0s autopkgtest [13:11:53]: starting date and time: 2026-01-23 13:11:53+0000 0s autopkgtest [13:11:53]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [13:11:53]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9sib8u6g/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade openmm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.14.2-1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-s390x-18.secgroup --name adt-resolute-s390x-openmm-20260123-105857-juju-7f2275-prod-proposed-migration-environment-20-8bc0d2a3-6e9a-4e6c-be4a-039f9ce44cf9 --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-s390x-openmm-20260123-105857-juju-7f2275-prod-proposed-migration-environment-20-8bc0d2a3-6e9a-4e6c-be4a-039f9ce44cf9 from image adt/ubuntu-resolute-s390x-server-20260123.img (UUID 5f2e306c-5dfc-4ef6-8be2-414f657c7562)... 88s autopkgtest [13:13:21]: testbed dpkg architecture: s390x 88s autopkgtest [13:13:21]: testbed apt version: 3.1.13 88s autopkgtest [13:13:21]: @@@@@@@@@@@@@@@@@@@@ test bed setup 88s autopkgtest [13:13:21]: testbed release detected to be: None 89s autopkgtest [13:13:22]: updating testbed package index (apt update) 89s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 89s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 90s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 90s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 90s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [23.6 kB] 90s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2820 B] 90s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1023 kB] 90s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [97.1 kB] 90s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [119 kB] 90s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [838 kB] 90s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [9152 B] 90s Fetched 2237 kB in 1s (3731 kB/s) 92s Reading package lists... 94s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 94s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 94s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 94s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 96s Reading package lists... 96s Reading package lists... 97s Building dependency tree... 97s Reading state information... 97s Calculating upgrade... 98s The following packages were automatically installed and are no longer required: 98s python3.13 python3.13-minimal 98s Use 'sudo apt autoremove' to remove them. 98s The following NEW packages will be installed: 98s libpython3.14-minimal libpython3.14-stdlib python3.14 python3.14-minimal 98s The following packages will be upgraded: 98s libpython3-stdlib python3 python3-gdbm python3-jaraco.context 98s python3-minimal 98s 5 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. 98s Need to get 6697 kB of archives. 98s After this operation, 24.3 MB of additional disk space will be used. 98s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-minimal s390x 3.14.2-1 [917 kB] 98s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14-minimal s390x 3.14.2-1 [2510 kB] 99s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-minimal s390x 3.14.2-1 [28.2 kB] 99s Get:4 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3 s390x 3.14.2-1 [22.9 kB] 99s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-stdlib s390x 3.14.2-1 [2373 kB] 99s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14 s390x 3.14.2-1 [816 kB] 100s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x libpython3-stdlib s390x 3.14.2-1 [10.9 kB] 100s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-gdbm s390x 3.14.2-1 [11.1 kB] 100s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x python3-jaraco.context all 6.0.1-2 [8198 B] 100s dpkg-preconfigure: unable to re-open stdin: No such file or directory 100s Fetched 6697 kB in 2s (3604 kB/s) 100s Selecting previously unselected package libpython3.14-minimal:s390x. 100s (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 ... 87685 files and directories currently installed.) 100s Preparing to unpack .../libpython3.14-minimal_3.14.2-1_s390x.deb ... 100s Unpacking libpython3.14-minimal:s390x (3.14.2-1) ... 101s Selecting previously unselected package python3.14-minimal. 101s Preparing to unpack .../python3.14-minimal_3.14.2-1_s390x.deb ... 101s Unpacking python3.14-minimal (3.14.2-1) ... 101s Setting up libpython3.14-minimal:s390x (3.14.2-1) ... 101s Setting up python3.14-minimal (3.14.2-1) ... 105s (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 ... 88027 files and directories currently installed.) 105s Preparing to unpack .../python3-minimal_3.14.2-1_s390x.deb ... 105s Unpacking python3-minimal (3.14.2-1) over (3.13.9-3) ... 105s Setting up python3-minimal (3.14.2-1) ... 105s (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 ... 88027 files and directories currently installed.) 105s Preparing to unpack .../0-python3_3.14.2-1_s390x.deb ... 106s running python pre-rtupdate hooks for python3.14... 106s Unpacking python3 (3.14.2-1) over (3.13.9-3) ... 106s Selecting previously unselected package libpython3.14-stdlib:s390x. 106s Preparing to unpack .../1-libpython3.14-stdlib_3.14.2-1_s390x.deb ... 106s Unpacking libpython3.14-stdlib:s390x (3.14.2-1) ... 106s Selecting previously unselected package python3.14. 106s Preparing to unpack .../2-python3.14_3.14.2-1_s390x.deb ... 106s Unpacking python3.14 (3.14.2-1) ... 106s Preparing to unpack .../3-libpython3-stdlib_3.14.2-1_s390x.deb ... 106s Unpacking libpython3-stdlib:s390x (3.14.2-1) over (3.13.9-3) ... 106s Preparing to unpack .../4-python3-gdbm_3.14.2-1_s390x.deb ... 106s Unpacking python3-gdbm (3.14.2-1) over (3.13.9-3) ... 106s Preparing to unpack .../5-python3-jaraco.context_6.0.1-2_all.deb ... 106s Unpacking python3-jaraco.context (6.0.1-2) over (6.0.1-1build1) ... 106s Setting up libpython3.14-stdlib:s390x (3.14.2-1) ... 106s Setting up python3.14 (3.14.2-1) ... 111s Setting up libpython3-stdlib:s390x (3.14.2-1) ... 111s Setting up python3-gdbm (3.14.2-1) ... 111s Setting up python3 (3.14.2-1) ... 111s running python rtupdate hooks for python3.14... 111s running python post-rtupdate hooks for python3.14... 111s Setting up python3-jaraco.context (6.0.1-2) ... 111s Processing triggers for man-db (2.13.1-1) ... 113s Processing triggers for systemd (259-1ubuntu2) ... 114s autopkgtest [13:13:47]: upgrading testbed (apt dist-upgrade and autopurge) 114s Reading package lists... 114s Building dependency tree... 114s Reading state information... 115s Calculating upgrade... 115s The following packages were automatically installed and are no longer required: 115s python3.13 python3.13-minimal 115s Use 'sudo apt autoremove' to remove them. 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 116s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s Solving dependencies... 118s The following packages will be REMOVED: 118s python3.13* python3.13-minimal* 119s 0 upgraded, 0 newly installed, 2 to remove and 0 not upgraded. 119s After this operation, 8012 kB disk space will be freed. 119s (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 ... 88457 files and directories currently installed.) 119s Removing python3.13 (3.13.11-1) ... 119s Removing python3.13-minimal (3.13.11-1) ... 122s Processing triggers for man-db (2.13.1-1) ... 123s Processing triggers for systemd (259-1ubuntu2) ... 124s (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 ... 88430 files and directories currently installed.) 124s Purging configuration files for python3.13-minimal (3.13.11-1) ... 127s autopkgtest [13:14:00]: testbed running kernel: Linux 6.18.0-9-generic #9-Ubuntu SMP Mon Jan 12 15:39:23 UTC 2026 128s autopkgtest [13:14:01]: @@@@@@@@@@@@@@@@@@@@ apt-source openmm 132s Get:1 http://ftpmaster.internal/ubuntu resolute/universe openmm 8.1.2+dfsg-12 (dsc) [2579 B] 132s Get:2 http://ftpmaster.internal/ubuntu resolute/universe openmm 8.1.2+dfsg-12 (tar) [11.5 MB] 132s Get:3 http://ftpmaster.internal/ubuntu resolute/universe openmm 8.1.2+dfsg-12 (diff) [23.7 kB] 132s gpgv: Signature made Mon Sep 29 08:59:53 2025 UTC 132s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 132s gpgv: issuer "merkys@debian.org" 132s gpgv: Can't check signature: No public key 132s dpkg-source: warning: cannot verify inline signature for ./openmm_8.1.2+dfsg-12.dsc: no acceptable signature found 135s dpkg-source: warning: diff 'src/debian/patches/4602.patch' patches file src/wrappers/python/openmm/app/internal/amber_file_parser.py more than once 136s autopkgtest [13:14:09]: testing package openmm version 8.1.2+dfsg-12 136s autopkgtest [13:14:09]: build not needed 143s autopkgtest [13:14:16]: test test-python: preparing testbed 143s Reading package lists... 144s Building dependency tree... 144s Reading state information... 144s Solving dependencies... 144s The following NEW packages will be installed: 144s cpp cpp-15 cpp-15-s390x-linux-gnu cpp-s390x-linux-gnu gcc gcc-15 144s gcc-15-s390x-linux-gnu gcc-s390x-linux-gnu libasan8 libblas3 libcc1-0 144s libgcc-15-dev libgfortran5 libgomp1 libisl23 libitm1 liblapack3 libmpc3 144s libopenmm-dev libopenmm8.1 libubsan1 python3-all python3-iniconfig 144s python3-numpy python3-numpy-dev python3-openmm python3-pluggy python3-pytest 144s python3.13 python3.13-minimal 144s 0 upgraded, 30 newly installed, 0 to remove and 0 not upgraded. 144s Need to get 58.6 MB of archives. 144s After this operation, 255 MB of additional disk space will be used. 144s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3.13-minimal s390x 3.13.11-1 [2405 kB] 145s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.3.5+ds-3 [146 kB] 145s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-7ubuntu1 [255 kB] 145s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-11ubuntu1 [629 kB] 145s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-7ubuntu1 [2983 kB] 145s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.3.5+ds-3 [5305 kB] 145s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x python3.13 s390x 3.13.11-1 [758 kB] 145s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x libisl23 s390x 0.27-1build1 [702 kB] 145s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x libmpc3 s390x 1.3.1-2 [57.4 kB] 146s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-15-s390x-linux-gnu s390x 15.2.0-11ubuntu1 [10.2 MB] 146s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-15 s390x 15.2.0-11ubuntu1 [1028 B] 146s Get:12 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [5746 B] 146s Get:13 http://ftpmaster.internal/ubuntu resolute/main s390x cpp s390x 4:15.2.0-4ubuntu1 [22.4 kB] 146s Get:14 http://ftpmaster.internal/ubuntu resolute/main s390x libcc1-0 s390x 15.2.0-11ubuntu1 [50.0 kB] 146s Get:15 http://ftpmaster.internal/ubuntu resolute/main s390x libgomp1 s390x 15.2.0-11ubuntu1 [154 kB] 146s Get:16 http://ftpmaster.internal/ubuntu resolute/main s390x libitm1 s390x 15.2.0-11ubuntu1 [30.9 kB] 146s Get:17 http://ftpmaster.internal/ubuntu resolute/main s390x libasan8 s390x 15.2.0-11ubuntu1 [2968 kB] 146s Get:18 http://ftpmaster.internal/ubuntu resolute/main s390x libubsan1 s390x 15.2.0-11ubuntu1 [1211 kB] 146s Get:19 http://ftpmaster.internal/ubuntu resolute/main s390x libgcc-15-dev s390x 15.2.0-11ubuntu1 [1045 kB] 146s Get:20 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15-s390x-linux-gnu s390x 15.2.0-11ubuntu1 [19.9 MB] 147s Get:21 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15 s390x 15.2.0-11ubuntu1 [517 kB] 147s Get:22 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [1208 B] 147s Get:23 http://ftpmaster.internal/ubuntu resolute/main s390x gcc s390x 4:15.2.0-4ubuntu1 [5018 B] 147s Get:24 http://ftpmaster.internal/ubuntu resolute/universe s390x libopenmm8.1 s390x 8.1.2+dfsg-12 [847 kB] 147s Get:25 http://ftpmaster.internal/ubuntu resolute/universe s390x libopenmm-dev s390x 8.1.2+dfsg-12 [341 kB] 147s Get:26 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-all s390x 3.14.2-1 [890 B] 147s Get:27 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-iniconfig all 2.1.0-2 [6962 B] 147s Get:28 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-openmm s390x 8.1.2+dfsg-12 [7759 kB] 148s Get:29 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pluggy all 1.6.0-2 [21.1 kB] 148s Get:30 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pytest all 9.0.2-2 [277 kB] 148s Fetched 58.6 MB in 4s (15.2 MB/s) 148s Selecting previously unselected package python3.13-minimal. 149s (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 ... 88432 files and directories currently installed.) 149s Preparing to unpack .../00-python3.13-minimal_3.13.11-1_s390x.deb ... 149s Unpacking python3.13-minimal (3.13.11-1) ... 149s Selecting previously unselected package python3-numpy-dev:s390x. 149s Preparing to unpack .../01-python3-numpy-dev_1%3a2.3.5+ds-3_s390x.deb ... 149s Unpacking python3-numpy-dev:s390x (1:2.3.5+ds-3) ... 149s Selecting previously unselected package libblas3:s390x. 149s Preparing to unpack .../02-libblas3_3.12.1-7ubuntu1_s390x.deb ... 149s Unpacking libblas3:s390x (3.12.1-7ubuntu1) ... 149s Selecting previously unselected package libgfortran5:s390x. 149s Preparing to unpack .../03-libgfortran5_15.2.0-11ubuntu1_s390x.deb ... 150s Unpacking libgfortran5:s390x (15.2.0-11ubuntu1) ... 150s Selecting previously unselected package liblapack3:s390x. 150s Preparing to unpack .../04-liblapack3_3.12.1-7ubuntu1_s390x.deb ... 150s Unpacking liblapack3:s390x (3.12.1-7ubuntu1) ... 150s Selecting previously unselected package python3-numpy. 150s Preparing to unpack .../05-python3-numpy_1%3a2.3.5+ds-3_s390x.deb ... 150s Unpacking python3-numpy (1:2.3.5+ds-3) ... 150s Selecting previously unselected package python3.13. 150s Preparing to unpack .../06-python3.13_3.13.11-1_s390x.deb ... 150s Unpacking python3.13 (3.13.11-1) ... 150s Selecting previously unselected package libisl23:s390x. 150s Preparing to unpack .../07-libisl23_0.27-1build1_s390x.deb ... 150s Unpacking libisl23:s390x (0.27-1build1) ... 150s Selecting previously unselected package libmpc3:s390x. 150s Preparing to unpack .../08-libmpc3_1.3.1-2_s390x.deb ... 150s Unpacking libmpc3:s390x (1.3.1-2) ... 150s Selecting previously unselected package cpp-15-s390x-linux-gnu. 150s Preparing to unpack .../09-cpp-15-s390x-linux-gnu_15.2.0-11ubuntu1_s390x.deb ... 150s Unpacking cpp-15-s390x-linux-gnu (15.2.0-11ubuntu1) ... 150s Selecting previously unselected package cpp-15. 150s Preparing to unpack .../10-cpp-15_15.2.0-11ubuntu1_s390x.deb ... 150s Unpacking cpp-15 (15.2.0-11ubuntu1) ... 150s Selecting previously unselected package cpp-s390x-linux-gnu. 150s Preparing to unpack .../11-cpp-s390x-linux-gnu_4%3a15.2.0-4ubuntu1_s390x.deb ... 150s Unpacking cpp-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 150s Selecting previously unselected package cpp. 150s Preparing to unpack .../12-cpp_4%3a15.2.0-4ubuntu1_s390x.deb ... 151s Unpacking cpp (4:15.2.0-4ubuntu1) ... 151s Selecting previously unselected package libcc1-0:s390x. 151s Preparing to unpack .../13-libcc1-0_15.2.0-11ubuntu1_s390x.deb ... 151s Unpacking libcc1-0:s390x (15.2.0-11ubuntu1) ... 151s Selecting previously unselected package libgomp1:s390x. 151s Preparing to unpack .../14-libgomp1_15.2.0-11ubuntu1_s390x.deb ... 151s Unpacking libgomp1:s390x (15.2.0-11ubuntu1) ... 151s Selecting previously unselected package libitm1:s390x. 151s Preparing to unpack .../15-libitm1_15.2.0-11ubuntu1_s390x.deb ... 151s Unpacking libitm1:s390x (15.2.0-11ubuntu1) ... 151s Selecting previously unselected package libasan8:s390x. 151s Preparing to unpack .../16-libasan8_15.2.0-11ubuntu1_s390x.deb ... 151s Unpacking libasan8:s390x (15.2.0-11ubuntu1) ... 151s Selecting previously unselected package libubsan1:s390x. 151s Preparing to unpack .../17-libubsan1_15.2.0-11ubuntu1_s390x.deb ... 151s Unpacking libubsan1:s390x (15.2.0-11ubuntu1) ... 151s Selecting previously unselected package libgcc-15-dev:s390x. 151s Preparing to unpack .../18-libgcc-15-dev_15.2.0-11ubuntu1_s390x.deb ... 151s Unpacking libgcc-15-dev:s390x (15.2.0-11ubuntu1) ... 151s Selecting previously unselected package gcc-15-s390x-linux-gnu. 151s Preparing to unpack .../19-gcc-15-s390x-linux-gnu_15.2.0-11ubuntu1_s390x.deb ... 151s Unpacking gcc-15-s390x-linux-gnu (15.2.0-11ubuntu1) ... 154s Selecting previously unselected package gcc-15. 154s Preparing to unpack .../20-gcc-15_15.2.0-11ubuntu1_s390x.deb ... 154s Unpacking gcc-15 (15.2.0-11ubuntu1) ... 154s Selecting previously unselected package gcc-s390x-linux-gnu. 154s Preparing to unpack .../21-gcc-s390x-linux-gnu_4%3a15.2.0-4ubuntu1_s390x.deb ... 154s Unpacking gcc-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 154s Selecting previously unselected package gcc. 154s Preparing to unpack .../22-gcc_4%3a15.2.0-4ubuntu1_s390x.deb ... 154s Unpacking gcc (4:15.2.0-4ubuntu1) ... 154s Selecting previously unselected package libopenmm8.1. 154s Preparing to unpack .../23-libopenmm8.1_8.1.2+dfsg-12_s390x.deb ... 154s Unpacking libopenmm8.1 (8.1.2+dfsg-12) ... 154s Selecting previously unselected package libopenmm-dev. 154s Preparing to unpack .../24-libopenmm-dev_8.1.2+dfsg-12_s390x.deb ... 154s Unpacking libopenmm-dev (8.1.2+dfsg-12) ... 154s Selecting previously unselected package python3-all. 154s Preparing to unpack .../25-python3-all_3.14.2-1_s390x.deb ... 154s Unpacking python3-all (3.14.2-1) ... 154s Selecting previously unselected package python3-iniconfig. 154s Preparing to unpack .../26-python3-iniconfig_2.1.0-2_all.deb ... 154s Unpacking python3-iniconfig (2.1.0-2) ... 154s Selecting previously unselected package python3-openmm. 154s Preparing to unpack .../27-python3-openmm_8.1.2+dfsg-12_s390x.deb ... 154s Unpacking python3-openmm (8.1.2+dfsg-12) ... 157s Selecting previously unselected package python3-pluggy. 157s Preparing to unpack .../28-python3-pluggy_1.6.0-2_all.deb ... 157s Unpacking python3-pluggy (1.6.0-2) ... 157s Selecting previously unselected package python3-pytest. 157s Preparing to unpack .../29-python3-pytest_9.0.2-2_all.deb ... 157s Unpacking python3-pytest (9.0.2-2) ... 157s Setting up python3-iniconfig (2.1.0-2) ... 157s Setting up libgomp1:s390x (15.2.0-11ubuntu1) ... 157s Setting up libblas3:s390x (3.12.1-7ubuntu1) ... 157s 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 157s Setting up libmpc3:s390x (1.3.1-2) ... 157s Setting up python3-numpy-dev:s390x (1:2.3.5+ds-3) ... 157s Setting up libgfortran5:s390x (15.2.0-11ubuntu1) ... 157s Setting up python3-pluggy (1.6.0-2) ... 157s Setting up libubsan1:s390x (15.2.0-11ubuntu1) ... 157s Setting up libasan8:s390x (15.2.0-11ubuntu1) ... 157s Setting up python3.13-minimal (3.13.11-1) ... 159s Setting up libisl23:s390x (0.27-1build1) ... 159s Setting up libopenmm8.1 (8.1.2+dfsg-12) ... 159s Setting up libcc1-0:s390x (15.2.0-11ubuntu1) ... 159s Setting up libitm1:s390x (15.2.0-11ubuntu1) ... 159s Setting up liblapack3:s390x (3.12.1-7ubuntu1) ... 159s 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 159s Setting up libgcc-15-dev:s390x (15.2.0-11ubuntu1) ... 159s Setting up python3.13 (3.13.11-1) ... 162s Setting up python3-pytest (9.0.2-2) ... 164s Setting up python3-all (3.14.2-1) ... 164s Setting up libopenmm-dev (8.1.2+dfsg-12) ... 164s Setting up python3-numpy (1:2.3.5+ds-3) ... 175s Setting up python3-openmm (8.1.2+dfsg-12) ... 175s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:426: SyntaxWarning: invalid escape sequence '\S' 175s r"(?:_(.+?)[.](\S+))" "|" # _category.attribute 175s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' 175s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 175s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' 175s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 175s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' 175s "(?:\s*#.*$)" "|" # comments (dumped) 175s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' 175s "(\S+)" # unquoted words 176s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:426: SyntaxWarning: "\S" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\S"? A raw string is also an option. 176s r"(?:_(.+?)[.](\S+))" "|" # _category.attribute 176s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: "\S" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\S"? A raw string is also an option. 176s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 176s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: "\s" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\s"? A raw string is also an option. 176s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 176s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: "\s" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\s"? A raw string is also an option. 176s "(?:\s*#.*$)" "|" # comments (dumped) 176s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: "\S" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\S"? A raw string is also an option. 176s "(\S+)" # unquoted words 176s Setting up cpp-15-s390x-linux-gnu (15.2.0-11ubuntu1) ... 176s Setting up gcc-15-s390x-linux-gnu (15.2.0-11ubuntu1) ... 176s Setting up cpp-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 176s Setting up gcc-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 176s Setting up cpp-15 (15.2.0-11ubuntu1) ... 176s Setting up cpp (4:15.2.0-4ubuntu1) ... 176s Setting up gcc-15 (15.2.0-11ubuntu1) ... 176s Setting up gcc (4:15.2.0-4ubuntu1) ... 176s Processing triggers for systemd (259-1ubuntu2) ... 176s Processing triggers for man-db (2.13.1-1) ... 178s Processing triggers for libc-bin (2.42-2ubuntu4) ... 180s autopkgtest [13:14:53]: test test-python: [----------------------- 180s 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 180s ============================= test session starts ============================== 180s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.13 180s cachedir: .pytest_cache 180s rootdir: /tmp/autopkgtest.ZtXIIb/build.0yO/src/wrappers/python/tests 180s configfile: pytest.ini 180s plugins: typeguard-4.4.4 183s collecting ... collected 327 items / 28 deselected / 299 selected 183s 183s TestAPIUnits.py::TestAPIUnits::testAmoebaMultipoleForce PASSED [ 0%] 183s TestAPIUnits.py::TestAPIUnits::testAmoebaTorsionTorsionForce PASSED [ 0%] 183s TestAPIUnits.py::TestAPIUnits::testAmoebaVdwForce PASSED [ 1%] 183s TestAPIUnits.py::TestAPIUnits::testAmoebaWcaDispersionForce PASSED [ 1%] 183s TestAPIUnits.py::TestAPIUnits::testAndersenThermostat PASSED [ 1%] 183s TestAPIUnits.py::TestAPIUnits::testBrownianIntegrator PASSED [ 2%] 183s TestAPIUnits.py::TestAPIUnits::testCmapForce PASSED [ 2%] 183s TestAPIUnits.py::TestAPIUnits::testCustomAngleForce PASSED [ 2%] 183s TestAPIUnits.py::TestAPIUnits::testCustomBondForce PASSED [ 3%] 183s TestAPIUnits.py::TestAPIUnits::testCustomCompoundBondForce PASSED [ 3%] 183s TestAPIUnits.py::TestAPIUnits::testCustomExternalForce PASSED [ 3%] 183s TestAPIUnits.py::TestAPIUnits::testCustomGBForce PASSED [ 4%] 183s TestAPIUnits.py::TestAPIUnits::testCustomHBondForce PASSED [ 4%] 183s TestAPIUnits.py::TestAPIUnits::testCustomIntegrator PASSED [ 4%] 183s TestAPIUnits.py::TestAPIUnits::testCustomManyParticleForce PASSED [ 5%] 183s TestAPIUnits.py::TestAPIUnits::testCustomNonbondedForce PASSED [ 5%] 183s TestAPIUnits.py::TestAPIUnits::testCustomTorsionForce PASSED [ 5%] 183s TestAPIUnits.py::TestAPIUnits::testDrudeForce PASSED [ 6%] 183s TestAPIUnits.py::TestAPIUnits::testDrudeLangevinIntegrator PASSED [ 6%] 183s TestAPIUnits.py::TestAPIUnits::testDrudeNoseHooverIntegrator PASSED [ 6%] 183s TestAPIUnits.py::TestAPIUnits::testDrudeSCFIntegrator PASSED [ 7%] 183s TestAPIUnits.py::TestAPIUnits::testGeneralizedKirkwood PASSED [ 7%] 183s TestAPIUnits.py::TestAPIUnits::testHarmonicAngleForce PASSED [ 7%] 183s TestAPIUnits.py::TestAPIUnits::testHarmonicBondForce PASSED [ 8%] 183s TestAPIUnits.py::TestAPIUnits::testLangevinIntegrator PASSED [ 8%] 183s TestAPIUnits.py::TestAPIUnits::testMonteCarloMembraneBarostat PASSED [ 8%] 183s TestAPIUnits.py::TestAPIUnits::testNonbondedForce PASSED [ 9%] 183s TestAPIUnits.py::TestAPIUnits::testNoseHooverIntegrator PASSED [ 9%] 183s TestAPIUnits.py::TestAPIUnits::testPeriodicTorsionForce PASSED [ 9%] 183s TestAPIUnits.py::TestAPIUnits::testRBTorsionForce PASSED [ 10%] 183s TestAPIUnits.py::TestAPIUnits::testVariableLangevinIntegrator PASSED [ 10%] 183s TestAPIUnits.py::TestAPIUnits::testVariableVerletIntegrator PASSED [ 10%] 183s TestAPIUnits.py::TestAPIUnits::testVerletIntegrator PASSED [ 11%] 183s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_CrdBox PASSED [ 11%] 183s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_CrdBoxTruncoct PASSED [ 11%] 183s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_CrdOnly PASSED [ 12%] 183s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_CrdVel PASSED [ 12%] 183s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_CrdVelBox PASSED [ 12%] 183s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_NetCDF SKIPPED (Sc...) 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[ 50%] 306s TestIntegrators.py::TestIntegrators::testBadGroups PASSED [ 51%] 306s TestIntegrators.py::TestIntegrators::testDrudeNoseHooverIntegrator SKIPPED [ 51%] 308s TestIntegrators.py::TestIntegrators::testMTSIntegratorConstraints PASSED [ 51%] 343s TestIntegrators.py::TestIntegrators::testMTSIntegratorExplicit PASSED [ 52%] 3019s TestIntegrators.py::TestIntegrators::testMTSLangevinIntegrator PASSED [ 52%] 3019s TestIntegrators.py::TestIntegrators::testMTSLangevinIntegratorFriction PASSED [ 52%] 3022s TestIntegrators.py::TestIntegrators::testNoseHooverIntegrator PASSED [ 53%] 3025s TestMetadynamics.py::TestMetadynamics::testHarmonicOscillator PASSED [ 53%] 3026s TestModeller.py::TestModeller::test_add PASSED [ 53%] 3027s TestModeller.py::TestModeller::test_addExtraParticles PASSED [ 54%] 3036s TestModeller.py::TestModeller::test_addHydrogensASH PASSED [ 54%] 3037s TestModeller.py::TestModeller::test_addHydrogensCYX PASSED [ 54%] 3047s TestModeller.py::TestModeller::test_addHydrogensGLH PASSED [ 55%] 3048s TestModeller.py::TestModeller::test_addHydrogensGlycam PASSED [ 55%] 3058s TestModeller.py::TestModeller::test_addHydrogensLYN PASSED [ 55%] 3067s TestModeller.py::TestModeller::test_addHydrogensPdb2 PASSED [ 56%] 3069s TestModeller.py::TestModeller::test_addHydrogensPdb3 PASSED [ 56%] 3071s TestModeller.py::TestModeller::test_addHydrogensPdb3_keepPositions PASSED [ 56%] 3083s TestModeller.py::TestModeller::test_addHydrogenspH11 PASSED [ 57%] 3094s TestModeller.py::TestModeller::test_addHydrogenspH4 PASSED [ 57%] 3095s TestModeller.py::TestModeller::test_addHydrogenspH9 PASSED [ 57%] 3095s TestModeller.py::TestModeller::test_addMembrane SKIPPED (Skipping a ...) [ 58%] 3097s TestModeller.py::TestModeller::test_addSolventBoxShape PASSED [ 58%] 3115s TestModeller.py::TestModeller::test_addSolventIons PASSED [ 58%] 3119s TestModeller.py::TestModeller::test_addSolventNegativeSolvent PASSED [ 59%] 3123s TestModeller.py::TestModeller::test_addSolventNeutralSolvent PASSED [ 59%] 3142s TestModeller.py::TestModeller::test_addSolventPeriodicBox PASSED [ 59%] 3146s TestModeller.py::TestModeller::test_addSolventPositiveSolvent PASSED [ 60%] 3160s TestModeller.py::TestModeller::test_addSolventWaterModels PASSED [ 60%] 3160s TestModeller.py::TestModeller::test_addVirtualSites PASSED [ 60%] 3170s TestModeller.py::TestModeller::test_convertWater PASSED [ 61%] 3171s TestModeller.py::TestModeller::test_delete PASSED [ 61%] 3172s TestModeller.py::TestModeller::test_deleteWater PASSED [ 61%] 3173s TestModeller.py::TestModeller::test_multiSiteIon PASSED [ 62%] 3174s TestModeller.py::TestModeller::test_removeExtraHydrogens PASSED [ 62%] 3174s TestNumpyCompatibility.py::TestNumpyCompatibility::test_CMAP PASSED [ 62%] 3174s TestNumpyCompatibility.py::TestNumpyCompatibility::test_int64 PASSED [ 63%] 3174s TestNumpyCompatibility.py::TestNumpyCompatibility::test_periodicBoxVectors PASSED [ 63%] 3174s TestNumpyCompatibility.py::TestNumpyCompatibility::test_setPositions PASSED [ 63%] 3174s TestNumpyCompatibility.py::TestNumpyCompatibility::test_setPositions_units PASSED [ 64%] 3175s TestNumpyCompatibility.py::TestNumpyCompatibility::test_setVelocities PASSED [ 64%] 3175s TestNumpyCompatibility.py::TestNumpyCompatibility::test_setVelocities_units PASSED [ 64%] 3175s TestNumpyCompatibility.py::TestNumpyCompatibility::test_tabulatedFunction PASSED [ 65%] 3175s TestNumpyCompatibility.py::TestNumpyUnits::testNumpyAttributes PASSED [ 65%] 3175s TestPatches.py::TestPatches::testAlaAlaAla PASSED [ 65%] 3175s TestPatches.py::TestPatches::testApplyPatch PASSED [ 66%] 3175s TestPatches.py::TestPatches::testParseMultiresiduePatch PASSED [ 66%] 3175s TestPatches.py::TestPatches::testParsePatch PASSED [ 66%] 3175s TestPdbFile.py::TestPdbFile::test_AltLocs PASSED [ 67%] 3175s TestPdbFile.py::TestPdbFile::test_BinaryStream PASSED [ 67%] 3175s TestPdbFile.py::TestPdbFile::test_ExtraParticles PASSED [ 67%] 3210s TestPdbFile.py::TestPdbFile::test_LargeFile PASSED [ 68%] 3210s TestPdbFile.py::TestPdbFile::test_Triclinic PASSED [ 68%] 3210s TestPdbFile.py::TestPdbFile::test_WriteFile PASSED [ 68%] 3221s TestPdbReporter.py::TestPDBReporter::testBondSubset PASSED [ 69%] 3223s TestPdbReporter.py::TestPDBReporter::testInvalidSubsets PASSED [ 69%] 3224s TestPdbReporter.py::TestPDBReporter::testSubset PASSED [ 69%] 3227s TestPdbReporter.py::TestPDBReporter::testWriteAll PASSED [ 70%] 3236s TestPdbReporter.py::TestPDBxReporter::testBondSubset PASSED [ 70%] 3238s TestPdbReporter.py::TestPDBxReporter::testInvalidSubsets PASSED [ 70%] 3240s TestPdbReporter.py::TestPDBxReporter::testSubset PASSED [ 71%] 3242s TestPdbReporter.py::TestPDBxReporter::testWriteAll PASSED [ 71%] 3242s TestPdbxFile.py::TestPdbxFile::testBonds PASSED [ 71%] 3242s TestPdbxFile.py::TestPdbxFile::testInsertionCodes PASSED [ 72%] 3242s TestPdbxFile.py::TestPdbxFile::testMultiChain PASSED [ 72%] 3250s TestPdbxFile.py::TestPdbxFile::testReporterExplicit PASSED [ 72%] 3250s TestPdbxFile.py::TestPdbxFile::testReporterImplicit PASSED [ 73%] 3250s TestPdbxFile.py::TestPdbxFile::test_FormatConversion PASSED [ 73%] 3250s TestPdbxFile.py::TestPdbxFile::test_Triclinic PASSED [ 73%] 3265s TestSimulatedTempering.py::TestSimulatedTempering::testHarmonicOscillator PASSED [ 74%] 3265s TestSimulatedTempering.py::TestSimulatedTempering::testHarmonicOscillatorNPT PASSED [ 74%] 3265s TestSimulation.py::TestSimulation::testCheckpointing PASSED [ 74%] 3266s TestSimulation.py::TestSimulation::testMinimizationReporter PASSED [ 75%] 3266s TestSimulation.py::TestSimulation::testStep PASSED [ 75%] 3452s TestSimulation.py::TestSimulation::testWrappedCoordinates PASSED [ 75%] 3453s TestStateDataReporter.py::TestStateDataReporter::testAppend PASSED [ 76%] 3453s TestTopology.py::TestTopology::test_bondtype_singleton PASSED [ 76%] 3453s TestTopology.py::TestTopology::test_getters PASSED [ 76%] 3453s TestTopology.py::TestTopology::test_residue_bonds PASSED [ 77%] 3453s TestUnitCell.py::TestUnitCell::testComputePBCVectors PASSED [ 77%] 3453s TestUnitCell.py::TestUnitCell::testReducePBCVectors PASSED [ 77%] 3453s TestUnits.py::TestUnits::testAngleQuantities PASSED [ 78%] 3453s TestUnits.py::TestUnits::testBadQuantityComparisons PASSED [ 78%] 3453s TestUnits.py::TestUnits::testBadQuantityConversions PASSED [ 78%] 3453s TestUnits.py::TestUnits::testBadQuantityMaths PASSED [ 79%] 3453s TestUnits.py::TestUnits::testBaseScaleMix PASSED [ 79%] 3453s TestUnits.py::TestUnits::testBaseUnit PASSED [ 79%] 3453s TestUnits.py::TestUnits::testCalorieConversion PASSED [ 80%] 3453s TestUnits.py::TestUnits::testChemistryProblems PASSED [ 80%] 3453s TestUnits.py::TestUnits::testCollectionQuantities PASSED [ 80%] 3453s TestUnits.py::TestUnits::testCollectionQuantityOperations PASSED [ 81%] 3453s TestUnits.py::TestUnits::testComparisonOperators PASSED [ 81%] 3453s TestUnits.py::TestUnits::testCompositeUnits PASSED [ 81%] 3453s TestUnits.py::TestUnits::testConversionFactorTo PASSED [ 82%] 3453s TestUnits.py::TestUnits::testCreateNewBaseUnit PASSED [ 82%] 3453s TestUnits.py::TestUnits::testCreateNewScaledUnit PASSED [ 82%] 3453s TestUnits.py::TestUnits::testCreateNewUnit PASSED [ 83%] 3453s TestUnits.py::TestUnits::testDimensionless PASSED [ 83%] 3453s TestUnits.py::TestUnits::testGetUnitAttributes PASSED [ 83%] 3453s TestUnits.py::TestUnits::testIllegalQuantityOps PASSED [ 84%] 3453s TestUnits.py::TestUnits::testIsCompatible PASSED [ 84%] 3453s TestUnits.py::TestUnits::testIsQuantity PASSED [ 84%] 3453s TestUnits.py::TestUnits::testIsUnit PASSED [ 85%] 3453s TestUnits.py::TestUnits::testMisc PASSED [ 85%] 3453s TestUnits.py::TestUnits::testMutableQuantityOperations PASSED [ 85%] 3453s TestUnits.py::TestUnits::testPresetUnitSystems PASSED [ 86%] 3453s TestUnits.py::TestUnits::testQuantityBadSqrt PASSED [ 86%] 3453s TestUnits.py::TestUnits::testQuantityCollectionMethods PASSED [ 86%] 3453s TestUnits.py::TestUnits::testQuantityComparisons PASSED [ 87%] 3453s TestUnits.py::TestUnits::testQuantityComplicatedMaths PASSED [ 87%] 3453s TestUnits.py::TestUnits::testQuantityFormat PASSED [ 87%] 3453s TestUnits.py::TestUnits::testQuantityMaths PASSED [ 88%] 3453s TestUnits.py::TestUnits::testQuantitySqrt PASSED [ 88%] 3453s TestUnits.py::TestUnits::testReduceUnit PASSED [ 88%] 3453s TestUnits.py::TestUnits::testScalarQuantityConstructor PASSED [ 89%] 3453s TestUnits.py::TestUnits::testScalarQuantityMultiplyDivide PASSED [ 89%] 3453s TestUnits.py::TestUnits::testScaledUnit PASSED [ 89%] 3453s TestUnits.py::TestUnits::testString PASSED [ 90%] 3453s TestUnits.py::TestUnits::testToBaseUnit PASSED [ 90%] 3453s TestUnits.py::TestUnits::testTruthiness PASSED [ 90%] 3453s TestUnits.py::TestUnits::testUnaryOperators PASSED [ 91%] 3453s TestUnits.py::TestUnits::testUnitBadSqrt PASSED [ 91%] 3453s TestUnits.py::TestUnits::testUnitDivision PASSED [ 91%] 3453s TestUnits.py::TestUnits::testUnitMathModule PASSED [ 92%] 3453s TestUnits.py::TestUnits::testUnitMathModuleBadInput PASSED [ 92%] 3453s TestUnits.py::TestUnits::testUnitSqrt PASSED [ 92%] 3453s TestUnits.py::TestUnits::testUnitString PASSED [ 93%] 3453s TestUnits.py::TestUnits::testUnitSystem PASSED [ 93%] 3453s TestUnits.py::TestUnits::testValueInUnit PASSED [ 93%] 3453s TestUnits.py::TestNumpyUnits::testMultiplication PASSED [ 94%] 3453s TestUnits.py::TestNumpyUnits::testNumpyDeepCopy PASSED [ 94%] 3453s TestUnits.py::TestNumpyUnits::testNumpyDivision PASSED [ 94%] 3453s TestUnits.py::TestNumpyUnits::testNumpyFunctions PASSED [ 95%] 3453s TestUnits.py::TestNumpyUnits::testNumpyIsString PASSED [ 95%] 3453s TestUnits.py::TestNumpyUnits::testNumpyQuantity PASSED [ 95%] 3453s TestVec3.py::TestVectors::testNegation PASSED [ 96%] 3453s TestVec3.py::TestVectors::testVec3Addition PASSED [ 96%] 3453s TestVec3.py::TestVectors::testVec3Attributes PASSED [ 96%] 3453s TestVec3.py::TestVectors::testVec3Division PASSED [ 97%] 3453s TestVec3.py::TestVectors::testVec3Equality PASSED [ 97%] 3453s TestVec3.py::TestVectors::testVec3Multiplication PASSED [ 97%] 3453s TestVec3.py::TestVectors::testVec3Subtraction PASSED [ 98%] 3453s TestXtcFile.py::TestXtcFile::testAppend PASSED [ 98%] 3453s TestXtcFile.py::TestXtcFile::testLongTrajectory PASSED [ 98%] 3453s TestXtcFile.py::TestXtcFile::test_xtc_box_from_topology PASSED [ 99%] 3453s TestXtcFile.py::TestXtcFile::test_xtc_cubic PASSED [ 99%] 3454s TestXtcFile.py::TestXtcFile::test_xtc_triclinic PASSED [100%] 3454s 3454s =============================== warnings summary =============================== 3454s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes 3454s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 3454s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 3454s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model GBn 3454s warnings.warn( 3454s 3454s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 3454s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 3454s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model HCT 3454s warnings.warn( 3454s 3454s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 3454s === 278 passed, 21 skipped, 28 deselected, 5 warnings in 3273.28s (0:54:33) ==== 3456s ============================= test session starts ============================== 3456s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.14 3456s cachedir: .pytest_cache 3456s rootdir: /tmp/autopkgtest.ZtXIIb/build.0yO/src/wrappers/python/tests 3456s configfile: pytest.ini 3456s plugins: typeguard-4.4.4 3460s collecting ... collected 327 items / 28 deselected / 299 selected 3460s 3460s TestAPIUnits.py::TestAPIUnits::testAmoebaMultipoleForce PASSED [ 0%] 3460s TestAPIUnits.py::TestAPIUnits::testAmoebaTorsionTorsionForce PASSED [ 0%] 3460s TestAPIUnits.py::TestAPIUnits::testAmoebaVdwForce PASSED [ 1%] 3460s TestAPIUnits.py::TestAPIUnits::testAmoebaWcaDispersionForce PASSED [ 1%] 3460s TestAPIUnits.py::TestAPIUnits::testAndersenThermostat PASSED [ 1%] 3460s TestAPIUnits.py::TestAPIUnits::testBrownianIntegrator PASSED [ 2%] 3460s TestAPIUnits.py::TestAPIUnits::testCmapForce PASSED [ 2%] 3460s TestAPIUnits.py::TestAPIUnits::testCustomAngleForce PASSED [ 2%] 3460s TestAPIUnits.py::TestAPIUnits::testCustomBondForce PASSED [ 3%] 3460s TestAPIUnits.py::TestAPIUnits::testCustomCompoundBondForce PASSED [ 3%] 3460s TestAPIUnits.py::TestAPIUnits::testCustomExternalForce PASSED [ 3%] 3460s TestAPIUnits.py::TestAPIUnits::testCustomGBForce PASSED [ 4%] 3460s TestAPIUnits.py::TestAPIUnits::testCustomHBondForce PASSED [ 4%] 3460s TestAPIUnits.py::TestAPIUnits::testCustomIntegrator PASSED [ 4%] 3460s TestAPIUnits.py::TestAPIUnits::testCustomManyParticleForce PASSED [ 5%] 3460s TestAPIUnits.py::TestAPIUnits::testCustomNonbondedForce PASSED [ 5%] 3460s TestAPIUnits.py::TestAPIUnits::testCustomTorsionForce PASSED [ 5%] 3460s TestAPIUnits.py::TestAPIUnits::testDrudeForce PASSED [ 6%] 3460s TestAPIUnits.py::TestAPIUnits::testDrudeLangevinIntegrator PASSED [ 6%] 3460s TestAPIUnits.py::TestAPIUnits::testDrudeNoseHooverIntegrator PASSED [ 6%] 3460s TestAPIUnits.py::TestAPIUnits::testDrudeSCFIntegrator PASSED [ 7%] 3460s TestAPIUnits.py::TestAPIUnits::testGeneralizedKirkwood PASSED [ 7%] 3460s TestAPIUnits.py::TestAPIUnits::testHarmonicAngleForce PASSED [ 7%] 3460s TestAPIUnits.py::TestAPIUnits::testHarmonicBondForce PASSED [ 8%] 3460s TestAPIUnits.py::TestAPIUnits::testLangevinIntegrator PASSED [ 8%] 3460s TestAPIUnits.py::TestAPIUnits::testMonteCarloMembraneBarostat PASSED [ 8%] 3460s TestAPIUnits.py::TestAPIUnits::testNonbondedForce PASSED [ 9%] 3460s TestAPIUnits.py::TestAPIUnits::testNoseHooverIntegrator PASSED [ 9%] 3460s TestAPIUnits.py::TestAPIUnits::testPeriodicTorsionForce PASSED [ 9%] 3460s TestAPIUnits.py::TestAPIUnits::testRBTorsionForce PASSED [ 10%] 3460s TestAPIUnits.py::TestAPIUnits::testVariableLangevinIntegrator PASSED [ 10%] 3460s TestAPIUnits.py::TestAPIUnits::testVariableVerletIntegrator PASSED [ 10%] 3460s TestAPIUnits.py::TestAPIUnits::testVerletIntegrator PASSED [ 11%] 3460s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_CrdBox PASSED [ 11%] 3460s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_CrdBoxTruncoct PASSED [ 11%] 3460s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_CrdOnly PASSED [ 12%] 3460s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_CrdVel PASSED [ 12%] 3460s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_CrdVelBox PASSED [ 12%] 3460s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_NetCDF SKIPPED (Sc...) [ 13%] 3464s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testAmberCMAP PASSED [ 13%] 3473s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testChamber PASSED [ 13%] 3473s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testEPConstraints PASSED [ 14%] 3473s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testGBneckRadii PASSED [ 14%] 3479s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes PASSED [ 14%] 3479s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testSwitchFunction PASSED [ 15%] 3480s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testWaterBonds PASSED [ 15%] 3481s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_Cutoff PASSED [ 15%] 3481s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_EwaldErrorTolerance PASSED [ 16%] 3482s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_HAngle PASSED [ 16%] 3482s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_HydrogenMass PASSED [ 16%] 3482s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent PASSED [ 17%] 3482s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters PASSED [ 17%] 3482s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventZeroSA PASSED [ 17%] 3483s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_LJ1264 PASSED [ 18%] 3483s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_NonbondedMethod PASSED [ 18%] 3483s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_RemoveCMMotion PASSED [ 18%] 3487s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_RigidWaterAndConstraints PASSED [ 19%] 3487s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_triclinicParm PASSED [ 19%] 3499s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_with_dcd_reporter PASSED [ 19%] 3499s TestBytes.py::TestBytes::test_createCheckpoint PASSED [ 20%] 3500s TestCharmmFiles.py::TestCharmmFiles::testSystemOptions PASSED [ 20%] 3500s TestCharmmFiles.py::TestCharmmFiles::test_Constraints PASSED [ 20%] 3500s TestCharmmFiles.py::TestCharmmFiles::test_Cutoff PASSED [ 21%] 3500s TestCharmmFiles.py::TestCharmmFiles::test_Drude SKIPPED (Skipping te...) [ 21%] 3503s TestCharmmFiles.py::TestCharmmFiles::test_DrudeMass PASSED [ 21%] 3503s TestCharmmFiles.py::TestCharmmFiles::test_HydrogenMass PASSED [ 22%] 3503s TestCharmmFiles.py::TestCharmmFiles::test_ImplicitSolvent PASSED [ 22%] 3503s TestCharmmFiles.py::TestCharmmFiles::test_ImplicitSolventParameters PASSED [ 22%] 3503s TestCharmmFiles.py::TestCharmmFiles::test_Impropers PASSED [ 23%] 3508s TestCharmmFiles.py::TestCharmmFiles::test_InsCode PASSED [ 23%] 3508s TestCharmmFiles.py::TestCharmmFiles::test_Lonepair PASSED [ 23%] 3508s TestCharmmFiles.py::TestCharmmFiles::test_NBThole SKIPPED (Skipping ...) [ 24%] 3508s TestCharmmFiles.py::TestCharmmFiles::test_NBXMod PASSED [ 24%] 3509s TestCharmmFiles.py::TestCharmmFiles::test_NoLongRangeCorrection PASSED [ 24%] 3509s TestCharmmFiles.py::TestCharmmFiles::test_NoPsfWarning PASSED [ 25%] 3509s TestCharmmFiles.py::TestCharmmFiles::test_NonbondedMethod PASSED [ 25%] 3509s TestCharmmFiles.py::TestCharmmFiles::test_Nonbonded_Exclusion PASSED [ 25%] 3510s TestCharmmFiles.py::TestCharmmFiles::test_PSFSetUnitCellDimensions PASSED [ 26%] 4292s TestCharmmFiles.py::TestCharmmFiles::test_PermissiveRead autopkgtest-virt-ssh [14:23:25]: ------- nova console-log 712d8bba-54bf-4a02-875a-58750231460b (adt-resolute-s390x-openmm-20260123-105857-juju-7f2275-prod-proposed-migration-environment-20-8bc0d2a3-6e9a-4e6c-be4a-039f9ce44cf9) ------ 4292s ERROR (CommandError): No server with a name or ID of '712d8bba-54bf-4a02-875a-58750231460b' exists. 4292s --------------------------------------------------- 4292s ------- nova show 712d8bba-54bf-4a02-875a-58750231460b (adt-resolute-s390x-openmm-20260123-105857-juju-7f2275-prod-proposed-migration-environment-20-8bc0d2a3-6e9a-4e6c-be4a-039f9ce44cf9) ------ 4292s ERROR (CommandError): No server with a name or ID of '712d8bba-54bf-4a02-875a-58750231460b' exists. 4292s --------------------------------------------------- 4292s 4296s autopkgtest [14:23:29]: ERROR: testbed failure: testbed auxverb failed with exit code 255