0s autopkgtest [09:46:18]: starting date and time: 2024-11-13 09:46:18+0000 0s autopkgtest [09:46:18]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [09:46:18]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.37hfqum4/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 autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-34.secgroup --name adt-plucky-arm64-openmm-20241113-094618-juju-7f2275-prod-proposed-migration-environment-2-db9e3f9a-83d3-45f8-9715-572424641acf --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/ 71s autopkgtest [09:47:29]: testbed dpkg architecture: arm64 71s autopkgtest [09:47:29]: testbed apt version: 2.9.8 71s autopkgtest [09:47:29]: @@@@@@@@@@@@@@@@@@@@ test bed setup 72s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 73s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 73s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 73s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 73s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 73s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 73s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 73s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 73s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 73s Fetched 1794 kB in 1s (1991 kB/s) 73s Reading package lists... 76s Reading package lists... 76s Building dependency tree... 76s Reading state information... 77s Calculating upgrade... 78s The following NEW packages will be installed: 78s python3.13-gdbm 78s The following packages will be upgraded: 78s libpython3-stdlib python3 python3-gdbm python3-minimal 78s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 78s Need to get 101 kB of archives. 78s After this operation, 141 kB of additional disk space will be used. 78s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 78s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 78s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 78s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 78s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 78s Fetched 101 kB in 0s (286 kB/s) 79s (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 ... 79924 files and directories currently installed.) 79s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 79s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 79s Setting up python3-minimal (3.12.7-1) ... 79s (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 ... 79924 files and directories currently installed.) 79s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 79s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 79s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 79s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 79s Selecting previously unselected package python3.13-gdbm. 79s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 79s Unpacking python3.13-gdbm (3.13.0-2) ... 79s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 79s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 79s Setting up python3.13-gdbm (3.13.0-2) ... 79s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 79s Setting up python3 (3.12.7-1) ... 80s Setting up python3-gdbm:arm64 (3.12.7-1) ... 80s Processing triggers for man-db (2.12.1-3) ... 80s Reading package lists... 81s Building dependency tree... 81s Reading state information... 81s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 82s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 82s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 82s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 82s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 83s Reading package lists... 83s Reading package lists... 83s Building dependency tree... 83s Reading state information... 84s Calculating upgrade... 84s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 84s Reading package lists... 85s Building dependency tree... 85s Reading state information... 85s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 88s autopkgtest [09:47:46]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 89s autopkgtest [09:47:47]: @@@@@@@@@@@@@@@@@@@@ apt-source openmm 93s Get:1 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-1 (dsc) [2508 B] 93s Get:2 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-1 (tar) [11.5 MB] 93s Get:3 http://ftpmaster.internal/ubuntu plucky/universe openmm 8.1.2+dfsg-1 (diff) [18.6 kB] 93s gpgv: Signature made Tue Sep 10 14:07:52 2024 UTC 93s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 93s gpgv: issuer "merkys@debian.org" 93s gpgv: Can't check signature: No public key 93s dpkg-source: warning: cannot verify inline signature for ./openmm_8.1.2+dfsg-1.dsc: no acceptable signature found 94s autopkgtest [09:47:52]: testing package openmm version 8.1.2+dfsg-1 94s autopkgtest [09:47:52]: build not needed 99s autopkgtest [09:47:57]: test command1: preparing testbed 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 101s Starting pkgProblemResolver with broken count: 0 101s Starting 2 pkgProblemResolver with broken count: 0 101s Done 101s The following additional packages will be installed: 101s libblas3 libgfortran5 liblapack3 libopenmm-dev libopenmm8.1 101s python3-iniconfig python3-numpy python3-openmm python3-packaging 101s python3-pluggy python3-pytest 101s Suggested packages: 101s gcc gfortran python-numpy-doc python3-dev 102s The following NEW packages will be installed: 102s autopkgtest-satdep libblas3 libgfortran5 liblapack3 libopenmm-dev 102s libopenmm8.1 python3-iniconfig python3-numpy python3-openmm 102s python3-packaging python3-pluggy python3-pytest 102s 0 upgraded, 12 newly installed, 0 to remove and 0 not upgraded. 102s Need to get 15.6 MB/15.6 MB of archives. 102s After this operation, 117 MB of additional disk space will be used. 102s Get:1 /tmp/autopkgtest.uy7uiy/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 102s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 102s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 102s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 102s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 libopenmm8.1 arm64 8.1.2+dfsg-1 [986 kB] 102s Get:6 http://ftpmaster.internal/ubuntu plucky/universe arm64 libopenmm-dev arm64 8.1.2+dfsg-1 [333 kB] 102s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 102s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 103s Get:9 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-openmm arm64 8.1.2+dfsg-1 [7401 kB] 103s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 103s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 103s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB] 104s Fetched 15.6 MB in 2s (9797 kB/s) 104s Selecting previously unselected package libblas3:arm64. 104s (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 ... 79931 files and directories currently installed.) 104s Preparing to unpack .../00-libblas3_3.12.0-3build2_arm64.deb ... 104s Unpacking libblas3:arm64 (3.12.0-3build2) ... 104s Selecting previously unselected package libgfortran5:arm64. 104s Preparing to unpack .../01-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 104s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 104s Selecting previously unselected package liblapack3:arm64. 104s Preparing to unpack .../02-liblapack3_3.12.0-3build2_arm64.deb ... 104s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 104s Selecting previously unselected package libopenmm8.1. 104s Preparing to unpack .../03-libopenmm8.1_8.1.2+dfsg-1_arm64.deb ... 104s Unpacking libopenmm8.1 (8.1.2+dfsg-1) ... 104s Selecting previously unselected package libopenmm-dev. 104s Preparing to unpack .../04-libopenmm-dev_8.1.2+dfsg-1_arm64.deb ... 104s Unpacking libopenmm-dev (8.1.2+dfsg-1) ... 104s Selecting previously unselected package python3-iniconfig. 104s Preparing to unpack .../05-python3-iniconfig_1.1.1-2_all.deb ... 104s Unpacking python3-iniconfig (1.1.1-2) ... 104s Selecting previously unselected package python3-numpy. 104s Preparing to unpack .../06-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 104s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 104s Selecting previously unselected package python3-openmm. 104s Preparing to unpack .../07-python3-openmm_8.1.2+dfsg-1_arm64.deb ... 104s Unpacking python3-openmm (8.1.2+dfsg-1) ... 105s Selecting previously unselected package python3-packaging. 105s Preparing to unpack .../08-python3-packaging_24.1-1_all.deb ... 105s Unpacking python3-packaging (24.1-1) ... 105s Selecting previously unselected package python3-pluggy. 105s Preparing to unpack .../09-python3-pluggy_1.5.0-1_all.deb ... 105s Unpacking python3-pluggy (1.5.0-1) ... 105s Selecting previously unselected package python3-pytest. 105s Preparing to unpack .../10-python3-pytest_8.3.3-1_all.deb ... 105s Unpacking python3-pytest (8.3.3-1) ... 105s Selecting previously unselected package autopkgtest-satdep. 105s Preparing to unpack .../11-1-autopkgtest-satdep.deb ... 105s Unpacking autopkgtest-satdep (0) ... 105s Setting up python3-iniconfig (1.1.1-2) ... 105s Setting up libblas3:arm64 (3.12.0-3build2) ... 105s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 105s Setting up python3-packaging (24.1-1) ... 105s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 105s Setting up python3-pluggy (1.5.0-1) ... 105s Setting up libopenmm8.1 (8.1.2+dfsg-1) ... 105s Setting up liblapack3:arm64 (3.12.0-3build2) ... 105s 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 105s Setting up python3-pytest (8.3.3-1) ... 106s Setting up libopenmm-dev (8.1.2+dfsg-1) ... 106s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 108s Setting up python3-openmm (8.1.2+dfsg-1) ... 108s /usr/lib/python3/dist-packages/openmm/__init__.py:16: SyntaxWarning: invalid escape sequence '\p' 108s os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % { 108s /usr/lib/python3/dist-packages/openmm/app/gromacsgrofile.py:62: SyntaxWarning: invalid escape sequence '\.' 108s return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) 108s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:65: SyntaxWarning: invalid escape sequence '\(' 108s FORMAT_RE_PATTERN=re.compile("([0-9]+)\(?([a-zA-Z]+)([0-9]+)\.?([0-9]*)\)?") 108s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1071: SyntaxWarning: invalid escape sequence '\.' 108s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 108s /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1082: SyntaxWarning: invalid escape sequence '\.' 108s if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): 108s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:358: SyntaxWarning: invalid escape sequence '\S' 108s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 108s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:360: SyntaxWarning: invalid escape sequence '\s' 108s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 108s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:361: SyntaxWarning: invalid escape sequence '\s' 108s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 108s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:363: SyntaxWarning: invalid escape sequence '\s' 108s "(?:\s*#.*$)" "|" # comments (dumped) 108s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:365: SyntaxWarning: invalid escape sequence '\S' 108s "(\S+)" # unquoted words 108s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:416: SyntaxWarning: invalid escape sequence '\S' 108s """ Tokenizer method for the mmCIF syntax file - 108s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' 108s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 108s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' 108s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 108s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' 108s "(?:\s*#.*$)" "|" # comments (dumped) 108s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' 108s "(\S+)" # unquoted words 108s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:347: SyntaxWarning: invalid escape sequence '\S' 108s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 108s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:349: SyntaxWarning: invalid escape sequence '\s' 108s "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings 108s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:350: SyntaxWarning: invalid escape sequence '\s' 108s "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings 108s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:352: SyntaxWarning: invalid escape sequence '\s' 108s "(?:\s*#.*$)" "|" # comments (dumped) 108s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:354: SyntaxWarning: invalid escape sequence '\S' 108s "(\S+)" # unquoted words 108s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:419: SyntaxWarning: invalid escape sequence '\S' 108s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 108s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:421: SyntaxWarning: invalid escape sequence '\s' 108s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 108s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:423: SyntaxWarning: invalid escape sequence '\s' 108s "(?:\s*#.*$)" "|" # comments (dumped) 108s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:425: SyntaxWarning: invalid escape sequence '\S' 108s "(\S+)" # unquoted words 108s /usr/lib/python3/dist-packages/openmm/app/metadynamics.py:247: SyntaxWarning: invalid escape sequence '\.' 108s pattern = re.compile('bias_(.*)_(.*)\.npy') 108s /usr/lib/python3/dist-packages/openmm/openmm.py:10429: SyntaxWarning: invalid escape sequence '\S' 108s match = re.search("<([^?]\S*)", inputString) 108s Setting up autopkgtest-satdep (0) ... 108s Processing triggers for man-db (2.12.1-3) ... 108s Processing triggers for libc-bin (2.40-1ubuntu3) ... 112s (Reading database ... 81561 files and directories currently installed.) 112s Removing autopkgtest-satdep (0) ... 113s autopkgtest [09:48:11]: test command1: cd wrappers/python/tests && pytest-3 113s autopkgtest [09:48:11]: test command1: [----------------------- 115s ============================= test session starts ============================== 115s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 115s rootdir: /tmp/autopkgtest.uy7uiy/build.6xD/src/wrappers/python/tests 115s configfile: pytest.ini 115s plugins: typeguard-4.4.1 115s collected 327 items 115s 115s TestAPIUnits.py .................................. [ 10%] 115s TestATMForce.py . [ 10%] 115s TestAmberInpcrdFile.py .....s [ 12%] 122s TestAmberPrmtopFile.py ....................... [ 19%] 122s TestBytes.py . [ 19%] 156s TestCharmmFiles.py ....s..........s......... [ 27%] 156s TestCheckpointReporter.py . [ 27%] 156s TestDcdFile.py ... [ 28%] 158s TestDesmondDMSFile.py ....... [ 30%] 159s TestElement.py .... [ 32%] 189s TestForceField.py s........................................ss..s.. [ 46%] 189s TestForceGroups.py ... [ 47%] 190s TestGenerators.py .. [ 48%] 190s TestGromacsGroFile.py . [ 48%] 190s TestGromacsTopFile.py sssssssssssss [ 52%] 645s TestIntegrators.py .s..... [ 54%] 647s TestMetadynamics.py . [ 55%] 697s TestModeller.py .............s............. [ 63%] 697s TestNumpyCompatibility.py ......... [ 66%] 697s TestPatches.py ..... [ 67%] 706s TestPdbFile.py ...... [ 69%] 713s TestPdbReporter.py ........ [ 71%] 715s TestPdbxFile.py ....... [ 74%] 717s TestPickle.py ... [ 74%] 720s TestSimulatedTempering.py .. [ 75%] 753s TestSimulation.py ....... [ 77%] 753s TestStateDataReporter.py . [ 77%] 753s TestSwigWrappers.py . [ 78%] 753s TestTopology.py ... [ 79%] 753s TestUnitCell.py .. [ 79%] 753s TestUnits.py ...................................................... [ 96%] 753s TestVec3.py ....... [ 98%] 753s TestXtcFile.py ..... [100%] 753s 753s =============================== warnings summary =============================== 753s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes 753s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 753s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 753s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 753s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model GBn 753s warnings.warn( 753s 753s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 753s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventForces 753s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 753s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model HCT 753s warnings.warn( 753s 753s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 753s =========== 305 passed, 22 skipped, 7 warnings in 639.78s (0:10:39) ============ 754s autopkgtest [09:58:52]: test command1: -----------------------] 754s autopkgtest [09:58:52]: test command1: - - - - - - - - - - results - - - - - - - - - - 754s command1 PASS 755s autopkgtest [09:58:53]: @@@@@@@@@@@@@@@@@@@@ summary 755s command1 PASS 768s virt: nova [W] Skipping flock in bos03-arm64 768s virt: Creating nova instance adt-plucky-arm64-openmm-20241113-094618-juju-7f2275-prod-proposed-migration-environment-2-db9e3f9a-83d3-45f8-9715-572424641acf from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...