0s autopkgtest [23:23:06]: starting date and time: 2025-01-09 23:23:06+0000 0s autopkgtest [23:23:06]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [23:23:06]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.hnb_ragk/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-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-16.secgroup --name adt-plucky-ppc64el-tm-align-20250109-232306-juju-7f2275-prod-proposed-migration-environment-15-590de691-9c82-4aa8-bfd2-d798d23b807d --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 67s autopkgtest [23:24:13]: testbed dpkg architecture: ppc64el 67s autopkgtest [23:24:13]: testbed apt version: 2.9.18 68s autopkgtest [23:24:14]: @@@@@@@@@@@@@@@@@@@@ test bed setup 68s autopkgtest [23:24:14]: testbed release detected to be: None 69s autopkgtest [23:24:15]: updating testbed package index (apt update) 69s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 69s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 69s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 69s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 69s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [126 kB] 70s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.0 kB] 70s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [9708 B] 70s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [781 kB] 70s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [268 kB] 70s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted ppc64el Packages [756 B] 70s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [1002 kB] 70s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [5088 B] 70s Fetched 2281 kB in 1s (2056 kB/s) 71s Reading package lists... 72s Reading package lists... 72s Building dependency tree... 72s Reading state information... 72s Calculating upgrade... 72s The following packages will be upgraded: 72s firmware-sof-signed 72s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 72s Need to get 7093 kB of archives. 72s After this operation, 0 B of additional disk space will be used. 72s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el firmware-sof-signed all 2024.06-1ubuntu4 [7093 kB] 73s Fetched 7093 kB in 1s (8421 kB/s) 74s (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 ... 74025 files and directories currently installed.) 74s Preparing to unpack .../firmware-sof-signed_2024.06-1ubuntu4_all.deb ... 74s Unpacking firmware-sof-signed (2024.06-1ubuntu4) over (2024.06-1ubuntu3) ... 74s Setting up firmware-sof-signed (2024.06-1ubuntu4) ... 74s Reading package lists... 74s Building dependency tree... 74s Reading state information... 74s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 74s autopkgtest [23:24:20]: upgrading testbed (apt dist-upgrade and autopurge) 75s Reading package lists... 75s Building dependency tree... 75s Reading state information... 75s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 75s Starting 2 pkgProblemResolver with broken count: 0 75s Done 76s Entering ResolveByKeep 76s 76s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 76s Reading package lists... 76s Building dependency tree... 76s Reading state information... 77s Starting pkgProblemResolver with broken count: 0 77s Starting 2 pkgProblemResolver with broken count: 0 77s Done 77s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 80s autopkgtest [23:24:26]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024 80s autopkgtest [23:24:26]: @@@@@@@@@@@@@@@@@@@@ apt-source tm-align 82s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (dsc) [2077 B] 82s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (tar) [52.8 kB] 82s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (diff) [818 kB] 82s gpgv: Signature made Mon Sep 16 11:21:36 2024 UTC 82s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 82s gpgv: issuer "tille@debian.org" 82s gpgv: Can't check signature: No public key 82s dpkg-source: warning: cannot verify inline signature for ./tm-align_20190822+dfsg-3.dsc: no acceptable signature found 82s autopkgtest [23:24:28]: testing package tm-align version 20190822+dfsg-3 82s autopkgtest [23:24:28]: build not needed 83s autopkgtest [23:24:29]: test run-unit-test: preparing testbed 83s Reading package lists... 83s Building dependency tree... 83s Reading state information... 83s Starting pkgProblemResolver with broken count: 0 83s Starting 2 pkgProblemResolver with broken count: 0 83s Done 84s The following NEW packages will be installed: 84s libgfortran5 tm-align 84s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 84s Need to get 1464 kB of archives. 84s After this operation, 3633 kB of additional disk space will be used. 84s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-12ubuntu1 [571 kB] 84s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el tm-align ppc64el 20190822+dfsg-3 [893 kB] 84s Fetched 1464 kB in 1s (2377 kB/s) 85s Selecting previously unselected package libgfortran5:ppc64el. 85s (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 ... 74025 files and directories currently installed.) 85s Preparing to unpack .../libgfortran5_14.2.0-12ubuntu1_ppc64el.deb ... 85s Unpacking libgfortran5:ppc64el (14.2.0-12ubuntu1) ... 85s Selecting previously unselected package tm-align. 85s Preparing to unpack .../tm-align_20190822+dfsg-3_ppc64el.deb ... 85s Unpacking tm-align (20190822+dfsg-3) ... 85s Setting up libgfortran5:ppc64el (14.2.0-12ubuntu1) ... 85s Setting up tm-align (20190822+dfsg-3) ... 85s Processing triggers for libc-bin (2.40-4ubuntu1) ... 85s Processing triggers for man-db (2.13.0-1) ... 86s autopkgtest [23:24:32]: test run-unit-test: [----------------------- 86s Run TMalign... 86s 86s ************************************************************************** 86s * TM-align (Version 20190822) * 86s * An algorithm for protein structure alignment and comparison * 86s * Based on statistics: * 86s * 0.0 < TM-score < 0.30, random structural similarity * 86s * 0.5 < TM-score < 1.00, in about the same fold * 86s * Reference: Y Zhang and J Skolnick, Nucl Acids Res 33, 2302-9 (2005) * 86s * Please email your comments and suggestions to: zhng@umich.edu * 86s ************************************************************************** 86s 86s Name of Chain_1: 1ni7.pdb 86s Name of Chain_2: 5eep.pdb 86s Length of Chain_1: 149 residues 86s Length of Chain_2: 140 residues 86s 86s Aligned length= 140, RMSD= 1.60, Seq_ID=n_identical/n_aligned= 0.986 86s TM-score= 0.85044 (if normalized by length of Chain_1) 86s TM-score= 0.90009 (if normalized by length of Chain_2) 86s (You should use TM-score normalized by length of the reference protein) 86s 86s (":" denotes aligned residue pairs of d < 5.0 A, "." denotes other aligned residues) 86s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 86s : ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 86s ------G-HPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 86s 86s Run TMscore... 86s Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 86s 86s ***************************************************************************** 86s * TM-SCORE * 86s * A scoring function to assess the similarity of protein structures * 86s * Based on statistics: * 86s * 0.0 < TM-score < 0.17, random structural similarity * 86s * 0.5 < TM-score < 1.00, in about the same fold * 86s * Reference: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710 * 86s * For comments, please email to: zhng@umich.edu * 86s ***************************************************************************** 86s 86s Structure1: 1ni7.pdb Length= 149 86s Structure2: 5eep.pdb Length= 140 (by which all scores are normalized) 86s Number of residues in common= 140 86s RMSD of the common residues= 1.616 86s 86s TM-score = 0.8987 (d0= 4.40) 86s MaxSub-score= 0.8459 (d0= 3.50) 86s GDT-TS-score= 0.8321 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 %(d<8)=1.0000 86s GDT-HA-score= 0.6214 %(d<0.5)=0.1571 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 86s 86s -------- rotation matrix to rotate Chain-1 to Chain-2 ------ 86s i t(i) u(i,1) u(i,2) u(i,3) 86s 1 0.9977278941 -0.2584957318 -0.9156232244 -0.3079189302 86s 2 13.5083713477 -0.8848339137 0.0965207762 0.4557989522 86s 3 45.5856492856 -0.3876195322 0.3902791958 -0.8351246898 86s 86s Superposition in the TM-score: Length(d<5.0)=140 RMSD= 1.62 86s (":" denotes the residue pairs of distance < 5.0 Angstrom) 86s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 86s :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 86s -------GHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 86s 12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789 86s 87s autopkgtest [23:24:33]: test run-unit-test: -----------------------] 87s autopkgtest [23:24:33]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 87s run-unit-test FAIL stderr: Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 87s autopkgtest [23:24:33]: test run-unit-test: - - - - - - - - - - stderr - - - - - - - - - - 87s Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 88s autopkgtest [23:24:34]: @@@@@@@@@@@@@@@@@@@@ summary 88s run-unit-test FAIL stderr: Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 104s nova [W] Using flock in prodstack6-ppc64el 104s Creating nova instance adt-plucky-ppc64el-tm-align-20250109-232306-juju-7f2275-prod-proposed-migration-environment-15-590de691-9c82-4aa8-bfd2-d798d23b807d from image adt/ubuntu-plucky-ppc64el-server-20250109.img (UUID 64b5f774-d527-428e-8e51-6eba74faf5f9)... 104s nova [W] Timed out waiting for e6733ce7-c7a1-4f42-99d2-5f283f3551ec to get deleted.