0s autopkgtest [01:13:33]: starting date and time: 2024-03-19 01:13:33+0000 0s autopkgtest [01:13:33]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [01:13:33]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.ju9p682t/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:openmpi,src:ampliconnoise,src:eztrace,src:gatb-core,src:gyoto,src:murasaki,src:pmix --apt-upgrade phyml --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=openmpi/4.1.6-7ubuntu1 ampliconnoise/1.29-10build2 eztrace/2.1-6 gatb-core/1.4.2+dfsg-13build1 gyoto/2.0.2-1.1build2 murasaki/1.68.6-13build5 pmix/5.0.1-4.1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos01-ppc64el-2.secgroup --name adt-noble-ppc64el-phyml-20240319-011333-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -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,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 495s autopkgtest [01:21:48]: testbed dpkg architecture: ppc64el 495s autopkgtest [01:21:48]: testbed apt version: 2.7.12 495s autopkgtest [01:21:48]: @@@@@@@@@@@@@@@@@@@@ test bed setup 496s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 497s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 497s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3748 kB] 498s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 498s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.0 kB] 498s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [645 kB] 498s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 498s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 498s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 498s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [4015 kB] 499s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 499s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [47.3 kB] 499s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 502s Fetched 9129 kB in 3s (2847 kB/s) 502s Reading package lists... 505s Reading package lists... 505s Building dependency tree... 505s Reading state information... 506s Calculating upgrade... 506s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 506s Reading package lists... 506s Building dependency tree... 506s Reading state information... 507s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 507s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 507s Get:2 http://ftpmaster.internal/ubuntu noble InRelease [255 kB] 508s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 508s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 508s Get:5 http://ftpmaster.internal/ubuntu noble/multiverse Sources [295 kB] 508s Get:6 http://ftpmaster.internal/ubuntu noble/universe Sources [19.8 MB] 510s Get:7 http://ftpmaster.internal/ubuntu noble/main Sources [1377 kB] 510s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el Packages [1377 kB] 510s Get:9 http://ftpmaster.internal/ubuntu noble/universe ppc64el Packages [14.9 MB] 510s Get:10 http://ftpmaster.internal/ubuntu noble/multiverse ppc64el Packages [185 kB] 516s Fetched 38.3 MB in 8s (4518 kB/s) 517s Reading package lists... 517s Reading package lists... 517s Building dependency tree... 517s Reading state information... 518s Calculating upgrade... 518s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 518s Reading package lists... 518s Building dependency tree... 518s Reading state information... 519s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 521s autopkgtest [01:22:14]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 522s autopkgtest [01:22:15]: @@@@@@@@@@@@@@@@@@@@ apt-source phyml 524s Get:1 http://ftpmaster.internal/ubuntu noble/universe phyml 3:3.3.20220408-3 (dsc) [2258 B] 524s Get:2 http://ftpmaster.internal/ubuntu noble/universe phyml 3:3.3.20220408-3 (tar) [1804 kB] 524s Get:3 http://ftpmaster.internal/ubuntu noble/universe phyml 3:3.3.20220408-3 (diff) [26.9 kB] 524s gpgv: Signature made Wed Oct 26 18:18:47 2022 UTC 524s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 524s gpgv: issuer "emollier@debian.org" 524s gpgv: Can't check signature: No public key 524s dpkg-source: warning: cannot verify inline signature for ./phyml_3.3.20220408-3.dsc: no acceptable signature found 524s autopkgtest [01:22:17]: testing package phyml version 3:3.3.20220408-3 524s autopkgtest [01:22:17]: build not needed 525s autopkgtest [01:22:18]: test run-unit-test: preparing testbed 526s Reading package lists... 527s Building dependency tree... 527s Reading state information... 527s Starting pkgProblemResolver with broken count: 0 527s Starting 2 pkgProblemResolver with broken count: 0 527s Done 528s The following additional packages will be installed: 528s libamd-comgr2 libamdhip64-5 libdrm-amdgpu1 libevent-pthreads-2.1-7 528s libfabric1 libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 528s libllvm17 libmunge2 libopenmpi3t64 libpciaccess0 libpmix2t64 librdmacm1t64 528s libucx0 libxnvctrl0 ocl-icd-libopencl1 openmpi-bin openmpi-common phyml 528s Suggested packages: 528s opencl-icd gfortran | fortran-compiler 528s The following NEW packages will be installed: 528s autopkgtest-satdep libamd-comgr2 libamdhip64-5 libdrm-amdgpu1 528s libevent-pthreads-2.1-7 libfabric1 libhsa-runtime64-1 libhsakmt1 528s libhwloc-plugins libhwloc15 libllvm17 libmunge2 libopenmpi3t64 libpciaccess0 528s libpmix2t64 librdmacm1t64 libucx0 libxnvctrl0 ocl-icd-libopencl1 openmpi-bin 528s openmpi-common phyml 528s 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. 528s Need to get 55.3 MB/55.3 MB of archives. 528s After this operation, 257 MB of additional disk space will be used. 528s Get:1 /tmp/autopkgtest.TGIKov/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [708 B] 528s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libllvm17 ppc64el 1:17.0.6-5build1 [27.3 MB] 529s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libamd-comgr2 ppc64el 6.0+git20231212.4510c28+dfsg-3 [15.3 MB] 530s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libdrm-amdgpu1 ppc64el 2.4.120-2 [24.5 kB] 530s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhsakmt1 ppc64el 5.7.0-1 [76.5 kB] 530s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhsa-runtime64-1 ppc64el 5.7.1-1 [330 kB] 530s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el libamdhip64-5 ppc64el 5.2.3-12 [5004 kB] 530s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el libevent-pthreads-2.1-7 ppc64el 2.1.12-stable-9 [7844 B] 530s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el librdmacm1t64 ppc64el 50.0-2 [80.9 kB] 530s Get:10 http://ftpmaster.internal/ubuntu noble/universe ppc64el libfabric1 ppc64el 1.17.0-3 [677 kB] 530s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhwloc15 ppc64el 2.10.0-1 [216 kB] 530s Get:12 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmunge2 ppc64el 0.5.15-3ubuntu1 [17.6 kB] 530s Get:13 http://ftpmaster.internal/ubuntu noble/main ppc64el libpciaccess0 ppc64el 0.17-3 [20.8 kB] 530s Get:14 http://ftpmaster.internal/ubuntu noble/main ppc64el libxnvctrl0 ppc64el 510.47.03-0ubuntu1 [11.7 kB] 530s Get:15 http://ftpmaster.internal/ubuntu noble/universe ppc64el ocl-icd-libopencl1 ppc64el 2.3.2-1 [41.7 kB] 530s Get:16 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhwloc-plugins ppc64el 2.10.0-1 [17.3 kB] 530s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libpmix2t64 ppc64el 5.0.1-4.1 [765 kB] 530s Get:18 http://ftpmaster.internal/ubuntu noble/universe ppc64el libucx0 ppc64el 1.16.0+ds-4 [1203 kB] 530s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libopenmpi3t64 ppc64el 4.1.6-7ubuntu1 [2721 kB] 530s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el openmpi-common all 4.1.6-7ubuntu1 [170 kB] 530s Get:21 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el openmpi-bin ppc64el 4.1.6-7ubuntu1 [118 kB] 530s Get:22 http://ftpmaster.internal/ubuntu noble/universe ppc64el phyml ppc64el 3:3.3.20220408-3 [1199 kB] 531s Fetched 55.3 MB in 3s (21.1 MB/s) 531s Selecting previously unselected package libllvm17:ppc64el. 531s (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 ... 70095 files and directories currently installed.) 531s Preparing to unpack .../00-libllvm17_1%3a17.0.6-5build1_ppc64el.deb ... 531s Unpacking libllvm17:ppc64el (1:17.0.6-5build1) ... 532s Selecting previously unselected package libamd-comgr2:ppc64el. 532s Preparing to unpack .../01-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3_ppc64el.deb ... 532s Unpacking libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3) ... 532s Selecting previously unselected package libdrm-amdgpu1:ppc64el. 532s Preparing to unpack .../02-libdrm-amdgpu1_2.4.120-2_ppc64el.deb ... 532s Unpacking libdrm-amdgpu1:ppc64el (2.4.120-2) ... 532s Selecting previously unselected package libhsakmt1:ppc64el. 532s Preparing to unpack .../03-libhsakmt1_5.7.0-1_ppc64el.deb ... 532s Unpacking libhsakmt1:ppc64el (5.7.0-1) ... 532s Selecting previously unselected package libhsa-runtime64-1. 532s Preparing to unpack .../04-libhsa-runtime64-1_5.7.1-1_ppc64el.deb ... 532s Unpacking libhsa-runtime64-1 (5.7.1-1) ... 532s Selecting previously unselected package libamdhip64-5. 532s Preparing to unpack .../05-libamdhip64-5_5.2.3-12_ppc64el.deb ... 532s Unpacking libamdhip64-5 (5.2.3-12) ... 532s Selecting previously unselected package libevent-pthreads-2.1-7:ppc64el. 532s Preparing to unpack .../06-libevent-pthreads-2.1-7_2.1.12-stable-9_ppc64el.deb ... 532s Unpacking libevent-pthreads-2.1-7:ppc64el (2.1.12-stable-9) ... 532s Selecting previously unselected package librdmacm1t64:ppc64el. 532s Preparing to unpack .../07-librdmacm1t64_50.0-2_ppc64el.deb ... 532s Unpacking librdmacm1t64:ppc64el (50.0-2) ... 532s Selecting previously unselected package libfabric1:ppc64el. 532s Preparing to unpack .../08-libfabric1_1.17.0-3_ppc64el.deb ... 532s Unpacking libfabric1:ppc64el (1.17.0-3) ... 532s Selecting previously unselected package libhwloc15:ppc64el. 533s Preparing to unpack .../09-libhwloc15_2.10.0-1_ppc64el.deb ... 533s Unpacking libhwloc15:ppc64el (2.10.0-1) ... 533s Selecting previously unselected package libmunge2:ppc64el. 533s Preparing to unpack .../10-libmunge2_0.5.15-3ubuntu1_ppc64el.deb ... 533s Unpacking libmunge2:ppc64el (0.5.15-3ubuntu1) ... 533s Selecting previously unselected package libpciaccess0:ppc64el. 533s Preparing to unpack .../11-libpciaccess0_0.17-3_ppc64el.deb ... 533s Unpacking libpciaccess0:ppc64el (0.17-3) ... 533s Selecting previously unselected package libxnvctrl0:ppc64el. 533s Preparing to unpack .../12-libxnvctrl0_510.47.03-0ubuntu1_ppc64el.deb ... 533s Unpacking libxnvctrl0:ppc64el (510.47.03-0ubuntu1) ... 533s Selecting previously unselected package ocl-icd-libopencl1:ppc64el. 533s Preparing to unpack .../13-ocl-icd-libopencl1_2.3.2-1_ppc64el.deb ... 533s Unpacking ocl-icd-libopencl1:ppc64el (2.3.2-1) ... 533s Selecting previously unselected package libhwloc-plugins:ppc64el. 533s Preparing to unpack .../14-libhwloc-plugins_2.10.0-1_ppc64el.deb ... 533s Unpacking libhwloc-plugins:ppc64el (2.10.0-1) ... 533s Selecting previously unselected package libpmix2t64:ppc64el. 533s Preparing to unpack .../15-libpmix2t64_5.0.1-4.1_ppc64el.deb ... 533s Unpacking libpmix2t64:ppc64el (5.0.1-4.1) ... 533s Selecting previously unselected package libucx0:ppc64el. 533s Preparing to unpack .../16-libucx0_1.16.0+ds-4_ppc64el.deb ... 533s Unpacking libucx0:ppc64el (1.16.0+ds-4) ... 533s Selecting previously unselected package libopenmpi3t64:ppc64el. 533s Preparing to unpack .../17-libopenmpi3t64_4.1.6-7ubuntu1_ppc64el.deb ... 533s Unpacking libopenmpi3t64:ppc64el (4.1.6-7ubuntu1) ... 533s Selecting previously unselected package openmpi-common. 533s Preparing to unpack .../18-openmpi-common_4.1.6-7ubuntu1_all.deb ... 533s Unpacking openmpi-common (4.1.6-7ubuntu1) ... 533s Selecting previously unselected package openmpi-bin. 533s Preparing to unpack .../19-openmpi-bin_4.1.6-7ubuntu1_ppc64el.deb ... 533s Unpacking openmpi-bin (4.1.6-7ubuntu1) ... 533s Selecting previously unselected package phyml. 533s Preparing to unpack .../20-phyml_3%3a3.3.20220408-3_ppc64el.deb ... 533s Unpacking phyml (3:3.3.20220408-3) ... 533s Selecting previously unselected package autopkgtest-satdep. 533s Preparing to unpack .../21-1-autopkgtest-satdep.deb ... 533s Unpacking autopkgtest-satdep (0) ... 533s Setting up libpciaccess0:ppc64el (0.17-3) ... 533s Setting up libxnvctrl0:ppc64el (510.47.03-0ubuntu1) ... 533s Setting up libmunge2:ppc64el (0.5.15-3ubuntu1) ... 533s Setting up libhwloc15:ppc64el (2.10.0-1) ... 533s Setting up ocl-icd-libopencl1:ppc64el (2.3.2-1) ... 533s Setting up openmpi-common (4.1.6-7ubuntu1) ... 533s Setting up librdmacm1t64:ppc64el (50.0-2) ... 533s Setting up libllvm17:ppc64el (1:17.0.6-5build1) ... 533s Setting up libevent-pthreads-2.1-7:ppc64el (2.1.12-stable-9) ... 533s Setting up libdrm-amdgpu1:ppc64el (2.4.120-2) ... 533s Setting up libfabric1:ppc64el (1.17.0-3) ... 533s Setting up libhwloc-plugins:ppc64el (2.10.0-1) ... 533s Setting up libpmix2t64:ppc64el (5.0.1-4.1) ... 533s Setting up libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3) ... 533s Setting up libhsakmt1:ppc64el (5.7.0-1) ... 533s Setting up libhsa-runtime64-1 (5.7.1-1) ... 533s Setting up libamdhip64-5 (5.2.3-12) ... 533s Setting up libucx0:ppc64el (1.16.0+ds-4) ... 533s Setting up libopenmpi3t64:ppc64el (4.1.6-7ubuntu1) ... 533s Setting up openmpi-bin (4.1.6-7ubuntu1) ... 533s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 533s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 533s Setting up phyml (3:3.3.20220408-3) ... 533s Setting up autopkgtest-satdep (0) ... 533s Processing triggers for man-db (2.12.0-3) ... 534s Processing triggers for libc-bin (2.39-0ubuntu2) ... 537s (Reading database ... 70664 files and directories currently installed.) 537s Removing autopkgtest-satdep (0) ... 538s autopkgtest [01:22:31]: test run-unit-test: [----------------------- 538s DNA interleaved sequence file, default parameters single processor: 538s + export PHYMLCPUS=1 538s + PHYMLCPUS=1 538s + echo 'DNA interleaved sequence file, default parameters single processor:' 538s + /usr/bin/phyml -i nucleic 538s 538s 538s . Command line: /usr/lib/phyml/bin/phyml -i nucleic 538s 538s 538s 538s 538s 538s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 538s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 538s 538s . Sequence filename: nucleic 538s . Data type: dna 538s . Alphabet size: 4 538s . Sequence format: interleaved 538s . Number of data sets: 1 538s . Nb of bootstrapped data sets: 0 538s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 538s . Model name: HKY85 538s . Ts/tv ratio: estimated 538s . Proportion of invariable sites: 0.000000 538s . RAS model: discrete Gamma 538s . Number of subst. rate catgs: 4 538s . Gamma distribution parameter: estimated 538s . 'Middle' of each rate class: mean 538s . Nucleotide equilibrium frequencies: empirical 538s . Optimise tree topology: yes 538s . Starting tree: BioNJ 538s . Add random input tree: no 538s . Optimise branch lengths: yes 538s . Minimum length of an edge: 1e-08 538s . Optimise substitution model parameters: yes 538s . Run ID: none 538s . Random seed: 1710811351 538s . Subtree patterns aliasing: no 538s . Version: 3.3.3:3.3.20220408-3 538s . Byte alignment: 1 538s . AVX enabled: no 538s . SSE enabled: no 538s 538s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 538s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 538s 538s 538s 538s . 382 patterns found (out of a total of 886 sites). 538s 538s . 582 sites without polymorphism (65.69%). 538s 538s 538s . Computing pairwise distances... 538s 538s . Building BioNJ tree... 538s 538s . This analysis requires at least 11 MB of memory space. 538s 538s 539s . Score of initial tree: -5680.04 539s 539s . Starting first round of SPRs... 541s 544s 3s | 1 | lnL= -5426.7 | depth= 6/ 40 | improvements= 17 | delta_lnL= 15.7/ 1000.0 + 544s 6s | 2 | lnL= -5428.0 | depth= 3/ 24 | improvements= 9 | delta_lnL= 4.6/ 1000.0 544s 544s . Second round of optimization... 546s 548s 8s | 3 | lnL= -5431.7 | depth= 2/ 21 | improvements= 12 | delta_lnL= 18.3/ 1000.0 550s 10s | 4 | lnL= -5430.6 | depth= 2/ 16 | improvements= 14 | delta_lnL= 12.8/ 1000.0 550s 12s | 5 | lnL= -5430.0 | depth= 2/ 12 | improvements= 22 | delta_lnL= 4.9/ 1000.0 551s 12s | 6 | lnL= -5438.1 | depth= 1/ 9 | improvements= 10 | delta_lnL= 0.0/ 36.6 551s 13s | 7 | lnL= -5428.7 | depth= 2/ 7 | improvements= 22 | delta_lnL= 11.8/ 36.6 552s 13s | 8 | lnL= -5429.7 | depth= 1/ 6 | improvements= 11 | delta_lnL= 0.0/ 36.6 552s 14s | 9 | lnL= -5427.3 | depth= 1/ 5 | improvements= 11 | delta_lnL= 0.0/ 36.6 553s 14s | 10 | lnL= -5449.0 | depth= 1/ 5 | improvements= 12 | delta_lnL= 0.0/ 23.6 554s 15s | 11 | lnL= -5455.3 | depth= 2/ 5 | improvements= 25 | delta_lnL= 11.7/ 23.6 554s 16s | 12 | lnL= -5429.1 | depth= 2/ 6 | improvements= 16 | delta_lnL= 4.3/ 23.6 554s 554s . Third round of optimization... 556s 559s 18s | 13 | lnL= -5421.0 | depth= 1/ 10 | improvements= 9 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 561s 21s | 14 | lnL= -5420.4 | depth= 1/ 8 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 564s 23s | 15 | lnL= -5420.3 | depth= 0/ 6 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 564s 26s | 16 | lnL= -5420.3 | depth= 0/ 5 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 564s 564s . Final optimisation steps... 566s 566s 566s . Log likelihood of the current tree: -5420.255955030107543279882520437240601. 566s 567s . Calculating fast branch supports (using 'aBayes'). 567s 567s . Printing the most likely tree in file 'nucleic_phyml_tree.txt'. 567s 567s . Time used 0h0m29s 567s 567s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 567s + echo 'AA interleaved sequence file, default parameters single processor:' 567s + /usr/bin/phyml -i proteic -d aa 567s AA interleaved sequence file, default parameters single processor: 567s 567s 567s . Command line: /usr/lib/phyml/bin/phyml -i proteic -d aa 567s 567s 567s 567s 567s 567s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 567s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 567s 567s . Sequence filename: proteic 567s . Data type: aa 567s . Alphabet size: 20 567s . Sequence format: interleaved 567s . Number of data sets: 1 567s . Nb of bootstrapped data sets: 0 567s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 567s . Model name: LG 567s . Proportion of invariable sites: 0.000000 567s . RAS model: discrete Gamma 567s . Number of subst. rate catgs: 4 567s . Gamma distribution parameter: estimated 567s . 'Middle' of each rate class: mean 567s . Amino-acid equilibrium frequencies: empirical 567s . Optimise tree topology: yes 567s . Starting tree: BioNJ 567s . Add random input tree: no 567s . Optimise branch lengths: yes 567s . Minimum length of an edge: 1e-08 567s . Optimise substitution model parameters: yes 567s . Run ID: none 567s . Random seed: 1710811380 567s . Subtree patterns aliasing: no 567s . Version: 3.3.3:3.3.20220408-3 567s . Byte alignment: 1 567s . AVX enabled: no 567s . SSE enabled: no 567s 567s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 567s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 567s 567s 567s 567s . 429 patterns found (out of a total of 547 sites). 567s 567s . 136 sites without polymorphism (24.86%). 567s 567s 567s . Computing pairwise distances... 567s 567s . Building BioNJ tree... 567s 567s . This analysis requires at least 39 MB of memory space. 567s 567s 572s . Score of initial tree: -12569.85 572s 572s . Starting first round of SPRs... 596s 596s 29s | 1 | lnL= -12476.8 | depth= 2/ 40 | improvements= 15 | delta_lnL= 2.4/ 1000.0 596s 596s . Second round of optimization... 619s 640s 52s | 2 | lnL= -12499.8 | depth= 2/ 36 | improvements= 21 | delta_lnL= 16.4/ 1000.0 664s 73s | 3 | lnL= -12516.0 | depth= 5/ 20 | improvements= 25 | delta_lnL= 15.1/ 1000.0 688s 97s | 4 | lnL= -12464.6 | depth= 4/ 16 | improvements= 18 | delta_lnL= 19.6/ 1000.0 693s 121s | 5 | lnL= -12483.4 | depth= 3/ 12 | improvements= 12 | delta_lnL= 10.0/ 1000.0 699s 126s | 6 | lnL= -12523.3 | depth= 3/ 9 | improvements= 18 | delta_lnL= 30.3/ 39.2 705s 132s | 7 | lnL= -12519.5 | depth= 3/ 7 | improvements= 23 | delta_lnL= 14.2/ 39.2 710s 138s | 8 | lnL= -12460.3 | depth= 2/ 7 | improvements= 19 | delta_lnL= 38.4/ 39.2 717s 143s | 9 | lnL= -12456.7 | depth= 1/ 6 | improvements= 14 | delta_lnL= 0.0/ 39.2 732s 150s | 10 | lnL= -12471.1 | depth= 2/ 5 | improvements= 15 | delta_lnL= 15.5/ 76.8 732s 164s | 11 | lnL= -12460.1 | depth= 1/ 6 | improvements= 21 | delta_lnL= 0.0/ 76.8 732s 732s . Third round of optimization... 752s 782s 185s | 12 | lnL= -12443.1 | depth= 1/ 10 | improvements= 6 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 782s 215s | 13 | lnL= -12443.1 | depth= 0/ 8 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 782s 782s . Final optimisation steps... 795s 795s 795s . Log likelihood of the current tree: -12443.048746567137641250155866146087646. 795s 804s . Calculating fast branch supports (using 'aBayes'). 804s 804s . Printing the most likely tree in file 'proteic_phyml_tree.txt'. 804s 804s . Time used 0h3m57s 804s 804s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 804s + echo 'AA sequential sequence file, with customization single processor:' 804s AA sequential sequence file, with customization single processor: 804s + /usr/bin/phyml -i example.nex -d nt -c 4 -a e 804s 804s 804s . Command line: /usr/lib/phyml/bin/phyml -i example.nex -d nt -c 4 -a e 804s 804s 804s 804s 804s 804s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 804s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 804s 804s . Sequence filename: example.nex 804s . Data type: dna 804s . Alphabet size: 4 804s . Sequence format: interleaved 804s . Number of data sets: 1 804s . Nb of bootstrapped data sets: 0 804s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 804s . Model name: HKY85 804s . Ts/tv ratio: estimated 804s . Proportion of invariable sites: 0.000000 804s . RAS model: discrete Gamma 804s . Number of subst. rate catgs: 4 804s . Gamma distribution parameter: estimated 804s . 'Middle' of each rate class: mean 804s . Nucleotide equilibrium frequencies: empirical 804s . Optimise tree topology: yes 804s . Starting tree: BioNJ 804s . Add random input tree: no 804s . Optimise branch lengths: yes 804s . Minimum length of an edge: 1e-08 804s . Optimise substitution model parameters: yes 804s . Run ID: none 804s . Random seed: 1710811617 804s . Subtree patterns aliasing: no 804s . Version: 3.3.3:3.3.20220408-3 804s . Byte alignment: 1 804s . AVX enabled: no 804s . SSE enabled: no 804s 804s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 804s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 804s 804s 804s 804s . 1037 patterns found (out of a total of 2888 sites). 804s 804s . 1378 sites without polymorphism (47.71%). 804s 804s 804s . Computing pairwise distances... 804s 804s . Building BioNJ tree... 804s 804s . This analysis requires at least 3 MB of memory space. 804s 804s 804s . Score of initial tree: -12664.54 804s 804s . Starting first round of SPRs... 804s 804s 0s | 1 | lnL= -12582.6 | depth= 1/ 40 | improvements= 5 | delta_lnL= 0.0/ 1000.0 804s 804s . Second round of optimization... 804s 804s 0s | 2 | lnL= -12588.8 | depth= 1/ 36 | improvements= 3 | delta_lnL= 0.0/ 1000.0 804s 804s . Third round of optimization... 805s 805s 0s | 3 | lnL= -12564.0 | depth= 1/ 20 | improvements= 3 | delta_lnL= 0.0/ 1000.0 | triple moves= 5 805s 1s | 4 | lnL= -12563.5 | depth= 0/ 16 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 805s 805s . Final optimisation steps... 805s 805s 805s . Log likelihood of the current tree: -12563.118859055624852771870791912078857. 805s 806s . Calculating fast branch supports (using 'aBayes'). 806s 806s . Printing the most likely tree in file 'example.nex_phyml_tree.txt'. 806s 806s . Time used 0h0m2s 806s 806s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 806s + export PHYMLCPUS=2 806s + PHYMLCPUS=2 806s + echo 'DNA interleaved sequence file, default parameters using 2 processors:' 806s DNA interleaved sequence file, default parameters using 2 processors: 806s + /usr/bin/phyml -i nucleic 806s 806s 806s . Command line: /usr/lib/phyml/bin/phyml -i nucleic 806s 806s 806s 806s 806s 806s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 806s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 806s 806s . Sequence filename: nucleic 806s . Data type: dna 806s . Alphabet size: 4 806s . Sequence format: interleaved 806s . Number of data sets: 1 806s . Nb of bootstrapped data sets: 0 806s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 806s . Model name: HKY85 806s . Ts/tv ratio: estimated 806s . Proportion of invariable sites: 0.000000 806s . RAS model: discrete Gamma 806s . Number of subst. rate catgs: 4 806s . Gamma distribution parameter: estimated 806s . 'Middle' of each rate class: mean 806s . Nucleotide equilibrium frequencies: empirical 806s . Optimise tree topology: yes 806s . Starting tree: BioNJ 806s . Add random input tree: no 806s . Optimise branch lengths: yes 806s . Minimum length of an edge: 1e-08 806s . Optimise substitution model parameters: yes 806s . Run ID: none 806s . Random seed: 1710811619 806s . Subtree patterns aliasing: no 806s . Version: 3.3.3:3.3.20220408-3 806s . Byte alignment: 1 806s . AVX enabled: no 806s . SSE enabled: no 806s 806s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 806s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 806s 806s 806s 806s . 382 patterns found (out of a total of 886 sites). 806s 806s . 582 sites without polymorphism (65.69%). 806s 806s 806s . Computing pairwise distances... 806s 806s . Building BioNJ tree... 806s 806s . This analysis requires at least 11 MB of memory space. 806s 806s 806s . Score of initial tree: -5680.04 806s 806s . Starting first round of SPRs... 809s 812s 3s | 1 | lnL= -5441.6 | depth= 6/ 40 | improvements= 20 | delta_lnL= 17.8/ 1000.0 812s 6s | 2 | lnL= -5427.8 | depth= 2/ 24 | improvements= 14 | delta_lnL= 3.1/ 1000.0 + 812s 812s . Second round of optimization... 814s 815s 8s | 3 | lnL= -5429.0 | depth= 1/ 21 | improvements= 13 | delta_lnL= 0.0/ 1000.0 817s 9s | 4 | lnL= -5422.9 | depth= 3/ 16 | improvements= 13 | delta_lnL= 5.3/ 1000.0 + 818s 11s | 5 | lnL= -5429.8 | depth= 1/ 12 | improvements= 8 | delta_lnL= 0.0/ 1000.0 818s 12s | 6 | lnL= -5446.5 | depth= 2/ 9 | improvements= 15 | delta_lnL= 5.2/ 20.0 818s 12s | 7 | lnL= -5442.1 | depth= 2/ 7 | improvements= 18 | delta_lnL= 21.1/ 20.0 819s 12s | 8 | lnL= -5425.7 | depth= 5/ 6 | improvements= 13 | delta_lnL= 5.6/ 20.0 819s 13s | 9 | lnL= -5439.6 | depth= 2/ 9 | improvements= 16 | delta_lnL= 4.3/ 20.0 821s 13s | 10 | lnL= -5426.6 | depth= 4/ 7 | improvements= 13 | delta_lnL= 2.5/ 42.2 821s 15s | 11 | lnL= -5435.0 | depth= 1/ 8 | improvements= 7 | delta_lnL= 0.0/ 42.2 822s 15s | 12 | lnL= -5432.4 | depth= 1/ 6 | improvements= 16 | delta_lnL= 0.0/ 42.2 822s 16s | 13 | lnL= -5427.5 | depth= 1/ 5 | improvements= 12 | delta_lnL= 0.0/ 42.2 822s 822s . Third round of optimization... 824s 827s 18s | 14 | lnL= -5421.6 | depth= 1/ 10 | improvements= 6 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 829s 21s | 15 | lnL= -5420.7 | depth= 3/ 8 | improvements= 1 | delta_lnL= 5.3/ 100.0 | triple moves= 5 + 832s 23s | 16 | lnL= -5420.6 | depth= 0/ 6 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 832s 26s | 17 | lnL= -5420.6 | depth= 0/ 5 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 832s 832s . Final optimisation steps... 834s 834s 834s . Log likelihood of the current tree: -5420.255856286204107163939625024795532. 834s 834s . Calculating fast branch supports (using 'aBayes'). 834s 834s . Printing the most likely tree in file 'nucleic_phyml_tree.txt'. 834s 834s . Time used 0h0m28s 834s 834s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 834s + echo 'AA interleaved sequence file, default parameters using 2 processors:' 834s AA interleaved sequence file, default parameters using 2 processors: 834s + /usr/bin/phyml -i proteic -d aa 834s 834s 834s . Command line: /usr/lib/phyml/bin/phyml -i proteic -d aa 834s 834s 834s 834s 834s 834s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 834s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 834s 834s . Sequence filename: proteic 834s . Data type: aa 834s . Alphabet size: 20 834s . Sequence format: interleaved 834s . Number of data sets: 1 834s . Nb of bootstrapped data sets: 0 834s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 834s . Model name: LG 834s . Proportion of invariable sites: 0.000000 834s . RAS model: discrete Gamma 834s . Number of subst. rate catgs: 4 834s . Gamma distribution parameter: estimated 834s . 'Middle' of each rate class: mean 834s . Amino-acid equilibrium frequencies: empirical 834s . Optimise tree topology: yes 834s . Starting tree: BioNJ 834s . Add random input tree: no 834s . Optimise branch lengths: yes 834s . Minimum length of an edge: 1e-08 834s . Optimise substitution model parameters: yes 834s . Run ID: none 834s . Random seed: 1710811647 834s . Subtree patterns aliasing: no 834s . Version: 3.3.3:3.3.20220408-3 834s . Byte alignment: 1 834s . AVX enabled: no 834s . SSE enabled: no 834s 834s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 834s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 834s 834s 834s 834s . 429 patterns found (out of a total of 547 sites). 834s 834s . 136 sites without polymorphism (24.86%). 834s 834s 835s . Computing pairwise distances... 835s 835s . Building BioNJ tree... 835s 835s . This analysis requires at least 39 MB of memory space. 835s 835s 840s . Score of initial tree: -12569.85 840s 840s . Starting first round of SPRs... 863s 863s 28s | 1 | lnL= -12461.3 | depth= 1/ 40 | improvements= 13 | delta_lnL= 0.0/ 1000.0 863s 863s . Second round of optimization... 886s 909s 51s | 2 | lnL= -12478.1 | depth= 1/ 36 | improvements= 17 | delta_lnL= 0.0/ 1000.0 932s 74s | 3 | lnL= -12474.6 | depth= 3/ 20 | improvements= 15 | delta_lnL= 14.2/ 1000.0 954s 97s | 4 | lnL= -12458.7 | depth= 1/ 16 | improvements= 18 | delta_lnL= 0.0/ 1000.0 958s 118s | 5 | lnL= -12497.4 | depth= 2/ 12 | improvements= 20 | delta_lnL= 20.1/ 1000.0 963s 123s | 6 | lnL= -12478.8 | depth= 1/ 9 | improvements= 10 | delta_lnL= 0.0/ 28.3 968s 128s | 7 | lnL= -12474.7 | depth= 1/ 7 | improvements= 14 | delta_lnL= 0.0/ 28.3 973s 133s | 8 | lnL= -12517.5 | depth= 3/ 5 | improvements= 19 | delta_lnL= 15.1/ 28.3 978s 138s | 9 | lnL= -12494.0 | depth= 1/ 7 | improvements= 16 | delta_lnL= 0.0/ 28.3 988s 143s | 10 | lnL= -12462.2 | depth= 4/ 5 | improvements= 20 | delta_lnL= 22.1/ 30.2 988s 153s | 11 | lnL= -12458.8 | depth= 2/ 8 | improvements= 16 | delta_lnL= 23.1/ 30.2 988s 988s . Third round of optimization... 1008s 1040s 173s | 12 | lnL= -12443.1 | depth= 2/ 10 | improvements= 5 | delta_lnL= 1.8/ 100.0 | triple moves= 5 + 1040s 205s | 13 | lnL= -12443.1 | depth= 0/ 8 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 6 + 1040s 1040s . Final optimisation steps... 1052s 1052s 1053s . Log likelihood of the current tree: -12443.048807328075781697407364845275879. 1053s 1062s . Calculating fast branch supports (using 'aBayes'). 1062s 1062s . Printing the most likely tree in file 'proteic_phyml_tree.txt'. 1062s 1062s . Time used 0h3m47s 1062s 1062s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1062s + echo 'AA sequential sequence file, with customization using 2 processors:' 1062s + /usr/bin/phyml -i example.nex -d nt -c 4 -a e 1062s AA sequential sequence file, with customization using 2 processors: 1062s 1062s 1062s . Command line: /usr/lib/phyml/bin/phyml -i example.nex -d nt -c 4 -a e 1062s 1062s 1062s 1062s 1062s 1062s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 1062s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 1062s 1062s . Sequence filename: example.nex 1062s . Data type: dna 1062s . Alphabet size: 4 1062s . Sequence format: interleaved 1062s . Number of data sets: 1 1062s . Nb of bootstrapped data sets: 0 1062s . Compute approximate likelihood ratio test: yes (aBayes branch supports) 1062s . Model name: HKY85 1062s . Ts/tv ratio: estimated 1062s . Proportion of invariable sites: 0.000000 1062s . RAS model: discrete Gamma 1062s . Number of subst. rate catgs: 4 1062s . Gamma distribution parameter: estimated 1062s . 'Middle' of each rate class: mean 1062s . Nucleotide equilibrium frequencies: empirical 1062s . Optimise tree topology: yes 1062s . Starting tree: BioNJ 1062s . Add random input tree: no 1062s . Optimise branch lengths: yes 1062s . Minimum length of an edge: 1e-08 1062s . Optimise substitution model parameters: yes 1062s . Run ID: none 1062s . Random seed: 1710811875 1062s . Subtree patterns aliasing: no 1062s . Version: 3.3.3:3.3.20220408-3 1062s . Byte alignment: 1 1062s . AVX enabled: no 1062s . SSE enabled: no 1062s 1062s ////////////////////////////////////.\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ 1062s \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\.////////////////////////////////////////// 1062s 1062s 1062s 1062s . 1037 patterns found (out of a total of 2888 sites). 1062s 1062s . 1378 sites without polymorphism (47.71%). 1062s 1062s 1062s . Computing pairwise distances... 1062s 1062s . Building BioNJ tree... 1062s 1062s . This analysis requires at least 3 MB of memory space. 1062s 1062s 1062s . Score of initial tree: -12664.54 1062s 1062s . Starting first round of SPRs... 1062s 1062s 0s | 1 | lnL= -12585.6 | depth= 1/ 40 | improvements= 2 | delta_lnL= 0.0/ 1000.0 1062s 1062s . Second round of optimization... 1062s 1062s 0s | 2 | lnL= -12581.1 | depth= 1/ 36 | improvements= 4 | delta_lnL= 0.0/ 1000.0 1062s 1062s . Third round of optimization... 1062s 1063s 0s | 3 | lnL= -12569.9 | depth= 1/ 20 | improvements= 4 | delta_lnL= 0.0/ 1000.0 | triple moves= 5 1063s 1s | 4 | lnL= -12563.5 | depth= 1/ 16 | improvements= 1 | delta_lnL= 0.0/ 100.0 | triple moves= 5 1063s 1s | 5 | lnL= -12563.5 | depth= 0/ 12 | improvements= 0 | delta_lnL= 0.0/ 100.0 | triple moves= 5 + 1063s 1063s . Final optimisation steps... 1064s 1064s 1064s . Log likelihood of the current tree: -12563.119093425872051739133894443511963. 1064s 1064s . Calculating fast branch supports (using 'aBayes'). 1064s 1064s . Printing the most likely tree in file 'example.nex_phyml_tree.txt'. 1064s 1064s . Time used 0h0m2s 1064s 1064s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1064s + echo PASS 1064s PASS 1064s autopkgtest [01:31:17]: test run-unit-test: -----------------------] 1065s autopkgtest [01:31:18]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 1065s run-unit-test PASS 1065s autopkgtest [01:31:18]: @@@@@@@@@@@@@@@@@@@@ summary 1065s run-unit-test PASS 1086s Creating nova instance adt-noble-ppc64el-phyml-20240319-011333-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240316.img (UUID 1492b190-05c5-462d-b1de-84bc330afe32)...