187s Preparing to unpack .../53-libucx0_1.17.0+ds-3build1_arm64.deb ... 187s Unpacking libucx0:arm64 (1.17.0+ds-3build1) ... 187s Selecting previously unselected package libopenmpi3t64:arm64. 187s Preparing to unpack .../54-libopenmpi3t64_5.0.5-6_arm64.deb ... 187s Unpacking libopenmpi3t64:arm64 (5.0.5-6) ... 187s Selecting previously unselected package libgromacs9:arm64. 187s Preparing to unpack .../55-libgromacs9_2024.2-1_arm64.deb ... 187s Unpacking libgromacs9:arm64 (2024.2-1) ... 188s Selecting previously unselected package libnblib-gmx0:arm64. 188s Preparing to unpack .../56-libnblib-gmx0_2024.2-1_arm64.deb ... 188s Unpacking libnblib-gmx0:arm64 (2024.2-1) ... 188s Selecting previously unselected package libnblib-gmx-dev. 188s Preparing to unpack .../57-libnblib-gmx-dev_2024.2-1_arm64.deb ... 188s Unpacking libnblib-gmx-dev (2024.2-1) ... 188s Selecting previously unselected package openmpi-common. 188s Preparing to unpack .../58-openmpi-common_5.0.5-6_all.deb ... 188s Unpacking openmpi-common (5.0.5-6) ... 188s Selecting previously unselected package openmpi-bin. 188s Preparing to unpack .../59-openmpi-bin_5.0.5-6_arm64.deb 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(3.3.10-1ubuntu4) ... 192s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 192s Setting up libubsan1:arm64 (14.2.0-8ubuntu1) ... 192s Setting up ocl-icd-libopencl1:arm64 (2.3.2-1build1) ... 192s Setting up libhwasan0:arm64 (14.2.0-8ubuntu1) ... 192s Setting up libasan8:arm64 (14.2.0-8ubuntu1) ... 192s Setting up openmpi-common (5.0.5-6) ... 192s Setting up librdmacm1t64:arm64 (52.0-2ubuntu1) ... 192s Setting up libamd-comgr2:arm64 (6.0+git20231212.4510c28+dfsg-3build2) ... 192s Setting up libmuparser2v5:arm64 (2.3.4-1) ... 192s Setting up libtsan2:arm64 (14.2.0-8ubuntu1) ... 192s Setting up libisl23:arm64 (0.27-1) ... 192s Setting up libcc1-0:arm64 (14.2.0-8ubuntu1) ... 192s Setting up liblsan0:arm64 (14.2.0-8ubuntu1) ... 192s Setting up libitm1:arm64 (14.2.0-8ubuntu1) ... 192s Setting up libdrm-amdgpu1:arm64 (2.4.123-1) ... 192s Setting up libfabric1:arm64 (1.17.0-3ubuntu1) ... 192s Setting up gromacs-data (2024.2-1) ... 192s Setting up liblapack3:arm64 (3.12.0-3build2) ... 192s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 192s Setting up libfftw3-single3:arm64 (3.3.10-1ubuntu4) ... 192s Setting up libfftw3-long3:arm64 (3.3.10-1ubuntu4) ... 192s Setting up libhwloc-plugins:arm64 (2.11.2-1) ... 192s Setting up libpmix2t64:arm64 (5.0.3-2) ... 192s Setting up cpp-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 192s Setting up libgcc-14-dev:arm64 (14.2.0-8ubuntu1) ... 192s Setting up libstdc++-14-dev:arm64 (14.2.0-8ubuntu1) ... 192s Setting up libhsakmt1:arm64 (5.7.0-1build1) ... 192s Setting up libfftw3-bin (3.3.10-1ubuntu4) ... 192s Setting up cpp-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 192s Setting up cpp-14 (14.2.0-8ubuntu1) ... 192s Setting up libhsa-runtime64-1 (5.7.1-2build1) ... 192s Setting up cpp (4:14.1.0-2ubuntu1) ... 192s Setting up gcc-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 192s Setting up libfftw3-dev:arm64 (3.3.10-1ubuntu4) ... 192s Setting up gcc-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 192s Setting up g++-14-aarch64-linux-gnu (14.2.0-8ubuntu1) ... 192s Setting up gcc-14 (14.2.0-8ubuntu1) ... 192s Setting up libamdhip64-5 (5.7.1-5) ... 192s Setting up g++-aarch64-linux-gnu (4:14.1.0-2ubuntu1) ... 192s Setting up g++-14 (14.2.0-8ubuntu1) ... 192s Setting up libucx0:arm64 (1.17.0+ds-3build1) ... 192s Setting up gcc (4:14.1.0-2ubuntu1) ... 192s Setting up libopenmpi3t64:arm64 (5.0.5-6) ... 192s Setting up g++ (4:14.1.0-2ubuntu1) ... 192s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 192s Setting up build-essential (12.10ubuntu1) ... 192s Setting up openmpi-bin (5.0.5-6) ... 192s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 192s 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 192s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 192s Setting up libgromacs9:arm64 (2024.2-1) ... 192s Setting up mpi-default-bin (1.17) ... 192s Setting up gromacs (2024.2-1) ... 192s Setting up libgromacs-dev (2024.2-1) ... 192s Setting up libnblib-gmx0:arm64 (2024.2-1) ... 192s Setting up libnblib-gmx-dev (2024.2-1) ... 192s Setting up autopkgtest-satdep (0) ... 192s Processing triggers for man-db (2.13.0-1) ... 193s Processing triggers for libc-bin (2.40-1ubuntu3) ... 198s (Reading database ... 110359 files and directories currently installed.) 198s Removing autopkgtest-satdep (0) ... 199s autopkgtest [20:34:33]: test gromacs-regressiontests: [----------------------- 199s ======================================================== 199s Starting regression tests: basic build, single precision 199s ======================================================== 199s Testing acetonitrilRF . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/acetonitrilRF/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/acetonitrilRF/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/acetonitrilRF/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/acetonitrilRF/topol -maxwarn 10 >grompp.out 2>grompp.err 199s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/acetonitrilRF/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 199s gmx mdrun -nb cpu -notunepme >mdrun.out 2>&1 199s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/acetonitrilRF/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 199s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/acetonitrilRF/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 199s PASSED but check mdp file differences 199s Testing aminoacids . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/aminoacids/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/aminoacids/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/aminoacids/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/aminoacids/topol -maxwarn 10 >grompp.out 2>grompp.err 199s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/aminoacids/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 199s gmx mdrun -notunepme >mdrun.out 2>&1 200s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/aminoacids/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 200s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/aminoacids/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 200s PASSED but check mdp file differences 200s Testing argon . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/argon/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/argon/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/argon/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/argon/topol -maxwarn 10 >grompp.out 2>grompp.err 200s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/argon/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 200s gmx mdrun -nb cpu -notunepme >mdrun.out 2>&1 200s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/argon/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 200s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/argon/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 200s PASSED but check mdp file differences 200s Testing awh_multibias . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/index >grompp.out 2>grompp.err 200s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 200s gmx mdrun -notunepme -cpi /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/continue -noappend >mdrun.out 2>&1 200s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 200s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/reference_s.trr -f2 traj.part0002.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 200s PASSED but check mdp file differences 200s Testing awh_multidim . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim/index >grompp.out 2>grompp.err 200s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 200s gmx mdrun -notunepme >mdrun.out 2>&1 200s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 200s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 200s PASSED but check mdp file differences 200s Testing butane . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/butane/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/butane/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/butane/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/butane/topol -maxwarn 10 >grompp.out 2>grompp.err 200s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/butane/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 200s gmx mdrun -notunepme >mdrun.out 2>&1 200s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/butane/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 200s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/butane/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 200s PASSED but check mdp file differences 200s Testing cbt . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/cbt/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/cbt/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/cbt/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/cbt/topol -maxwarn 10 >grompp.out 2>grompp.err 200s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/cbt/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 200s gmx mdrun -nb cpu -notunepme >mdrun.out 2>&1 200s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/cbt/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 200s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/cbt/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 200s PASSED but check mdp file differences 200s Testing dd121 . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dd121/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dd121/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dd121/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dd121/topol -maxwarn 10 >grompp.out 2>grompp.err 200s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dd121/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 200s gmx mdrun -ntmpi 12 -notunepme >mdrun.out 2>&1 243s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dd121/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 243s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dd121/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 243s PASSED but check mdp file differences 243s Testing dec+water . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dec+water/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dec+water/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dec+water/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dec+water/topol -maxwarn 10 >grompp.out 2>grompp.err 243s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dec+water/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 243s gmx mdrun -nb cpu -notunepme >mdrun.out 2>&1 244s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dec+water/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 244s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dec+water/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 244s PASSED but check mdp file differences 244s Testing distance_restraints . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/distance_restraints/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/distance_restraints/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/distance_restraints/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/distance_restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 244s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/distance_restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 244s gmx mdrun -ntmpi 1 -notunepme >mdrun.out 2>&1 244s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/distance_restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 244s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/distance_restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 244s PASSED but check mdp file differences 244s Testing ethyleenglycol . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/ethyleenglycol/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/ethyleenglycol/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/ethyleenglycol/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/ethyleenglycol/topol -maxwarn 10 >grompp.out 2>grompp.err 244s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/ethyleenglycol/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 244s gmx mdrun -notunepme >mdrun.out 2>&1 244s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/ethyleenglycol/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 244s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/ethyleenglycol/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 244s PASSED but check mdp file differences 244s Testing field . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/field/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/field/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/field/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/field/topol -maxwarn 10 >grompp.out 2>grompp.err 244s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/field/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 244s gmx mdrun -notunepme >mdrun.out 2>&1 244s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/field/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 244s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/field/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 244s PASSED but check mdp file differences 244s Testing nacl . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nacl/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nacl/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nacl/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nacl/topol -maxwarn 10 >grompp.out 2>grompp.err 245s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nacl/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 245s gmx mdrun -notunepme >mdrun.out 2>&1 268s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nacl/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 268s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nacl/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 268s PASSED but check mdp file differences 268s Testing nbnxn-energy-groups . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-energy-groups/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-energy-groups/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-energy-groups/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-energy-groups/topol -maxwarn 10 >grompp.out 2>grompp.err 268s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-energy-groups/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 268s gmx mdrun -nb cpu -notunepme >mdrun.out 2>&1 287s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 287s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-energy-groups/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 287s PASSED but check mdp file differences 287s Testing nbnxn-free-energy . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy/topol -maxwarn 10 >grompp.out 2>grompp.err 287s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 287s gmx mdrun -notunepme >mdrun.out 2>&1 304s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 304s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 304s PASSED but check mdp file differences 304s Testing nbnxn-free-energy-vv . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy-vv/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy-vv/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy-vv/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy-vv/topol -maxwarn 10 >grompp.out 2>grompp.err 304s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy-vv/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 304s gmx mdrun -notunepme >mdrun.out 2>&1 321s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 321s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy-vv/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 321s PASSED but check mdp file differences 321s Testing nbnxn-ljpme-geometric . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-geometric/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-geometric/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-geometric/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-geometric/topol -maxwarn 10 >grompp.out 2>grompp.err 321s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-geometric/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 321s gmx mdrun -notunepme >mdrun.out 2>&1 335s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 335s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-geometric/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 335s PASSED but check mdp file differences 335s Testing nbnxn-ljpme-LB . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB/topol -maxwarn 10 >grompp.out 2>grompp.err 335s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 335s gmx mdrun -notunepme >mdrun.out 2>&1 400s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 400s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 400s PASSED but check mdp file differences 400s Testing nbnxn-ljpme-LB-geometric . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/topol -maxwarn 10 >grompp.out 2>grompp.err 400s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 400s gmx mdrun -notunepme >mdrun.out 2>&1 464s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 464s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 464s PASSED but check mdp file differences 464s Testing nbnxn-vdw-force-switch . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-force-switch/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-force-switch/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-force-switch/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-force-switch/topol -maxwarn 10 >grompp.out 2>grompp.err 464s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-force-switch/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 464s gmx mdrun -notunepme >mdrun.out 2>&1 483s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 483s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-force-switch/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 483s PASSED but check mdp file differences 483s Testing nbnxn-vdw-potential-switch . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch/topol -maxwarn 10 >grompp.out 2>grompp.err 483s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 483s gmx mdrun -notunepme >mdrun.out 2>&1 501s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 501s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 501s PASSED but check mdp file differences 501s Testing nbnxn-vdw-potential-switch-argon . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/topol -maxwarn 10 >grompp.out 2>grompp.err 501s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/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 501s gmx mdrun -notunepme >mdrun.out 2>&1 502s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 502s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/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 502s PASSED but check mdp file differences 502s Testing nbnxn_pme . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme/topol -maxwarn 10 >grompp.out 2>grompp.err 502s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 502s gmx mdrun -notunepme >mdrun.out 2>&1 520s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 520s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 520s PASSED but check mdp file differences 520s Testing nbnxn_pme_order5 . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order5/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order5/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order5/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order5/topol -maxwarn 10 >grompp.out 2>grompp.err 520s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order5/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 520s gmx mdrun -notunepme >mdrun.out 2>&1 539s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 539s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order5/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 539s PASSED but check mdp file differences 539s Testing nbnxn_pme_order6 . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order6/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order6/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order6/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order6/topol -maxwarn 10 >grompp.out 2>grompp.err 539s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order6/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 539s gmx mdrun -notunepme >mdrun.out 2>&1 557s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 557s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order6/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 557s PASSED but check mdp file differences 557s Testing nbnxn_rf . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rf/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rf/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rf/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rf/topol -maxwarn 10 >grompp.out 2>grompp.err 557s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rf/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 557s gmx mdrun -notunepme >mdrun.out 2>&1 557s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rf/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 557s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rf/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 557s PASSED but check mdp file differences 557s Testing nbnxn_rzero . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rzero/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rzero/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rzero/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rzero/topol -maxwarn 10 >grompp.out 2>grompp.err 557s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rzero/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 557s gmx mdrun -notunepme >mdrun.out 2>&1 557s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rzero/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 557s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rzero/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 557s PASSED but check mdp file differences 557s Testing nbnxn_vsite . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_vsite/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_vsite/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_vsite/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_vsite/topol -maxwarn 10 >grompp.out 2>grompp.err 557s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_vsite/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 557s gmx mdrun -ntmpi 6 -notunepme >mdrun.out 2>&1 591s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_vsite/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 591s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_vsite/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 591s PASSED but check mdp file differences 591s Testing nst_mismatch . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nst_mismatch/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nst_mismatch/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nst_mismatch/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nst_mismatch/topol -maxwarn 10 >grompp.out 2>grompp.err 591s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nst_mismatch/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 591s gmx mdrun -notunepme >mdrun.out 2>&1 592s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nst_mismatch/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 592s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nst_mismatch/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 592s PASSED but check mdp file differences 592s Testing octahedron . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/octahedron/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/octahedron/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/octahedron/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/octahedron/topol -maxwarn 10 >grompp.out 2>grompp.err 592s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/octahedron/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 592s gmx mdrun -notunepme >mdrun.out 2>&1 626s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/octahedron/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 626s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/octahedron/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 626s PASSED but check mdp file differences 626s Testing orientation-restraints . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/orientation-restraints/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/orientation-restraints/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/orientation-restraints/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/orientation-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 627s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/orientation-restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 627s gmx mdrun -ntmpi 1 -notunepme >mdrun.out 2>&1 695s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/orientation-restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 695s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/orientation-restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 695s PASSED but check mdp file differences 695s Testing position-restraints . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/position-restraints/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/position-restraints/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/position-restraints/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/position-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 696s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/position-restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 696s gmx mdrun -notunepme >mdrun.out 2>&1 696s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/position-restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 696s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/position-restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 696s PASSED but check mdp file differences 696s Testing pr-vrescale . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pr-vrescale/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pr-vrescale/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pr-vrescale/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pr-vrescale/topol -maxwarn 10 >grompp.out 2>grompp.err 696s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pr-vrescale/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 696s gmx mdrun -notunepme >mdrun.out 2>&1 714s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pr-vrescale/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 714s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pr-vrescale/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 714s PASSED but check mdp file differences 714s Testing pull_constraint . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint/index >grompp.out 2>grompp.err 715s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 715s gmx mdrun -notunepme >mdrun.out 2>&1 715s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 715s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 715s PASSED but check mdp file differences 715s Testing pull_cylinder . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder/index >grompp.out 2>grompp.err 715s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 715s gmx mdrun -notunepme >mdrun.out 2>&1 715s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 715s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 715s PASSED but check mdp file differences 715s Testing pull_geometry_angle . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle/index >grompp.out 2>grompp.err 715s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 715s gmx mdrun -notunepme >mdrun.out 2>&1 738s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 738s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 738s PASSED but check mdp file differences 738s Testing pull_geometry_angle-axis . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle-axis/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle-axis/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle-axis/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle-axis/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle-axis/index >grompp.out 2>grompp.err 738s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle-axis/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 738s gmx mdrun -notunepme >mdrun.out 2>&1 762s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 762s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle-axis/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 762s PASSED but check mdp file differences 762s Testing pull_geometry_dihedral . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_dihedral/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_dihedral/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_dihedral/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_dihedral/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_dihedral/index >grompp.out 2>grompp.err 762s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_dihedral/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 762s gmx mdrun -notunepme >mdrun.out 2>&1 786s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 786s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_dihedral/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 786s PASSED but check mdp file differences 786s Testing reb . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/reb/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/reb/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/reb/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/reb/topol -maxwarn 10 >grompp.out 2>grompp.err 786s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/reb/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 786s gmx mdrun -nb cpu -notunepme >mdrun.out 2>&1 786s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/reb/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 786s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/reb/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 786s PASSED but check mdp file differences 786s Testing sw . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/sw/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/sw/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/sw/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/sw/topol -maxwarn 10 >grompp.out 2>grompp.err 786s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/sw/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 786s gmx mdrun -ntmpi 1 -notunepme >mdrun.out 2>&1 798s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/sw/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 798s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/sw/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 798s PASSED but check mdp file differences 798s Testing swap_x . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x/index >grompp.out 2>grompp.err 798s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 798s gmx mdrun -notunepme >mdrun.out 2>&1 841s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 841s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 841s PASSED but check mdp file differences 841s Testing swap_y . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y/index >grompp.out 2>grompp.err 842s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 842s gmx mdrun -notunepme >mdrun.out 2>&1 884s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 884s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 884s PASSED but check mdp file differences 884s Testing swap_z . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z/index >grompp.out 2>grompp.err 885s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 885s gmx mdrun -notunepme >mdrun.out 2>&1 934s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 934s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 934s PASSED but check mdp file differences 934s Testing tip4p . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p/topol -maxwarn 10 >grompp.out 2>grompp.err 935s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 935s gmx mdrun -notunepme >mdrun.out 2>&1 936s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 936s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 936s PASSED but check mdp file differences 936s Testing tip4p_continue . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue/topol -maxwarn 10 >grompp.out 2>grompp.err 936s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 936s gmx mdrun -notunepme -cpi /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue/continue -noappend >mdrun.out 2>&1 937s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 937s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue/reference_s.trr -f2 traj.part0002.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 937s PASSED but check mdp file differences 937s Testing tip4pflex . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4pflex/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4pflex/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4pflex/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4pflex/topol -maxwarn 10 >grompp.out 2>grompp.err 937s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4pflex/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 937s gmx mdrun -notunepme >mdrun.out 2>&1 953s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4pflex/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 953s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4pflex/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 953s PASSED but check mdp file differences 953s Testing urea . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/urea/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/urea/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/urea/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/urea/topol -maxwarn 10 >grompp.out 2>grompp.err 953s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/urea/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 953s gmx mdrun -notunepme >mdrun.out 2>&1 953s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/urea/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 953s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/urea/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 953s PASSED but check mdp file differences 953s Testing walls . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/walls/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/walls/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/walls/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/walls/topol -maxwarn 10 >grompp.out 2>grompp.err 953s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/walls/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 953s gmx mdrun -notunepme >mdrun.out 2>&1 969s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/walls/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 969s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/walls/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 969s PASSED but check mdp file differences 969s All 48 complex tests PASSED 969s Testing coulandvdwsequential_coul . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_coul/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_coul/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_coul/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_coul/topol -maxwarn 10 >grompp.out 2>grompp.err 969s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_coul/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 969s gmx mdrun -notunepme >mdrun.out 2>&1 985s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_coul/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 985s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_coul/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 985s PASSED but check mdp file differences 985s Testing coulandvdwsequential_vdw . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_vdw/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_vdw/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_vdw/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_vdw/topol -maxwarn 10 >grompp.out 2>grompp.err 986s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_vdw/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 986s gmx mdrun -notunepme >mdrun.out 2>&1 1002s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_vdw/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1002s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_vdw/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1002s PASSED but check mdp file differences 1002s Testing coulandvdwtogether . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwtogether/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwtogether/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwtogether/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwtogether/topol -maxwarn 10 >grompp.out 2>grompp.err 1002s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwtogether/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1002s gmx mdrun -notunepme >mdrun.out 2>&1 1019s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwtogether/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1019s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwtogether/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1019s PASSED but check mdp file differences 1019s Testing expanded . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/expanded/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/expanded/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/expanded/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/expanded/topol -maxwarn 10 >grompp.out 2>grompp.err 1019s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/expanded/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1019s gmx mdrun -notunepme >mdrun.out 2>&1 1031s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/expanded/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1031s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/expanded/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1032s PASSED but check mdp file differences 1032s Testing relative . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative/topol -maxwarn 10 >grompp.out 2>grompp.err 1032s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1032s gmx mdrun -notunepme >mdrun.out 2>&1 1066s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1066s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1066s PASSED but check mdp file differences 1066s Testing relative-position-restraints . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative-position-restraints/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative-position-restraints/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative-position-restraints/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative-position-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 1067s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative-position-restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1067s gmx mdrun -notunepme >mdrun.out 2>&1 1101s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1101s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative-position-restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1101s PASSED but check mdp file differences 1101s Testing restraints . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/restraints/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/restraints/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/restraints/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 1102s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1102s gmx mdrun -notunepme >mdrun.out 2>&1 1188s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1188s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1188s PASSED but check mdp file differences 1188s Testing simtemp . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/simtemp/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/simtemp/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/simtemp/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/simtemp/topol -maxwarn 10 >grompp.out 2>grompp.err 1188s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/simtemp/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1188s gmx mdrun -notunepme >mdrun.out 2>&1 1200s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/simtemp/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1200s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/simtemp/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1200s PASSED but check mdp file differences 1200s Testing transformAtoB . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/transformAtoB/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/transformAtoB/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/transformAtoB/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/transformAtoB/topol -maxwarn 10 >grompp.out 2>grompp.err 1200s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/transformAtoB/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1200s gmx mdrun -notunepme >mdrun.out 2>&1 1213s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/transformAtoB/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1213s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/transformAtoB/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1213s PASSED but check mdp file differences 1213s Testing vdwalone . . . gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/vdwalone/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/vdwalone/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/vdwalone/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/vdwalone/topol -maxwarn 10 >grompp.out 2>grompp.err 1213s gmx check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/vdwalone/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1213s gmx mdrun -notunepme >mdrun.out 2>&1 1225s gmx check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/vdwalone/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1225s gmx check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/vdwalone/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1225s PASSED but check mdp file differences 1225s All 10 freeenergy tests PASSED 1225s All 0 extra tests PASSED 1225s Testing linfix . . . 1225s gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix/topol -maxwarn 2 >grompp.out 2>grompp.err 1225s echo 0 | gmx make_edi -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix/eigenvec.trr -outfrq 1 -linfix 1 -linstep 0.0013 -o sam.edi 1>make_edi.out 2>make_edi.err 1225s gmx mdrun -ei sam.edi -eo linfix.xvg >mdrun.out 2>&1 1225s Comparing column #0 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix/edsam_reference.xvg and linfix.xvg ... all within tolerance of 0 1225s Comparing column #1 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix/edsam_reference.xvg and linfix.xvg ... all within tolerance of 0.05 1225s Comparing column #2 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix/edsam_reference.xvg and linfix.xvg ... all within tolerance of 1e-06 1225s Testing linacc . . . 1225s gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc/topol -maxwarn 2 >grompp.out 2>grompp.err 1226s echo 0 | gmx make_edi -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc/eigenvec.trr -outfrq 2 -linacc 1 -accdir +1 -o sam.edi 1>make_edi.out 2>make_edi.err 1226s gmx mdrun -ei sam.edi -eo linacc.xvg >mdrun.out 2>&1 1226s Comparing column #0 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc/edsam_reference.xvg and linacc.xvg ... all within tolerance of 0 1226s Comparing column #1 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc/edsam_reference.xvg and linacc.xvg ... all within tolerance of 0.005 1226s Comparing column #2 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc/edsam_reference.xvg and linacc.xvg ... all within tolerance of 0.001 1226s Checking monotonicity for column 2 of file linacc.xvg ... values of column 2 are increasing monotonically. 1226s Testing radfix . . . 1226s gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radfix/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radfix/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radfix/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radfix/topol -maxwarn 2 >grompp.out 2>grompp.err 1226s echo 0 | gmx make_edi -f /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1226s gmx mdrun -ei sam.edi -eo radfix.xvg >mdrun.out 2>&1 1226s Comparing column #0 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radfix/edsam_reference.xvg and radfix.xvg ... all within tolerance of 0 1226s Comparing column #1 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radfix/edsam_reference.xvg and radfix.xvg ... all within tolerance of 0.05 1226s Comparing column #4 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radfix/edsam_reference.xvg and radfix.xvg ... all within tolerance of 0 1226s Checking radius for file radfix.xvg ... all values within tolerance of 1e-05 1226s Testing radacc . . . 1226s gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radacc/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radacc/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radacc/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radacc/topol -maxwarn 2 >grompp.out 2>grompp.err 1226s echo 0 | gmx make_edi -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radacc/eigenvec.trr -outfrq 3 -radacc 1-2 -o sam.edi 1>make_edi.out 2>make_edi.err 1226s gmx mdrun -ei sam.edi -eo radacc.xvg >mdrun.out 2>&1 1226s Comparing column #0 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radacc/edsam_reference.xvg and radacc.xvg ... all within tolerance of 0 1226s Comparing column #1 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radacc/edsam_reference.xvg and radacc.xvg ... all within tolerance of 0.05 1226s Checking radius for file radacc.xvg ... all values within tolerance of 1e-05 1226s Checking monotonicity for column 4 of file radacc.xvg ... values of column 4 are increasing monotonically. 1226s Testing radcon . . . 1226s gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon/topol -maxwarn 2 >grompp.out 2>grompp.err 1226s echo 0 0 | gmx make_edi -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon/eigenvec.trr -outfrq 1 -radcon 1-2 -tar /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon/target.pdb -o sam.edi 1>make_edi.out 2>make_edi.err 1226s gmx mdrun -ei sam.edi -eo radcon.xvg >mdrun.out 2>&1 1226s Comparing column #0 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon/edsam_reference.xvg and radcon.xvg ... all within tolerance of 0 1226s Comparing column #1 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon/edsam_reference.xvg and radcon.xvg ... all within tolerance of 0.05 1226s Checking radius for file radcon.xvg ... all values within tolerance of 1e-05 1226s Checking monotonicity for column 4 of file radcon.xvg ... values of column 4 are decreasing monotonically. 1226s Testing flooding1 . . . 1226s gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/topol -maxwarn 2 >grompp.out 2>grompp.err 1226s gmx mdrun -ei /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/sam.edi -eo flooding1.xvg >mdrun.out 2>&1 1236s Comparing column #0 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 0 1236s Comparing column #1 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1e-05 1236s Comparing column #2 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1e-05 1236s Comparing column #3 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1 1236s Comparing column #4 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1 1236s Comparing column #5 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1e-05 1236s Comparing column #6 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1 1236s Comparing column #7 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1 1236s Testing flooding2 . . . 1236s gmx grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/topol -maxwarn 2 >grompp.out 2>grompp.err 1236s gmx mdrun -ei /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/sam.edi -eo flooding2.xvg >mdrun.out 2>&1 1246s Comparing column #0 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 0 1246s Comparing column #1 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 0.05 1246s Comparing column #2 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 0.025 1246s Comparing column #3 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 250 1246s Comparing column #4 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 1000 1246s Comparing column #5 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 0.025 1246s Comparing column #6 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 250 1246s Comparing column #7 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 1000 1246s All 7 essential dynamics tests PASSED 1246s ======================================================== 1246s Starting regression tests: basic build, double precision 1246s ======================================================== 1246s Testing acetonitrilRF . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/acetonitrilRF/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/acetonitrilRF/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/acetonitrilRF/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/acetonitrilRF/topol -maxwarn 10 >grompp.out 2>grompp.err 1246s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/acetonitrilRF/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1246s gmx_d mdrun -nb cpu -notunepme >mdrun.out 2>&1 1246s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/acetonitrilRF/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1246s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/acetonitrilRF/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1246s PASSED but check mdp file differences 1246s Testing aminoacids . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/aminoacids/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/aminoacids/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/aminoacids/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/aminoacids/topol -maxwarn 10 >grompp.out 2>grompp.err 1247s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/aminoacids/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1247s gmx_d mdrun -notunepme >mdrun.out 2>&1 1247s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/aminoacids/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1247s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/aminoacids/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1247s PASSED but check mdp file differences 1247s Testing argon . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/argon/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/argon/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/argon/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/argon/topol -maxwarn 10 >grompp.out 2>grompp.err 1247s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/argon/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1247s gmx_d mdrun -nb cpu -notunepme >mdrun.out 2>&1 1247s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/argon/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1247s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/argon/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1247s PASSED but check mdp file differences 1247s Testing awh_multibias . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/index >grompp.out 2>grompp.err 1247s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1247s gmx_d mdrun -notunepme -cpi /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/continue -noappend >mdrun.out 2>&1 1247s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1247s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/reference_d.trr -f2 traj.part0002.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1247s PASSED but check mdp file differences 1247s Testing awh_multidim . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim/index >grompp.out 2>grompp.err 1247s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1247s gmx_d mdrun -notunepme >mdrun.out 2>&1 1247s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1247s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1247s PASSED but check mdp file differences 1247s Testing butane . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/butane/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/butane/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/butane/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/butane/topol -maxwarn 10 >grompp.out 2>grompp.err 1247s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/butane/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1247s gmx_d mdrun -notunepme >mdrun.out 2>&1 1247s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/butane/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1247s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/butane/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1247s PASSED but check mdp file differences 1247s Testing cbt . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/cbt/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/cbt/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/cbt/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/cbt/topol -maxwarn 10 >grompp.out 2>grompp.err 1247s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/cbt/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1247s gmx_d mdrun -nb cpu -notunepme >mdrun.out 2>&1 1247s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/cbt/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1247s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/cbt/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1247s PASSED but check mdp file differences 1247s Testing dd121 . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dd121/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dd121/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dd121/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dd121/topol -maxwarn 10 >grompp.out 2>grompp.err 1247s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dd121/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1247s gmx_d mdrun -ntmpi 12 -notunepme >mdrun.out 2>&1 1263s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dd121/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1263s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dd121/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1263s PASSED but check mdp file differences 1263s Testing dec+water . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dec+water/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dec+water/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dec+water/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dec+water/topol -maxwarn 10 >grompp.out 2>grompp.err 1263s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dec+water/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1263s gmx_d mdrun -nb cpu -notunepme >mdrun.out 2>&1 1263s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dec+water/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1263s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dec+water/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1263s PASSED but check mdp file differences 1263s Testing distance_restraints . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/distance_restraints/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/distance_restraints/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/distance_restraints/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/distance_restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 1263s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/distance_restraints/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1263s gmx_d mdrun -ntmpi 1 -notunepme >mdrun.out 2>&1 1263s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/distance_restraints/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1263s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/distance_restraints/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1263s PASSED but check mdp file differences 1263s Testing ethyleenglycol . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/ethyleenglycol/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/ethyleenglycol/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/ethyleenglycol/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/ethyleenglycol/topol -maxwarn 10 >grompp.out 2>grompp.err 1263s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/ethyleenglycol/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1263s gmx_d mdrun -notunepme >mdrun.out 2>&1 1263s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/ethyleenglycol/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1264s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/ethyleenglycol/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1264s PASSED but check mdp file differences 1264s Testing field . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/field/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/field/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/field/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/field/topol -maxwarn 10 >grompp.out 2>grompp.err 1264s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/field/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1264s gmx_d mdrun -notunepme >mdrun.out 2>&1 1264s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/field/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1264s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/field/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1264s PASSED but check mdp file differences 1264s Testing nacl . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nacl/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nacl/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nacl/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nacl/topol -maxwarn 10 >grompp.out 2>grompp.err 1264s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nacl/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1264s gmx_d mdrun -notunepme >mdrun.out 2>&1 1264s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nacl/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1264s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nacl/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1264s PASSED but check mdp file differences 1264s Testing nbnxn-energy-groups . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-energy-groups/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-energy-groups/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-energy-groups/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-energy-groups/topol -maxwarn 10 >grompp.out 2>grompp.err 1264s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-energy-groups/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1264s gmx_d mdrun -nb cpu -notunepme >mdrun.out 2>&1 1264s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1264s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-energy-groups/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1264s PASSED but check mdp file differences 1264s Testing nbnxn-free-energy . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy/topol -maxwarn 10 >grompp.out 2>grompp.err 1265s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1265s gmx_d mdrun -notunepme >mdrun.out 2>&1 1265s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1265s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1265s PASSED but check mdp file differences 1265s Testing nbnxn-free-energy-vv . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy-vv/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy-vv/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy-vv/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy-vv/topol -maxwarn 10 >grompp.out 2>grompp.err 1265s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy-vv/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1265s gmx_d mdrun -notunepme >mdrun.out 2>&1 1265s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1265s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy-vv/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1265s PASSED but check mdp file differences 1265s Testing nbnxn-ljpme-geometric . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-geometric/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-geometric/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-geometric/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-geometric/topol -maxwarn 10 >grompp.out 2>grompp.err 1265s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-geometric/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1265s gmx_d mdrun -notunepme >mdrun.out 2>&1 1265s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1265s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-geometric/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1265s PASSED but check mdp file differences 1265s Testing nbnxn-ljpme-LB . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB/topol -maxwarn 10 >grompp.out 2>grompp.err 1265s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1265s gmx_d mdrun -notunepme >mdrun.out 2>&1 1266s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1266s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1266s PASSED but check mdp file differences 1266s Testing nbnxn-ljpme-LB-geometric . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/topol -maxwarn 10 >grompp.out 2>grompp.err 1266s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1266s gmx_d mdrun -notunepme >mdrun.out 2>&1 1266s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1266s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1266s PASSED but check mdp file differences 1266s Testing nbnxn-vdw-force-switch . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-force-switch/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-force-switch/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-force-switch/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-force-switch/topol -maxwarn 10 >grompp.out 2>grompp.err 1266s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-force-switch/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1266s gmx_d mdrun -notunepme >mdrun.out 2>&1 1266s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1266s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-force-switch/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1266s PASSED but check mdp file differences 1266s Testing nbnxn-vdw-potential-switch . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch/topol -maxwarn 10 >grompp.out 2>grompp.err 1266s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1266s gmx_d mdrun -notunepme >mdrun.out 2>&1 1267s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1267s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1267s PASSED but check mdp file differences 1267s Testing nbnxn-vdw-potential-switch-argon . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/topol -maxwarn 10 >grompp.out 2>grompp.err 1267s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1267s gmx_d mdrun -notunepme >mdrun.out 2>&1 1267s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1267s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1267s PASSED but check mdp file differences 1267s Testing nbnxn_pme . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme/topol -maxwarn 10 >grompp.out 2>grompp.err 1267s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1267s gmx_d mdrun -notunepme >mdrun.out 2>&1 1267s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1267s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1267s PASSED but check mdp file differences 1267s Testing nbnxn_pme_order5 . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order5/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order5/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order5/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order5/topol -maxwarn 10 >grompp.out 2>grompp.err 1267s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order5/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1267s gmx_d mdrun -notunepme >mdrun.out 2>&1 1267s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1267s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order5/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1267s PASSED but check mdp file differences 1267s Testing nbnxn_pme_order6 . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order6/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order6/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order6/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order6/topol -maxwarn 10 >grompp.out 2>grompp.err 1267s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order6/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1267s gmx_d mdrun -notunepme >mdrun.out 2>&1 1267s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1267s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order6/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1267s PASSED but check mdp file differences 1267s Testing nbnxn_rf . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rf/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rf/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rf/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rf/topol -maxwarn 10 >grompp.out 2>grompp.err 1267s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rf/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1267s gmx_d mdrun -notunepme >mdrun.out 2>&1 1267s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rf/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1267s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rf/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1267s PASSED but check mdp file differences 1267s Testing nbnxn_rzero . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rzero/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rzero/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rzero/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rzero/topol -maxwarn 10 >grompp.out 2>grompp.err 1267s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rzero/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1267s gmx_d mdrun -notunepme >mdrun.out 2>&1 1267s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rzero/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1267s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rzero/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1267s PASSED but check mdp file differences 1267s Testing nbnxn_vsite . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_vsite/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_vsite/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_vsite/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_vsite/topol -maxwarn 10 >grompp.out 2>grompp.err 1267s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_vsite/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1268s gmx_d mdrun -ntmpi 6 -notunepme >mdrun.out 2>&1 1272s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_vsite/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1272s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_vsite/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1272s PASSED but check mdp file differences 1272s Testing nst_mismatch . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nst_mismatch/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nst_mismatch/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nst_mismatch/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nst_mismatch/topol -maxwarn 10 >grompp.out 2>grompp.err 1272s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nst_mismatch/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1272s gmx_d mdrun -notunepme >mdrun.out 2>&1 1273s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nst_mismatch/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1273s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nst_mismatch/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1273s PASSED but check mdp file differences 1273s Testing octahedron . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/octahedron/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/octahedron/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/octahedron/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/octahedron/topol -maxwarn 10 >grompp.out 2>grompp.err 1273s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/octahedron/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1273s gmx_d mdrun -notunepme >mdrun.out 2>&1 1273s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/octahedron/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1273s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/octahedron/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1273s PASSED but check mdp file differences 1273s Testing orientation-restraints . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/orientation-restraints/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/orientation-restraints/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/orientation-restraints/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/orientation-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 1273s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/orientation-restraints/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1273s gmx_d mdrun -ntmpi 1 -notunepme >mdrun.out 2>&1 1277s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/orientation-restraints/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1277s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/orientation-restraints/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1277s PASSED but check mdp file differences 1277s Testing position-restraints . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/position-restraints/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/position-restraints/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/position-restraints/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/position-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 1277s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/position-restraints/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1277s gmx_d mdrun -notunepme >mdrun.out 2>&1 1277s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/position-restraints/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1277s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/position-restraints/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1277s PASSED but check mdp file differences 1277s Testing pr-vrescale . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pr-vrescale/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pr-vrescale/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pr-vrescale/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pr-vrescale/topol -maxwarn 10 >grompp.out 2>grompp.err 1277s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pr-vrescale/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1277s gmx_d mdrun -notunepme >mdrun.out 2>&1 1277s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pr-vrescale/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1277s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pr-vrescale/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1277s PASSED but check mdp file differences 1277s Testing pull_constraint . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint/index >grompp.out 2>grompp.err 1277s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1277s gmx_d mdrun -notunepme >mdrun.out 2>&1 1278s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1278s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1278s PASSED but check mdp file differences 1278s Testing pull_cylinder . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder/index >grompp.out 2>grompp.err 1278s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1278s gmx_d mdrun -notunepme >mdrun.out 2>&1 1278s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1278s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1278s PASSED but check mdp file differences 1278s Testing pull_geometry_angle . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle/index >grompp.out 2>grompp.err 1278s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1278s gmx_d mdrun -notunepme >mdrun.out 2>&1 1278s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1278s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1278s PASSED but check mdp file differences 1278s Testing pull_geometry_angle-axis . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle-axis/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle-axis/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle-axis/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle-axis/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle-axis/index >grompp.out 2>grompp.err 1278s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle-axis/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1278s gmx_d mdrun -notunepme >mdrun.out 2>&1 1278s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1278s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle-axis/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1278s PASSED but check mdp file differences 1278s Testing pull_geometry_dihedral . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_dihedral/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_dihedral/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_dihedral/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_dihedral/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_dihedral/index >grompp.out 2>grompp.err 1278s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_dihedral/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1278s gmx_d mdrun -notunepme >mdrun.out 2>&1 1278s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1278s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_dihedral/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1278s PASSED but check mdp file differences 1278s Testing reb . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/reb/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/reb/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/reb/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/reb/topol -maxwarn 10 >grompp.out 2>grompp.err 1278s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/reb/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1278s gmx_d mdrun -nb cpu -notunepme >mdrun.out 2>&1 1278s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/reb/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1278s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/reb/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1278s PASSED but check mdp file differences 1278s Testing sw . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/sw/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/sw/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/sw/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/sw/topol -maxwarn 10 >grompp.out 2>grompp.err 1278s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/sw/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1278s gmx_d mdrun -ntmpi 1 -notunepme >mdrun.out 2>&1 1279s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/sw/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1279s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/sw/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1279s PASSED but check mdp file differences 1279s Testing swap_x . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x/index >grompp.out 2>grompp.err 1279s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1279s gmx_d mdrun -notunepme >mdrun.out 2>&1 1279s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1279s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1279s PASSED but check mdp file differences 1279s Testing swap_y . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y/index >grompp.out 2>grompp.err 1280s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1280s gmx_d mdrun -notunepme >mdrun.out 2>&1 1280s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1280s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1280s PASSED but check mdp file differences 1280s Testing swap_z . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z/index >grompp.out 2>grompp.err 1280s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1280s gmx_d mdrun -notunepme >mdrun.out 2>&1 1281s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1281s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1281s PASSED but check mdp file differences 1281s Testing tip4p . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p/topol -maxwarn 10 >grompp.out 2>grompp.err 1281s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1281s gmx_d mdrun -notunepme >mdrun.out 2>&1 1281s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1281s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1281s PASSED but check mdp file differences 1281s Testing tip4p_continue . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue/topol -maxwarn 10 >grompp.out 2>grompp.err 1282s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1282s gmx_d mdrun -notunepme -cpi /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue/continue -noappend >mdrun.out 2>&1 1282s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1282s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue/reference_d.trr -f2 traj.part0002.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1282s PASSED but check mdp file differences 1282s Testing tip4pflex . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4pflex/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4pflex/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4pflex/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4pflex/topol -maxwarn 10 >grompp.out 2>grompp.err 1282s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4pflex/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1282s gmx_d mdrun -notunepme >mdrun.out 2>&1 1282s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4pflex/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1282s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4pflex/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1282s PASSED but check mdp file differences 1282s Testing urea . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/urea/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/urea/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/urea/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/urea/topol -maxwarn 10 >grompp.out 2>grompp.err 1282s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/urea/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1282s gmx_d mdrun -notunepme >mdrun.out 2>&1 1282s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/urea/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1282s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/urea/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1282s PASSED but check mdp file differences 1282s Testing walls . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/walls/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/walls/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/walls/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/walls/topol -maxwarn 10 >grompp.out 2>grompp.err 1282s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/walls/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1282s gmx_d mdrun -notunepme >mdrun.out 2>&1 1282s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/walls/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1282s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/walls/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1282s PASSED but check mdp file differences 1282s All 48 complex tests PASSED 1282s Testing coulandvdwsequential_coul . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_coul/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_coul/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_coul/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_coul/topol -maxwarn 10 >grompp.out 2>grompp.err 1283s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_coul/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1283s gmx_d mdrun -notunepme >mdrun.out 2>&1 1283s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_coul/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1283s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_coul/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1283s PASSED but check mdp file differences 1283s Testing coulandvdwsequential_vdw . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_vdw/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_vdw/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_vdw/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_vdw/topol -maxwarn 10 >grompp.out 2>grompp.err 1283s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_vdw/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1283s gmx_d mdrun -notunepme >mdrun.out 2>&1 1284s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_vdw/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1284s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_vdw/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1284s PASSED but check mdp file differences 1284s Testing coulandvdwtogether . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwtogether/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwtogether/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwtogether/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwtogether/topol -maxwarn 10 >grompp.out 2>grompp.err 1284s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwtogether/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1284s gmx_d mdrun -notunepme >mdrun.out 2>&1 1284s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwtogether/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1284s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwtogether/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1284s PASSED but check mdp file differences 1284s Testing expanded . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/expanded/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/expanded/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/expanded/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/expanded/topol -maxwarn 10 >grompp.out 2>grompp.err 1284s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/expanded/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1284s gmx_d mdrun -notunepme >mdrun.out 2>&1 1285s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/expanded/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1285s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/expanded/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1285s PASSED but check mdp file differences 1285s Testing relative . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative/topol -maxwarn 10 >grompp.out 2>grompp.err 1285s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1285s gmx_d mdrun -notunepme >mdrun.out 2>&1 1286s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1286s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1286s PASSED but check mdp file differences 1286s Testing relative-position-restraints . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative-position-restraints/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative-position-restraints/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative-position-restraints/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative-position-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 1286s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative-position-restraints/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1286s gmx_d mdrun -notunepme >mdrun.out 2>&1 1287s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1287s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative-position-restraints/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1287s PASSED but check mdp file differences 1287s Testing restraints . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/restraints/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/restraints/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/restraints/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 1288s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/restraints/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1288s gmx_d mdrun -notunepme >mdrun.out 2>&1 1301s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/restraints/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1301s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/restraints/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1301s PASSED but check mdp file differences 1301s Testing simtemp . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/simtemp/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/simtemp/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/simtemp/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/simtemp/topol -maxwarn 10 >grompp.out 2>grompp.err 1301s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/simtemp/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1301s gmx_d mdrun -notunepme >mdrun.out 2>&1 1301s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/simtemp/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1301s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/simtemp/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1301s PASSED but check mdp file differences 1301s Testing transformAtoB . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/transformAtoB/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/transformAtoB/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/transformAtoB/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/transformAtoB/topol -maxwarn 10 >grompp.out 2>grompp.err 1301s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/transformAtoB/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1301s gmx_d mdrun -notunepme >mdrun.out 2>&1 1301s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/transformAtoB/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1301s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/transformAtoB/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1301s PASSED but check mdp file differences 1301s Testing vdwalone . . . gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/vdwalone/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/vdwalone/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/vdwalone/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/vdwalone/topol -maxwarn 10 >grompp.out 2>grompp.err 1301s gmx_d check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/vdwalone/reference_d.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1301s gmx_d mdrun -notunepme >mdrun.out 2>&1 1302s gmx_d check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/vdwalone/reference_d.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1302s gmx_d check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/vdwalone/reference_d.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1302s PASSED but check mdp file differences 1302s All 10 freeenergy tests PASSED 1302s All 0 extra tests PASSED 1302s Testing linfix . . . 1302s gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix/topol -maxwarn 2 >grompp.out 2>grompp.err 1302s echo 0 | gmx_d make_edi -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix/eigenvec.trr -outfrq 1 -linfix 1 -linstep 0.0013 -o sam.edi 1>make_edi.out 2>make_edi.err 1302s gmx_d mdrun -ei sam.edi -eo linfix.xvg >mdrun.out 2>&1 1302s Comparing column #0 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix/edsam_reference.xvg and linfix.xvg ... all within tolerance of 0 1302s Comparing column #1 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix/edsam_reference.xvg and linfix.xvg ... all within tolerance of 0.05 1302s Comparing column #2 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix/edsam_reference.xvg and linfix.xvg ... all within tolerance of 1e-06 1302s Testing linacc . . . 1302s gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc/topol -maxwarn 2 >grompp.out 2>grompp.err 1302s echo 0 | gmx_d make_edi -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc/eigenvec.trr -outfrq 2 -linacc 1 -accdir +1 -o sam.edi 1>make_edi.out 2>make_edi.err 1302s gmx_d mdrun -ei sam.edi -eo linacc.xvg >mdrun.out 2>&1 1302s Comparing column #0 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc/edsam_reference.xvg and linacc.xvg ... all within tolerance of 0 1302s Comparing column #1 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc/edsam_reference.xvg and linacc.xvg ... all within tolerance of 0.005 1302s Comparing column #2 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc/edsam_reference.xvg and linacc.xvg ... all within tolerance of 0.001 1302s Checking monotonicity for column 2 of file linacc.xvg ... values of column 2 are increasing monotonically. 1302s Testing radfix . . . 1302s gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radfix/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radfix/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radfix/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radfix/topol -maxwarn 2 >grompp.out 2>grompp.err 1302s echo 0 | gmx_d make_edi -f /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1302s gmx_d mdrun -ei sam.edi -eo radfix.xvg >mdrun.out 2>&1 1302s Comparing column #0 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radfix/edsam_reference.xvg and radfix.xvg ... all within tolerance of 0 1302s Comparing column #1 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radfix/edsam_reference.xvg and radfix.xvg ... all within tolerance of 0.05 1302s Comparing column #4 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radfix/edsam_reference.xvg and radfix.xvg ... all within tolerance of 0 1302s Checking radius for file radfix.xvg ... all values within tolerance of 1e-05 1302s Testing radacc . . . 1302s gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radacc/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radacc/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radacc/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radacc/topol -maxwarn 2 >grompp.out 2>grompp.err 1302s echo 0 | gmx_d make_edi -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radacc/eigenvec.trr -outfrq 3 -radacc 1-2 -o sam.edi 1>make_edi.out 2>make_edi.err 1302s gmx_d mdrun -ei sam.edi -eo radacc.xvg >mdrun.out 2>&1 1302s Comparing column #0 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radacc/edsam_reference.xvg and radacc.xvg ... all within tolerance of 0 1302s Comparing column #1 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radacc/edsam_reference.xvg and radacc.xvg ... all within tolerance of 0.05 1302s Checking radius for file radacc.xvg ... all values within tolerance of 1e-05 1302s Checking monotonicity for column 4 of file radacc.xvg ... values of column 4 are increasing monotonically. 1302s Testing radcon . . . 1302s gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon/topol -maxwarn 2 >grompp.out 2>grompp.err 1302s echo 0 0 | gmx_d make_edi -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon/eigenvec.trr -outfrq 1 -radcon 1-2 -tar /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon/target.pdb -o sam.edi 1>make_edi.out 2>make_edi.err 1302s gmx_d mdrun -ei sam.edi -eo radcon.xvg >mdrun.out 2>&1 1302s Comparing column #0 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon/edsam_reference.xvg and radcon.xvg ... all within tolerance of 0 1302s Comparing column #1 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon/edsam_reference.xvg and radcon.xvg ... all within tolerance of 0.05 1302s Checking radius for file radcon.xvg ... all values within tolerance of 1e-05 1302s Checking monotonicity for column 4 of file radcon.xvg ... values of column 4 are decreasing monotonically. 1302s Testing flooding1 . . . 1302s gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/topol -maxwarn 2 >grompp.out 2>grompp.err 1303s gmx_d mdrun -ei /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/sam.edi -eo flooding1.xvg >mdrun.out 2>&1 1303s Comparing column #0 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 0 1303s Comparing column #1 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1e-05 1303s Comparing column #2 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1e-05 1303s Comparing column #3 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1 1303s Comparing column #4 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1 1303s Comparing column #5 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1e-05 1303s Comparing column #6 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1 1303s Comparing column #7 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/edsam_reference.xvg and flooding1.xvg ... all within tolerance of 1 1303s Testing flooding2 . . . 1303s gmx_d grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/topol -maxwarn 2 >grompp.out 2>grompp.err 1303s gmx_d mdrun -ei /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/sam.edi -eo flooding2.xvg >mdrun.out 2>&1 1304s Comparing column #0 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 0 1304s Comparing column #1 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 0.05 1304s Comparing column #2 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 0.025 1304s Comparing column #3 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 250 1304s Comparing column #4 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 1000 1304s Comparing column #5 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 0.025 1304s Comparing column #6 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 250 1304s Comparing column #7 of .xvg files /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/edsam_reference.xvg and flooding2.xvg ... all within tolerance of 1000 1304s All 7 essential dynamics tests PASSED 1304s ============================================================= 1304s Starting regression tests: MPI build, single precision (only) 1304s ============================================================= 1304s Will test on 4 MPI ranks (if possible) 1304s Testing acetonitrilRF . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/acetonitrilRF/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/acetonitrilRF/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/acetonitrilRF/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/acetonitrilRF/topol -maxwarn 10 >grompp.out 2>grompp.err 1304s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/acetonitrilRF/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1304s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/acetonitrilRF gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1 1304s 1304s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/acetonitrilRF gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1' was -1 1304s FAILED. Check mdrun.out, md.log file(s) in acetonitrilRF for acetonitrilRF 1304s Testing aminoacids . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/aminoacids/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/aminoacids/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/aminoacids/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/aminoacids/topol -maxwarn 10 >grompp.out 2>grompp.err 1304s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/aminoacids/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1305s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/aminoacids gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1305s 1305s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/aminoacids gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1305s FAILED. Check mdrun.out, md.log file(s) in aminoacids for aminoacids 1305s Testing argon . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/argon/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/argon/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/argon/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/argon/topol -maxwarn 10 >grompp.out 2>grompp.err 1305s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/argon/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1305s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/argon gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1 1305s 1305s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/argon gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1' was -1 1305s FAILED. Check mdrun.out, md.log file(s) in argon for argon 1305s Testing awh_multibias . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/index >grompp.out 2>grompp.err 1305s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1305s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias gmx_mpi mdrun -notunepme -cpi /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/continue -noappend >mdrun.out 2>&1 1305s 1305s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias gmx_mpi mdrun -notunepme -cpi /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multibias/continue -noappend >mdrun.out 2>&1' was -1 1305s FAILED. Check mdrun.out, md.log file(s) in awh_multibias for awh_multibias 1305s Testing awh_multidim . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim/index >grompp.out 2>grompp.err 1305s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1305s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1305s 1305s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/awh_multidim gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1305s FAILED. Check mdrun.out, md.log file(s) in awh_multidim for awh_multidim 1305s Testing butane . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/butane/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/butane/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/butane/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/butane/topol -maxwarn 10 >grompp.out 2>grompp.err 1305s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/butane/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1305s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/butane gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1305s 1305s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/butane gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1305s FAILED. Check mdrun.out, md.log file(s) in butane for butane 1305s Testing cbt . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/cbt/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/cbt/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/cbt/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/cbt/topol -maxwarn 10 >grompp.out 2>grompp.err 1305s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/cbt/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1305s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/cbt gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1 1305s 1305s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/cbt gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1' was -1 1305s FAILED. Check mdrun.out, md.log file(s) in cbt for cbt 1305s Testing dd121 . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dd121/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dd121/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dd121/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dd121/topol -maxwarn 10 >grompp.out 2>grompp.err 1306s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dd121/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1306s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dd121 gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1306s 1306s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dd121 gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1306s FAILED. Check mdrun.out, md.log file(s) in dd121 for dd121 1306s Testing dec+water . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dec+water/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dec+water/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dec+water/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dec+water/topol -maxwarn 10 >grompp.out 2>grompp.err 1306s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dec+water/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1306s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dec+water gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1 1306s 1306s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/dec+water gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1' was -1 1306s FAILED. Check mdrun.out, md.log file(s) in dec+water for dec+water 1306s Testing distance_restraints . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/distance_restraints/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/distance_restraints/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/distance_restraints/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/distance_restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 1306s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/distance_restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1306s mpirun -np 1 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/distance_restraints gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1306s gmx_mpi check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/distance_restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1306s gmx_mpi check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/distance_restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1307s PASSED but check mdp file differences 1307s Testing ethyleenglycol . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/ethyleenglycol/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/ethyleenglycol/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/ethyleenglycol/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/ethyleenglycol/topol -maxwarn 10 >grompp.out 2>grompp.err 1307s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/ethyleenglycol/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1307s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/ethyleenglycol gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1307s 1307s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/ethyleenglycol gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1307s FAILED. Check mdrun.out, md.log file(s) in ethyleenglycol for ethyleenglycol 1307s Testing field . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/field/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/field/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/field/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/field/topol -maxwarn 10 >grompp.out 2>grompp.err 1307s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/field/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1307s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/field gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1307s 1307s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/field gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1307s FAILED. Check mdrun.out, md.log file(s) in field for field 1307s Testing nacl . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nacl/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nacl/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nacl/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nacl/topol -maxwarn 10 >grompp.out 2>grompp.err 1307s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nacl/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1307s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nacl gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1307s 1307s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nacl gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1307s FAILED. Check mdrun.out, md.log file(s) in nacl for nacl 1307s Testing nbnxn-energy-groups . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-energy-groups/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-energy-groups/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-energy-groups/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-energy-groups/topol -maxwarn 10 >grompp.out 2>grompp.err 1308s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-energy-groups/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1308s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-energy-groups gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1 1308s 1308s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-energy-groups gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1' was -1 1308s FAILED. Check mdrun.out, md.log file(s) in nbnxn-energy-groups for nbnxn-energy-groups 1308s Testing nbnxn-free-energy . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy/topol -maxwarn 10 >grompp.out 2>grompp.err 1308s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1308s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1308s 1308s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1308s FAILED. Check mdrun.out, md.log file(s) in nbnxn-free-energy for nbnxn-free-energy 1308s Testing nbnxn-free-energy-vv . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy-vv/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy-vv/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy-vv/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy-vv/topol -maxwarn 10 >grompp.out 2>grompp.err 1308s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy-vv/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1308s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy-vv gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1308s 1308s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-free-energy-vv gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1308s FAILED. Check mdrun.out, md.log file(s) in nbnxn-free-energy-vv for nbnxn-free-energy-vv 1308s Testing nbnxn-ljpme-geometric . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-geometric/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-geometric/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-geometric/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-geometric/topol -maxwarn 10 >grompp.out 2>grompp.err 1308s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-geometric/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1308s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-geometric gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1308s 1308s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-geometric gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1308s FAILED. Check mdrun.out, md.log file(s) in nbnxn-ljpme-geometric for nbnxn-ljpme-geometric 1308s Testing nbnxn-ljpme-LB . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB/topol -maxwarn 10 >grompp.out 2>grompp.err 1308s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1308s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1308s 1308s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1308s FAILED. Check mdrun.out, md.log file(s) in nbnxn-ljpme-LB for nbnxn-ljpme-LB 1308s Testing nbnxn-ljpme-LB-geometric . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/topol -maxwarn 10 >grompp.out 2>grompp.err 1309s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB-geometric/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1309s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB-geometric gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1309s 1309s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-ljpme-LB-geometric gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1309s FAILED. Check mdrun.out, md.log file(s) in nbnxn-ljpme-LB-geometric for nbnxn-ljpme-LB-geometric 1309s Testing nbnxn-vdw-force-switch . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-force-switch/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-force-switch/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-force-switch/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-force-switch/topol -maxwarn 10 >grompp.out 2>grompp.err 1309s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-force-switch/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1309s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-force-switch gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1309s 1309s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-force-switch gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1309s FAILED. Check mdrun.out, md.log file(s) in nbnxn-vdw-force-switch for nbnxn-vdw-force-switch 1309s Testing nbnxn-vdw-potential-switch . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch/topol -maxwarn 10 >grompp.out 2>grompp.err 1309s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1309s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1309s 1309s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1309s FAILED. Check mdrun.out, md.log file(s) in nbnxn-vdw-potential-switch for nbnxn-vdw-potential-switch 1309s Testing nbnxn-vdw-potential-switch-argon . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon/topol -maxwarn 10 >grompp.out 2>grompp.err 1309s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1309s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1309s 1309s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn-vdw-potential-switch-argon gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1309s FAILED. Check mdrun.out, md.log file(s) in nbnxn-vdw-potential-switch-argon for nbnxn-vdw-potential-switch-argon 1309s Testing nbnxn_pme . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme/topol -maxwarn 10 >grompp.out 2>grompp.err 1309s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1309s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1309s 1309s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1309s FAILED. Check mdrun.out, md.log file(s) in nbnxn_pme for nbnxn_pme 1309s Testing nbnxn_pme_order5 . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order5/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order5/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order5/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order5/topol -maxwarn 10 >grompp.out 2>grompp.err 1309s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order5/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1310s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order5 gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1310s 1310s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order5 gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1310s FAILED. Check mdrun.out, md.log file(s) in nbnxn_pme_order5 for nbnxn_pme_order5 1310s Testing nbnxn_pme_order6 . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order6/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order6/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order6/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order6/topol -maxwarn 10 >grompp.out 2>grompp.err 1310s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order6/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1310s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order6 gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1310s 1310s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_pme_order6 gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1310s FAILED. Check mdrun.out, md.log file(s) in nbnxn_pme_order6 for nbnxn_pme_order6 1310s Testing nbnxn_rf . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rf/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rf/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rf/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rf/topol -maxwarn 10 >grompp.out 2>grompp.err 1310s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rf/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1310s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rf gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1310s 1310s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rf gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1310s FAILED. Check mdrun.out, md.log file(s) in nbnxn_rf for nbnxn_rf 1310s Testing nbnxn_rzero . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rzero/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rzero/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rzero/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rzero/topol -maxwarn 10 >grompp.out 2>grompp.err 1310s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rzero/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1310s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rzero gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1310s 1310s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_rzero gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1310s FAILED. Check mdrun.out, md.log file(s) in nbnxn_rzero for nbnxn_rzero 1310s Testing nbnxn_vsite . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_vsite/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_vsite/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_vsite/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_vsite/topol -maxwarn 10 >grompp.out 2>grompp.err 1310s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_vsite/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1310s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_vsite gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1310s 1310s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nbnxn_vsite gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1310s FAILED. Check mdrun.out, md.log file(s) in nbnxn_vsite for nbnxn_vsite 1310s Testing nst_mismatch . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nst_mismatch/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nst_mismatch/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nst_mismatch/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nst_mismatch/topol -maxwarn 10 >grompp.out 2>grompp.err 1311s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nst_mismatch/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1311s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nst_mismatch gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1311s 1311s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/nst_mismatch gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1311s FAILED. Check mdrun.out, md.log file(s) in nst_mismatch for nst_mismatch 1311s Testing octahedron . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/octahedron/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/octahedron/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/octahedron/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/octahedron/topol -maxwarn 10 >grompp.out 2>grompp.err 1311s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/octahedron/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1311s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/octahedron gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1311s 1311s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/octahedron gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1311s FAILED. Check mdrun.out, md.log file(s) in octahedron for octahedron 1311s Testing orientation-restraints . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/orientation-restraints/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/orientation-restraints/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/orientation-restraints/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/orientation-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 1311s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/orientation-restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1311s mpirun -np 1 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/orientation-restraints gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1380s gmx_mpi check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/orientation-restraints/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1380s gmx_mpi check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/orientation-restraints/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1380s PASSED but check mdp file differences 1380s Testing position-restraints . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/position-restraints/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/position-restraints/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/position-restraints/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/position-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 1380s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/position-restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1380s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/position-restraints gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1380s 1380s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/position-restraints gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1380s FAILED. Check mdrun.out, md.log file(s) in position-restraints for position-restraints 1380s Testing pr-vrescale . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pr-vrescale/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pr-vrescale/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pr-vrescale/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pr-vrescale/topol -maxwarn 10 >grompp.out 2>grompp.err 1381s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pr-vrescale/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1381s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pr-vrescale gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1381s 1381s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pr-vrescale gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1381s FAILED. Check mdrun.out, md.log file(s) in pr-vrescale for pr-vrescale 1381s Testing pull_constraint . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint/index >grompp.out 2>grompp.err 1381s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1381s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1381s 1381s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_constraint gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1381s FAILED. Check mdrun.out, md.log file(s) in pull_constraint for pull_constraint 1381s Testing pull_cylinder . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder/index >grompp.out 2>grompp.err 1381s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1381s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1381s 1381s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_cylinder gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1381s FAILED. Check mdrun.out, md.log file(s) in pull_cylinder for pull_cylinder 1381s Testing pull_geometry_angle . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle/index >grompp.out 2>grompp.err 1381s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1381s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1381s 1381s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1381s FAILED. Check mdrun.out, md.log file(s) in pull_geometry_angle for pull_geometry_angle 1381s Testing pull_geometry_angle-axis . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle-axis/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle-axis/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle-axis/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle-axis/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle-axis/index >grompp.out 2>grompp.err 1381s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle-axis/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1382s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle-axis gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1382s 1382s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_angle-axis gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1382s FAILED. Check mdrun.out, md.log file(s) in pull_geometry_angle-axis for pull_geometry_angle-axis 1382s Testing pull_geometry_dihedral . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_dihedral/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_dihedral/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_dihedral/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_dihedral/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_dihedral/index >grompp.out 2>grompp.err 1382s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_dihedral/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1382s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_dihedral gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1382s 1382s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/pull_geometry_dihedral gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1382s FAILED. Check mdrun.out, md.log file(s) in pull_geometry_dihedral for pull_geometry_dihedral 1382s Testing reb . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/reb/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/reb/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/reb/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/reb/topol -maxwarn 10 >grompp.out 2>grompp.err 1382s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/reb/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1382s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/reb gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1 1382s 1382s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/reb gmx_mpi mdrun -nb cpu -notunepme >mdrun.out 2>&1' was -1 1382s FAILED. Check mdrun.out, md.log file(s) in reb for reb 1382s Testing sw . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/sw/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/sw/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/sw/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/sw/topol -maxwarn 10 >grompp.out 2>grompp.err 1382s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/sw/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1382s mpirun -np 1 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/sw gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1395s gmx_mpi check -e /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/sw/reference_s.edr -e2 ener.edr -tol 0.001 -abstol 0.05 -lastener Potential >checkpot.out 2>checkpot.err 1395s gmx_mpi check -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/sw/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err 1395s PASSED but check mdp file differences 1395s Testing swap_x . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x/index >grompp.out 2>grompp.err 1395s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1396s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1396s 1396s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_x gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1396s FAILED. Check mdrun.out, md.log file(s) in swap_x for swap_x 1396s Testing swap_y . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y/index >grompp.out 2>grompp.err 1396s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1396s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1396s 1396s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_y gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1396s FAILED. Check mdrun.out, md.log file(s) in swap_y for swap_y 1396s Testing swap_z . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z/topol -maxwarn 10 -n /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z/index >grompp.out 2>grompp.err 1396s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1396s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1397s 1397s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/swap_z gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1397s FAILED. Check mdrun.out, md.log file(s) in swap_z for swap_z 1397s Testing tip4p . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p/topol -maxwarn 10 >grompp.out 2>grompp.err 1397s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1397s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1397s 1397s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1397s FAILED. Check mdrun.out, md.log file(s) in tip4p for tip4p 1397s Testing tip4p_continue . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue/topol -maxwarn 10 >grompp.out 2>grompp.err 1397s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1397s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue gmx_mpi mdrun -notunepme -cpi /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue/continue -noappend >mdrun.out 2>&1 1397s 1397s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue gmx_mpi mdrun -notunepme -cpi /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4p_continue/continue -noappend >mdrun.out 2>&1' was -1 1397s FAILED. Check mdrun.out, md.log file(s) in tip4p_continue for tip4p_continue 1397s Testing tip4pflex . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4pflex/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4pflex/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4pflex/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4pflex/topol -maxwarn 10 >grompp.out 2>grompp.err 1397s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4pflex/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1397s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4pflex gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1397s 1397s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/tip4pflex gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1397s FAILED. Check mdrun.out, md.log file(s) in tip4pflex for tip4pflex 1397s Testing urea . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/urea/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/urea/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/urea/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/urea/topol -maxwarn 10 >grompp.out 2>grompp.err 1398s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/urea/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1398s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/urea gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1398s 1398s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/urea gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1398s FAILED. Check mdrun.out, md.log file(s) in urea for urea 1398s Testing walls . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/walls/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/walls/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/walls/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/walls/topol -maxwarn 10 >grompp.out 2>grompp.err 1398s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/walls/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1398s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/walls gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1398s 1398s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/complex/walls gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1398s FAILED. Check mdrun.out, md.log file(s) in walls for walls 1398s 45 out of 48 complex tests FAILED 1398s Testing coulandvdwsequential_coul . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_coul/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_coul/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_coul/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_coul/topol -maxwarn 10 >grompp.out 2>grompp.err 1398s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_coul/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1398s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_coul gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1398s 1398s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_coul gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1398s FAILED. Check mdrun.out, md.log file(s) in coulandvdwsequential_coul for coulandvdwsequential_coul 1398s Testing coulandvdwsequential_vdw . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_vdw/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_vdw/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_vdw/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_vdw/topol -maxwarn 10 >grompp.out 2>grompp.err 1399s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_vdw/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1399s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_vdw gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1399s 1399s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwsequential_vdw gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1399s FAILED. Check mdrun.out, md.log file(s) in coulandvdwsequential_vdw for coulandvdwsequential_vdw 1399s Testing coulandvdwtogether . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwtogether/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwtogether/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwtogether/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwtogether/topol -maxwarn 10 >grompp.out 2>grompp.err 1399s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwtogether/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1399s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwtogether gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1399s 1399s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/coulandvdwtogether gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1399s FAILED. Check mdrun.out, md.log file(s) in coulandvdwtogether for coulandvdwtogether 1399s Testing expanded . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/expanded/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/expanded/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/expanded/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/expanded/topol -maxwarn 10 >grompp.out 2>grompp.err 1399s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/expanded/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1399s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/expanded gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1399s 1399s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/expanded gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1399s FAILED. Check mdrun.out, md.log file(s) in expanded for expanded 1399s Testing relative . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative/topol -maxwarn 10 >grompp.out 2>grompp.err 1400s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1400s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1400s 1400s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1400s FAILED. Check mdrun.out, md.log file(s) in relative for relative 1400s Testing relative-position-restraints . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative-position-restraints/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative-position-restraints/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative-position-restraints/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative-position-restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 1400s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative-position-restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1400s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative-position-restraints gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1400s 1400s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/relative-position-restraints gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1400s FAILED. Check mdrun.out, md.log file(s) in relative-position-restraints for relative-position-restraints 1400s Testing restraints . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/restraints/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/restraints/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/restraints/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/restraints/topol -maxwarn 10 >grompp.out 2>grompp.err 1400s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/restraints/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1400s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/restraints gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1400s 1400s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/restraints gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1400s FAILED. Check mdrun.out, md.log file(s) in restraints for restraints 1400s Testing simtemp . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/simtemp/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/simtemp/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/simtemp/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/simtemp/topol -maxwarn 10 >grompp.out 2>grompp.err 1400s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/simtemp/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1400s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/simtemp gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1400s 1400s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/simtemp gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1400s FAILED. Check mdrun.out, md.log file(s) in simtemp for simtemp 1400s Testing transformAtoB . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/transformAtoB/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/transformAtoB/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/transformAtoB/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/transformAtoB/topol -maxwarn 10 >grompp.out 2>grompp.err 1400s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/transformAtoB/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1401s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/transformAtoB gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1401s 1401s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/transformAtoB gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1401s FAILED. Check mdrun.out, md.log file(s) in transformAtoB for transformAtoB 1401s Testing vdwalone . . . gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/vdwalone/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/vdwalone/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/vdwalone/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/vdwalone/topol -maxwarn 10 >grompp.out 2>grompp.err 1401s gmx_mpi check -s1 /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/vdwalone/reference_s.tpr -s2 topol.tpr -tol 0.0001 -abstol 0.001 >checktpr.out 2>checktpr.err 1401s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/vdwalone gmx_mpi mdrun -notunepme >mdrun.out 2>&1 1401s 1401s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/freeenergy/vdwalone gmx_mpi mdrun -notunepme >mdrun.out 2>&1' was -1 1401s FAILED. Check mdrun.out, md.log file(s) in vdwalone for vdwalone 1401s 10 out of 10 freeenergy tests FAILED 1401s All 0 extra tests PASSED 1401s Testing linfix . . . 1401s gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix/topol -maxwarn 2 >grompp.out 2>grompp.err 1401s echo 0 | gmx_mpi make_edi -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix/eigenvec.trr -outfrq 1 -linfix 1 -linstep 0.0013 -o sam.edi 1>make_edi.out 2>make_edi.err 1401s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix gmx_mpi mdrun -ei sam.edi -eo linfix.xvg >mdrun.out 2>&1 1401s 1401s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linfix gmx_mpi mdrun -ei sam.edi -eo linfix.xvg >mdrun.out 2>&1' was -1 1401s Testing linacc . . . 1401s gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc/topol -maxwarn 2 >grompp.out 2>grompp.err 1401s echo 0 | gmx_mpi make_edi -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc/eigenvec.trr -outfrq 2 -linacc 1 -accdir +1 -o sam.edi 1>make_edi.out 2>make_edi.err 1401s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc gmx_mpi mdrun -ei sam.edi -eo linacc.xvg >mdrun.out 2>&1 1401s 1401s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/linacc gmx_mpi mdrun -ei sam.edi -eo linacc.xvg >mdrun.out 2>&1' was -1 1401s Testing radfix . . . 1401s gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radfix/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radfix/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radfix/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radfix/topol -maxwarn 2 >grompp.out 2>grompp.err 1401s echo 0 | gmx_mpi make_edi -f /tmp/autopkgtest.K5CJ0h/build.Kdk/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 1401s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radfix gmx_mpi mdrun -ei sam.edi -eo radfix.xvg >mdrun.out 2>&1 1401s 1401s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radfix gmx_mpi mdrun -ei sam.edi -eo radfix.xvg >mdrun.out 2>&1' was -1 1401s Testing radacc . . . 1401s gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radacc/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radacc/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radacc/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radacc/topol -maxwarn 2 >grompp.out 2>grompp.err 1401s echo 0 | gmx_mpi make_edi -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radacc/eigenvec.trr -outfrq 3 -radacc 1-2 -o sam.edi 1>make_edi.out 2>make_edi.err 1401s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radacc gmx_mpi mdrun -ei sam.edi -eo radacc.xvg >mdrun.out 2>&1 1401s 1401s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radacc gmx_mpi mdrun -ei sam.edi -eo radacc.xvg >mdrun.out 2>&1' was -1 1401s Testing radcon . . . 1401s gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon/topol -maxwarn 2 >grompp.out 2>grompp.err 1401s echo 0 0 | gmx_mpi make_edi -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon/eigenvec.trr -outfrq 1 -radcon 1-2 -tar /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon/target.pdb -o sam.edi 1>make_edi.out 2>make_edi.err 1402s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon gmx_mpi mdrun -ei sam.edi -eo radcon.xvg >mdrun.out 2>&1 1402s 1402s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/radcon gmx_mpi mdrun -ei sam.edi -eo radcon.xvg >mdrun.out 2>&1' was -1 1402s Testing flooding1 . . . 1402s gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/topol -maxwarn 2 >grompp.out 2>grompp.err 1402s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1 gmx_mpi mdrun -ei /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/sam.edi -eo flooding1.xvg >mdrun.out 2>&1 1402s 1402s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1 gmx_mpi mdrun -ei /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding1/sam.edi -eo flooding1.xvg >mdrun.out 2>&1' was -1 1402s Testing flooding2 . . . 1402s gmx_mpi grompp -f /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/grompp.mdp -c /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/conf -r /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/conf -p /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/topol -maxwarn 2 >grompp.out 2>grompp.err 1402s mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2 gmx_mpi mdrun -ei /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/sam.edi -eo flooding2.xvg >mdrun.out 2>&1 1402s 1402s Abnormal return value for 'mpirun -np 4 -wdir /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2 gmx_mpi mdrun -ei /tmp/autopkgtest.K5CJ0h/build.Kdk/src/regressiontests/essentialdynamics/flooding2/sam.edi -eo flooding2.xvg >mdrun.out 2>&1' was -1 1402s Essential dynamics tests FAILED with 7 errors! 1403s autopkgtest [20:54:37]: test gromacs-regressiontests: -----------------------] 1403s gromacs-regressiontests FAIL non-zero exit status 1 1403s autopkgtest [20:54:37]: test gromacs-regressiontests: - - - - - - - - - - results - - - - - - - - - - 1404s autopkgtest [20:54:38]: @@@@@@@@@@@@@@@@@@@@ summary 1404s gromacs-regressiontests FAIL non-zero exit status 1 1408s virt: nova [W] Skipping flock in bos03-arm64 1408s virt: Creating nova instance adt-plucky-arm64-gromacs-20241123-203114-juju-7f2275-prod-proposed-migration-environment-2-005610bb-975c-42e0-87dd-328e71ec5fde from image adt/ubuntu-plucky-arm64-server-20241119.img (UUID 254dc414-4366-404b-b85c-a4e26b3194ad)...