0s autopkgtest [22:25:19]: starting date and time: 2025-03-25 22:25:19+0000 0s autopkgtest [22:25:19]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [22:25:19]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.3w12f_5i/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-2@bos03-ppc64el-20.secgroup --name adt-plucky-ppc64el-tm-align-20250325-220802-juju-7f2275-prod-proposed-migration-environment-2-c5bbb970-c2ce-49d8-a221-94409c682ecc --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 77s autopkgtest [22:26:36]: testbed dpkg architecture: ppc64el 78s autopkgtest [22:26:37]: testbed apt version: 2.9.34 78s autopkgtest [22:26:37]: @@@@@@@@@@@@@@@@@@@@ test bed setup 78s autopkgtest [22:26:37]: testbed release detected to be: None 79s autopkgtest [22:26:38]: updating testbed package index (apt update) 79s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 80s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 80s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 80s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 80s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [28.1 kB] 80s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [262 kB] 80s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [10.9 kB] 80s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [1232 B] 80s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [66.2 kB] 80s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el c-n-f Metadata [616 B] 80s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/restricted ppc64el c-n-f Metadata [120 B] 80s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [169 kB] 80s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el c-n-f Metadata [10.2 kB] 80s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [2660 B] 80s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el c-n-f Metadata [172 B] 82s Fetched 677 kB in 1s (828 kB/s) 83s Reading package lists... 83s autopkgtest [22:26:42]: upgrading testbed (apt dist-upgrade and autopurge) 84s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 84s Starting 2 pkgProblemResolver with broken count: 0 84s Done 85s Entering ResolveByKeep 85s 85s Calculating upgrade... 86s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 86s Reading package lists... 86s Building dependency tree... 86s Reading state information... 86s Starting pkgProblemResolver with broken count: 0 87s Starting 2 pkgProblemResolver with broken count: 0 87s Done 87s Solving dependencies... 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 90s autopkgtest [22:26:49]: testbed running kernel: Linux 6.14.0-11-generic #11-Ubuntu SMP Mon Mar 17 12:33:11 UTC 2025 90s autopkgtest [22:26:49]: @@@@@@@@@@@@@@@@@@@@ apt-source tm-align 92s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (dsc) [2077 B] 92s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (tar) [52.8 kB] 92s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (diff) [818 kB] 92s gpgv: Signature made Mon Sep 16 11:21:36 2024 UTC 92s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 92s gpgv: issuer "tille@debian.org" 92s gpgv: Can't check signature: No public key 92s dpkg-source: warning: cannot verify inline signature for ./tm-align_20190822+dfsg-3.dsc: no acceptable signature found 92s autopkgtest [22:26:51]: testing package tm-align version 20190822+dfsg-3 93s autopkgtest [22:26:52]: build not needed 93s autopkgtest [22:26:52]: test run-unit-test: preparing testbed 94s Reading package lists... 94s Building dependency tree... 94s Reading state information... 94s Starting pkgProblemResolver with broken count: 0 94s Starting 2 pkgProblemResolver with broken count: 0 94s Done 94s The following NEW packages will be installed: 94s libgfortran5 tm-align 95s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 95s Need to get 1507 kB of archives. 95s After this operation, 4036 kB of additional disk space will be used. 95s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 15-20250319-1ubuntu1 [614 kB] 95s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el tm-align ppc64el 20190822+dfsg-3 [893 kB] 95s Fetched 1507 kB in 1s (2358 kB/s) 96s Selecting previously unselected package libgfortran5:ppc64el. 96s (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 ... 107156 files and directories currently installed.) 96s Preparing to unpack .../libgfortran5_15-20250319-1ubuntu1_ppc64el.deb ... 96s Unpacking libgfortran5:ppc64el (15-20250319-1ubuntu1) ... 96s Selecting previously unselected package tm-align. 96s Preparing to unpack .../tm-align_20190822+dfsg-3_ppc64el.deb ... 96s Unpacking tm-align (20190822+dfsg-3) ... 96s Setting up libgfortran5:ppc64el (15-20250319-1ubuntu1) ... 96s Setting up tm-align (20190822+dfsg-3) ... 96s Processing triggers for libc-bin (2.41-6ubuntu1) ... 96s Processing triggers for man-db (2.13.0-1) ... 97s autopkgtest [22:26:56]: test run-unit-test: [----------------------- 98s Run TMalign... 98s 98s ************************************************************************** 98s * TM-align (Version 20190822) * 98s * An algorithm for protein structure alignment and comparison * 98s * Based on statistics: * 98s * 0.0 < TM-score < 0.30, random structural similarity * 98s * 0.5 < TM-score < 1.00, in about the same fold * 98s * Reference: Y Zhang and J Skolnick, Nucl Acids Res 33, 2302-9 (2005) * 98s * Please email your comments and suggestions to: zhng@umich.edu * 98s ************************************************************************** 98s 98s Name of Chain_1: 1ni7.pdb 98s Name of Chain_2: 5eep.pdb 98s Length of Chain_1: 149 residues 98s Length of Chain_2: 140 residues 98s 98s Aligned length= 140, RMSD= 1.60, Seq_ID=n_identical/n_aligned= 0.986 98s TM-score= 0.85044 (if normalized by length of Chain_1) 98s TM-score= 0.90009 (if normalized by length of Chain_2) 98s (You should use TM-score normalized by length of the reference protein) 98s 98s (":" denotes aligned residue pairs of d < 5.0 A, "." denotes other aligned residues) 98s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 98s : ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 98s ------G-HPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 98s 98s Run TMscore... 98s Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 98s 98s ***************************************************************************** 98s * TM-SCORE * 98s * A scoring function to assess the similarity of protein structures * 98s * Based on statistics: * 98s * 0.0 < TM-score < 0.17, random structural similarity * 98s * 0.5 < TM-score < 1.00, in about the same fold * 98s * Reference: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710 * 98s * For comments, please email to: zhng@umich.edu * 98s ***************************************************************************** 98s 98s Structure1: 1ni7.pdb Length= 149 98s Structure2: 5eep.pdb Length= 140 (by which all scores are normalized) 98s Number of residues in common= 140 98s RMSD of the common residues= 1.616 98s 98s TM-score = 0.8987 (d0= 4.40) 98s MaxSub-score= 0.8459 (d0= 3.50) 98s GDT-TS-score= 0.8321 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 %(d<8)=1.0000 98s GDT-HA-score= 0.6214 %(d<0.5)=0.1571 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 98s 98s -------- rotation matrix to rotate Chain-1 to Chain-2 ------ 98s i t(i) u(i,1) u(i,2) u(i,3) 98s 1 0.9977278941 -0.2584957318 -0.9156232244 -0.3079189302 98s 2 13.5083713477 -0.8848339137 0.0965207762 0.4557989522 98s 3 45.5856492856 -0.3876195322 0.3902791958 -0.8351246898 98s 98s Superposition in the TM-score: Length(d<5.0)=140 RMSD= 1.62 98s (":" denotes the residue pairs of distance < 5.0 Angstrom) 98s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 98s :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 98s -------GHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 98s 12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789 98s 98s autopkgtest [22:26:57]: test run-unit-test: -----------------------] 98s autopkgtest [22:26:57]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 98s run-unit-test FAIL stderr: Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 99s autopkgtest [22:26:58]: test run-unit-test: - - - - - - - - - - stderr - - - - - - - - - - 99s Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 99s autopkgtest [22:26:58]: @@@@@@@@@@@@@@@@@@@@ summary 99s run-unit-test FAIL stderr: Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 116s nova [W] Using flock in prodstack6-ppc64el 116s Creating nova instance adt-plucky-ppc64el-tm-align-20250325-220802-juju-7f2275-prod-proposed-migration-environment-2-c5bbb970-c2ce-49d8-a221-94409c682ecc from image adt/ubuntu-plucky-ppc64el-server-20250325.img (UUID f67a8b0d-e022-4e3c-aea9-7883e99ef9b4)... 116s nova [W] Timed out waiting for 5056fc84-3842-4381-b183-7ce37cfd472e to get deleted.