1s autopkgtest [16:30:55]: starting date and time: 2025-10-20 16:30:55+0000 1s autopkgtest [16:30:55]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 1s autopkgtest [16:30:55]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ig_94c7_/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest,src:python-pluggy --apt-upgrade openmm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.4.2-1 python-pluggy/1.6.0-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-s390x-14.secgroup --name adt-resolute-s390x-openmm-20251020-163054-juju-7f2275-prod-proposed-migration-environment-2-598d943f-6cfc-4aad-bc29-ae42f9271bb6 --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 6s Creating nova instance adt-resolute-s390x-openmm-20251020-163054-juju-7f2275-prod-proposed-migration-environment-2-598d943f-6cfc-4aad-bc29-ae42f9271bb6 from image adt/ubuntu-resolute-s390x-server-20251020.img (UUID af6042e7-5f94-4102-8fd4-5557e2338897)... 54s autopkgtest [16:31:48]: testbed dpkg architecture: s390x 54s autopkgtest [16:31:48]: testbed apt version: 3.1.8ubuntu1 54s autopkgtest [16:31:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 55s autopkgtest [16:31:49]: testbed release detected to be: None 55s autopkgtest [16:31:49]: updating testbed package index (apt update) 56s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [83.3 kB] 56s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 56s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 56s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 56s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [646 kB] 56s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [56.9 kB] 56s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [14.3 kB] 56s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [5028 B] 56s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [107 kB] 57s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted s390x Packages [940 B] 57s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [400 kB] 57s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [3812 B] 57s Fetched 1318 kB in 1s (1173 kB/s) 57s Reading package lists... 58s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 58s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 58s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 58s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 59s Reading package lists... 59s Reading package lists... 59s Building dependency tree... 59s Reading state information... 59s Calculating upgrade... 59s The following packages will be upgraded: 59s libjson-c5 python3-inflect python3-oauthlib python3-zipp 60s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 60s Need to get 175 kB of archives. 60s After this operation, 31.7 kB of additional disk space will be used. 60s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x libjson-c5 s390x 0.18+ds-1.1 [36.8 kB] 60s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x python3-inflect all 7.5.0-1 [33.9 kB] 60s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x python3-oauthlib all 3.3.1-1 [93.5 kB] 60s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x python3-zipp all 3.23.0-1 [10.4 kB] 60s dpkg-preconfigure: unable to re-open stdin: No such file or directory 60s Fetched 175 kB in 0s (421 kB/s) 60s (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 ... 56857 files and directories currently installed.) 60s Preparing to unpack .../libjson-c5_0.18+ds-1.1_s390x.deb ... 60s Unpacking libjson-c5:s390x (0.18+ds-1.1) over (0.18+ds-1) ... 60s Preparing to unpack .../python3-inflect_7.5.0-1_all.deb ... 60s Unpacking python3-inflect (7.5.0-1) over (7.3.1-2) ... 60s Preparing to unpack .../python3-oauthlib_3.3.1-1_all.deb ... 60s Unpacking python3-oauthlib (3.3.1-1) over (3.2.2-3) ... 60s Preparing to unpack .../python3-zipp_3.23.0-1_all.deb ... 60s Unpacking python3-zipp (3.23.0-1) over (3.21.0-1) ... 60s Setting up python3-zipp (3.23.0-1) ... 60s Setting up python3-inflect (7.5.0-1) ... 61s Setting up python3-oauthlib (3.3.1-1) ... 61s Setting up libjson-c5:s390x (0.18+ds-1.1) ... 61s Processing triggers for libc-bin (2.42-0ubuntu3) ... 61s autopkgtest [16:31:55]: upgrading testbed (apt dist-upgrade and autopurge) 61s Reading package lists... 61s Building dependency tree... 61s Reading state information... 61s Calculating upgrade... 61s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 61s Reading package lists... 62s Building dependency tree... 62s Reading state information... 62s Solving dependencies... 62s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 64s autopkgtest [16:31:58]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP Mon Sep 22 08:56:47 UTC 2025 64s autopkgtest [16:31:58]: @@@@@@@@@@@@@@@@@@@@ apt-source openmm 68s Get:1 http://ftpmaster.internal/ubuntu resolute/universe openmm 8.1.2+dfsg-11 (dsc) [2584 B] 68s Get:2 http://ftpmaster.internal/ubuntu resolute/universe openmm 8.1.2+dfsg-11 (tar) [11.5 MB] 68s Get:3 http://ftpmaster.internal/ubuntu resolute/universe openmm 8.1.2+dfsg-11 (diff) [23.3 kB] 69s gpgv: Signature made Fri Mar 21 00:11:20 2025 UTC 69s gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA 69s gpgv: issuer "dparsons@debian.org" 69s gpgv: Can't check signature: No public key 69s dpkg-source: warning: cannot verify inline signature for ./openmm_8.1.2+dfsg-11.dsc: no acceptable signature found 69s dpkg-source: warning: diff 'src/debian/patches/4602.patch' patches file src/wrappers/python/openmm/app/internal/amber_file_parser.py more than once 69s autopkgtest [16:32:03]: testing package openmm version 8.1.2+dfsg-11 70s autopkgtest [16:32:04]: build not needed 90s autopkgtest [16:32:24]: test test-python: preparing testbed 90s Reading package lists... 90s Building dependency tree... 90s Reading state information... 90s Solving dependencies... 91s The following NEW packages will be installed: 91s cpp cpp-15 cpp-15-s390x-linux-gnu cpp-s390x-linux-gnu gcc gcc-15 91s gcc-15-s390x-linux-gnu gcc-s390x-linux-gnu libasan8 libblas3 libcc1-0 91s libgcc-15-dev libgfortran5 libgomp1 libisl23 libitm1 liblapack3 libmpc3 91s libopenmm-dev libopenmm8.1 libubsan1 python3-all python3-iniconfig 91s python3-numpy python3-numpy-dev python3-openmm python3-packaging 91s python3-pluggy python3-pytest 91s 0 upgraded, 29 newly installed, 0 to remove and 0 not upgraded. 91s Need to get 54.1 MB of archives. 91s After this operation, 232 MB of additional disk space will be used. 91s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.2.4+ds-1ubuntu1 [147 kB] 91s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-6build1 [245 kB] 91s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-5ubuntu1 [629 kB] 91s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-6build1 [2910 kB] 92s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.2.4+ds-1ubuntu1 [4399 kB] 92s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x libisl23 s390x 0.27-1 [704 kB] 92s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x libmpc3 s390x 1.3.1-1build3 [57.6 kB] 92s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-15-s390x-linux-gnu s390x 15.2.0-5ubuntu1 [10.2 MB] 92s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-15 s390x 15.2.0-5ubuntu1 [1024 B] 92s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [5746 B] 92s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x cpp s390x 4:15.2.0-4ubuntu1 [22.4 kB] 92s Get:12 http://ftpmaster.internal/ubuntu resolute/main s390x libcc1-0 s390x 15.2.0-5ubuntu1 [50.0 kB] 92s Get:13 http://ftpmaster.internal/ubuntu resolute/main s390x libgomp1 s390x 15.2.0-5ubuntu1 [154 kB] 92s Get:14 http://ftpmaster.internal/ubuntu resolute/main s390x libitm1 s390x 15.2.0-5ubuntu1 [30.9 kB] 92s Get:15 http://ftpmaster.internal/ubuntu resolute/main s390x libasan8 s390x 15.2.0-5ubuntu1 [2969 kB] 92s Get:16 http://ftpmaster.internal/ubuntu resolute/main s390x libubsan1 s390x 15.2.0-5ubuntu1 [1211 kB] 92s Get:17 http://ftpmaster.internal/ubuntu resolute/main s390x libgcc-15-dev s390x 15.2.0-5ubuntu1 [1045 kB] 92s Get:18 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15-s390x-linux-gnu s390x 15.2.0-5ubuntu1 [19.9 MB] 93s Get:19 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15 s390x 15.2.0-5ubuntu1 [512 kB] 93s Get:20 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [1208 B] 93s Get:21 http://ftpmaster.internal/ubuntu resolute/main s390x gcc s390x 4:15.2.0-4ubuntu1 [5018 B] 93s Get:22 http://ftpmaster.internal/ubuntu resolute/universe s390x libopenmm8.1 s390x 8.1.2+dfsg-11 [867 kB] 93s Get:23 http://ftpmaster.internal/ubuntu resolute/universe s390x libopenmm-dev s390x 8.1.2+dfsg-11 [344 kB] 93s Get:24 http://ftpmaster.internal/ubuntu resolute/main s390x python3-all s390x 3.13.7-1 [886 B] 93s Get:25 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-iniconfig all 1.1.1-2 [6024 B] 93s Get:26 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-openmm s390x 8.1.2+dfsg-11 [7417 kB] 93s Get:27 http://ftpmaster.internal/ubuntu resolute/main s390x python3-packaging all 25.0-1 [52.8 kB] 93s Get:28 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x python3-pluggy all 1.6.0-1 [21.0 kB] 93s Get:29 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x python3-pytest all 8.4.2-1 [268 kB] 93s Fetched 54.1 MB in 2s (21.7 MB/s) 93s Selecting previously unselected package python3-numpy-dev:s390x. 93s (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 ... 56867 files and directories currently installed.) 93s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 93s Unpacking python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 93s Selecting previously unselected package libblas3:s390x. 93s Preparing to unpack .../01-libblas3_3.12.1-6build1_s390x.deb ... 93s Unpacking libblas3:s390x (3.12.1-6build1) ... 93s Selecting previously unselected package libgfortran5:s390x. 93s Preparing to unpack .../02-libgfortran5_15.2.0-5ubuntu1_s390x.deb ... 93s Unpacking libgfortran5:s390x (15.2.0-5ubuntu1) ... 93s Selecting previously unselected package liblapack3:s390x. 93s Preparing to unpack .../03-liblapack3_3.12.1-6build1_s390x.deb ... 93s Unpacking liblapack3:s390x (3.12.1-6build1) ... 93s Selecting previously unselected package python3-numpy. 93s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 93s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 94s Selecting previously unselected package libisl23:s390x. 94s Preparing to unpack .../05-libisl23_0.27-1_s390x.deb ... 94s Unpacking libisl23:s390x (0.27-1) ... 94s Selecting previously unselected package libmpc3:s390x. 94s Preparing to unpack .../06-libmpc3_1.3.1-1build3_s390x.deb ... 94s Unpacking libmpc3:s390x (1.3.1-1build3) ... 94s Selecting previously unselected package cpp-15-s390x-linux-gnu. 94s Preparing to unpack .../07-cpp-15-s390x-linux-gnu_15.2.0-5ubuntu1_s390x.deb ... 94s Unpacking cpp-15-s390x-linux-gnu (15.2.0-5ubuntu1) ... 94s Selecting previously unselected package cpp-15. 94s Preparing to unpack .../08-cpp-15_15.2.0-5ubuntu1_s390x.deb ... 94s Unpacking cpp-15 (15.2.0-5ubuntu1) ... 94s Selecting previously unselected package cpp-s390x-linux-gnu. 94s Preparing to unpack .../09-cpp-s390x-linux-gnu_4%3a15.2.0-4ubuntu1_s390x.deb ... 94s Unpacking cpp-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 94s Selecting previously unselected package cpp. 94s Preparing to unpack .../10-cpp_4%3a15.2.0-4ubuntu1_s390x.deb ... 94s Unpacking cpp (4:15.2.0-4ubuntu1) ... 94s Selecting previously unselected package libcc1-0:s390x. 94s Preparing to unpack .../11-libcc1-0_15.2.0-5ubuntu1_s390x.deb ... 94s Unpacking libcc1-0:s390x (15.2.0-5ubuntu1) ... 94s Selecting previously unselected package libgomp1:s390x. 94s Preparing to unpack .../12-libgomp1_15.2.0-5ubuntu1_s390x.deb ... 94s Unpacking libgomp1:s390x (15.2.0-5ubuntu1) ... 94s Selecting previously unselected package libitm1:s390x. 94s Preparing to unpack .../13-libitm1_15.2.0-5ubuntu1_s390x.deb ... 94s Unpacking libitm1:s390x (15.2.0-5ubuntu1) ... 94s Selecting previously unselected package libasan8:s390x. 94s Preparing to unpack .../14-libasan8_15.2.0-5ubuntu1_s390x.deb ... 94s Unpacking libasan8:s390x (15.2.0-5ubuntu1) ... 94s Selecting previously unselected package libubsan1:s390x. 94s Preparing to unpack .../15-libubsan1_15.2.0-5ubuntu1_s390x.deb ... 94s Unpacking libubsan1:s390x (15.2.0-5ubuntu1) ... 94s Selecting previously unselected package libgcc-15-dev:s390x. 94s Preparing to unpack .../16-libgcc-15-dev_15.2.0-5ubuntu1_s390x.deb ... 94s Unpacking libgcc-15-dev:s390x (15.2.0-5ubuntu1) ... 94s Selecting previously unselected package gcc-15-s390x-linux-gnu. 94s Preparing to unpack .../17-gcc-15-s390x-linux-gnu_15.2.0-5ubuntu1_s390x.deb ... 94s Unpacking gcc-15-s390x-linux-gnu (15.2.0-5ubuntu1) ... 94s Selecting previously unselected package gcc-15. 94s Preparing to unpack .../18-gcc-15_15.2.0-5ubuntu1_s390x.deb ... 94s Unpacking gcc-15 (15.2.0-5ubuntu1) ... 94s Selecting previously unselected package gcc-s390x-linux-gnu. 94s Preparing to unpack .../19-gcc-s390x-linux-gnu_4%3a15.2.0-4ubuntu1_s390x.deb ... 94s Unpacking gcc-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 94s Selecting previously unselected package gcc. 94s Preparing to unpack .../20-gcc_4%3a15.2.0-4ubuntu1_s390x.deb ... 94s Unpacking gcc (4:15.2.0-4ubuntu1) ... 94s Selecting previously unselected package libopenmm8.1. 94s Preparing to unpack .../21-libopenmm8.1_8.1.2+dfsg-11_s390x.deb ... 94s Unpacking libopenmm8.1 (8.1.2+dfsg-11) ... 94s Selecting previously unselected package libopenmm-dev. 94s Preparing to unpack .../22-libopenmm-dev_8.1.2+dfsg-11_s390x.deb ... 94s Unpacking libopenmm-dev (8.1.2+dfsg-11) ... 94s Selecting previously unselected package python3-all. 94s Preparing to unpack .../23-python3-all_3.13.7-1_s390x.deb ... 94s Unpacking python3-all (3.13.7-1) ... 94s Selecting previously unselected package python3-iniconfig. 94s Preparing to unpack .../24-python3-iniconfig_1.1.1-2_all.deb ... 94s Unpacking python3-iniconfig (1.1.1-2) ... 94s Selecting previously unselected package python3-openmm. 94s Preparing to unpack .../25-python3-openmm_8.1.2+dfsg-11_s390x.deb ... 94s Unpacking python3-openmm (8.1.2+dfsg-11) ... 95s Selecting previously unselected package python3-packaging. 95s Preparing to unpack .../26-python3-packaging_25.0-1_all.deb ... 95s Unpacking python3-packaging (25.0-1) ... 95s Selecting previously unselected package python3-pluggy. 95s Preparing to unpack .../27-python3-pluggy_1.6.0-1_all.deb ... 95s Unpacking python3-pluggy (1.6.0-1) ... 95s Selecting previously unselected package python3-pytest. 95s Preparing to unpack .../28-python3-pytest_8.4.2-1_all.deb ... 95s Unpacking python3-pytest (8.4.2-1) ... 95s Setting up python3-iniconfig (1.1.1-2) ... 95s Setting up python3-all (3.13.7-1) ... 95s Setting up libgomp1:s390x (15.2.0-5ubuntu1) ... 95s Setting up libblas3:s390x (3.12.1-6build1) ... 95s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 95s Setting up python3-packaging (25.0-1) ... 95s Setting up libmpc3:s390x (1.3.1-1build3) ... 95s Setting up python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 95s Setting up libgfortran5:s390x (15.2.0-5ubuntu1) ... 95s Setting up python3-pluggy (1.6.0-1) ... 95s Setting up libubsan1:s390x (15.2.0-5ubuntu1) ... 95s Setting up libasan8:s390x (15.2.0-5ubuntu1) ... 95s Setting up libisl23:s390x (0.27-1) ... 95s Setting up libopenmm8.1 (8.1.2+dfsg-11) ... 95s Setting up libcc1-0:s390x (15.2.0-5ubuntu1) ... 95s Setting up libitm1:s390x (15.2.0-5ubuntu1) ... 95s Setting up liblapack3:s390x (3.12.1-6build1) ... 95s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 95s Setting up libgcc-15-dev:s390x (15.2.0-5ubuntu1) ... 95s Setting up python3-pytest (8.4.2-1) ... 95s Setting up libopenmm-dev (8.1.2+dfsg-11) ... 95s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 96s Setting up python3-openmm (8.1.2+dfsg-11) ... 97s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:426: SyntaxWarning: invalid escape sequence '\S' 97s r"(?:_(.+?)[.](\S+))" "|" # _category.attribute 97s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' 97s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 97s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' 97s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 97s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' 97s "(?:\s*#.*$)" "|" # comments (dumped) 97s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' 97s "(\S+)" # unquoted words 97s Setting up cpp-15-s390x-linux-gnu (15.2.0-5ubuntu1) ... 97s Setting up gcc-15-s390x-linux-gnu (15.2.0-5ubuntu1) ... 97s Setting up cpp-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 97s Setting up gcc-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 97s Setting up cpp-15 (15.2.0-5ubuntu1) ... 97s Setting up cpp (4:15.2.0-4ubuntu1) ... 97s Setting up gcc-15 (15.2.0-5ubuntu1) ... 97s Setting up gcc (4:15.2.0-4ubuntu1) ... 97s Processing triggers for man-db (2.13.1-1) ... 97s Processing triggers for libc-bin (2.42-0ubuntu3) ... 98s autopkgtest [16:32:32]: test test-python: [----------------------- 99s skipping tests with SKIP_TEST_LIST=TestATMForce test_Constraints_charmm test_1 test_DispersionCorrection test_Disulfides test_IdenticalTemplates test_LennardJonesGenerator test_NBFix test_ProgrammaticForceField testDisulfidePatch testCopyForce test_deepcopy testLoadFromXML testRunForClockTime testSaveState test_ImplicitSolventForces test_ImplicitSolventForces test_Forces test_ImplicitSolventForces testCopyIntegrator 99s ============================= test session starts ============================== 99s platform linux -- Python 3.13.7, pytest-8.4.2, pluggy-1.6.0 -- /usr/bin/python3.13 99s cachedir: .pytest_cache 99s rootdir: /tmp/autopkgtest.NfVoX5/build.D0g/src/wrappers/python/tests 99s configfile: pytest.ini 99s plugins: typeguard-4.4.2 100s collecting ... collected 327 items / 28 deselected / 299 selected 100s 100s TestAPIUnits.py::TestAPIUnits::testAmoebaMultipoleForce PASSED [ 0%] 100s TestAPIUnits.py::TestAPIUnits::testAmoebaTorsionTorsionForce PASSED [ 0%] 100s TestAPIUnits.py::TestAPIUnits::testAmoebaVdwForce PASSED [ 1%] 100s TestAPIUnits.py::TestAPIUnits::testAmoebaWcaDispersionForce PASSED [ 1%] 100s TestAPIUnits.py::TestAPIUnits::testAndersenThermostat PASSED [ 1%] 100s 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[ 24%] 111s TestCharmmFiles.py::TestCharmmFiles::test_NBXMod PASSED [ 24%] 111s TestCharmmFiles.py::TestCharmmFiles::test_NoLongRangeCorrection PASSED [ 24%] 111s TestCharmmFiles.py::TestCharmmFiles::test_NoPsfWarning PASSED [ 25%] 111s TestCharmmFiles.py::TestCharmmFiles::test_NonbondedMethod PASSED [ 25%] 111s TestCharmmFiles.py::TestCharmmFiles::test_Nonbonded_Exclusion PASSED [ 25%] 112s TestCharmmFiles.py::TestCharmmFiles::test_PSFSetUnitCellDimensions PASSED [ 26%] 115s TestCharmmFiles.py::TestCharmmFiles::test_PermissiveRead PASSED [ 26%] 115s TestCharmmFiles.py::TestCharmmFiles::test_RemoveCMMotion PASSED [ 26%] 115s TestCharmmFiles.py::TestCharmmFiles::test_Residues PASSED [ 27%] 116s TestDcdFile.py::TestDCDFile::testAppend PASSED [ 27%] 116s TestDcdFile.py::TestDCDFile::testLongTrajectory PASSED [ 27%] 116s TestDcdFile.py::TestDCDFile::test_dcd PASSED [ 28%] 116s TestDesmondDMSFile.py::TestDesmondDMSFile::test_Cutoff PASSED [ 28%] 116s TestDesmondDMSFile.py::TestDesmondDMSFile::test_EwaldErrorTolerance PASSED [ 28%] 116s TestDesmondDMSFile.py::TestDesmondDMSFile::test_HydrogenMass PASSED [ 29%] 117s TestDesmondDMSFile.py::TestDesmondDMSFile::test_NonbondedMethod PASSED [ 29%] 117s TestDesmondDMSFile.py::TestDesmondDMSFile::test_OPLS1 PASSED [ 29%] 117s TestDesmondDMSFile.py::TestDesmondDMSFile::test_OPLS2 PASSED [ 30%] 117s TestDesmondDMSFile.py::TestDesmondDMSFile::test_RemoveCMMotion PASSED [ 30%] 117s TestElement.py::TestElement::test_attributes PASSED [ 30%] 118s TestElement.py::TestElement::test_getByMass PASSED [ 31%] 118s TestElement.py::TestElement::test_immutable PASSED [ 31%] 118s TestElement.py::TestElement::test_pickleable PASSED [ 31%] 118s TestForceField.py::TestForceField::test_CharmmPolar SKIPPED (Skippin...) 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[ 50%] 128s TestIntegrators.py::TestIntegrators::testBadGroups PASSED [ 51%] 128s TestIntegrators.py::TestIntegrators::testDrudeNoseHooverIntegrator SKIPPED [ 51%] 128s TestIntegrators.py::TestIntegrators::testMTSIntegratorConstraints PASSED [ 51%] 136s TestIntegrators.py::TestIntegrators::testMTSIntegratorExplicit PASSED [ 52%] 731s TestIntegrators.py::TestIntegrators::testMTSLangevinIntegrator PASSED [ 52%] 731s TestIntegrators.py::TestIntegrators::testMTSLangevinIntegratorFriction PASSED [ 52%] 732s TestIntegrators.py::TestIntegrators::testNoseHooverIntegrator PASSED [ 53%] 733s TestMetadynamics.py::TestMetadynamics::testHarmonicOscillator PASSED [ 53%] 733s TestModeller.py::TestModeller::test_add PASSED [ 53%] 734s TestModeller.py::TestModeller::test_addExtraParticles PASSED [ 54%] 736s TestModeller.py::TestModeller::test_addHydrogensASH PASSED [ 54%] 736s TestModeller.py::TestModeller::test_addHydrogensCYX PASSED [ 54%] 739s TestModeller.py::TestModeller::test_addHydrogensGLH PASSED [ 55%] 739s TestModeller.py::TestModeller::test_addHydrogensGlycam PASSED [ 55%] 741s TestModeller.py::TestModeller::test_addHydrogensLYN PASSED [ 55%] 744s TestModeller.py::TestModeller::test_addHydrogensPdb2 PASSED [ 56%] 744s TestModeller.py::TestModeller::test_addHydrogensPdb3 PASSED [ 56%] 745s TestModeller.py::TestModeller::test_addHydrogensPdb3_keepPositions PASSED [ 56%] 747s TestModeller.py::TestModeller::test_addHydrogenspH11 PASSED [ 57%] 750s TestModeller.py::TestModeller::test_addHydrogenspH4 PASSED [ 57%] 750s TestModeller.py::TestModeller::test_addHydrogenspH9 PASSED [ 57%] 750s TestModeller.py::TestModeller::test_addMembrane SKIPPED (Skipping a ...) [ 58%] 750s TestModeller.py::TestModeller::test_addSolventBoxShape PASSED [ 58%] 755s TestModeller.py::TestModeller::test_addSolventIons PASSED [ 58%] 756s TestModeller.py::TestModeller::test_addSolventNegativeSolvent PASSED [ 59%] 757s TestModeller.py::TestModeller::test_addSolventNeutralSolvent PASSED [ 59%] 761s TestModeller.py::TestModeller::test_addSolventPeriodicBox PASSED [ 59%] 763s TestModeller.py::TestModeller::test_addSolventPositiveSolvent PASSED [ 60%] 765s TestModeller.py::TestModeller::test_addSolventWaterModels PASSED [ 60%] 766s TestModeller.py::TestModeller::test_addVirtualSites PASSED [ 60%] 768s TestModeller.py::TestModeller::test_convertWater PASSED [ 61%] 768s TestModeller.py::TestModeller::test_delete PASSED [ 61%] 768s TestModeller.py::TestModeller::test_deleteWater PASSED [ 61%] 768s TestModeller.py::TestModeller::test_multiSiteIon PASSED [ 62%] 769s TestModeller.py::TestModeller::test_removeExtraHydrogens PASSED [ 62%] 769s TestNumpyCompatibility.py::TestNumpyCompatibility::test_CMAP PASSED [ 62%] 769s TestNumpyCompatibility.py::TestNumpyCompatibility::test_int64 PASSED [ 63%] 769s TestNumpyCompatibility.py::TestNumpyCompatibility::test_periodicBoxVectors PASSED [ 63%] 769s TestNumpyCompatibility.py::TestNumpyCompatibility::test_setPositions PASSED [ 63%] 769s TestNumpyCompatibility.py::TestNumpyCompatibility::test_setPositions_units PASSED [ 64%] 769s TestNumpyCompatibility.py::TestNumpyCompatibility::test_setVelocities PASSED [ 64%] 769s TestNumpyCompatibility.py::TestNumpyCompatibility::test_setVelocities_units PASSED [ 64%] 769s TestNumpyCompatibility.py::TestNumpyCompatibility::test_tabulatedFunction PASSED [ 65%] 769s TestNumpyCompatibility.py::TestNumpyUnits::testNumpyAttributes PASSED [ 65%] 769s TestPatches.py::TestPatches::testAlaAlaAla PASSED [ 65%] 769s TestPatches.py::TestPatches::testApplyPatch PASSED [ 66%] 769s TestPatches.py::TestPatches::testParseMultiresiduePatch PASSED [ 66%] 769s TestPatches.py::TestPatches::testParsePatch PASSED [ 66%] 769s TestPdbFile.py::TestPdbFile::test_AltLocs PASSED [ 67%] 769s TestPdbFile.py::TestPdbFile::test_BinaryStream PASSED [ 67%] 769s TestPdbFile.py::TestPdbFile::test_ExtraParticles PASSED [ 67%] 775s TestPdbFile.py::TestPdbFile::test_LargeFile PASSED [ 68%] 775s TestPdbFile.py::TestPdbFile::test_Triclinic PASSED [ 68%] 775s TestPdbFile.py::TestPdbFile::test_WriteFile PASSED [ 68%] 778s TestPdbReporter.py::TestPDBReporter::testBondSubset PASSED [ 69%] 778s TestPdbReporter.py::TestPDBReporter::testInvalidSubsets PASSED [ 69%] 778s TestPdbReporter.py::TestPDBReporter::testSubset PASSED [ 69%] 779s TestPdbReporter.py::TestPDBReporter::testWriteAll PASSED [ 70%] 780s TestPdbReporter.py::TestPDBxReporter::testBondSubset PASSED [ 70%] 781s TestPdbReporter.py::TestPDBxReporter::testInvalidSubsets PASSED [ 70%] 781s TestPdbReporter.py::TestPDBxReporter::testSubset PASSED [ 71%] 781s TestPdbReporter.py::TestPDBxReporter::testWriteAll 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TestStateDataReporter.py::TestStateDataReporter::testAppend PASSED [ 76%] 822s TestTopology.py::TestTopology::test_bondtype_singleton PASSED [ 76%] 822s TestTopology.py::TestTopology::test_getters PASSED [ 76%] 822s TestTopology.py::TestTopology::test_residue_bonds PASSED [ 77%] 822s TestUnitCell.py::TestUnitCell::testComputePBCVectors PASSED [ 77%] 822s TestUnitCell.py::TestUnitCell::testReducePBCVectors PASSED [ 77%] 822s TestUnits.py::TestUnits::testAngleQuantities PASSED [ 78%] 822s TestUnits.py::TestUnits::testBadQuantityComparisons PASSED [ 78%] 822s TestUnits.py::TestUnits::testBadQuantityConversions PASSED [ 78%] 822s TestUnits.py::TestUnits::testBadQuantityMaths PASSED [ 79%] 822s TestUnits.py::TestUnits::testBaseScaleMix PASSED [ 79%] 822s TestUnits.py::TestUnits::testBaseUnit PASSED [ 79%] 822s TestUnits.py::TestUnits::testCalorieConversion PASSED [ 80%] 822s TestUnits.py::TestUnits::testChemistryProblems PASSED [ 80%] 822s TestUnits.py::TestUnits::testCollectionQuantities PASSED [ 80%] 822s TestUnits.py::TestUnits::testCollectionQuantityOperations PASSED [ 81%] 822s TestUnits.py::TestUnits::testComparisonOperators PASSED [ 81%] 822s TestUnits.py::TestUnits::testCompositeUnits PASSED [ 81%] 822s TestUnits.py::TestUnits::testConversionFactorTo PASSED [ 82%] 822s TestUnits.py::TestUnits::testCreateNewBaseUnit PASSED [ 82%] 822s TestUnits.py::TestUnits::testCreateNewScaledUnit PASSED [ 82%] 822s TestUnits.py::TestUnits::testCreateNewUnit PASSED [ 83%] 822s TestUnits.py::TestUnits::testDimensionless PASSED [ 83%] 822s TestUnits.py::TestUnits::testGetUnitAttributes PASSED [ 83%] 822s TestUnits.py::TestUnits::testIllegalQuantityOps PASSED [ 84%] 822s TestUnits.py::TestUnits::testIsCompatible PASSED [ 84%] 822s TestUnits.py::TestUnits::testIsQuantity PASSED [ 84%] 822s TestUnits.py::TestUnits::testIsUnit PASSED [ 85%] 822s TestUnits.py::TestUnits::testMisc PASSED [ 85%] 822s TestUnits.py::TestUnits::testMutableQuantityOperations PASSED [ 85%] 822s TestUnits.py::TestUnits::testPresetUnitSystems PASSED [ 86%] 822s TestUnits.py::TestUnits::testQuantityBadSqrt PASSED [ 86%] 822s TestUnits.py::TestUnits::testQuantityCollectionMethods PASSED [ 86%] 822s TestUnits.py::TestUnits::testQuantityComparisons PASSED [ 87%] 822s TestUnits.py::TestUnits::testQuantityComplicatedMaths PASSED [ 87%] 822s TestUnits.py::TestUnits::testQuantityFormat PASSED [ 87%] 822s TestUnits.py::TestUnits::testQuantityMaths PASSED [ 88%] 822s TestUnits.py::TestUnits::testQuantitySqrt PASSED [ 88%] 822s TestUnits.py::TestUnits::testReduceUnit PASSED [ 88%] 822s TestUnits.py::TestUnits::testScalarQuantityConstructor PASSED [ 89%] 822s TestUnits.py::TestUnits::testScalarQuantityMultiplyDivide PASSED [ 89%] 822s TestUnits.py::TestUnits::testScaledUnit PASSED [ 89%] 822s TestUnits.py::TestUnits::testString PASSED [ 90%] 822s TestUnits.py::TestUnits::testToBaseUnit PASSED [ 90%] 822s TestUnits.py::TestUnits::testTruthiness PASSED [ 90%] 822s TestUnits.py::TestUnits::testUnaryOperators PASSED [ 91%] 822s TestUnits.py::TestUnits::testUnitBadSqrt PASSED [ 91%] 822s TestUnits.py::TestUnits::testUnitDivision PASSED [ 91%] 822s TestUnits.py::TestUnits::testUnitMathModule PASSED [ 92%] 822s TestUnits.py::TestUnits::testUnitMathModuleBadInput PASSED [ 92%] 822s TestUnits.py::TestUnits::testUnitSqrt PASSED [ 92%] 822s TestUnits.py::TestUnits::testUnitString PASSED [ 93%] 822s TestUnits.py::TestUnits::testUnitSystem PASSED [ 93%] 822s TestUnits.py::TestUnits::testValueInUnit PASSED [ 93%] 822s TestUnits.py::TestNumpyUnits::testMultiplication PASSED [ 94%] 822s TestUnits.py::TestNumpyUnits::testNumpyDeepCopy PASSED [ 94%] 822s TestUnits.py::TestNumpyUnits::testNumpyDivision PASSED [ 94%] 822s TestUnits.py::TestNumpyUnits::testNumpyFunctions PASSED [ 95%] 822s TestUnits.py::TestNumpyUnits::testNumpyIsString PASSED [ 95%] 822s TestUnits.py::TestNumpyUnits::testNumpyQuantity PASSED [ 95%] 822s TestVec3.py::TestVectors::testNegation PASSED [ 96%] 822s TestVec3.py::TestVectors::testVec3Addition PASSED [ 96%] 822s TestVec3.py::TestVectors::testVec3Attributes PASSED [ 96%] 822s TestVec3.py::TestVectors::testVec3Division PASSED [ 97%] 822s TestVec3.py::TestVectors::testVec3Equality PASSED [ 97%] 822s TestVec3.py::TestVectors::testVec3Multiplication PASSED [ 97%] 822s TestVec3.py::TestVectors::testVec3Subtraction PASSED [ 98%] 822s TestXtcFile.py::TestXtcFile::testAppend PASSED [ 98%] 822s TestXtcFile.py::TestXtcFile::testLongTrajectory PASSED [ 98%] 822s TestXtcFile.py::TestXtcFile::test_xtc_box_from_topology PASSED [ 99%] 822s TestXtcFile.py::TestXtcFile::test_xtc_cubic PASSED [ 99%] 823s TestXtcFile.py::TestXtcFile::test_xtc_triclinic PASSED [100%] 823s 823s =============================== warnings summary =============================== 823s :488 823s :488: DeprecationWarning: builtin type SwigPyPacked has no __module__ attribute 823s 823s :488 823s :488: DeprecationWarning: builtin type SwigPyObject has no __module__ attribute 823s 823s :488 823s :488: DeprecationWarning: builtin type swigvarlink has no __module__ attribute 823s 823s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes 823s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 823s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 823s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model GBn 823s warnings.warn( 823s 823s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 823s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 823s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model HCT 823s warnings.warn( 823s 823s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 823s ==== 278 passed, 21 skipped, 28 deselected, 8 warnings in 723.52s (0:12:03) ==== 823s autopkgtest [16:44:37]: test test-python: -----------------------] 824s test-python PASS 824s autopkgtest [16:44:38]: test test-python: - - - - - - - - - - results - - - - - - - - - - 824s autopkgtest [16:44:38]: @@@@@@@@@@@@@@@@@@@@ summary 824s test-python PASS