0s autopkgtest [13:45:38]: starting date and time: 2026-02-09 13:45:38+0000 0s autopkgtest [13:45:38]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [13:45:38]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.zrzu1hkc/out --timeout-copy=6000 --needs-internet=try --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade openmm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.42-2ubuntu5 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@sto01-s390x-12.secgroup --name adt-resolute-s390x-openmm-20260209-134538-juju-7f2275-prod-proposed-migration-environment-15-fadda868-78cd-433b-972b-ee37db40f02d --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-autopkgtest-workers-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 4s Creating nova instance adt-resolute-s390x-openmm-20260209-134538-juju-7f2275-prod-proposed-migration-environment-15-fadda868-78cd-433b-972b-ee37db40f02d from image adt/ubuntu-resolute-s390x-server-20260209.img (UUID 9cc437fa-9eb6-47c5-b3be-2034f91c6244)... 255s autopkgtest [13:49:53]: testbed dpkg architecture: s390x 256s autopkgtest [13:49:54]: testbed apt version: 3.1.15 258s autopkgtest [13:49:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup 259s autopkgtest [13:49:57]: testbed release detected to be: None 262s autopkgtest [13:50:00]: updating testbed package index (apt update) 263s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [124 kB] 263s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 263s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 263s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 263s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [173 kB] 263s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [2744 B] 263s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [1622 kB] 263s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [29.4 kB] 263s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [243 kB] 263s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [1436 kB] 263s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [8136 B] 266s Fetched 3638 kB in 4s (945 kB/s) 272s Reading package lists... 275s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 275s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 275s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 275s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 281s Reading package lists... 281s Reading package lists... 282s Building dependency tree... 282s Reading state information... 283s Calculating upgrade... 284s The following packages will be upgraded: 284s cryptsetup-bin dracut-install libc-bin libc-gconv-modules-extra libc6 284s libcryptsetup12 locales 285s 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 285s Need to get 8469 kB of archives. 285s After this operation, 0 B of additional disk space will be used. 285s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x libc-gconv-modules-extra s390x 2.42-2ubuntu5 [1369 kB] 285s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x libc6 s390x 2.42-2ubuntu5 [1623 kB] 286s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x libc-bin s390x 2.42-2ubuntu5 [674 kB] 286s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x libcryptsetup12 s390x 2:2.8.0-1ubuntu3 [273 kB] 286s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x locales all 2.42-2ubuntu5 [4255 kB] 286s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x cryptsetup-bin s390x 2:2.8.0-1ubuntu3 [227 kB] 286s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x dracut-install s390x 109-11ubuntu1 [46.9 kB] 290s dpkg-preconfigure: unable to re-open stdin: No such file or directory 291s Fetched 8469 kB in 1s (6414 kB/s) 298s (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 ... 88641 files and directories currently installed.) 298s Preparing to unpack .../libc-gconv-modules-extra_2.42-2ubuntu5_s390x.deb ... 298s Unpacking libc-gconv-modules-extra:s390x (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 301s Setting up libc-gconv-modules-extra:s390x (2.42-2ubuntu5) ... 305s (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 ... 88641 files and directories currently installed.) 305s Preparing to unpack .../libc6_2.42-2ubuntu5_s390x.deb ... 307s Unpacking libc6:s390x (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 308s Setting up libc6:s390x (2.42-2ubuntu5) ... 310s (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 ... 88641 files and directories currently installed.) 310s Preparing to unpack .../libc-bin_2.42-2ubuntu5_s390x.deb ... 311s Unpacking libc-bin (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 313s Setting up libc-bin (2.42-2ubuntu5) ... 315s (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 ... 88641 files and directories currently installed.) 316s Preparing to unpack .../libcryptsetup12_2%3a2.8.0-1ubuntu3_s390x.deb ... 316s Unpacking libcryptsetup12:s390x (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 318s Preparing to unpack .../locales_2.42-2ubuntu5_all.deb ... 318s Unpacking locales (2.42-2ubuntu5) over (2.42-2ubuntu4) ... 323s Preparing to unpack .../cryptsetup-bin_2%3a2.8.0-1ubuntu3_s390x.deb ... 323s Unpacking cryptsetup-bin (2:2.8.0-1ubuntu3) over (2:2.8.0-1ubuntu2) ... 326s Preparing to unpack .../dracut-install_109-11ubuntu1_s390x.deb ... 327s Unpacking dracut-install (109-11ubuntu1) over (109-9ubuntu1) ... 328s Setting up locales (2.42-2ubuntu5) ... 334s Generating locales (this might take a while)... 343s en_US.UTF-8... done 343s Generation complete. 345s Setting up dracut-install (109-11ubuntu1) ... 346s Setting up libcryptsetup12:s390x (2:2.8.0-1ubuntu3) ... 346s Setting up cryptsetup-bin (2:2.8.0-1ubuntu3) ... 346s Processing triggers for systemd (259-1ubuntu3) ... 350s Processing triggers for man-db (2.13.1-1build1) ... 398s Processing triggers for libc-bin (2.42-2ubuntu5) ... 402s autopkgtest [13:52:20]: upgrading testbed (apt dist-upgrade and autopurge) 402s Reading package lists... 404s Building dependency tree... 404s Reading state information... 405s Calculating upgrade... 405s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 406s Reading package lists... 408s Building dependency tree... 408s Reading state information... 409s Solving dependencies... 410s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 417s autopkgtest [13:52:35]: testbed running kernel: Linux 6.19.0-3-generic #3-Ubuntu SMP Fri Jan 23 19:02:49 UTC 2026 418s autopkgtest [13:52:36]: @@@@@@@@@@@@@@@@@@@@ apt-source openmm 434s Get:1 http://ftpmaster.internal/ubuntu resolute/universe openmm 8.1.2+dfsg-12 (dsc) [2579 B] 434s Get:2 http://ftpmaster.internal/ubuntu resolute/universe openmm 8.1.2+dfsg-12 (tar) [11.5 MB] 434s Get:3 http://ftpmaster.internal/ubuntu resolute/universe openmm 8.1.2+dfsg-12 (diff) [23.7 kB] 436s gpgv: Signature made Mon Sep 29 08:59:53 2025 UTC 436s gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 436s gpgv: issuer "merkys@debian.org" 436s gpgv: Can't check signature: No public key 436s dpkg-source: warning: cannot verify inline signature for ./openmm_8.1.2+dfsg-12.dsc: no acceptable signature found 444s dpkg-source: warning: diff 'src/debian/patches/4602.patch' patches file src/wrappers/python/openmm/app/internal/amber_file_parser.py more than once 444s autopkgtest [13:53:02]: testing package openmm version 8.1.2+dfsg-12 445s autopkgtest [13:53:03]: build not needed 464s autopkgtest [13:53:22]: test test-python: preparing testbed 465s Reading package lists... 467s Building dependency tree... 467s Reading state information... 467s Solving dependencies... 469s The following NEW packages will be installed: 469s cpp cpp-15 cpp-15-s390x-linux-gnu cpp-s390x-linux-gnu gcc gcc-15 469s gcc-15-s390x-linux-gnu gcc-s390x-linux-gnu libasan8 libblas3 libcc1-0 469s libgcc-15-dev libgfortran5 libgomp1 libisl23 libitm1 liblapack3 liblsan0 469s libmpc3 libopenmm-dev libopenmm8.1 libtsan2 libubsan1 python3-all 469s python3-iniconfig python3-numpy python3-numpy-dev python3-openmm 469s python3-pluggy python3-pytest python3.14 python3.14-minimal 470s 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. 470s Need to get 63.0 MB of archives. 470s After this operation, 273 MB of additional disk space will be used. 470s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.3.5+ds-3 [146 kB] 470s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-7ubuntu1 [255 kB] 470s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-12ubuntu1 [629 kB] 470s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-7ubuntu1 [2983 kB] 470s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.3.5+ds-3 [5305 kB] 471s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14-minimal s390x 3.14.2-1 [2510 kB] 471s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x libisl23 s390x 0.27-1build1 [702 kB] 471s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x libmpc3 s390x 1.3.1-2 [57.4 kB] 471s Get:9 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-15-s390x-linux-gnu s390x 15.2.0-12ubuntu1 [10.2 MB] 474s Get:10 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-15 s390x 15.2.0-12ubuntu1 [1028 B] 474s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x cpp-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [5746 B] 474s Get:12 http://ftpmaster.internal/ubuntu resolute/main s390x cpp s390x 4:15.2.0-4ubuntu1 [22.4 kB] 474s Get:13 http://ftpmaster.internal/ubuntu resolute/main s390x libcc1-0 s390x 15.2.0-12ubuntu1 [50.0 kB] 474s Get:14 http://ftpmaster.internal/ubuntu resolute/main s390x libgomp1 s390x 15.2.0-12ubuntu1 [154 kB] 474s Get:15 http://ftpmaster.internal/ubuntu resolute/main s390x libitm1 s390x 15.2.0-12ubuntu1 [30.9 kB] 474s Get:16 http://ftpmaster.internal/ubuntu resolute/main s390x libasan8 s390x 15.2.0-12ubuntu1 [2968 kB] 474s Get:17 http://ftpmaster.internal/ubuntu resolute/main s390x liblsan0 s390x 15.2.0-12ubuntu1 [1354 kB] 474s Get:18 http://ftpmaster.internal/ubuntu resolute/main s390x libtsan2 s390x 15.2.0-12ubuntu1 [2685 kB] 475s Get:19 http://ftpmaster.internal/ubuntu resolute/main s390x libubsan1 s390x 15.2.0-12ubuntu1 [1211 kB] 475s Get:20 http://ftpmaster.internal/ubuntu resolute/main s390x libgcc-15-dev s390x 15.2.0-12ubuntu1 [1294 kB] 475s Get:21 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15-s390x-linux-gnu s390x 15.2.0-12ubuntu1 [19.9 MB] 476s Get:22 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-15 s390x 15.2.0-12ubuntu1 [519 kB] 476s Get:23 http://ftpmaster.internal/ubuntu resolute/main s390x gcc-s390x-linux-gnu s390x 4:15.2.0-4ubuntu1 [1208 B] 477s Get:24 http://ftpmaster.internal/ubuntu resolute/main s390x gcc s390x 4:15.2.0-4ubuntu1 [5018 B] 477s Get:25 http://ftpmaster.internal/ubuntu resolute/universe s390x libopenmm8.1 s390x 8.1.2+dfsg-12 [847 kB] 477s Get:26 http://ftpmaster.internal/ubuntu resolute/universe s390x libopenmm-dev s390x 8.1.2+dfsg-12 [341 kB] 478s Get:27 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14 s390x 3.14.2-1 [816 kB] 478s Get:28 http://ftpmaster.internal/ubuntu resolute/main s390x python3-all s390x 3.13.9-3 [890 B] 478s Get:29 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-iniconfig all 2.1.0-2 [6962 B] 478s Get:30 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-openmm s390x 8.1.2+dfsg-12 [7759 kB] 479s Get:31 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pluggy all 1.6.0-2 [21.1 kB] 479s Get:32 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pytest all 9.0.2-2 [277 kB] 482s Fetched 63.0 MB in 10s (6237 kB/s) 482s Selecting previously unselected package python3-numpy-dev:s390x. 482s (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 ... 88641 files and directories currently installed.) 482s Preparing to unpack .../00-python3-numpy-dev_1%3a2.3.5+ds-3_s390x.deb ... 482s Unpacking python3-numpy-dev:s390x (1:2.3.5+ds-3) ... 483s Selecting previously unselected package libblas3:s390x. 483s Preparing to unpack .../01-libblas3_3.12.1-7ubuntu1_s390x.deb ... 483s Unpacking libblas3:s390x (3.12.1-7ubuntu1) ... 483s Selecting previously unselected package libgfortran5:s390x. 483s Preparing to unpack .../02-libgfortran5_15.2.0-12ubuntu1_s390x.deb ... 483s Unpacking libgfortran5:s390x (15.2.0-12ubuntu1) ... 483s Selecting previously unselected package liblapack3:s390x. 484s Preparing to unpack .../03-liblapack3_3.12.1-7ubuntu1_s390x.deb ... 484s Unpacking liblapack3:s390x (3.12.1-7ubuntu1) ... 485s Selecting previously unselected package python3-numpy. 485s Preparing to unpack .../04-python3-numpy_1%3a2.3.5+ds-3_s390x.deb ... 485s Unpacking python3-numpy (1:2.3.5+ds-3) ... 488s Selecting previously unselected package python3.14-minimal. 488s Preparing to unpack .../05-python3.14-minimal_3.14.2-1_s390x.deb ... 488s Unpacking python3.14-minimal (3.14.2-1) ... 488s Selecting previously unselected package libisl23:s390x. 488s Preparing to unpack .../06-libisl23_0.27-1build1_s390x.deb ... 488s Unpacking libisl23:s390x (0.27-1build1) ... 489s Selecting previously unselected package libmpc3:s390x. 489s Preparing to unpack .../07-libmpc3_1.3.1-2_s390x.deb ... 489s Unpacking libmpc3:s390x (1.3.1-2) ... 489s Selecting previously unselected package cpp-15-s390x-linux-gnu. 489s Preparing to unpack .../08-cpp-15-s390x-linux-gnu_15.2.0-12ubuntu1_s390x.deb ... 489s Unpacking cpp-15-s390x-linux-gnu (15.2.0-12ubuntu1) ... 493s Selecting previously unselected package cpp-15. 493s Preparing to unpack .../09-cpp-15_15.2.0-12ubuntu1_s390x.deb ... 493s Unpacking cpp-15 (15.2.0-12ubuntu1) ... 493s Selecting previously unselected package cpp-s390x-linux-gnu. 493s Preparing to unpack .../10-cpp-s390x-linux-gnu_4%3a15.2.0-4ubuntu1_s390x.deb ... 493s Unpacking cpp-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 493s Selecting previously unselected package cpp. 493s Preparing to unpack .../11-cpp_4%3a15.2.0-4ubuntu1_s390x.deb ... 493s Unpacking cpp (4:15.2.0-4ubuntu1) ... 493s Selecting previously unselected package libcc1-0:s390x. 493s Preparing to unpack .../12-libcc1-0_15.2.0-12ubuntu1_s390x.deb ... 493s Unpacking libcc1-0:s390x (15.2.0-12ubuntu1) ... 493s Selecting previously unselected package libgomp1:s390x. 493s Preparing to unpack .../13-libgomp1_15.2.0-12ubuntu1_s390x.deb ... 493s Unpacking libgomp1:s390x (15.2.0-12ubuntu1) ... 493s Selecting previously unselected package libitm1:s390x. 493s Preparing to unpack .../14-libitm1_15.2.0-12ubuntu1_s390x.deb ... 493s Unpacking libitm1:s390x (15.2.0-12ubuntu1) ... 493s Selecting previously unselected package libasan8:s390x. 493s Preparing to unpack .../15-libasan8_15.2.0-12ubuntu1_s390x.deb ... 493s Unpacking libasan8:s390x (15.2.0-12ubuntu1) ... 495s Selecting previously unselected package liblsan0:s390x. 495s Preparing to unpack .../16-liblsan0_15.2.0-12ubuntu1_s390x.deb ... 495s Unpacking liblsan0:s390x (15.2.0-12ubuntu1) ... 496s Selecting previously unselected package libtsan2:s390x. 496s Preparing to unpack .../17-libtsan2_15.2.0-12ubuntu1_s390x.deb ... 496s Unpacking libtsan2:s390x (15.2.0-12ubuntu1) ... 498s Selecting previously unselected package libubsan1:s390x. 498s Preparing to unpack .../18-libubsan1_15.2.0-12ubuntu1_s390x.deb ... 498s Unpacking libubsan1:s390x (15.2.0-12ubuntu1) ... 498s Selecting previously unselected package libgcc-15-dev:s390x. 498s Preparing to unpack .../19-libgcc-15-dev_15.2.0-12ubuntu1_s390x.deb ... 498s Unpacking libgcc-15-dev:s390x (15.2.0-12ubuntu1) ... 500s Selecting previously unselected package gcc-15-s390x-linux-gnu. 500s Preparing to unpack .../20-gcc-15-s390x-linux-gnu_15.2.0-12ubuntu1_s390x.deb ... 500s Unpacking gcc-15-s390x-linux-gnu (15.2.0-12ubuntu1) ... 507s Selecting previously unselected package gcc-15. 507s Preparing to unpack .../21-gcc-15_15.2.0-12ubuntu1_s390x.deb ... 507s Unpacking gcc-15 (15.2.0-12ubuntu1) ... 507s Selecting previously unselected package gcc-s390x-linux-gnu. 507s Preparing to unpack .../22-gcc-s390x-linux-gnu_4%3a15.2.0-4ubuntu1_s390x.deb ... 507s Unpacking gcc-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 507s Selecting previously unselected package gcc. 507s Preparing to unpack .../23-gcc_4%3a15.2.0-4ubuntu1_s390x.deb ... 507s Unpacking gcc (4:15.2.0-4ubuntu1) ... 507s Selecting previously unselected package libopenmm8.1. 507s Preparing to unpack .../24-libopenmm8.1_8.1.2+dfsg-12_s390x.deb ... 508s Unpacking libopenmm8.1 (8.1.2+dfsg-12) ... 508s Selecting previously unselected package libopenmm-dev. 508s Preparing to unpack .../25-libopenmm-dev_8.1.2+dfsg-12_s390x.deb ... 508s Unpacking libopenmm-dev (8.1.2+dfsg-12) ... 508s Selecting previously unselected package python3.14. 508s Preparing to unpack .../26-python3.14_3.14.2-1_s390x.deb ... 508s Unpacking python3.14 (3.14.2-1) ... 509s Selecting previously unselected package python3-all. 509s Preparing to unpack .../27-python3-all_3.13.9-3_s390x.deb ... 509s Unpacking python3-all (3.13.9-3) ... 509s Selecting previously unselected package python3-iniconfig. 509s Preparing to unpack .../28-python3-iniconfig_2.1.0-2_all.deb ... 509s Unpacking python3-iniconfig (2.1.0-2) ... 509s Selecting previously unselected package python3-openmm. 509s Preparing to unpack .../29-python3-openmm_8.1.2+dfsg-12_s390x.deb ... 509s Unpacking python3-openmm (8.1.2+dfsg-12) ... 517s Selecting previously unselected package python3-pluggy. 517s Preparing to unpack .../30-python3-pluggy_1.6.0-2_all.deb ... 517s Unpacking python3-pluggy (1.6.0-2) ... 517s Selecting previously unselected package python3-pytest. 517s Preparing to unpack .../31-python3-pytest_9.0.2-2_all.deb ... 517s Unpacking python3-pytest (9.0.2-2) ... 517s Setting up python3-iniconfig (2.1.0-2) ... 524s Setting up libgomp1:s390x (15.2.0-12ubuntu1) ... 524s Setting up libblas3:s390x (3.12.1-7ubuntu1) ... 526s 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 526s Setting up libmpc3:s390x (1.3.1-2) ... 526s Setting up python3-numpy-dev:s390x (1:2.3.5+ds-3) ... 526s Setting up libgfortran5:s390x (15.2.0-12ubuntu1) ... 526s Setting up python3-pluggy (1.6.0-2) ... 527s Setting up libubsan1:s390x (15.2.0-12ubuntu1) ... 527s Setting up libasan8:s390x (15.2.0-12ubuntu1) ... 527s Setting up libtsan2:s390x (15.2.0-12ubuntu1) ... 527s Setting up libisl23:s390x (0.27-1build1) ... 527s Setting up libopenmm8.1 (8.1.2+dfsg-12) ... 527s Setting up python3.14-minimal (3.14.2-1) ... 539s Setting up libcc1-0:s390x (15.2.0-12ubuntu1) ... 539s Setting up liblsan0:s390x (15.2.0-12ubuntu1) ... 539s Setting up libitm1:s390x (15.2.0-12ubuntu1) ... 539s Setting up liblapack3:s390x (3.12.1-7ubuntu1) ... 539s 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 539s Setting up libgcc-15-dev:s390x (15.2.0-12ubuntu1) ... 539s Setting up python3-pytest (9.0.2-2) ... 545s Setting up libopenmm-dev (8.1.2+dfsg-12) ... 545s Setting up python3-numpy (1:2.3.5+ds-3) ... 571s Setting up python3-openmm (8.1.2+dfsg-12) ... 573s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:426: SyntaxWarning: invalid escape sequence '\S' 573s r"(?:_(.+?)[.](\S+))" "|" # _category.attribute 573s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' 573s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 573s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' 573s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 573s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' 573s "(?:\s*#.*$)" "|" # comments (dumped) 573s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' 573s "(\S+)" # unquoted words 576s /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. 576s r"(?:_(.+?)[.](\S+))" "|" # _category.attribute 576s /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. 576s "(?:_(.+?)[.](\S+))" "|" # _category.attribute 576s /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. 576s "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings 576s /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: "\s" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\s"? A raw string is also an option. 576s "(?:\s*#.*$)" "|" # comments (dumped) 576s /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. 576s "(\S+)" # unquoted words 577s Setting up cpp-15-s390x-linux-gnu (15.2.0-12ubuntu1) ... 577s Setting up python3.14 (3.14.2-1) ... 603s Setting up gcc-15-s390x-linux-gnu (15.2.0-12ubuntu1) ... 603s Setting up cpp-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 603s Setting up python3-all (3.13.9-3) ... 603s Setting up gcc-s390x-linux-gnu (4:15.2.0-4ubuntu1) ... 603s Setting up cpp-15 (15.2.0-12ubuntu1) ... 603s Setting up cpp (4:15.2.0-4ubuntu1) ... 603s Setting up gcc-15 (15.2.0-12ubuntu1) ... 603s Setting up gcc (4:15.2.0-4ubuntu1) ... 603s Processing triggers for systemd (259-1ubuntu3) ... 604s Processing triggers for man-db (2.13.1-1build1) ... 614s Processing triggers for libc-bin (2.42-2ubuntu5) ... 621s autopkgtest [13:55:59]: test test-python: [----------------------- 622s 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 627s ============================= test session starts ============================== 627s platform linux -- Python 3.14.2, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.14 627s cachedir: .pytest_cache 627s rootdir: /tmp/autopkgtest.Ym6bjl/build.fRO/src/wrappers/python/tests 627s configfile: pytest.ini 627s plugins: typeguard-4.4.4 635s collecting ... collected 327 items / 28 deselected / 299 selected 635s 635s TestAPIUnits.py::TestAPIUnits::testAmoebaMultipoleForce PASSED [ 0%] 635s TestAPIUnits.py::TestAPIUnits::testAmoebaTorsionTorsionForce PASSED [ 0%] 635s TestAPIUnits.py::TestAPIUnits::testAmoebaVdwForce PASSED [ 1%] 635s TestAPIUnits.py::TestAPIUnits::testAmoebaWcaDispersionForce PASSED [ 1%] 635s TestAPIUnits.py::TestAPIUnits::testAndersenThermostat PASSED [ 1%] 635s TestAPIUnits.py::TestAPIUnits::testBrownianIntegrator PASSED [ 2%] 635s TestAPIUnits.py::TestAPIUnits::testCmapForce PASSED [ 2%] 635s TestAPIUnits.py::TestAPIUnits::testCustomAngleForce PASSED [ 2%] 635s TestAPIUnits.py::TestAPIUnits::testCustomBondForce PASSED [ 3%] 635s TestAPIUnits.py::TestAPIUnits::testCustomCompoundBondForce PASSED [ 3%] 635s TestAPIUnits.py::TestAPIUnits::testCustomExternalForce PASSED [ 3%] 635s TestAPIUnits.py::TestAPIUnits::testCustomGBForce PASSED [ 4%] 635s TestAPIUnits.py::TestAPIUnits::testCustomHBondForce PASSED [ 4%] 635s TestAPIUnits.py::TestAPIUnits::testCustomIntegrator PASSED [ 4%] 635s TestAPIUnits.py::TestAPIUnits::testCustomManyParticleForce PASSED [ 5%] 635s TestAPIUnits.py::TestAPIUnits::testCustomNonbondedForce PASSED [ 5%] 635s TestAPIUnits.py::TestAPIUnits::testCustomTorsionForce PASSED [ 5%] 635s TestAPIUnits.py::TestAPIUnits::testDrudeForce PASSED [ 6%] 635s TestAPIUnits.py::TestAPIUnits::testDrudeLangevinIntegrator PASSED [ 6%] 635s TestAPIUnits.py::TestAPIUnits::testDrudeNoseHooverIntegrator PASSED [ 6%] 635s TestAPIUnits.py::TestAPIUnits::testDrudeSCFIntegrator PASSED [ 7%] 635s TestAPIUnits.py::TestAPIUnits::testGeneralizedKirkwood PASSED [ 7%] 635s TestAPIUnits.py::TestAPIUnits::testHarmonicAngleForce PASSED [ 7%] 635s TestAPIUnits.py::TestAPIUnits::testHarmonicBondForce PASSED [ 8%] 635s TestAPIUnits.py::TestAPIUnits::testLangevinIntegrator PASSED [ 8%] 635s TestAPIUnits.py::TestAPIUnits::testMonteCarloMembraneBarostat PASSED [ 8%] 635s TestAPIUnits.py::TestAPIUnits::testNonbondedForce PASSED [ 9%] 635s TestAPIUnits.py::TestAPIUnits::testNoseHooverIntegrator PASSED [ 9%] 635s TestAPIUnits.py::TestAPIUnits::testPeriodicTorsionForce PASSED [ 9%] 635s TestAPIUnits.py::TestAPIUnits::testRBTorsionForce PASSED [ 10%] 635s TestAPIUnits.py::TestAPIUnits::testVariableLangevinIntegrator PASSED [ 10%] 635s TestAPIUnits.py::TestAPIUnits::testVariableVerletIntegrator PASSED [ 10%] 635s TestAPIUnits.py::TestAPIUnits::testVerletIntegrator PASSED [ 11%] 635s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_CrdBox PASSED [ 11%] 635s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_CrdBoxTruncoct PASSED [ 11%] 635s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_CrdOnly PASSED [ 12%] 635s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_CrdVel PASSED [ 12%] 636s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_CrdVelBox PASSED [ 12%] 636s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_NetCDF SKIPPED (Sc...) [ 13%] 643s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testAmberCMAP PASSED [ 13%] 661s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testChamber PASSED [ 13%] 661s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testEPConstraints PASSED [ 14%] 661s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testGBneckRadii PASSED [ 14%] 676s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes PASSED [ 14%] 676s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testSwitchFunction PASSED [ 15%] 679s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testWaterBonds PASSED [ 15%] 679s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_Cutoff PASSED [ 15%] 680s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_EwaldErrorTolerance PASSED [ 16%] 682s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_HAngle PASSED [ 16%] 683s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_HydrogenMass PASSED [ 16%] 683s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent PASSED [ 17%] 683s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters PASSED [ 17%] 683s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventZeroSA PASSED [ 17%] 685s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_LJ1264 PASSED [ 18%] 686s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_NonbondedMethod PASSED [ 18%] 686s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_RemoveCMMotion PASSED [ 18%] 691s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_RigidWaterAndConstraints PASSED [ 19%] 691s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_triclinicParm PASSED [ 19%] 727s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_with_dcd_reporter PASSED [ 19%] 727s TestBytes.py::TestBytes::test_createCheckpoint PASSED [ 20%] 728s TestCharmmFiles.py::TestCharmmFiles::testSystemOptions PASSED [ 20%] 728s TestCharmmFiles.py::TestCharmmFiles::test_Constraints PASSED [ 20%] 729s TestCharmmFiles.py::TestCharmmFiles::test_Cutoff PASSED [ 21%] 729s TestCharmmFiles.py::TestCharmmFiles::test_Drude SKIPPED (Skipping te...) 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[ 24%] 746s TestCharmmFiles.py::TestCharmmFiles::test_NBXMod PASSED [ 24%] 747s TestCharmmFiles.py::TestCharmmFiles::test_NoLongRangeCorrection PASSED [ 24%] 747s TestCharmmFiles.py::TestCharmmFiles::test_NoPsfWarning PASSED [ 25%] 748s TestCharmmFiles.py::TestCharmmFiles::test_NonbondedMethod PASSED [ 25%] 748s TestCharmmFiles.py::TestCharmmFiles::test_Nonbonded_Exclusion PASSED [ 25%] 749s TestCharmmFiles.py::TestCharmmFiles::test_PSFSetUnitCellDimensions PASSED [ 26%] 778s TestCharmmFiles.py::TestCharmmFiles::test_PermissiveRead PASSED [ 26%] 778s TestCharmmFiles.py::TestCharmmFiles::test_RemoveCMMotion PASSED [ 26%] 778s TestCharmmFiles.py::TestCharmmFiles::test_Residues PASSED [ 27%] 779s TestDcdFile.py::TestDCDFile::testAppend PASSED [ 27%] 779s TestDcdFile.py::TestDCDFile::testLongTrajectory PASSED [ 27%] 779s TestDcdFile.py::TestDCDFile::test_dcd PASSED [ 28%] 783s TestDesmondDMSFile.py::TestDesmondDMSFile::test_Cutoff PASSED [ 28%] 784s TestDesmondDMSFile.py::TestDesmondDMSFile::test_EwaldErrorTolerance PASSED [ 28%] 786s TestDesmondDMSFile.py::TestDesmondDMSFile::test_HydrogenMass PASSED [ 29%] 789s TestDesmondDMSFile.py::TestDesmondDMSFile::test_NonbondedMethod PASSED [ 29%] 790s TestDesmondDMSFile.py::TestDesmondDMSFile::test_OPLS1 PASSED [ 29%] 792s TestDesmondDMSFile.py::TestDesmondDMSFile::test_OPLS2 PASSED [ 30%] 793s TestDesmondDMSFile.py::TestDesmondDMSFile::test_RemoveCMMotion PASSED [ 30%] 793s TestElement.py::TestElement::test_attributes PASSED [ 30%] 796s TestElement.py::TestElement::test_getByMass PASSED [ 31%] 796s TestElement.py::TestElement::test_immutable PASSED [ 31%] 796s TestElement.py::TestElement::test_pickleable PASSED [ 31%] 796s TestForceField.py::TestForceField::test_CharmmPolar SKIPPED (Skippin...) [ 32%] 798s TestForceField.py::TestForceField::test_CustomNonbondedGenerator PASSED [ 32%] 801s TestForceField.py::TestForceField::test_Cutoff PASSED [ 32%] 805s TestForceField.py::TestForceField::test_DrudeMass PASSED [ 33%] 809s TestForceField.py::TestForceField::test_Glycam PASSED [ 33%] 811s TestForceField.py::TestForceField::test_HydrogenMass PASSED [ 33%] 812s TestForceField.py::TestForceField::test_IgnoreExternalBonds PASSED [ 34%] 812s TestForceField.py::TestForceField::test_ImplicitSolvent PASSED [ 34%] 814s TestForceField.py::TestForceField::test_ImplicitSolventParameters PASSED [ 34%] 817s TestForceField.py::TestForceField::test_ImpropersOrdering PASSED [ 35%] 817s TestForceField.py::TestForceField::test_ImpropersOrdering_smirnoff PASSED [ 35%] 820s TestForceField.py::TestForceField::test_Includes PASSED [ 35%] 821s TestForceField.py::TestForceField::test_InitializationScript PASSED [ 36%] 824s TestForceField.py::TestForceField::test_MultipleFilesandForceTags PASSED [ 36%] 828s TestForceField.py::TestForceField::test_NonbondedMethod PASSED [ 36%] 830s TestForceField.py::TestForceField::test_Opc3Energy PASSED [ 37%] 832s TestForceField.py::TestForceField::test_OpcEnergy PASSED [ 37%] 834s TestForceField.py::TestForceField::test_PeriodicBoxVectors PASSED [ 37%] 836s TestForceField.py::TestForceField::test_RemoveCMMotion PASSED [ 38%] 842s TestForceField.py::TestForceField::test_ResidueAttributes PASSED [ 38%] 844s TestForceField.py::TestForceField::test_ResidueOverriding PASSED [ 38%] 845s TestForceField.py::TestForceField::test_ResidueTemplateUserChoice PASSED [ 39%] 857s TestForceField.py::TestForceField::test_RigidWaterAndConstraints PASSED [ 39%] 860s TestForceField.py::TestForceField::test_ScalingFactorCombining PASSED [ 39%] 861s TestForceField.py::TestForceField::test_SwitchingDistance PASSED [ 40%] 863s TestForceField.py::TestForceField::test_UnusedArgs PASSED [ 40%] 865s TestForceField.py::TestForceField::test_Wildcard PASSED [ 40%] 869s TestForceField.py::TestForceField::test_flexibleConstraints PASSED [ 41%] 873s TestForceField.py::TestForceField::test_generateTemplatesForUnmatchedResidues PASSED [ 41%] 875s TestForceField.py::TestForceField::test_getMatchingTemplates PASSED [ 41%] 878s TestForceField.py::TestForceField::test_getUnmatchedResidues PASSED [ 42%] 880s TestForceField.py::TestForceField::test_residueMatcher PASSED [ 42%] 887s TestForceField.py::TestForceField::test_residueTemplateGenerator PASSED [ 42%] 887s TestForceField.py::AmoebaTestForceField::test_Amoeba18BPTI SKIPPED (...) 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[ 50%] 896s TestIntegrators.py::TestIntegrators::testBadGroups PASSED [ 51%] 896s TestIntegrators.py::TestIntegrators::testDrudeNoseHooverIntegrator SKIPPED [ 51%] 901s TestIntegrators.py::TestIntegrators::testMTSIntegratorConstraints PASSED [ 51%] 977s TestIntegrators.py::TestIntegrators::testMTSIntegratorExplicit PASSED [ 52%] 6664s TestIntegrators.py::TestIntegrators::testMTSLangevinIntegrator PASSED [ 52%] 6664s TestIntegrators.py::TestIntegrators::testMTSLangevinIntegratorFriction PASSED [ 52%] 6674s TestIntegrators.py::TestIntegrators::testNoseHooverIntegrator PASSED [ 53%] 6686s TestMetadynamics.py::TestMetadynamics::testHarmonicOscillator PASSED [ 53%] 6688s TestModeller.py::TestModeller::test_add PASSED [ 53%] 6691s TestModeller.py::TestModeller::test_addExtraParticles PASSED [ 54%] 6713s TestModeller.py::TestModeller::test_addHydrogensASH PASSED [ 54%] 6715s TestModeller.py::TestModeller::test_addHydrogensCYX PASSED [ 54%] 6737s TestModeller.py::TestModeller::test_addHydrogensGLH PASSED [ 55%] 6738s TestModeller.py::TestModeller::test_addHydrogensGlycam PASSED [ 55%] 6761s TestModeller.py::TestModeller::test_addHydrogensLYN PASSED [ 55%] 6783s TestModeller.py::TestModeller::test_addHydrogensPdb2 PASSED [ 56%] 6786s TestModeller.py::TestModeller::test_addHydrogensPdb3 PASSED [ 56%] 6789s TestModeller.py::TestModeller::test_addHydrogensPdb3_keepPositions PASSED [ 56%] 6812s TestModeller.py::TestModeller::test_addHydrogenspH11 PASSED [ 57%] 6834s TestModeller.py::TestModeller::test_addHydrogenspH4 PASSED [ 57%] 6836s TestModeller.py::TestModeller::test_addHydrogenspH9 PASSED [ 57%] 6836s TestModeller.py::TestModeller::test_addMembrane SKIPPED (Skipping a ...) [ 58%] 6842s TestModeller.py::TestModeller::test_addSolventBoxShape PASSED [ 58%] 6890s TestModeller.py::TestModeller::test_addSolventIons PASSED [ 58%] 6899s TestModeller.py::TestModeller::test_addSolventNegativeSolvent PASSED [ 59%] 6905s TestModeller.py::TestModeller::test_addSolventNeutralSolvent PASSED [ 59%] 6945s TestModeller.py::TestModeller::test_addSolventPeriodicBox PASSED [ 59%] 6956s TestModeller.py::TestModeller::test_addSolventPositiveSolvent PASSED [ 60%] 6981s TestModeller.py::TestModeller::test_addSolventWaterModels PASSED [ 60%] 6983s TestModeller.py::TestModeller::test_addVirtualSites PASSED [ 60%] 7000s TestModeller.py::TestModeller::test_convertWater PASSED [ 61%] 7002s TestModeller.py::TestModeller::test_delete PASSED [ 61%] 7003s TestModeller.py::TestModeller::test_deleteWater PASSED [ 61%] 7005s TestModeller.py::TestModeller::test_multiSiteIon PASSED [ 62%] 7007s TestModeller.py::TestModeller::test_removeExtraHydrogens PASSED [ 62%] 7007s TestNumpyCompatibility.py::TestNumpyCompatibility::test_CMAP PASSED [ 62%] 7007s TestNumpyCompatibility.py::TestNumpyCompatibility::test_int64 PASSED [ 63%] 7007s TestNumpyCompatibility.py::TestNumpyCompatibility::test_periodicBoxVectors PASSED [ 63%] 7007s TestNumpyCompatibility.py::TestNumpyCompatibility::test_setPositions PASSED [ 63%] 7007s TestNumpyCompatibility.py::TestNumpyCompatibility::test_setPositions_units PASSED [ 64%] 7007s TestNumpyCompatibility.py::TestNumpyCompatibility::test_setVelocities PASSED [ 64%] 7007s TestNumpyCompatibility.py::TestNumpyCompatibility::test_setVelocities_units PASSED [ 64%] 7007s TestNumpyCompatibility.py::TestNumpyCompatibility::test_tabulatedFunction PASSED [ 65%] 7007s TestNumpyCompatibility.py::TestNumpyUnits::testNumpyAttributes PASSED [ 65%] 7007s TestPatches.py::TestPatches::testAlaAlaAla PASSED [ 65%] 7007s TestPatches.py::TestPatches::testApplyPatch PASSED [ 66%] 7007s TestPatches.py::TestPatches::testParseMultiresiduePatch PASSED [ 66%] 7007s TestPatches.py::TestPatches::testParsePatch PASSED [ 66%] 7007s TestPdbFile.py::TestPdbFile::test_AltLocs PASSED [ 67%] 7007s TestPdbFile.py::TestPdbFile::test_BinaryStream PASSED [ 67%] 7007s TestPdbFile.py::TestPdbFile::test_ExtraParticles PASSED [ 67%] 7056s TestPdbFile.py::TestPdbFile::test_LargeFile PASSED [ 68%] 7056s TestPdbFile.py::TestPdbFile::test_Triclinic PASSED [ 68%] 7056s TestPdbFile.py::TestPdbFile::test_WriteFile PASSED [ 68%] 7074s TestPdbReporter.py::TestPDBReporter::testBondSubset PASSED [ 69%] 7078s TestPdbReporter.py::TestPDBReporter::testInvalidSubsets PASSED [ 69%] 7081s TestPdbReporter.py::TestPDBReporter::testSubset PASSED [ 69%] 7084s TestPdbReporter.py::TestPDBReporter::testWriteAll PASSED [ 70%] 7099s TestPdbReporter.py::TestPDBxReporter::testBondSubset PASSED [ 70%] 7103s TestPdbReporter.py::TestPDBxReporter::testInvalidSubsets PASSED [ 70%] 7104s TestPdbReporter.py::TestPDBxReporter::testSubset PASSED [ 71%] 7108s TestPdbReporter.py::TestPDBxReporter::testWriteAll PASSED [ 71%] 7108s TestPdbxFile.py::TestPdbxFile::testBonds PASSED [ 71%] 7108s TestPdbxFile.py::TestPdbxFile::testInsertionCodes PASSED [ 72%] 7108s TestPdbxFile.py::TestPdbxFile::testMultiChain PASSED [ 72%] 7126s TestPdbxFile.py::TestPdbxFile::testReporterExplicit PASSED [ 72%] 7127s TestPdbxFile.py::TestPdbxFile::testReporterImplicit PASSED [ 73%] 7127s TestPdbxFile.py::TestPdbxFile::test_FormatConversion PASSED [ 73%] 7127s TestPdbxFile.py::TestPdbxFile::test_Triclinic PASSED [ 73%] 7151s TestSimulatedTempering.py::TestSimulatedTempering::testHarmonicOscillator PASSED [ 74%] 7151s TestSimulatedTempering.py::TestSimulatedTempering::testHarmonicOscillatorNPT PASSED [ 74%] 7152s TestSimulation.py::TestSimulation::testCheckpointing PASSED [ 74%] 7152s TestSimulation.py::TestSimulation::testMinimizationReporter PASSED [ 75%] 7152s TestSimulation.py::TestSimulation::testStep PASSED [ 75%] 7522s TestSimulation.py::TestSimulation::testWrappedCoordinates PASSED [ 75%] 7522s TestStateDataReporter.py::TestStateDataReporter::testAppend PASSED [ 76%] 7522s TestTopology.py::TestTopology::test_bondtype_singleton PASSED [ 76%] 7522s TestTopology.py::TestTopology::test_getters PASSED [ 76%] 7522s TestTopology.py::TestTopology::test_residue_bonds PASSED [ 77%] 7522s TestUnitCell.py::TestUnitCell::testComputePBCVectors PASSED [ 77%] 7522s TestUnitCell.py::TestUnitCell::testReducePBCVectors PASSED [ 77%] 7522s TestUnits.py::TestUnits::testAngleQuantities PASSED [ 78%] 7522s TestUnits.py::TestUnits::testBadQuantityComparisons PASSED [ 78%] 7522s TestUnits.py::TestUnits::testBadQuantityConversions PASSED [ 78%] 7522s TestUnits.py::TestUnits::testBadQuantityMaths PASSED [ 79%] 7522s TestUnits.py::TestUnits::testBaseScaleMix PASSED [ 79%] 7522s TestUnits.py::TestUnits::testBaseUnit PASSED [ 79%] 7522s TestUnits.py::TestUnits::testCalorieConversion PASSED [ 80%] 7522s TestUnits.py::TestUnits::testChemistryProblems PASSED [ 80%] 7522s TestUnits.py::TestUnits::testCollectionQuantities PASSED [ 80%] 7522s TestUnits.py::TestUnits::testCollectionQuantityOperations PASSED [ 81%] 7522s TestUnits.py::TestUnits::testComparisonOperators PASSED [ 81%] 7523s TestUnits.py::TestUnits::testCompositeUnits PASSED [ 81%] 7523s TestUnits.py::TestUnits::testConversionFactorTo PASSED [ 82%] 7523s TestUnits.py::TestUnits::testCreateNewBaseUnit PASSED [ 82%] 7523s TestUnits.py::TestUnits::testCreateNewScaledUnit PASSED [ 82%] 7523s TestUnits.py::TestUnits::testCreateNewUnit PASSED [ 83%] 7523s TestUnits.py::TestUnits::testDimensionless PASSED [ 83%] 7523s TestUnits.py::TestUnits::testGetUnitAttributes PASSED [ 83%] 7523s TestUnits.py::TestUnits::testIllegalQuantityOps PASSED [ 84%] 7523s TestUnits.py::TestUnits::testIsCompatible PASSED [ 84%] 7523s TestUnits.py::TestUnits::testIsQuantity PASSED [ 84%] 7523s TestUnits.py::TestUnits::testIsUnit PASSED [ 85%] 7523s TestUnits.py::TestUnits::testMisc PASSED [ 85%] 7523s TestUnits.py::TestUnits::testMutableQuantityOperations PASSED [ 85%] 7523s TestUnits.py::TestUnits::testPresetUnitSystems PASSED [ 86%] 7523s TestUnits.py::TestUnits::testQuantityBadSqrt PASSED [ 86%] 7523s TestUnits.py::TestUnits::testQuantityCollectionMethods PASSED [ 86%] 7523s TestUnits.py::TestUnits::testQuantityComparisons PASSED [ 87%] 7523s TestUnits.py::TestUnits::testQuantityComplicatedMaths PASSED [ 87%] 7523s TestUnits.py::TestUnits::testQuantityFormat PASSED [ 87%] 7523s TestUnits.py::TestUnits::testQuantityMaths PASSED [ 88%] 7523s TestUnits.py::TestUnits::testQuantitySqrt PASSED [ 88%] 7523s TestUnits.py::TestUnits::testReduceUnit PASSED [ 88%] 7523s TestUnits.py::TestUnits::testScalarQuantityConstructor PASSED [ 89%] 7523s TestUnits.py::TestUnits::testScalarQuantityMultiplyDivide PASSED [ 89%] 7523s TestUnits.py::TestUnits::testScaledUnit PASSED [ 89%] 7523s TestUnits.py::TestUnits::testString PASSED [ 90%] 7523s TestUnits.py::TestUnits::testToBaseUnit PASSED [ 90%] 7523s TestUnits.py::TestUnits::testTruthiness PASSED [ 90%] 7523s TestUnits.py::TestUnits::testUnaryOperators PASSED [ 91%] 7523s TestUnits.py::TestUnits::testUnitBadSqrt PASSED [ 91%] 7523s TestUnits.py::TestUnits::testUnitDivision PASSED [ 91%] 7523s TestUnits.py::TestUnits::testUnitMathModule PASSED [ 92%] 7523s TestUnits.py::TestUnits::testUnitMathModuleBadInput PASSED [ 92%] 7523s TestUnits.py::TestUnits::testUnitSqrt PASSED [ 92%] 7523s TestUnits.py::TestUnits::testUnitString PASSED [ 93%] 7523s TestUnits.py::TestUnits::testUnitSystem PASSED [ 93%] 7523s TestUnits.py::TestUnits::testValueInUnit PASSED [ 93%] 7523s TestUnits.py::TestNumpyUnits::testMultiplication PASSED [ 94%] 7523s TestUnits.py::TestNumpyUnits::testNumpyDeepCopy PASSED [ 94%] 7523s TestUnits.py::TestNumpyUnits::testNumpyDivision PASSED [ 94%] 7523s TestUnits.py::TestNumpyUnits::testNumpyFunctions PASSED [ 95%] 7523s TestUnits.py::TestNumpyUnits::testNumpyIsString PASSED [ 95%] 7523s TestUnits.py::TestNumpyUnits::testNumpyQuantity PASSED [ 95%] 7523s TestVec3.py::TestVectors::testNegation PASSED [ 96%] 7523s TestVec3.py::TestVectors::testVec3Addition PASSED [ 96%] 7523s TestVec3.py::TestVectors::testVec3Attributes PASSED [ 96%] 7523s TestVec3.py::TestVectors::testVec3Division PASSED [ 97%] 7523s TestVec3.py::TestVectors::testVec3Equality PASSED [ 97%] 7523s TestVec3.py::TestVectors::testVec3Multiplication PASSED [ 97%] 7523s TestVec3.py::TestVectors::testVec3Subtraction PASSED [ 98%] 7524s TestXtcFile.py::TestXtcFile::testAppend PASSED [ 98%] 7524s TestXtcFile.py::TestXtcFile::testLongTrajectory PASSED [ 98%] 7524s TestXtcFile.py::TestXtcFile::test_xtc_box_from_topology PASSED [ 99%] 7524s TestXtcFile.py::TestXtcFile::test_xtc_cubic PASSED [ 99%] 7531s TestXtcFile.py::TestXtcFile::test_xtc_triclinic PASSED [100%] 7531s 7531s =============================== warnings summary =============================== 7531s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes 7531s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 7531s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 7531s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model GBn 7531s warnings.warn( 7531s 7531s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent 7531s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters 7531s /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:1168: UserWarning: Non-optimal GB parameters detected for GB model HCT 7531s warnings.warn( 7531s 7531s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 7531s === 278 passed, 21 skipped, 28 deselected, 5 warnings in 6897.70s (1:54:57) ==== 7540s ============================= test session starts ============================== 7540s platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0 -- /usr/bin/python3.13 7540s cachedir: .pytest_cache 7540s rootdir: /tmp/autopkgtest.Ym6bjl/build.fRO/src/wrappers/python/tests 7540s configfile: pytest.ini 7540s plugins: typeguard-4.4.4 7548s collecting ... collected 327 items / 28 deselected / 299 selected 7548s 7548s TestAPIUnits.py::TestAPIUnits::testAmoebaMultipoleForce PASSED [ 0%] 7548s TestAPIUnits.py::TestAPIUnits::testAmoebaTorsionTorsionForce PASSED [ 0%] 7548s TestAPIUnits.py::TestAPIUnits::testAmoebaVdwForce PASSED [ 1%] 7548s TestAPIUnits.py::TestAPIUnits::testAmoebaWcaDispersionForce PASSED [ 1%] 7548s TestAPIUnits.py::TestAPIUnits::testAndersenThermostat PASSED [ 1%] 7548s TestAPIUnits.py::TestAPIUnits::testBrownianIntegrator PASSED [ 2%] 7548s TestAPIUnits.py::TestAPIUnits::testCmapForce PASSED [ 2%] 7548s TestAPIUnits.py::TestAPIUnits::testCustomAngleForce PASSED [ 2%] 7548s TestAPIUnits.py::TestAPIUnits::testCustomBondForce PASSED [ 3%] 7548s TestAPIUnits.py::TestAPIUnits::testCustomCompoundBondForce PASSED [ 3%] 7548s TestAPIUnits.py::TestAPIUnits::testCustomExternalForce PASSED [ 3%] 7548s TestAPIUnits.py::TestAPIUnits::testCustomGBForce PASSED [ 4%] 7548s TestAPIUnits.py::TestAPIUnits::testCustomHBondForce PASSED [ 4%] 7548s TestAPIUnits.py::TestAPIUnits::testCustomIntegrator PASSED [ 4%] 7548s TestAPIUnits.py::TestAPIUnits::testCustomManyParticleForce PASSED [ 5%] 7548s TestAPIUnits.py::TestAPIUnits::testCustomNonbondedForce PASSED [ 5%] 7548s TestAPIUnits.py::TestAPIUnits::testCustomTorsionForce PASSED [ 5%] 7548s TestAPIUnits.py::TestAPIUnits::testDrudeForce PASSED [ 6%] 7548s TestAPIUnits.py::TestAPIUnits::testDrudeLangevinIntegrator PASSED [ 6%] 7548s TestAPIUnits.py::TestAPIUnits::testDrudeNoseHooverIntegrator PASSED [ 6%] 7548s TestAPIUnits.py::TestAPIUnits::testDrudeSCFIntegrator PASSED [ 7%] 7548s TestAPIUnits.py::TestAPIUnits::testGeneralizedKirkwood PASSED [ 7%] 7548s TestAPIUnits.py::TestAPIUnits::testHarmonicAngleForce PASSED [ 7%] 7548s TestAPIUnits.py::TestAPIUnits::testHarmonicBondForce PASSED [ 8%] 7548s TestAPIUnits.py::TestAPIUnits::testLangevinIntegrator PASSED [ 8%] 7548s TestAPIUnits.py::TestAPIUnits::testMonteCarloMembraneBarostat PASSED [ 8%] 7548s TestAPIUnits.py::TestAPIUnits::testNonbondedForce PASSED [ 9%] 7548s TestAPIUnits.py::TestAPIUnits::testNoseHooverIntegrator PASSED [ 9%] 7548s TestAPIUnits.py::TestAPIUnits::testPeriodicTorsionForce PASSED [ 9%] 7548s TestAPIUnits.py::TestAPIUnits::testRBTorsionForce PASSED [ 10%] 7548s TestAPIUnits.py::TestAPIUnits::testVariableLangevinIntegrator PASSED [ 10%] 7548s TestAPIUnits.py::TestAPIUnits::testVariableVerletIntegrator PASSED [ 10%] 7548s TestAPIUnits.py::TestAPIUnits::testVerletIntegrator PASSED [ 11%] 7548s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_CrdBox PASSED [ 11%] 7548s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_CrdBoxTruncoct PASSED [ 11%] 7548s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_CrdOnly PASSED [ 12%] 7548s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_CrdVel PASSED [ 12%] 7548s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_CrdVelBox PASSED [ 12%] 7548s TestAmberInpcrdFile.py::TestAmberInpcrdFile::test_NetCDF SKIPPED (Sc...) [ 13%] 7558s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testAmberCMAP PASSED [ 13%] 7577s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testChamber PASSED [ 13%] 7577s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testEPConstraints PASSED [ 14%] 7577s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testGBneckRadii PASSED [ 14%] 7590s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testNucleicGBParametes PASSED [ 14%] 7591s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testSwitchFunction PASSED [ 15%] 7593s TestAmberPrmtopFile.py::TestAmberPrmtopFile::testWaterBonds PASSED [ 15%] 7593s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_Cutoff PASSED [ 15%] 7594s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_EwaldErrorTolerance PASSED [ 16%] 7596s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_HAngle PASSED [ 16%] 7597s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_HydrogenMass PASSED [ 16%] 7597s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolvent PASSED [ 17%] 7597s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventParameters PASSED [ 17%] 7597s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_ImplicitSolventZeroSA PASSED [ 17%] 7599s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_LJ1264 PASSED [ 18%] 7599s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_NonbondedMethod PASSED [ 18%] 7600s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_RemoveCMMotion PASSED [ 18%] 7605s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_RigidWaterAndConstraints PASSED [ 19%] 7606s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_triclinicParm PASSED [ 19%] 7649s TestAmberPrmtopFile.py::TestAmberPrmtopFile::test_with_dcd_reporter PASSED [ 19%] 7649s TestBytes.py::TestBytes::test_createCheckpoint PASSED [ 20%] 7651s TestCharmmFiles.py::TestCharmmFiles::testSystemOptions PASSED [ 20%] 7651s TestCharmmFiles.py::TestCharmmFiles::test_Constraints PASSED [ 20%] 7651s TestCharmmFiles.py::TestCharmmFiles::test_Cutoff PASSED [ 21%] 7651s TestCharmmFiles.py::TestCharmmFiles::test_Drude SKIPPED (Skipping te...) [ 21%] 7657s TestCharmmFiles.py::TestCharmmFiles::test_DrudeMass PASSED [ 21%] 7657s TestCharmmFiles.py::TestCharmmFiles::test_HydrogenMass PASSED [ 22%] 7657s TestCharmmFiles.py::TestCharmmFiles::test_ImplicitSolvent PASSED [ 22%] 7657s TestCharmmFiles.py::TestCharmmFiles::test_ImplicitSolventParameters PASSED [ 22%] 7657s TestCharmmFiles.py::TestCharmmFiles::test_Impropers PASSED [ 23%] 7681s TestCharmmFiles.py::TestCharmmFiles::test_InsCode PASSED [ 23%] 7681s TestCharmmFiles.py::TestCharmmFiles::test_Lonepair PASSED [ 23%] 7681s TestCharmmFiles.py::TestCharmmFiles::test_NBThole SKIPPED (Skipping ...) [ 24%] 7682s TestCharmmFiles.py::TestCharmmFiles::test_NBXMod PASSED [ 24%] 7683s TestCharmmFiles.py::TestCharmmFiles::test_NoLongRangeCorrection PASSED [ 24%] 7684s TestCharmmFiles.py::TestCharmmFiles::test_NoPsfWarning PASSED [ 25%] 7685s TestCharmmFiles.py::TestCharmmFiles::test_NonbondedMethod PASSED [ 25%] 7685s TestCharmmFiles.py::TestCharmmFiles::test_Nonbonded_Exclusion PASSED [ 25%] 7686s TestCharmmFiles.py::TestCharmmFiles::test_PSFSetUnitCellDimensions PASSED [ 26%] 7728s TestCharmmFiles.py::TestCharmmFiles::test_PermissiveRead PASSED [ 26%] 7729s TestCharmmFiles.py::TestCharmmFiles::test_RemoveCMMotion PASSED [ 26%] 7729s TestCharmmFiles.py::TestCharmmFiles::test_Residues PASSED [ 27%] 7732s TestDcdFile.py::TestDCDFile::testAppend PASSED [ 27%] 7732s TestDcdFile.py::TestDCDFile::testLongTrajectory PASSED [ 27%] 7732s TestDcdFile.py::TestDCDFile::test_dcd PASSED [ 28%] 7737s TestDesmondDMSFile.py::TestDesmondDMSFile::test_Cutoff PASSED [ 28%] 7740s TestDesmondDMSFile.py::TestDesmondDMSFile::test_EwaldErrorTolerance PASSED [ 28%] 7742s TestDesmondDMSFile.py::TestDesmondDMSFile::test_HydrogenMass PASSED [ 29%] 7747s TestDesmondDMSFile.py::TestDesmondDMSFile::test_NonbondedMethod PASSED [ 29%] 7747s TestDesmondDMSFile.py::TestDesmondDMSFile::test_OPLS1 PASSED [ 29%] 7748s TestDesmondDMSFile.py::TestDesmondDMSFile::test_OPLS2 PASSED [ 30%] 7750s TestDesmondDMSFile.py::TestDesmondDMSFile::test_RemoveCMMotion PASSED [ 30%] 7750s TestElement.py::TestElement::test_attributes PASSED [ 30%] 7754s TestElement.py::TestElement::test_getByMass PASSED [ 31%] 7754s TestElement.py::TestElement::test_immutable PASSED [ 31%] 7754s TestElement.py::TestElement::test_pickleable PASSED [ 31%] 7754s TestForceField.py::TestForceField::test_CharmmPolar SKIPPED (Skippin...) [ 32%] 7756s TestForceField.py::TestForceField::test_CustomNonbondedGenerator PASSED [ 32%] 7759s TestForceField.py::TestForceField::test_Cutoff PASSED [ 32%] 7764s TestForceField.py::TestForceField::test_DrudeMass PASSED [ 33%] 7770s TestForceField.py::TestForceField::test_Glycam PASSED [ 33%] 7775s TestForceField.py::TestForceField::test_HydrogenMass PASSED [ 33%] 7776s TestForceField.py::TestForceField::test_IgnoreExternalBonds PASSED [ 34%] 7778s TestForceField.py::TestForceField::test_ImplicitSolvent PASSED [ 34%] 7779s TestForceField.py::TestForceField::test_ImplicitSolventParameters PASSED [ 34%] 7783s TestForceField.py::TestForceField::test_ImpropersOrdering PASSED [ 35%] 7784s TestForceField.py::TestForceField::test_ImpropersOrdering_smirnoff PASSED [ 35%] 7788s TestForceField.py::TestForceField::test_Includes PASSED [ 35%] 7789s TestForceField.py::TestForceField::test_InitializationScript PASSED [ 36%] 7791s TestForceField.py::TestForceField::test_MultipleFilesandForceTags PASSED [ 36%] 7796s TestForceField.py::TestForceField::test_NonbondedMethod PASSED [ 36%] 7797s TestForceField.py::TestForceField::test_Opc3Energy PASSED [ 37%] 7800s TestForceField.py::TestForceField::test_OpcEnergy PASSED [ 37%] 7802s TestForceField.py::TestForceField::test_PeriodicBoxVectors PASSED [ 37%] 7804s TestForceField.py::TestForceField::test_RemoveCMMotion PASSED [ 38%] 7811s TestForceField.py::TestForceField::test_ResidueAttributes PASSED [ 38%] 7812s TestForceField.py::TestForceField::test_ResidueOverriding PASSED [ 38%] 7814s TestForceField.py::TestForceField::test_ResidueTemplateUserChoice PASSED [ 39%] 7829s TestForceField.py::TestForceField::test_RigidWaterAndConstraints PASSED [ 39%] 7832s TestForceField.py::TestForceField::test_ScalingFactorCombining PASSED [ 39%] 7834s TestForceField.py::TestForceField::test_SwitchingDistance PASSED [ 40%] 7837s TestForceField.py::TestForceField::test_UnusedArgs PASSED [ 40%] 7838s TestForceField.py::TestForceField::test_Wildcard PASSED [ 40%] 7846s TestForceField.py::TestForceField::test_flexibleConstraints PASSED [ 41%] 7853s TestForceField.py::TestForceField::test_generateTemplatesForUnmatchedResidues PASSED [ 41%] 7856s TestForceField.py::TestForceField::test_getMatchingTemplates PASSED [ 41%] 7859s TestForceField.py::TestForceField::test_getUnmatchedResidues PASSED [ 42%] 7863s TestForceField.py::TestForceField::test_residueMatcher PASSED [ 42%] 7872s TestForceField.py::TestForceField::test_residueTemplateGenerator PASSED [ 42%] 7872s TestForceField.py::AmoebaTestForceField::test_Amoeba18BPTI SKIPPED (...) [ 43%] 7872s TestForceField.py::AmoebaTestForceField::test_Amoeba18Nucleic SKIPPED [ 43%] 7873s TestForceField.py::AmoebaTestForceField::test_Cutoff PASSED [ 43%] 7873s TestForceField.py::AmoebaTestForceField::test_NonbondedMethod PASSED [ 44%] 7875s TestForceField.py::AmoebaTestForceField::test_RigidWater PASSED [ 44%] 7875s TestForceGroups.py::TestForceGroups::test1 PASSED [ 44%] 7875s TestForceGroups.py::TestForceGroups::test2 PASSED [ 45%] 7875s TestForceGroups.py::TestForceGroups::test3 PASSED [ 45%] 7878s TestGenerators.py::TestGenerators::test_CustomHbondGenerator PASSED [ 45%] 7878s TestGenerators.py::TestGenerators::test_CustomHbondGenerator2 PASSED [ 46%] 7878s TestGromacsGroFile.py::TestGromacsGroFile::test_Triclinic PASSED [ 46%] 7878s TestGromacsTopFile.py::TestGromacsTopFile::test_Cutoff SKIPPED (GROM...) [ 46%] 7878s TestGromacsTopFile.py::TestGromacsTopFile::test_EwaldErrorTolerance SKIPPED [ 47%] 7878s TestGromacsTopFile.py::TestGromacsTopFile::test_GROMOS SKIPPED (GROM...) [ 47%] 7878s TestGromacsTopFile.py::TestGromacsTopFile::test_HydrogenMass SKIPPED [ 47%] 7878s TestGromacsTopFile.py::TestGromacsTopFile::test_NonbondedMethod SKIPPED [ 48%] 7878s TestGromacsTopFile.py::TestGromacsTopFile::test_RemoveCMMotion SKIPPED [ 48%] 7878s TestGromacsTopFile.py::TestGromacsTopFile::test_RigidWaterAndConstraints SKIPPED [ 48%] 7878s TestGromacsTopFile.py::TestGromacsTopFile::test_SMOG SKIPPED (GROMAC...) [ 49%] 7878s TestGromacsTopFile.py::TestGromacsTopFile::test_SwitchingFunction SKIPPED [ 49%] 7878s TestGromacsTopFile.py::TestGromacsTopFile::test_VirtualParticle SKIPPED [ 49%] 7878s TestGromacsTopFile.py::TestGromacsTopFile::test_Vsite3 SKIPPED (GROM...) [ 50%] 7878s TestGromacsTopFile.py::TestGromacsTopFile::test_ff99SBILDN SKIPPED (...) [ 50%] 7878s TestGromacsTopFile.py::TestGromacsTopFile::test_ionic SKIPPED (GROMA...) [ 50%] 7879s TestIntegrators.py::TestIntegrators::testBadGroups PASSED [ 51%] 7879s TestIntegrators.py::TestIntegrators::testDrudeNoseHooverIntegrator SKIPPED [ 51%] 7884s TestIntegrators.py::TestIntegrators::testMTSIntegratorConstraints PASSED [ 51%] 7962s TestIntegrators.py::TestIntegrators::testMTSIntegratorExplicit PASSED [ 52%] 10621s TestIntegrators.py::TestIntegrators::testMTSLangevinIntegrator autopkgtest [16:42:39]: ERROR: timed out on command "su -s /bin/bash ubuntu -c set -e; exec /tmp/autopkgtest.Ym6bjl/wrapper.sh --artifacts=/tmp/autopkgtest.Ym6bjl/test-python-artifacts --chdir=/tmp/autopkgtest.Ym6bjl/build.fRO/src --env=AUTOPKGTEST_TESTBED_ARCH=s390x --env=AUTOPKGTEST_TEST_ARCH=s390x --env=DEB_BUILD_OPTIONS=parallel=2 --env=DEBIAN_FRONTEND=noninteractive --env=LANG=C.UTF-8 --unset-env=LANGUAGE --unset-env=LC_ADDRESS --unset-env=LC_ALL --unset-env=LC_COLLATE --unset-env=LC_CTYPE --unset-env=LC_IDENTIFICATION --unset-env=LC_MEASUREMENT --unset-env=LC_MESSAGES --unset-env=LC_MONETARY --unset-env=LC_NAME --unset-env=LC_NUMERIC --unset-env=LC_PAPER --unset-env=LC_TELEPHONE --unset-env=LC_TIME --script-pid-file=/tmp/autopkgtest_script_pid --source-profile --stderr=/tmp/autopkgtest.Ym6bjl/test-python-stderr --stdout=/tmp/autopkgtest.Ym6bjl/test-python-stdout --tmp=/tmp/autopkgtest.Ym6bjl/autopkgtest_tmp --env=ADT_TEST_TRIGGERS=glibc/2.42-2ubuntu5 --make-executable=/tmp/autopkgtest.Ym6bjl/build.fRO/src/debian/tests/test-python -- /tmp/autopkgtest.Ym6bjl/build.fRO/src/debian/tests/test-python" (kind: test) 10621s autopkgtest [16:42:39]: test test-python: -----------------------] 10624s test-python FAIL timed out 10624s autopkgtest [16:42:42]: test test-python: - - - - - - - - - - results - - - - - - - - - - 10626s autopkgtest [16:42:43]: @@@@@@@@@@@@@@@@@@@@ summary 10626s test-python FAIL timed out