0s autopkgtest [10:24:39]: starting date and time: 2025-04-14 10:24:39+0000 0s autopkgtest [10:24:39]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [10:24:39]: host juju-7f2275-prod-proposed-migration-environment-20; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.1eg04fij/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-20@bos03-ppc64el-3.secgroup --name adt-plucky-ppc64el-tm-align-20250414-092728-juju-7f2275-prod-proposed-migration-environment-20-0a319856-aa68-4943-8212-109e3bcac0a4 --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-20 --net-id=net_prod-proposed-migration-ppc64el -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 62s autopkgtest [10:25:41]: testbed dpkg architecture: ppc64el 62s autopkgtest [10:25:41]: testbed apt version: 3.0.0 62s autopkgtest [10:25:41]: @@@@@@@@@@@@@@@@@@@@ test bed setup 62s autopkgtest [10:25:41]: testbed release detected to be: None 63s autopkgtest [10:25:42]: updating testbed package index (apt update) 63s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [265 kB] 64s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 64s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 64s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 64s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [9948 B] 64s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [5192 B] 64s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [204 kB] 64s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [3476 B] 64s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el c-n-f Metadata [288 B] 64s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted ppc64el c-n-f Metadata [120 B] 64s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [120 kB] 64s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el c-n-f Metadata [8688 B] 64s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [2008 B] 64s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el c-n-f Metadata [172 B] 65s Fetched 619 kB in 1s (832 kB/s) 66s Reading package lists... 67s autopkgtest [10:25:46]: upgrading testbed (apt dist-upgrade and autopurge) 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 68s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 68s Starting 2 pkgProblemResolver with broken count: 0 68s Done 68s Entering ResolveByKeep 69s 69s Calculating upgrade... 69s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 69s Reading package lists... 69s Building dependency tree... 69s Reading state information... 70s Starting pkgProblemResolver with broken count: 0 70s Starting 2 pkgProblemResolver with broken count: 0 70s Done 70s Solving dependencies... 70s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 72s autopkgtest [10:25:51]: testbed running kernel: Linux 6.14.0-15-generic #15-Ubuntu SMP Sun Apr 6 14:52:42 UTC 2025 73s autopkgtest [10:25:52]: @@@@@@@@@@@@@@@@@@@@ apt-source tm-align 74s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (dsc) [2077 B] 74s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (tar) [52.8 kB] 74s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe tm-align 20190822+dfsg-3 (diff) [818 kB] 75s gpgv: Signature made Mon Sep 16 11:21:36 2024 UTC 75s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 75s gpgv: issuer "tille@debian.org" 75s gpgv: Can't check signature: No public key 75s dpkg-source: warning: cannot verify inline signature for ./tm-align_20190822+dfsg-3.dsc: no acceptable signature found 75s autopkgtest [10:25:54]: testing package tm-align version 20190822+dfsg-3 75s autopkgtest [10:25:54]: build not needed 76s autopkgtest [10:25:55]: test run-unit-test: preparing testbed 76s Reading package lists... 76s Building dependency tree... 76s Reading state information... 76s Starting pkgProblemResolver with broken count: 0 76s Starting 2 pkgProblemResolver with broken count: 0 76s Done 77s The following NEW packages will be installed: 77s libgfortran5 tm-align 77s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 77s Need to get 1508 kB of archives. 77s After this operation, 4036 kB of additional disk space will be used. 77s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 15-20250404-0ubuntu1 [615 kB] 77s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el tm-align ppc64el 20190822+dfsg-3 [893 kB] 78s Fetched 1508 kB in 1s (2429 kB/s) 78s Selecting previously unselected package libgfortran5:ppc64el. 78s (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 ... 107206 files and directories currently installed.) 78s Preparing to unpack .../libgfortran5_15-20250404-0ubuntu1_ppc64el.deb ... 78s Unpacking libgfortran5:ppc64el (15-20250404-0ubuntu1) ... 78s Selecting previously unselected package tm-align. 78s Preparing to unpack .../tm-align_20190822+dfsg-3_ppc64el.deb ... 78s Unpacking tm-align (20190822+dfsg-3) ... 78s Setting up libgfortran5:ppc64el (15-20250404-0ubuntu1) ... 78s Setting up tm-align (20190822+dfsg-3) ... 78s Processing triggers for libc-bin (2.41-6ubuntu1) ... 78s Processing triggers for man-db (2.13.0-1) ... 79s autopkgtest [10:25:58]: test run-unit-test: [----------------------- 80s Run TMalign... 80s 80s ************************************************************************** 80s * TM-align (Version 20190822) * 80s * An algorithm for protein structure alignment and comparison * 80s * Based on statistics: * 80s * 0.0 < TM-score < 0.30, random structural similarity * 80s * 0.5 < TM-score < 1.00, in about the same fold * 80s * Reference: Y Zhang and J Skolnick, Nucl Acids Res 33, 2302-9 (2005) * 80s * Please email your comments and suggestions to: zhng@umich.edu * 80s ************************************************************************** 80s 80s Name of Chain_1: 1ni7.pdb 80s Name of Chain_2: 5eep.pdb 80s Length of Chain_1: 149 residues 80s Length of Chain_2: 140 residues 80s 80s Aligned length= 140, RMSD= 1.60, Seq_ID=n_identical/n_aligned= 0.986 80s TM-score= 0.85044 (if normalized by length of Chain_1) 80s TM-score= 0.90009 (if normalized by length of Chain_2) 80s (You should use TM-score normalized by length of the reference protein) 80s 80s (":" denotes aligned residue pairs of d < 5.0 A, "." denotes other aligned residues) 80s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 80s : ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 80s ------G-HPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 80s 80s Run TMscore... 80s Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 80s 80s ***************************************************************************** 80s * TM-SCORE * 80s * A scoring function to assess the similarity of protein structures * 80s * Based on statistics: * 80s * 0.0 < TM-score < 0.17, random structural similarity * 80s * 0.5 < TM-score < 1.00, in about the same fold * 80s * Reference: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710 * 80s * For comments, please email to: zhng@umich.edu * 80s ***************************************************************************** 80s 80s Structure1: 1ni7.pdb Length= 149 80s Structure2: 5eep.pdb Length= 140 (by which all scores are normalized) 80s Number of residues in common= 140 80s RMSD of the common residues= 1.616 80s 80s TM-score = 0.8987 (d0= 4.40) 80s MaxSub-score= 0.8459 (d0= 3.50) 80s GDT-TS-score= 0.8321 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 %(d<8)=1.0000 80s GDT-HA-score= 0.6214 %(d<0.5)=0.1571 %(d<1)=0.4786 %(d<2)=0.8571 %(d<4)=0.9929 80s 80s -------- rotation matrix to rotate Chain-1 to Chain-2 ------ 80s i t(i) u(i,1) u(i,2) u(i,3) 80s 1 0.9977278941 -0.2584957318 -0.9156232244 -0.3079189302 80s 2 13.5083713477 -0.8848339137 0.0965207762 0.4557989522 80s 3 45.5856492856 -0.3876195322 0.3902791958 -0.8351246898 80s 80s Superposition in the TM-score: Length(d<5.0)=140 RMSD= 1.62 80s (":" denotes the residue pairs of distance < 5.0 Angstrom) 80s MTNPQFAGHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAATKQVLE 80s :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: 80s -------GHPFGTTVTAETLRNTFAPLTQWEDKYRQLIMLGKQLPALPDELKAQAKEIAGCENRVWLGYTVAENGKMHFFGDSEGRIVRGLLAVLLTAVEGKTAAELQAQSPLALFDELGLRAQLSASRSQGLNALSEAIIAAAKQV-- 80s 12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890123456789 80s 80s autopkgtest [10:25:59]: test run-unit-test: -----------------------] 81s run-unit-test FAIL stderr: Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 81s autopkgtest [10:26:00]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 81s autopkgtest [10:26:00]: test run-unit-test: - - - - - - - - - - stderr - - - - - - - - - - 81s Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 81s autopkgtest [10:26:00]: @@@@@@@@@@@@@@@@@@@@ summary 81s run-unit-test FAIL stderr: Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG 86s nova [W] Using flock in prodstack6-ppc64el 86s Creating nova instance adt-plucky-ppc64el-tm-align-20250414-092728-juju-7f2275-prod-proposed-migration-environment-20-0a319856-aa68-4943-8212-109e3bcac0a4 from image adt/ubuntu-plucky-ppc64el-server-20250414.img (UUID 643589a2-ed02-4b24-8397-93850cd38c96)... 86s nova [W] Timed out waiting for 06a2a942-65b5-4c49-8ecc-a84a07041fb8 to get deleted.