0s autopkgtest [09:08:03]: starting date and time: 2024-11-13 09:08:03+0000 0s autopkgtest [09:08:03]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [09:08:03]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.1t2ipus5/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade openmm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-4.secgroup --name adt-plucky-amd64-openmm-20241113-090803-juju-7f2275-prod-proposed-migration-environment-2-ad61b713-483e-4ac8-a59a-45b9323fb72b --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -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/ 83s autopkgtest [09:09:26]: testbed dpkg architecture: amd64 83s autopkgtest [09:09:26]: testbed apt version: 2.9.8 83s autopkgtest [09:09:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup 85s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 85s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 86s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 86s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 86s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 86s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [65.2 kB] 86s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [111 kB] 86s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 86s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [637 kB] 86s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [255 kB] 86s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 86s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 86s Fetched 2173 kB in 1s (1464 kB/s) 86s Reading package lists... 88s Reading package lists... 89s Building dependency tree... 89s Reading state information... 89s Calculating upgrade... 89s The following NEW packages will be installed: 89s python3.13-gdbm 89s The following packages will be upgraded: 89s libgpgme11t64 libpython3-stdlib python3 python3-gdbm python3-minimal 89s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 89s Need to get 253 kB of archives. 89s After this operation, 147 kB of additional disk space will be used. 89s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 89s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 89s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 89s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 89s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 89s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 libgpgme11t64 amd64 1.23.2-5ubuntu4 [152 kB] 90s Fetched 253 kB in 0s (557 kB/s) 90s (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 ... 75541 files and directories currently installed.) 90s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 90s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 90s Setting up python3-minimal (3.12.7-1) ... 90s (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 ... 75541 files and directories currently installed.) 90s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 90s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 90s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 90s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 90s Selecting previously unselected package python3.13-gdbm. 90s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 90s Unpacking python3.13-gdbm (3.13.0-2) ... 90s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 90s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 90s Preparing to unpack .../libgpgme11t64_1.23.2-5ubuntu4_amd64.deb ... 90s Unpacking libgpgme11t64:amd64 (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 90s Setting up libgpgme11t64:amd64 (1.23.2-5ubuntu4) ... 90s Setting up python3.13-gdbm (3.13.0-2) ... 90s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 90s Setting up python3 (3.12.7-1) ... 90s Setting up python3-gdbm:amd64 (3.12.7-1) ... 90s Processing triggers for man-db (2.12.1-3) ... 91s Processing triggers for libc-bin (2.40-1ubuntu3) ... 91s Reading package lists... 91s Building dependency tree... 91s Reading state information... 92s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 92s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 92s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 92s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 92s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 93s Reading package lists... 93s Reading package lists... 93s Building dependency tree... 93s Reading state information... 93s Calculating upgrade... 93s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 93s Reading package lists... 94s Building dependency tree... 94s Reading state information... 94s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 97s autopkgtest [09:09:40]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 97s autopkgtest [09:09:40]: @@@@@@@@@@@@@@@@@@@@ apt-source openmm 103s Get:1 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-1 (dsc) [2508 B] 103s Get:2 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-1 (tar) [11.5 MB] 103s Get:3 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-1 (diff) [18.6 kB] 103s gpgv: Signature made Tue Sep 10 14:07:52 2024 UTC 103s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 103s gpgv: issuer "merkys@debian.org" 103s gpgv: Can't check signature: No public key 103s dpkg-source: warning: cannot verify inline signature for ./openmm_8.1.2+dfsg-1.dsc: no acceptable signature found 104s autopkgtest [09:09:47]: testing package openmm version 8.1.2+dfsg-1 104s autopkgtest [09:09:47]: build not needed 112s autopkgtest [09:09:55]: test command1: preparing testbed 113s Reading package lists... 113s Building dependency tree... 113s Reading state information... 113s Starting pkgProblemResolver with broken count: 0 113s Starting 2 pkgProblemResolver with broken count: 0 113s Done 114s The following additional packages will be installed: 114s libblas3 libgfortran5 liblapack3 libopenmm-dev libopenmm8.1 114s python3-iniconfig python3-numpy python3-openmm python3-packaging 114s python3-pluggy python3-pytest 114s Suggested packages: 114s gcc gfortran python-numpy-doc python3-dev 114s The following NEW packages will be installed: 114s autopkgtest-satdep libblas3 libgfortran5 liblapack3 libopenmm-dev 114s libopenmm8.1 python3-iniconfig python3-numpy python3-openmm 114s python3-packaging python3-pluggy python3-pytest 114s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 114s Need to get 17.6 MB/17.6 MB of archives. 114s After this operation, 126 MB of additional disk space will be used. 114s Get:1 /tmp/autopkgtest.arku1n/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [716 B] 114s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 114s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 115s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 116s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmm8.1 amd64 8.1.2+dfsg-1 [1120 kB] 117s Get:6 http://ftpmaster.internal/ubuntu plucky/universe amd64 libopenmm-dev amd64 8.1.2+dfsg-1 [349 kB] 117s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 117s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 120s Get:9 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-openmm amd64 8.1.2+dfsg-1 [7536 kB] 125s Get:10 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 125s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 125s Get:12 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB] 125s Fetched 17.6 MB in 11s (1556 kB/s) 125s Selecting previously unselected package libblas3:amd64. 125s (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 ... 75548 files and directories currently installed.) 125s Preparing to unpack .../00-libblas3_3.12.0-3build2_amd64.deb ... 125s Unpacking libblas3:amd64 (3.12.0-3build2) ... 125s Selecting previously unselected package libgfortran5:amd64. 125s Preparing to unpack .../01-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 125s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 125s Selecting previously unselected package liblapack3:amd64. 125s Preparing to unpack .../02-liblapack3_3.12.0-3build2_amd64.deb ... 125s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 125s Selecting previously unselected package libopenmm8.1. 125s Preparing to unpack .../03-libopenmm8.1_8.1.2+dfsg-1_amd64.deb ... 125s Unpacking libopenmm8.1 (8.1.2+dfsg-1) ... 125s Selecting previously unselected package libopenmm-dev. 125s Preparing to unpack .../04-libopenmm-dev_8.1.2+dfsg-1_amd64.deb ... 125s Unpacking libopenmm-dev (8.1.2+dfsg-1) ... 125s Selecting previously unselected package python3-iniconfig. 125s Preparing to unpack .../05-python3-iniconfig_1.1.1-2_all.deb ... 125s Unpacking python3-iniconfig (1.1.1-2) ... 125s Selecting previously unselected package python3-numpy. 125s Preparing to unpack .../06-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 125s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 126s Selecting previously unselected package python3-openmm. 126s Preparing to unpack .../07-python3-openmm_8.1.2+dfsg-1_amd64.deb ... 126s Unpacking python3-openmm (8.1.2+dfsg-1) ... 126s Selecting previously unselected package python3-packaging. 126s Preparing to unpack .../08-python3-packaging_24.1-1_all.deb ... 126s Unpacking python3-packaging (24.1-1) ... 126s Selecting previously unselected package python3-pluggy. 126s Preparing to unpack .../09-python3-pluggy_1.5.0-1_all.deb ... 126s Unpacking python3-pluggy (1.5.0-1) ... 126s Selecting previously unselected package python3-pytest. 126s Preparing to unpack .../10-python3-pytest_8.3.3-1_all.deb ... 126s Unpacking python3-pytest (8.3.3-1) ... 126s Selecting previously unselected package autopkgtest-satdep. 126s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 126s Unpacking autopkgtest-satdep (0) ... 126s Setting up python3-iniconfig (1.1.1-2) ... 126s Setting up libblas3:amd64 (3.12.0-3build2) ... 126s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 126s Setting up python3-packaging (24.1-1) ... 126s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 126s Setting up python3-pluggy (1.5.0-1) ... 126s Setting up libopenmm8.1 (8.1.2+dfsg-1) ... 126s Setting up liblapack3:amd64 (3.12.0-3build2) ... 126s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 126s Setting up python3-pytest (8.3.3-1) ... 127s Setting up libopenmm-dev (8.1.2+dfsg-1) ... 127s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 128s Setting up python3-openmm (8.1.2+dfsg-1) ... 128s /usr/lib/python3/dist-packages/openmm/__init__.py:16: SyntaxWarning: invalid escape sequence '\p' 128s os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % { 128s /usr/lib/python3/dist-packages/openmm/app/gromacsgrofile.py:62: SyntaxWarning: invalid escape sequence '\.' 128s return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) 128s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:65: SyntaxWarning: invalid escape sequence '\(' 128s FORMAT_RE_PATTERN=re.compile("([0-9]+)\(?([a-zA-Z]+)([0-9]+)\.?([0-9]*)\)?") 128s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1071: SyntaxWarning: invalid escape sequence '\.' 128s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 128s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1082: SyntaxWarning: invalid escape sequence '\.' 128s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 128s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:358: SyntaxWarning: invalid escape sequence '\S' 128s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 128s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:360: SyntaxWarning: invalid escape sequence '\s' 128s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 128s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:361: SyntaxWarning: invalid escape sequence '\s' 128s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 128s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:363: SyntaxWarning: invalid escape sequence '\s' 128s "(?:\s*#.*$)" "|" # comments (dumped) 128s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:365: SyntaxWarning: invalid escape sequence '\S' 128s "(\S+)" # unquoted words 128s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:416: SyntaxWarning: invalid escape sequence '\S' 128s """ Tokenizer method for the mmCIF syntax file - 128s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' 128s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 128s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' 128s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 128s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' 128s "(?:\s*#.*$)" "|" # comments (dumped) 128s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' 128s "(\S+)" # unquoted words 128s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:347: SyntaxWarning: invalid escape sequence '\S' 128s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 128s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:349: SyntaxWarning: invalid escape sequence '\s' 128s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 128s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:350: SyntaxWarning: invalid escape sequence '\s' 128s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 128s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:352: SyntaxWarning: invalid escape sequence '\s' 128s "(?:\s*#.*$)" "|" # comments (dumped) 128s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:354: SyntaxWarning: invalid escape sequence '\S' 128s "(\S+)" # unquoted words 128s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:419: SyntaxWarning: invalid escape sequence '\S' 128s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 128s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:421: SyntaxWarning: invalid escape sequence '\s' 128s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 128s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:423: SyntaxWarning: invalid escape sequence '\s' 128s "(?:\s*#.*$)" "|" # comments (dumped) 128s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:425: SyntaxWarning: invalid escape sequence '\S' 128s "(\S+)" # unquoted words 128s /usr/lib/python3/dist-packages/openmm/app/metadynamics.py:247: SyntaxWarning: invalid escape sequence '\.' 128s pattern = re.compile('bias_(.*)_(.*)\.npy') 128s /usr/lib/python3/dist-packages/openmm/openmm.py:7208: SyntaxWarning: invalid escape sequence '\S' 128s match = re.search("<([^?]\S*)", inputString) 128s Setting up autopkgtest-satdep (0) ... 128s Processing triggers for man-db (2.12.1-3) ... 129s Processing triggers for libc-bin (2.40-1ubuntu3) ... 131s (Reading database ... 77178 files and directories currently installed.) 131s Removing autopkgtest-satdep (0) ... 132s autopkgtest [09:10:15]: test command1: cd wrappers/python/tests && pytest-3 132s autopkgtest [09:10:15]: test command1: [----------------------- 133s ============================= test session starts ============================== 133s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 133s rootdir: /tmp/autopkgtest.arku1n/build.Dzr/src/wrappers/python/tests 133s configfile: pytest.ini 133s plugins: typeguard-4.4.1 133s collected 327 items 133s 133s TestAPIUnits.py .................................. [ 10%] 133s TestATMForce.py . [ 10%] 133s TestAmberInpcrdFile.py .....s [ 12%] 139s TestAmberPrmtopFile.py ....................... [ 19%] 139s TestBytes.py . [ 19%] 163s TestCharmmFiles.py ....s..........s......... [ 27%] 163s TestCheckpointReporter.py . [ 27%] 163s TestDcdFile.py ... [ 28%] 165s TestDesmondDMSFile.py ....... [ 30%] 165s TestElement.py .... [ 32%] 183s TestForceField.py s........................................ss..s.. [ 46%] 183s TestForceGroups.py ... [ 47%] 183s TestGenerators.py .. [ 48%] 183s TestGromacsGroFile.py . [ 48%] 183s TestGromacsTopFile.py sssssssssssss [ 52%] 670s TestIntegrators.py .s..... [ 54%] 672s TestMetadynamics.py . [ 55%] 701s TestModeller.py .............s............. [ 63%] 701s TestNumpyCompatibility.py ......... [ 66%] 701s TestPatches.py ..... [ 67%] 707s TestPdbFile.py ...... [ 69%] 712s TestPdbReporter.py ........ [ 71%] 713s TestPdbxFile.py ....... [ 74%] 714s TestPickle.py ... [ 74%] 717s TestSimulatedTempering.py .. [ 75%] 750s TestSimulation.py ....... [ 77%] 750s TestStateDataReporter.py . [ 77%] 750s TestSwigWrappers.py . [ 78%] 750s TestTopology.py ... [ 79%] 750s TestUnitCell.py .. [ 79%] 750s TestUnits.py ...................................................... [ 96%] 750s TestVec3.py ....... [ 98%] 750s TestXtcFile.py ..... [100%] 750s 750s =============================== warnings summary =============================== 750s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes 750s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 750s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 750s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 750s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model GBn 750s warnings.warn( 750s 750s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 750s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 750s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 750s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model HCT 750s warnings.warn( 750s 750s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 750s =========== 305 passed, 22 skipped, 7 warnings in 617.96s (0:10:17) ============ 751s autopkgtest [09:20:34]: test command1: -----------------------] 751s autopkgtest [09:20:34]: test command1: - - - - - - - - - - results - - - - - - - - - - 751s command1 PASS 752s autopkgtest [09:20:35]: @@@@@@@@@@@@@@@@@@@@ summary 752s command1 PASS 1027s virt: nova [W] Skipping flock for amd64 1027s virt: Creating nova instance adt-plucky-amd64-openmm-20241113-090803-juju-7f2275-prod-proposed-migration-environment-2-ad61b713-483e-4ac8-a59a-45b9323fb72b from image adt/ubuntu-plucky-amd64-server-20241113.img (UUID 62c21ac4-2290-4c8d-8313-dddd18eacff4)...