0s autopkgtest [14:54:30]: starting date and time: 2025-06-19 14:54:30+0000 0s autopkgtest [14:54:30]: git checkout: 9986aa8c Merge branch 'skia/fix_network_interface' into 'ubuntu/production' 0s autopkgtest [14:54:30]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._kakduw6/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:tm-align --apt-upgrade tm-align --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=tm-align/20190822+dfsg-3 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-cpu2-ram4-disk20-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-20@sto01-ppc64el-25.secgroup --name adt-questing-ppc64el-tm-align-20250619-145430-juju-7f2275-prod-proposed-migration-environment-20-25ed9f14-098f-46ac-a3ec-689bc5b46d60 --image adt/ubuntu-questing-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-autopkgtest-workers-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 117s autopkgtest [14:56:27]: testbed dpkg architecture: ppc64el 118s autopkgtest [14:56:28]: testbed apt version: 3.1.2 118s autopkgtest [14:56:28]: @@@@@@@@@@@@@@@@@@@@ test bed setup 118s autopkgtest [14:56:28]: testbed release detected to be: None 119s autopkgtest [14:56:29]: updating testbed package index (apt update) 119s Get:1 http://ftpmaster.internal/ubuntu questing-proposed InRelease [249 kB] 119s Hit:2 http://ftpmaster.internal/ubuntu questing InRelease 119s Hit:3 http://ftpmaster.internal/ubuntu questing-updates InRelease 119s Hit:4 http://ftpmaster.internal/ubuntu questing-security InRelease 119s Get:5 http://ftpmaster.internal/ubuntu questing-proposed/multiverse Sources [17.4 kB] 119s Get:6 http://ftpmaster.internal/ubuntu questing-proposed/restricted Sources [4716 B] 119s Get:7 http://ftpmaster.internal/ubuntu questing-proposed/universe Sources [426 kB] 119s Get:8 http://ftpmaster.internal/ubuntu questing-proposed/main Sources [38.3 kB] 119s Get:9 http://ftpmaster.internal/ubuntu questing-proposed/main ppc64el Packages [66.7 kB] 119s Get:10 http://ftpmaster.internal/ubuntu questing-proposed/restricted ppc64el Packages [724 B] 119s Get:11 http://ftpmaster.internal/ubuntu questing-proposed/universe ppc64el Packages [340 kB] 119s Get:12 http://ftpmaster.internal/ubuntu questing-proposed/multiverse ppc64el Packages [6448 B] 119s Fetched 1149 kB in 1s (2227 kB/s) 120s Reading package lists... 121s autopkgtest [14:56:31]: upgrading testbed (apt dist-upgrade and autopurge) 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Calculating upgrade... 121s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 121s Reading package lists... 121s Building dependency tree... 121s Reading state information... 121s Solving dependencies... 122s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 124s autopkgtest [14:56:34]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP Sun Apr 6 14:52:42 UTC 2025 124s autopkgtest [14:56:34]: @@@@@@@@@@@@@@@@@@@@ apt-source tm-align 125s Get:1 http://ftpmaster.internal/ubuntu questing-proposed/universe tm-align 20190822+dfsg-3 (dsc) [2077 B] 125s Get:2 http://ftpmaster.internal/ubuntu questing-proposed/universe tm-align 20190822+dfsg-3 (tar) [52.8 kB] 125s Get:3 http://ftpmaster.internal/ubuntu questing-proposed/universe tm-align 20190822+dfsg-3 (diff) [818 kB] 126s gpgv: Signature made Mon Sep 16 11:21:36 2024 UTC 126s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 126s gpgv: issuer "tille@debian.org" 126s gpgv: Can't check signature: No public key 126s dpkg-source: warning: cannot verify inline signature for ./tm-align_20190822+dfsg-3.dsc: no acceptable signature found 126s autopkgtest [14:56:36]: testing package tm-align version 20190822+dfsg-3 126s autopkgtest [14:56:36]: build not needed 126s autopkgtest [14:56:36]: test run-unit-test: preparing testbed 126s Reading package lists... 126s Building dependency tree... 126s Reading state information... 127s Solving dependencies... 127s The following NEW packages will be installed: 127s libgfortran5 tm-align 127s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 127s Need to get 1509 kB of archives. 127s After this operation, 4102 kB of additional disk space will be used. 127s Get:1 http://ftpmaster.internal/ubuntu questing/main ppc64el libgfortran5 ppc64el 15.1.0-5ubuntu1 [617 kB] 127s Get:2 http://ftpmaster.internal/ubuntu questing-proposed/universe ppc64el tm-align ppc64el 20190822+dfsg-3 [893 kB] 127s Fetched 1509 kB in 0s (4502 kB/s) 127s Selecting previously unselected package libgfortran5:ppc64el. 128s (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 ... 79652 files and directories currently installed.) 128s Preparing to unpack .../libgfortran5_15.1.0-5ubuntu1_ppc64el.deb ... 128s Unpacking libgfortran5:ppc64el (15.1.0-5ubuntu1) ... 128s Selecting previously unselected package tm-align. 128s Preparing to unpack .../tm-align_20190822+dfsg-3_ppc64el.deb ... 128s Unpacking tm-align (20190822+dfsg-3) ... 128s Setting up libgfortran5:ppc64el (15.1.0-5ubuntu1) ... 128s Setting up tm-align (20190822+dfsg-3) ... 128s Processing triggers for libc-bin (2.41-6ubuntu2) ... 128s Processing triggers for man-db (2.13.1-1) ... 129s autopkgtest [14:56:39]: test run-unit-test: [----------------------- 130s ************************************************************************** 130s # A new feature in cloud-init identified possible datasources for # 130s # this system as: # 130s # [] # 130s # However, the datasource used was: OpenStack # 130s # # 130s # In the future, cloud-init will only attempt to use datasources that # 130s # are identified or specifically configured. # 130s # For more information see # 130s # https://bugs.launchpad.net/bugs/1669675 # 130s # # 130s # If you are seeing this message, please file a bug against # 130s # cloud-init at # 130s # https://github.com/canonical/cloud-init/issues # 130s # Make sure to include the cloud provider your instance is # 130s # running on. # 130s # # 130s # After you have filed a bug, you can disable this warning by launching # 130s # your instance with the cloud-config below, or putting that content # 130s # into /etc/cloud/cloud.cfg.d/99-warnings.cfg # 130s # # 130s # #cloud-config # 130s # warnings: # 130s # dsid_missing_source: off # 130s ************************************************************************** 130s 130s Disable the warnings above by: 130s touch /home/ubuntu/.cloud-warnings.skip 130s or 130s touch /var/lib/cloud/instance/warnings/.skip 130s Run TMalign... 130s Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 130s 130s ************************************************************************** 130s * TM-align (Version 20190822) * 130s * An algorithm for protein structure alignment and comparison * 130s * Based on statistics: * 130s * 0.0 < TM-score < 0.30, random structural similarity * 130s * 0.5 < TM-score < 1.00, in about the same fold * 130s * Reference: Y Zhang and J Skolnick, Nucl Acids Res 33, 2302-9 (2005) * 130s * Please email your comments and suggestions to: zhng@umich.edu * 130s ************************************************************************** 130s 130s Name of Chain_1: 1ni7.pdb 130s Name of Chain_2: 5eep.pdb 130s Length of Chain_1: 149 residues 130s Length of Chain_2: 140 residues 130s 130s Aligned length= 140, RMSD= 1.60, Seq_ID=n_identical/n_aligned= 0.986 130s TM-score= 0.85044 (if normalized by length of Chain_1) 130s TM-score= 0.90009 (if normalized by length of Chain_2) 130s (You should use TM-score normalized by length of the reference protein) 130s 130s (":" denotes aligned residue pairs of d < 5.0 A, "." denotes other aligned residues) 130s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 130s : ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 130s ------G-HPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 130s 130s Run TMscore... 130s 130s ***************************************************************************** 130s * TM-SCORE * 130s * A scoring function to assess the similarity of protein structures * 130s * Based on statistics: * 130s * 0.0 < TM-score < 0.17, random structural similarity * 130s * 0.5 < TM-score < 1.00, in about the same fold * 130s * Reference: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710 * 130s * For comments, please email to: zhng@umich.edu * 130s ***************************************************************************** 130s 130s Structure1: 1ni7.pdb Length= 149 130s Structure2: 5eep.pdb Length= 140 (by which all scores are normalized) 130s Number of residues in common= 140 130s RMSD of the common residues= 1.616 130s 130s TM-score = 0.8987 (d0= 4.40) 130s MaxSub-score= 0.8459 (d0= 3.50) 130s GDT-TS-score= 0.8321 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 %(d<8)=1.0000 130s GDT-HA-score= 0.6214 %(d<0.5)=0.1571 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 130s 130s -------- rotation matrix to rotate Chain-1 to Chain-2 ------ 130s i t(i) u(i,1) u(i,2) u(i,3) 130s 1 0.9977278941 -0.2584957318 -0.9156232244 -0.3079189302 130s 2 13.5083713477 -0.8848339137 0.0965207762 0.4557989522 130s 3 45.5856492856 -0.3876195322 0.3902791958 -0.8351246898 130s 130s Superposition in the TM-score: Length(d<5.0)=140 RMSD= 1.62 130s (":" denotes the residue pairs of distance < 5.0 Angstrom) 130s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 130s :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 130s -------GHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 130s 12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789 130s 130s autopkgtest [14:56:40]: test run-unit-test: -----------------------] 130s run-unit-test FAIL stderr: Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 130s autopkgtest [14:56:40]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 131s autopkgtest [14:56:41]: test run-unit-test: - - - - - - - - - - stderr - - - - - - - - - - 131s Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 131s autopkgtest [14:56:41]: @@@@@@@@@@@@@@@@@@@@ summary 131s run-unit-test FAIL stderr: Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 135s nova [W] Using flock in prodstack7-ppc64el 135s flock: timeout while waiting to get lock 135s Creating nova instance adt-questing-ppc64el-tm-align-20250619-145430-juju-7f2275-prod-proposed-migration-environment-20-25ed9f14-098f-46ac-a3ec-689bc5b46d60 from image adt/ubuntu-questing-ppc64el-server-20250619.img (UUID 1c97422d-c646-492e-9581-3c98f213de4b)... 135s nova [W] Timed out waiting for 0c92b07b-4538-4220-a9d0-9d8e04d88535 to get deleted.