0s autopkgtest [17:08:52]: starting date and time: 2024-07-12 17:08:52+0000 0s autopkgtest [17:08:52]: git checkout: fd3bed09 nova: allow more retries for quota issues 0s autopkgtest [17:08:52]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.9ksgfx8a/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:glibc --apt-upgrade gmap --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=glibc/2.39-3.1ubuntu3 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-ppc64el-6.secgroup --name adt-oracular-ppc64el-gmap-20240712-170852-juju-7f2275-prod-proposed-migration-environment-2-2ec113cf-a32e-4916-80d9-bd4112e68fca --image adt/ubuntu-oracular-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,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 146s autopkgtest [17:11:18]: testbed dpkg architecture: ppc64el 147s autopkgtest [17:11:19]: testbed apt version: 2.9.6 147s autopkgtest [17:11:19]: @@@@@@@@@@@@@@@@@@@@ test bed setup 160s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [126 kB] 160s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [46.6 kB] 160s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2576 B] 160s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [334 kB] 160s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [8548 B] 160s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el Packages [74.9 kB] 160s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el c-n-f Metadata [2104 B] 160s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/restricted ppc64el Packages [1368 B] 160s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/restricted ppc64el c-n-f Metadata [120 B] 160s Get:10 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el Packages [349 kB] 160s Get:11 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el c-n-f Metadata [8320 B] 160s Get:12 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse ppc64el Packages [1448 B] 160s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse ppc64el c-n-f Metadata [120 B] 162s Fetched 955 kB in 1s (1137 kB/s) 162s Reading package lists... 190s Reading package lists... 190s Building dependency tree... 190s Reading state information... 190s Calculating upgrade... 191s The following packages will be upgraded: 191s binutils binutils-common binutils-powerpc64le-linux-gnu gir1.2-glib-2.0 191s inetutils-telnet libbinutils libc-bin libc-dev-bin libc-devtools libc6 191s libc6-dev libctf-nobfd0 libctf0 libglib2.0-0t64 libglib2.0-data 191s libnghttp2-14 libnss3 libsframe1 libssl3t64 locales openssh-client 191s openssh-server openssh-sftp-server openssl telnet 191s 25 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 191s Need to get 23.0 MB of archives. 191s After this operation, 1586 kB disk space will be freed. 191s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libc-devtools ppc64el 2.39-3.1ubuntu3 [29.5 kB] 191s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libc6-dev ppc64el 2.39-3.1ubuntu3 [1982 kB] 191s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libc-dev-bin ppc64el 2.39-3.1ubuntu3 [21.0 kB] 191s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libc6 ppc64el 2.39-3.1ubuntu3 [3174 kB] 191s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el libc-bin ppc64el 2.39-3.1ubuntu3 [720 kB] 191s Get:6 http://ftpmaster.internal/ubuntu oracular/main ppc64el libssl3t64 ppc64el 3.2.2-1ubuntu1 [2345 kB] 191s Get:7 http://ftpmaster.internal/ubuntu oracular/main ppc64el openssh-sftp-server ppc64el 1:9.6p1-3ubuntu17 [43.6 kB] 191s Get:8 http://ftpmaster.internal/ubuntu oracular/main ppc64el openssh-server ppc64el 1:9.6p1-3ubuntu17 [624 kB] 191s Get:9 http://ftpmaster.internal/ubuntu oracular/main ppc64el openssh-client ppc64el 1:9.6p1-3ubuntu17 [1108 kB] 191s Get:10 http://ftpmaster.internal/ubuntu oracular/main ppc64el gir1.2-glib-2.0 ppc64el 2.80.4-1ubuntu1 [182 kB] 191s Get:11 http://ftpmaster.internal/ubuntu oracular/main ppc64el libglib2.0-0t64 ppc64el 2.80.4-1ubuntu1 [1763 kB] 191s Get:12 http://ftpmaster.internal/ubuntu oracular/main ppc64el libglib2.0-data all 2.80.4-1ubuntu1 [49.3 kB] 191s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el locales all 2.39-3.1ubuntu3 [4220 kB] 192s Get:14 http://ftpmaster.internal/ubuntu oracular/main ppc64el openssl ppc64el 3.2.2-1ubuntu1 [1147 kB] 192s Get:15 http://ftpmaster.internal/ubuntu oracular/main ppc64el inetutils-telnet ppc64el 2:2.5-5ubuntu1 [120 kB] 192s Get:16 http://ftpmaster.internal/ubuntu oracular/main ppc64el libnghttp2-14 ppc64el 1.62.1-2 [89.3 kB] 192s Get:17 http://ftpmaster.internal/ubuntu oracular/main ppc64el telnet all 0.17+2.5-5ubuntu1 [3688 B] 192s Get:18 http://ftpmaster.internal/ubuntu oracular/main ppc64el libctf0 ppc64el 2.42.50.20240710-1ubuntu1 [113 kB] 192s Get:19 http://ftpmaster.internal/ubuntu oracular/main ppc64el libctf-nobfd0 ppc64el 2.42.50.20240710-1ubuntu1 [113 kB] 192s Get:20 http://ftpmaster.internal/ubuntu oracular/main ppc64el binutils-powerpc64le-linux-gnu ppc64el 2.42.50.20240710-1ubuntu1 [2492 kB] 192s Get:21 http://ftpmaster.internal/ubuntu oracular/main ppc64el libbinutils ppc64el 2.42.50.20240710-1ubuntu1 [702 kB] 192s Get:22 http://ftpmaster.internal/ubuntu oracular/main ppc64el binutils ppc64el 2.42.50.20240710-1ubuntu1 [3092 B] 192s Get:23 http://ftpmaster.internal/ubuntu oracular/main ppc64el binutils-common ppc64el 2.42.50.20240710-1ubuntu1 [220 kB] 192s Get:24 http://ftpmaster.internal/ubuntu oracular/main ppc64el libsframe1 ppc64el 2.42.50.20240710-1ubuntu1 [15.8 kB] 192s Get:25 http://ftpmaster.internal/ubuntu oracular/main ppc64el libnss3 ppc64el 2:3.102-1 [1748 kB] 192s Preconfiguring packages ... 192s Fetched 23.0 MB in 1s (18.3 MB/s) 192s (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 ... 72755 files and directories currently installed.) 192s Preparing to unpack .../libc-devtools_2.39-3.1ubuntu3_ppc64el.deb ... 192s Unpacking libc-devtools (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 192s Preparing to unpack .../libc6-dev_2.39-3.1ubuntu3_ppc64el.deb ... 192s Unpacking libc6-dev:ppc64el (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 193s Preparing to unpack .../libc-dev-bin_2.39-3.1ubuntu3_ppc64el.deb ... 193s Unpacking libc-dev-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 193s Preparing to unpack .../libc6_2.39-3.1ubuntu3_ppc64el.deb ... 193s Unpacking libc6:ppc64el (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 193s Setting up libc6:ppc64el (2.39-3.1ubuntu3) ... 193s Error: Could not restart systemd, systemd binary not working 193s (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 ... 72755 files and directories currently installed.) 193s Preparing to unpack .../libc-bin_2.39-3.1ubuntu3_ppc64el.deb ... 193s Unpacking libc-bin (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 193s Setting up libc-bin (2.39-3.1ubuntu3) ... 193s (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 ... 72755 files and directories currently installed.) 193s Preparing to unpack .../libssl3t64_3.2.2-1ubuntu1_ppc64el.deb ... 193s Unpacking libssl3t64:ppc64el (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ... 193s Setting up libssl3t64:ppc64el (3.2.2-1ubuntu1) ... 194s (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 ... 72755 files and directories currently installed.) 194s Preparing to unpack .../00-openssh-sftp-server_1%3a9.6p1-3ubuntu17_ppc64el.deb ... 194s Unpacking openssh-sftp-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 194s Preparing to unpack .../01-openssh-server_1%3a9.6p1-3ubuntu17_ppc64el.deb ... 194s Unpacking openssh-server (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 194s Preparing to unpack .../02-openssh-client_1%3a9.6p1-3ubuntu17_ppc64el.deb ... 194s Unpacking openssh-client (1:9.6p1-3ubuntu17) over (1:9.6p1-3ubuntu15) ... 194s Preparing to unpack .../03-gir1.2-glib-2.0_2.80.4-1ubuntu1_ppc64el.deb ... 194s Unpacking gir1.2-glib-2.0:ppc64el (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ... 194s Preparing to unpack .../04-libglib2.0-0t64_2.80.4-1ubuntu1_ppc64el.deb ... 194s Unpacking libglib2.0-0t64:ppc64el (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ... 194s Preparing to unpack .../05-libglib2.0-data_2.80.4-1ubuntu1_all.deb ... 194s Unpacking libglib2.0-data (2.80.4-1ubuntu1) over (2.80.3-1ubuntu1) ... 194s Preparing to unpack .../06-locales_2.39-3.1ubuntu3_all.deb ... 194s Unpacking locales (2.39-3.1ubuntu3) over (2.39-0ubuntu9) ... 194s Preparing to unpack .../07-openssl_3.2.2-1ubuntu1_ppc64el.deb ... 194s Unpacking openssl (3.2.2-1ubuntu1) over (3.2.1-3ubuntu1) ... 194s Preparing to unpack .../08-inetutils-telnet_2%3a2.5-5ubuntu1_ppc64el.deb ... 194s Unpacking inetutils-telnet (2:2.5-5ubuntu1) over (2:2.5-3ubuntu4) ... 194s Preparing to unpack .../09-libnghttp2-14_1.62.1-2_ppc64el.deb ... 194s Unpacking libnghttp2-14:ppc64el (1.62.1-2) over (1.62.1-1) ... 194s Preparing to unpack .../10-telnet_0.17+2.5-5ubuntu1_all.deb ... 194s Unpacking telnet (0.17+2.5-5ubuntu1) over (0.17+2.5-3ubuntu4) ... 194s Preparing to unpack .../11-libctf0_2.42.50.20240710-1ubuntu1_ppc64el.deb ... 194s Unpacking libctf0:ppc64el (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 194s Preparing to unpack .../12-libctf-nobfd0_2.42.50.20240710-1ubuntu1_ppc64el.deb ... 194s Unpacking libctf-nobfd0:ppc64el (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 194s Preparing to unpack .../13-binutils-powerpc64le-linux-gnu_2.42.50.20240710-1ubuntu1_ppc64el.deb ... 194s Unpacking binutils-powerpc64le-linux-gnu (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 195s Preparing to unpack .../14-libbinutils_2.42.50.20240710-1ubuntu1_ppc64el.deb ... 195s Unpacking libbinutils:ppc64el (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 195s Preparing to unpack .../15-binutils_2.42.50.20240710-1ubuntu1_ppc64el.deb ... 195s Unpacking binutils (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 195s Preparing to unpack .../16-binutils-common_2.42.50.20240710-1ubuntu1_ppc64el.deb ... 195s Unpacking binutils-common:ppc64el (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 195s Preparing to unpack .../17-libsframe1_2.42.50.20240710-1ubuntu1_ppc64el.deb ... 195s Unpacking libsframe1:ppc64el (2.42.50.20240710-1ubuntu1) over (2.42.50.20240625-1ubuntu1) ... 195s Preparing to unpack .../18-libnss3_2%3a3.102-1_ppc64el.deb ... 195s Unpacking libnss3:ppc64el (2:3.102-1) over (2:3.101-1) ... 195s Setting up openssh-client (1:9.6p1-3ubuntu17) ... 195s Setting up binutils-common:ppc64el (2.42.50.20240710-1ubuntu1) ... 195s Setting up libnghttp2-14:ppc64el (1.62.1-2) ... 195s Setting up inetutils-telnet (2:2.5-5ubuntu1) ... 195s Setting up libctf-nobfd0:ppc64el (2.42.50.20240710-1ubuntu1) ... 195s Setting up libnss3:ppc64el (2:3.102-1) ... 195s Setting up locales (2.39-3.1ubuntu3) ... 195s Generating locales (this might take a while)... 197s en_US.UTF-8... done 197s Generation complete. 197s Setting up libsframe1:ppc64el (2.42.50.20240710-1ubuntu1) ... 197s Setting up libglib2.0-0t64:ppc64el (2.80.4-1ubuntu1) ... 197s No schema files found: doing nothing. 197s Setting up libglib2.0-data (2.80.4-1ubuntu1) ... 197s Setting up gir1.2-glib-2.0:ppc64el (2.80.4-1ubuntu1) ... 197s Setting up libbinutils:ppc64el (2.42.50.20240710-1ubuntu1) ... 197s Setting up libc-dev-bin (2.39-3.1ubuntu3) ... 197s Setting up openssl (3.2.2-1ubuntu1) ... 197s Installing new version of config file /etc/ssl/openssl.cnf ... 197s Setting up libc-devtools (2.39-3.1ubuntu3) ... 197s Setting up libctf0:ppc64el (2.42.50.20240710-1ubuntu1) ... 197s Setting up openssh-sftp-server (1:9.6p1-3ubuntu17) ... 197s Setting up telnet (0.17+2.5-5ubuntu1) ... 197s Setting up openssh-server (1:9.6p1-3ubuntu17) ... 197s Installing new version of config file /etc/pam.d/sshd ... 198s Setting up libc6-dev:ppc64el (2.39-3.1ubuntu3) ... 198s Setting up binutils-powerpc64le-linux-gnu (2.42.50.20240710-1ubuntu1) ... 198s Setting up binutils (2.42.50.20240710-1ubuntu1) ... 198s Processing triggers for libc-bin (2.39-3.1ubuntu3) ... 198s Processing triggers for ufw (0.36.2-6) ... 198s Processing triggers for systemd (256-1ubuntu1) ... 199s Processing triggers for man-db (2.12.1-2) ... 201s Reading package lists... 201s Building dependency tree... 201s Reading state information... 201s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 204s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 204s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 204s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 204s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 205s Reading package lists... 205s Reading package lists... 205s Building dependency tree... 206s Reading state information... 206s Calculating upgrade... 206s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 206s Reading package lists... 206s Building dependency tree... 206s Reading state information... 206s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 207s autopkgtest [17:12:19]: rebooting testbed after setup commands that affected boot 212s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 245s autopkgtest-virt-ssh: WARNING: ssh connection failed. Retrying in 3 seconds... 282s autopkgtest [17:13:34]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP Sat Apr 20 00:05:55 UTC 2024 314s autopkgtest [17:14:06]: @@@@@@@@@@@@@@@@@@@@ apt-source gmap 325s Get:1 http://ftpmaster.internal/ubuntu oracular/multiverse gmap 2024-05-20+ds-1 (dsc) [2191 B] 325s Get:2 http://ftpmaster.internal/ubuntu oracular/multiverse gmap 2024-05-20+ds-1 (tar) [2495 kB] 325s Get:3 http://ftpmaster.internal/ubuntu oracular/multiverse gmap 2024-05-20+ds-1 (diff) [13.3 kB] 325s gpgv: Signature made Sun May 26 10:21:41 2024 UTC 325s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 325s gpgv: issuer "emollier@debian.org" 325s gpgv: Can't check signature: No public key 325s dpkg-source: warning: cannot verify inline signature for ./gmap_2024-05-20+ds-1.dsc: no acceptable signature found 326s autopkgtest [17:14:18]: testing package gmap version 2024-05-20+ds-1 326s autopkgtest [17:14:18]: build not needed 374s autopkgtest [17:15:06]: test gmap-tests: preparing testbed 377s Reading package lists... 377s Building dependency tree... 377s Reading state information... 377s Starting pkgProblemResolver with broken count: 0 377s Starting 2 pkgProblemResolver with broken count: 0 377s Done 378s The following additional packages will be installed: 378s gmap 378s The following NEW packages will be installed: 378s autopkgtest-satdep gmap 378s 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. 378s Need to get 6206 kB/6207 kB of archives. 378s After this operation, 45.4 MB of additional disk space will be used. 378s Get:1 /tmp/autopkgtest.4FhG8B/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [704 B] 378s Get:2 http://ftpmaster.internal/ubuntu oracular/universe ppc64el gmap ppc64el 2024-05-20+ds-1 [6206 kB] 380s Fetched 6206 kB in 2s (2545 kB/s) 380s Selecting previously unselected package gmap. 380s (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 ... 72754 files and directories currently installed.) 380s Preparing to unpack .../gmap_2024-05-20+ds-1_ppc64el.deb ... 380s Unpacking gmap (2024-05-20+ds-1) ... 381s Selecting previously unselected package autopkgtest-satdep. 381s Preparing to unpack .../1-autopkgtest-satdep.deb ... 381s Unpacking autopkgtest-satdep (0) ... 381s Setting up gmap (2024-05-20+ds-1) ... 381s Setting up autopkgtest-satdep (0) ... 381s Processing triggers for man-db (2.12.1-2) ... 389s (Reading database ... 72817 files and directories currently installed.) 389s Removing autopkgtest-satdep (0) ... 395s autopkgtest [17:15:27]: test gmap-tests: [----------------------- 395s align.test 395s GMAP version 2024-05-20 called with args: gmap.nosimd -A -g /tmp/tmp.S8wFOtsNml/tests/ss.chr17test /tmp/tmp.S8wFOtsNml/tests/ss.her2 395s Finished checking compiler assumptions 395s Starting alignment 395s Processed 1 queries in 0.02 seconds (45.43 queries/sec) 395s coords1.test 395s Opening file /tmp/tmp.S8wFOtsNml/tests/ss.chr17test 395s Processed short contigs (<1000000 nt): . 395s ============================================================ 395s Contig mapping information has been written to file coords.chr17test. 395s ============================================================ 395s iit.test 395s Finished reading FASTA file -- total entries: 3 395s Maximum coordinate: 40000 395s Total label length: 3 + 3 separators 395s Total annotation length: 80 + 3 separators 395s Saw 0 distinct divisions/chromosomes 395s Saw 3 distinct tags/types 395s No divs/chromosomes provided, so storing as IIT version 1 400s Writing IIT file header information...coordinates require 4 bytes each...done 400s Processing null division/chromosome...sorting...writing...done (3 intervals) 400s Writing IIT file footer information...done 400s setup1.test 400s --local flag not specified, so building localdb by default 400s Writing files under . 400s Not sorting chromosomes. To sort chromosomes other ways, use the -s flag. 400s Creating files in directory ./chr17test 400s Running "/usr/lib/gmap/fa_coords" -o "./chr17test.coords" -f "./chr17test.sources" 400s Opening file /tmp/tmp.S8wFOtsNml/tests/ss.chr17test 400s Processed short contigs (<1000000 nt): . 400s ============================================================ 400s Contig mapping information has been written to file ./chr17test.coords. 400s ============================================================ 400s Running "/usr/lib/gmap/gmap_process" -c "./chr17test.coords" -f "./chr17test.sources" | "/usr/lib/gmap/gmapindex" -d chr17test -D "./chr17test" -A -s none 400s Reading coordinates from file ./chr17test.coords 400s Logging contig chr17test at chr17test:1..200000 in genome chr17test 400s => primary (linear) chromosome 400s Total genomic length = 200000 bp 400s divsort == NO_SORT 400s Have a total of 1 chromosomes 400s Writing chromosome file ./chr17test/chr17test.chromosome 400s Chromosome chr17test has universal coordinates 1..200000 400s Writing chromosome IIT file ./chr17test/chr17test.chromosome.iit 400s Writing IIT file header information...coordinates require 4 bytes each...done 400s Processing null division/chromosome...sorting...writing...done (1 intervals) 400s Writing IIT file footer information...done 400s Writing IIT file header information...coordinates require 4 bytes each...done 400s Processing null division/chromosome...sorting...writing...done (1 intervals) 400s Writing IIT file footer information...done 400s No alternate scaffolds observed 401s Running "/usr/lib/gmap/gmap_process" -c "./chr17test.coords" -f "./chr17test.sources" | "/usr/lib/gmap/gmapindex" -d chr17test -D "./chr17test" -G 401s Genome length is 200000 nt 401s Trying to allocate 18752*4 bytes of memory...succeeded. Building genome in memory. 402s Reading coordinates from file ./chr17test.coords 402s Writing contig chr17test to universal coordinates 1..200000 402s A total of 0 non-ACGTNX characters were seen in the genome. 403s Running cat "./chr17test/chr17test.genomecomp" | "/usr/lib/gmap/gmapindex" -d chr17test -D "./chr17test" -U 405s Running cat "./chr17test/chr17test.genomecomp" | "/usr/lib/gmap/gmapindex" -k 15 -q 3 -D "./chr17test" -d chr17test -N 405s Counting positions in genome chr17test (15 bp every 3 bp), position 0 406s Number of positions: 200000 => normal-sized genome 406s Number of offsets: 66662 => pages file not required 408s Running "/usr/lib/gmap/gmapindex" -k 15 -q 3 -D "./chr17test" -d chr17test -O "./chr17test/chr17test.genomecomp" 408s Offset compression types: bitpack64 408s Allocating 16777216*1 bytes for packsizes 408s Allocating 16777216*8 bytes for bitpacks 408s Indexing offsets of oligomers in genome chr17test (15 bp every 3 bp), position 0 410s Writing 1073741825 offsets compressed via bitpack64...done 412s Running "/usr/lib/gmap/gmapindex" -k 15 -q 3 -D "./chr17test" -d chr17test -P "./chr17test/chr17test.genomecomp" 412s Looking for genome chr17test in directory ./chr17test 412s Looking for index files in directory ./chr17test 412s Pointers file is chr17test.ref153offsets64meta 412s Offsets file is chr17test.ref153offsets64strm 412s Positions file is chr17test.ref153positions 412s Expanding offsetsstrm into counters...done 412s Allocating 1004928 bytes for counterstrm 413s Trying to allocate 66662*4 bytes of memory for positions...succeeded. Building positions in memory. 413s Indexing positions of oligomers in genome chr17test (15 bp every 3 bp), position 0 413s Writing 66662 genomic positions to file ./chr17test/chr17test.ref153positions ... 413s done 415s Running "/usr/lib/gmap/gmapindex" -D "./chr17test" -d chr17test -Q "./chr17test/chr17test.genomecomp" 415s Writing localdb sarrays 417s autopkgtest [17:15:49]: test gmap-tests: -----------------------] 424s gmap-tests PASS 424s autopkgtest [17:15:56]: test gmap-tests: - - - - - - - - - - results - - - - - - - - - - 430s autopkgtest [17:16:02]: @@@@@@@@@@@@@@@@@@@@ summary 430s gmap-tests PASS 476s nova [W] Using flock in scalingstack-bos02-ppc64el 476s Creating nova instance adt-oracular-ppc64el-gmap-20240712-170852-juju-7f2275-prod-proposed-migration-environment-2-2ec113cf-a32e-4916-80d9-bd4112e68fca from image adt/ubuntu-oracular-ppc64el-server-20240711.img (UUID 9c30bb8c-2214-40db-9e25-a03aa1f5d53f)...