0s autopkgtest [19:49:09]: starting date and time: 2024-03-14 19:49:09+0000 0s autopkgtest [19:49:09]: git checkout: b506e79c ssh-setup/nova: fix ARCH having two lines of data 0s autopkgtest [19:49:09]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.enaxlxdj/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:fftw3,src:openmpi,src:pmix --apt-upgrade relion --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=fftw3/3.3.10-1ubuntu2 openmpi/4.1.6-5.1ubuntu3 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@bos02-ppc64el-20.secgroup --name adt-noble-ppc64el-relion-20240314-194909-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://ftpmaster.internal/ubuntu/ 125s autopkgtest [19:51:14]: testbed dpkg architecture: ppc64el 126s autopkgtest [19:51:15]: testbed apt version: 2.7.12 126s autopkgtest [19:51:15]: @@@@@@@@@@@@@@@@@@@@ test bed setup 127s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 127s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [48.4 kB] 127s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3020 kB] 128s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [4812 B] 128s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [454 kB] 128s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el Packages [607 kB] 128s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el c-n-f Metadata [3116 B] 128s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el Packages [1372 B] 128s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted ppc64el c-n-f Metadata [116 B] 128s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el Packages [3317 kB] 128s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el c-n-f Metadata [8652 B] 128s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el Packages [42.8 kB] 128s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse ppc64el c-n-f Metadata [116 B] 131s Fetched 7625 kB in 3s (2955 kB/s) 132s Reading package lists... 135s Reading package lists... 135s Building dependency tree... 135s Reading state information... 135s Calculating upgrade... 135s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s Reading package lists... 135s Building dependency tree... 135s Reading state information... 135s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 136s Hit:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease 136s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 136s Hit:3 http://ftpmaster.internal/ubuntu noble-updates InRelease 136s Hit:4 http://ftpmaster.internal/ubuntu noble-security InRelease 137s Reading package lists... 137s Reading package lists... 138s Building dependency tree... 138s Reading state information... 138s Calculating upgrade... 138s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 138s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 142s autopkgtest [19:51:31]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Wed Feb 14 00:33:03 UTC 2024 142s autopkgtest [19:51:31]: @@@@@@@@@@@@@@@@@@@@ apt-source relion 145s Get:1 http://ftpmaster.internal/ubuntu noble/universe relion 3.1.3-3build1 (dsc) [2135 B] 145s Get:2 http://ftpmaster.internal/ubuntu noble/universe relion 3.1.3-3build1 (tar) [2345 kB] 145s Get:3 http://ftpmaster.internal/ubuntu noble/universe relion 3.1.3-3build1 (diff) [12.0 kB] 145s gpgv: Signature made Sat Feb 4 12:33:57 2023 UTC 145s gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D 145s gpgv: Can't check signature: No public key 145s dpkg-source: warning: cannot verify inline signature for ./relion_3.1.3-3build1.dsc: no acceptable signature found 145s autopkgtest [19:51:34]: testing package relion version 3.1.3-3build1 147s autopkgtest [19:51:36]: build not needed 162s autopkgtest [19:51:51]: test command1: preparing testbed 163s Reading package lists... 163s Building dependency tree... 163s Reading state information... 163s Starting pkgProblemResolver with broken count: 0 163s Starting 2 pkgProblemResolver with broken count: 0 163s Done 164s The following additional packages will be installed: 164s libamd-comgr2 libamdhip64-5 libdeflate0 libdrm-amdgpu1 164s libevent-pthreads-2.1-7 libfabric1 libfftw3-double3 libfftw3-single3 164s libgomp1 libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libjbig0 164s libjpeg-turbo8 libjpeg8 liblerc4 libllvm17 libmunge2 libopenmpi3t64 164s libpciaccess0 libpmix2t64 librdmacm1t64 libsharpyuv0 libtiff6 libucx0 164s libwebp7 libxnvctrl0 ocl-icd-libopencl1 openmpi-bin openmpi-common relion 164s Suggested packages: 164s libfftw3-bin libfftw3-dev opencl-icd gfortran | fortran-compiler 164s The following NEW packages will be installed: 164s autopkgtest-satdep libamd-comgr2 libamdhip64-5 libdeflate0 libdrm-amdgpu1 164s libevent-pthreads-2.1-7 libfabric1 libfftw3-double3 libfftw3-single3 164s libgomp1 libhsa-runtime64-1 libhsakmt1 libhwloc-plugins libhwloc15 libjbig0 164s libjpeg-turbo8 libjpeg8 liblerc4 libllvm17 libmunge2 libopenmpi3t64 164s libpciaccess0 libpmix2t64 librdmacm1t64 libsharpyuv0 libtiff6 libucx0 164s libwebp7 libxnvctrl0 ocl-icd-libopencl1 openmpi-bin openmpi-common relion 164s 0 upgraded, 33 newly installed, 0 to remove and 0 not upgraded. 164s Need to get 69.9 MB/69.9 MB of archives. 164s After this operation, 352 MB of additional disk space will be used. 164s Get:1 /tmp/autopkgtest.5moh26/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [708 B] 164s Get:2 http://ftpmaster.internal/ubuntu noble/main ppc64el libllvm17 ppc64el 1:17.0.6-5build1 [27.3 MB] 166s Get:3 http://ftpmaster.internal/ubuntu noble/universe ppc64el libamd-comgr2 ppc64el 6.0+git20231212.4510c28+dfsg-3 [15.3 MB] 166s Get:4 http://ftpmaster.internal/ubuntu noble/main ppc64el libdrm-amdgpu1 ppc64el 2.4.120-2 [24.5 kB] 166s Get:5 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhsakmt1 ppc64el 5.7.0-1 [76.5 kB] 166s Get:6 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhsa-runtime64-1 ppc64el 5.7.1-1 [330 kB] 166s Get:7 http://ftpmaster.internal/ubuntu noble/universe ppc64el libamdhip64-5 ppc64el 5.2.3-12 [5004 kB] 166s Get:8 http://ftpmaster.internal/ubuntu noble/main ppc64el libdeflate0 ppc64el 1.19-1 [61.9 kB] 166s Get:9 http://ftpmaster.internal/ubuntu noble/main ppc64el libevent-pthreads-2.1-7 ppc64el 2.1.12-stable-9 [7844 B] 166s Get:10 http://ftpmaster.internal/ubuntu noble/main ppc64el librdmacm1t64 ppc64el 50.0-2 [80.9 kB] 166s Get:11 http://ftpmaster.internal/ubuntu noble/universe ppc64el libfabric1 ppc64el 1.17.0-3 [677 kB] 166s Get:12 http://ftpmaster.internal/ubuntu noble/main ppc64el libgomp1 ppc64el 14-20240303-1ubuntu1 [161 kB] 166s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libfftw3-double3 ppc64el 3.3.10-1ubuntu2 [443 kB] 166s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/main ppc64el libfftw3-single3 ppc64el 3.3.10-1ubuntu2 [453 kB] 166s Get:15 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhwloc15 ppc64el 2.10.0-1 [216 kB] 166s Get:16 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu1 [212 kB] 166s Get:17 http://ftpmaster.internal/ubuntu noble/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B] 167s Get:18 http://ftpmaster.internal/ubuntu noble/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu1 [266 kB] 167s Get:19 http://ftpmaster.internal/ubuntu noble/universe ppc64el libmunge2 ppc64el 0.5.15-3ubuntu1 [17.6 kB] 167s Get:20 http://ftpmaster.internal/ubuntu noble/main ppc64el libpciaccess0 ppc64el 0.17-3 [20.8 kB] 167s Get:21 http://ftpmaster.internal/ubuntu noble/main ppc64el libxnvctrl0 ppc64el 510.47.03-0ubuntu1 [11.7 kB] 167s Get:22 http://ftpmaster.internal/ubuntu noble/universe ppc64el ocl-icd-libopencl1 ppc64el 2.3.2-1 [41.7 kB] 167s Get:23 http://ftpmaster.internal/ubuntu noble/universe ppc64el libhwloc-plugins ppc64el 2.10.0-1 [17.3 kB] 167s Get:24 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libpmix2t64 ppc64el 5.0.1-4.1 [765 kB] 167s Get:25 http://ftpmaster.internal/ubuntu noble/universe ppc64el libucx0 ppc64el 1.16.0+ds-4 [1203 kB] 167s Get:26 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el libopenmpi3t64 ppc64el 4.1.6-5.1ubuntu4 [2721 kB] 167s Get:27 http://ftpmaster.internal/ubuntu noble/main ppc64el libsharpyuv0 ppc64el 1.3.2-0.4 [28.7 kB] 167s Get:28 http://ftpmaster.internal/ubuntu noble/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu1 [34.7 kB] 167s Get:29 http://ftpmaster.internal/ubuntu noble/main ppc64el libwebp7 ppc64el 1.3.2-0.4 [312 kB] 167s Get:30 http://ftpmaster.internal/ubuntu noble/main ppc64el libtiff6 ppc64el 4.5.1+git230720-3ubuntu1 [323 kB] 167s Get:31 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el openmpi-common all 4.1.6-5.1ubuntu4 [170 kB] 167s Get:32 http://ftpmaster.internal/ubuntu noble-proposed/universe ppc64el openmpi-bin ppc64el 4.1.6-5.1ubuntu4 [118 kB] 167s Get:33 http://ftpmaster.internal/ubuntu noble/universe ppc64el relion ppc64el 3.1.3-3build1 [13.5 MB] 167s Fetched 69.9 MB in 3s (20.1 MB/s) 167s Selecting previously unselected package libllvm17:ppc64el. 168s (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.) 168s Preparing to unpack .../00-libllvm17_1%3a17.0.6-5build1_ppc64el.deb ... 168s Unpacking libllvm17:ppc64el (1:17.0.6-5build1) ... 168s Selecting previously unselected package libamd-comgr2:ppc64el. 168s Preparing to unpack .../01-libamd-comgr2_6.0+git20231212.4510c28+dfsg-3_ppc64el.deb ... 168s Unpacking libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3) ... 169s Selecting previously unselected package libdrm-amdgpu1:ppc64el. 169s Preparing to unpack .../02-libdrm-amdgpu1_2.4.120-2_ppc64el.deb ... 169s Unpacking libdrm-amdgpu1:ppc64el (2.4.120-2) ... 169s Selecting previously unselected package libhsakmt1:ppc64el. 169s Preparing to unpack .../03-libhsakmt1_5.7.0-1_ppc64el.deb ... 169s Unpacking libhsakmt1:ppc64el (5.7.0-1) ... 169s Selecting previously unselected package libhsa-runtime64-1. 169s Preparing to unpack .../04-libhsa-runtime64-1_5.7.1-1_ppc64el.deb ... 169s Unpacking libhsa-runtime64-1 (5.7.1-1) ... 169s Selecting previously unselected package libamdhip64-5. 169s Preparing to unpack .../05-libamdhip64-5_5.2.3-12_ppc64el.deb ... 169s Unpacking libamdhip64-5 (5.2.3-12) ... 169s Selecting previously unselected package libdeflate0:ppc64el. 169s Preparing to unpack .../06-libdeflate0_1.19-1_ppc64el.deb ... 169s Unpacking libdeflate0:ppc64el (1.19-1) ... 169s Selecting previously unselected package libevent-pthreads-2.1-7:ppc64el. 169s Preparing to unpack .../07-libevent-pthreads-2.1-7_2.1.12-stable-9_ppc64el.deb ... 169s Unpacking libevent-pthreads-2.1-7:ppc64el (2.1.12-stable-9) ... 169s Selecting previously unselected package librdmacm1t64:ppc64el. 169s Preparing to unpack .../08-librdmacm1t64_50.0-2_ppc64el.deb ... 169s Unpacking librdmacm1t64:ppc64el (50.0-2) ... 169s Selecting previously unselected package libfabric1:ppc64el. 169s Preparing to unpack .../09-libfabric1_1.17.0-3_ppc64el.deb ... 169s Unpacking libfabric1:ppc64el (1.17.0-3) ... 169s Selecting previously unselected package libgomp1:ppc64el. 169s Preparing to unpack .../10-libgomp1_14-20240303-1ubuntu1_ppc64el.deb ... 169s Unpacking libgomp1:ppc64el (14-20240303-1ubuntu1) ... 169s Selecting previously unselected package libfftw3-double3:ppc64el. 169s Preparing to unpack .../11-libfftw3-double3_3.3.10-1ubuntu2_ppc64el.deb ... 169s Unpacking libfftw3-double3:ppc64el (3.3.10-1ubuntu2) ... 169s Selecting previously unselected package libfftw3-single3:ppc64el. 169s Preparing to unpack .../12-libfftw3-single3_3.3.10-1ubuntu2_ppc64el.deb ... 169s Unpacking libfftw3-single3:ppc64el (3.3.10-1ubuntu2) ... 169s Selecting previously unselected package libhwloc15:ppc64el. 169s Preparing to unpack .../13-libhwloc15_2.10.0-1_ppc64el.deb ... 169s Unpacking libhwloc15:ppc64el (2.10.0-1) ... 169s Selecting previously unselected package libjpeg-turbo8:ppc64el. 169s Preparing to unpack .../14-libjpeg-turbo8_2.1.5-2ubuntu1_ppc64el.deb ... 169s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 169s Selecting previously unselected package libjpeg8:ppc64el. 169s Preparing to unpack .../15-libjpeg8_8c-2ubuntu11_ppc64el.deb ... 169s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ... 169s Selecting previously unselected package liblerc4:ppc64el. 169s Preparing to unpack .../16-liblerc4_4.0.0+ds-4ubuntu1_ppc64el.deb ... 169s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 169s Selecting previously unselected package libmunge2:ppc64el. 169s Preparing to unpack .../17-libmunge2_0.5.15-3ubuntu1_ppc64el.deb ... 169s Unpacking libmunge2:ppc64el (0.5.15-3ubuntu1) ... 169s Selecting previously unselected package libpciaccess0:ppc64el. 169s Preparing to unpack .../18-libpciaccess0_0.17-3_ppc64el.deb ... 169s Unpacking libpciaccess0:ppc64el (0.17-3) ... 169s Selecting previously unselected package libxnvctrl0:ppc64el. 169s Preparing to unpack .../19-libxnvctrl0_510.47.03-0ubuntu1_ppc64el.deb ... 169s Unpacking libxnvctrl0:ppc64el (510.47.03-0ubuntu1) ... 169s Selecting previously unselected package ocl-icd-libopencl1:ppc64el. 169s Preparing to unpack .../20-ocl-icd-libopencl1_2.3.2-1_ppc64el.deb ... 169s Unpacking ocl-icd-libopencl1:ppc64el (2.3.2-1) ... 169s Selecting previously unselected package libhwloc-plugins:ppc64el. 169s Preparing to unpack .../21-libhwloc-plugins_2.10.0-1_ppc64el.deb ... 169s Unpacking libhwloc-plugins:ppc64el (2.10.0-1) ... 169s Selecting previously unselected package libpmix2t64:ppc64el. 169s Preparing to unpack .../22-libpmix2t64_5.0.1-4.1_ppc64el.deb ... 169s Unpacking libpmix2t64:ppc64el (5.0.1-4.1) ... 169s Selecting previously unselected package libucx0:ppc64el. 169s Preparing to unpack .../23-libucx0_1.16.0+ds-4_ppc64el.deb ... 169s Unpacking libucx0:ppc64el (1.16.0+ds-4) ... 169s Selecting previously unselected package libopenmpi3t64:ppc64el. 169s Preparing to unpack .../24-libopenmpi3t64_4.1.6-5.1ubuntu4_ppc64el.deb ... 169s Unpacking libopenmpi3t64:ppc64el (4.1.6-5.1ubuntu4) ... 170s Selecting previously unselected package libsharpyuv0:ppc64el. 170s Preparing to unpack .../25-libsharpyuv0_1.3.2-0.4_ppc64el.deb ... 170s Unpacking libsharpyuv0:ppc64el (1.3.2-0.4) ... 170s Selecting previously unselected package libjbig0:ppc64el. 170s Preparing to unpack .../26-libjbig0_2.1-6.1ubuntu1_ppc64el.deb ... 170s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu1) ... 170s Selecting previously unselected package libwebp7:ppc64el. 170s Preparing to unpack .../27-libwebp7_1.3.2-0.4_ppc64el.deb ... 170s Unpacking libwebp7:ppc64el (1.3.2-0.4) ... 170s Selecting previously unselected package libtiff6:ppc64el. 170s Preparing to unpack .../28-libtiff6_4.5.1+git230720-3ubuntu1_ppc64el.deb ... 170s Unpacking libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 170s Selecting previously unselected package openmpi-common. 170s Preparing to unpack .../29-openmpi-common_4.1.6-5.1ubuntu4_all.deb ... 170s Unpacking openmpi-common (4.1.6-5.1ubuntu4) ... 170s Selecting previously unselected package openmpi-bin. 170s Preparing to unpack .../30-openmpi-bin_4.1.6-5.1ubuntu4_ppc64el.deb ... 170s Unpacking openmpi-bin (4.1.6-5.1ubuntu4) ... 170s Selecting previously unselected package relion. 170s Preparing to unpack .../31-relion_3.1.3-3build1_ppc64el.deb ... 170s Unpacking relion (3.1.3-3build1) ... 170s Selecting previously unselected package autopkgtest-satdep. 170s Preparing to unpack .../32-1-autopkgtest-satdep.deb ... 170s Unpacking autopkgtest-satdep (0) ... 170s Setting up libsharpyuv0:ppc64el (1.3.2-0.4) ... 170s Setting up libpciaccess0:ppc64el (0.17-3) ... 170s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu1) ... 170s Setting up libdeflate0:ppc64el (1.19-1) ... 170s Setting up libgomp1:ppc64el (14-20240303-1ubuntu1) ... 170s Setting up libjbig0:ppc64el (2.1-6.1ubuntu1) ... 170s Setting up libxnvctrl0:ppc64el (510.47.03-0ubuntu1) ... 170s Setting up libmunge2:ppc64el (0.5.15-3ubuntu1) ... 170s Setting up libhwloc15:ppc64el (2.10.0-1) ... 170s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu1) ... 170s Setting up libfftw3-double3:ppc64el (3.3.10-1ubuntu2) ... 170s Setting up libwebp7:ppc64el (1.3.2-0.4) ... 170s Setting up ocl-icd-libopencl1:ppc64el (2.3.2-1) ... 170s Setting up openmpi-common (4.1.6-5.1ubuntu4) ... 170s Setting up librdmacm1t64:ppc64el (50.0-2) ... 170s Setting up libllvm17:ppc64el (1:17.0.6-5build1) ... 170s Setting up libevent-pthreads-2.1-7:ppc64el (2.1.12-stable-9) ... 170s Setting up libdrm-amdgpu1:ppc64el (2.4.120-2) ... 170s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ... 170s Setting up libfabric1:ppc64el (1.17.0-3) ... 170s Setting up libfftw3-single3:ppc64el (3.3.10-1ubuntu2) ... 170s Setting up libhwloc-plugins:ppc64el (2.10.0-1) ... 170s Setting up libpmix2t64:ppc64el (5.0.1-4.1) ... 170s Setting up libtiff6:ppc64el (4.5.1+git230720-3ubuntu1) ... 170s Setting up libamd-comgr2:ppc64el (6.0+git20231212.4510c28+dfsg-3) ... 170s Setting up libhsakmt1:ppc64el (5.7.0-1) ... 170s Setting up libhsa-runtime64-1 (5.7.1-1) ... 170s Setting up libamdhip64-5 (5.2.3-12) ... 170s Setting up libucx0:ppc64el (1.16.0+ds-4) ... 170s Setting up libopenmpi3t64:ppc64el (4.1.6-5.1ubuntu4) ... 170s Setting up openmpi-bin (4.1.6-5.1ubuntu4) ... 170s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 170s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 170s Setting up relion (3.1.3-3build1) ... 170s Setting up autopkgtest-satdep (0) ... 170s Processing triggers for man-db (2.12.0-3) ... 171s Processing triggers for libc-bin (2.39-0ubuntu2) ... 173s (Reading database ... 70762 files and directories currently installed.) 173s Removing autopkgtest-satdep (0) ... 174s autopkgtest [19:52:03]: test command1: /usr/bin/relion_refine 174s autopkgtest [19:52:03]: test command1: [----------------------- 174s +++ RELION: command line arguments (with defaults for optional ones between parentheses) +++ 174s ====== General options ===== 174s --i () : Input images (in a star-file) 174s --o () : Output rootname 174s --iter (50) : Maximum number of iterations to perform 174s --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) 174s --K (1) : Number of references to be refined 174s --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) 174s --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) 174s --flatten_solvent (false) : Perform masking on the references as well? 174s --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) 174s --solvent_mask2 (None) : User-provided secondary mask (with its own average density) 174s --lowpass_mask (None) : User-provided mask for low-pass filtering 174s --lowpass (0) : User-provided cutoff for region specified above 174s --tau (None) : STAR file with input tau2-spectrum (to be kept constant) 174s --local_symmetry (None) : Local symmetry description file containing list of masks and their operators 174s --split_random_halves (false) : Refine two random halves of the data completely separately 174s --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations 174s ====== Initialisation ===== 174s --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) 174s --denovo_3dref (false) : Make an initial 3D model from randomly oriented 2D particles 174s --offset (10) : Initial estimated stddev for the origin offsets (in Angstroms) 174s --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) 174s --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration 174s ====== Orientations ===== 174s --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) 174s --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc 174s --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) 174s --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views 174s --sym (c1) : Symmetry group 174s --relax_sym () : Symmetry to be relaxed 174s --offset_range (6) : Search range for origin offsets (in pixels) 174s --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) 174s --helical_offset_step (-1) : Sampling rate (before oversampling) for offsets along helical axis (in Angstroms) 174s --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) 174s --auto_refine (false) : Perform 3D auto-refine procedure? 174s --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches 174s --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) 174s --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) 174s --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) 174s --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) 174s --skip_align (false) : Skip orientational assignment (only classify)? 174s --skip_rotate (false) : Skip rotational assignment (only translate and classify)? 174s --bimodal_psi (false) : Do bimodal searches of psi angle? 174s ====== Helical reconstruction (in development...) ===== 174s --helix (false) : Perform 3D classification or refinement for helices? 174s --ignore_helical_symmetry (false) : Ignore helical symmetry? 174s --helical_nr_asu (1) : Number of new helical asymmetric units (asu) per box (1 means no helical symmetry is present) 174s --helical_twist_initial (0.) : Helical twist (in degrees, positive values for right-handedness) 174s --helical_twist_min (0.) : Minimum helical twist (in degrees, positive values for right-handedness) 174s --helical_twist_max (0.) : Maximum helical twist (in degrees, positive values for right-handedness) 174s --helical_twist_inistep (0.) : Initial step of helical twist search (in degrees) 174s --helical_rise_initial (0.) : Helical rise (in Angstroms) 174s --helical_rise_min (0.) : Minimum helical rise (in Angstroms) 174s --helical_rise_max (0.) : Maximum helical rise (in Angstroms) 174s --helical_rise_inistep (0.) : Initial step of helical rise search (in Angstroms) 174s --helical_nstart (1) : N-number for the N-start helix (only useful for rotational priors) 174s --helical_z_percentage (0.3) : This box length along the center of Z axis contains good information of the helix. Important in imposing and refining symmetry 174s --helical_inner_diameter (-1.) : Inner diameter of helical tubes in Angstroms (for masks of helical references and particles) 174s --helical_outer_diameter (-1.) : Outer diameter of helical tubes in Angstroms (for masks of helical references and particles) 174s --helical_symmetry_search (false) : Perform local refinement of helical symmetry? 174s --helical_sigma_distance (-1.) : Sigma of distance along the helical tracks 174s --helical_keep_tilt_prior_fixed (false) : Keep helical tilt priors fixed (at 90 degrees) in global angular searches? 174s --helical_exclude_resols () : Resolutions (in A) along helical axis to exclude from refinement (comma-separated pairs, e.g. 50-5) 174s --fourier_mask (None) : Originally-sized, FFTW-centred image with Fourier mask for Projector 174s ====== Corrections ===== 174s --ctf (false) : Perform CTF correction? 174s --pad_ctf (false) : Perform CTF padding to treat CTF aliaising better? 174s --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? 174s --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? 174s --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? 174s --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) 174s --norm (false) : Perform normalisation-error correction? 174s --scale (false) : Perform intensity-scale corrections on image groups? 174s --no_norm (false) : Switch off normalisation-error correction? 174s --no_scale (false) : Switch off intensity-scale corrections on image groups? 174s ====== Stochastic Gradient Descent ===== 174s --sgd (false) : Perform stochastic gradient descent instead of default expectation-maximization 174s --stochastic_em (false) : Perform stochastic EM instead of SGD to avoid patent problems for initial model generation by commercial users 174s --sgd_ini_iter (50) : Number of initial SGD iterations 174s --sgd_fin_iter (50) : Number of final SGD iterations 174s --sgd_inbetween_iter (200) : Number of SGD iterations between the initial and final ones 174s --sgd_ini_resol (35) : Resolution cutoff during the initial SGD iterations (A) 174s --sgd_fin_resol (15) : Resolution cutoff during the final SGD iterations (A) 174s --sgd_ini_subset (100) : Mini-batch size during the initial SGD iterations 174s --sgd_fin_subset (500) : Mini-batch size during the final SGD iterations 174s --mu (0.9) : Momentum parameter for SGD updates 174s --sgd_stepsize (0.5) : Step size parameter for SGD updates 174s --sgd_sigma2fudge_initial (8) : Initial factor by which the noise variance will be multiplied for SGD (not used if halftime is negative) 174s --sgd_sigma2fudge_halflife (-1) : Initialise SGD with 8x higher noise-variance, and reduce with this half-life in # of particles (default is keep normal variance) 174s --sgd_skip_anneal (false) : By default, multiple references are annealed during the in_between iterations. Use this option to switch annealing off 174s --sgd_write_iter (1) : Write out model every so many iterations in SGD (default is writing out all iters) 174s ====== Computation ===== 174s --pool (1) : Number of images to pool for each thread task 174s --j (1) : Number of threads to run in parallel (only useful on multi-core machines) 174s --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc 174s --onthefly_shifts (false) : Calculate shifted images on-the-fly, do not store precalculated ones in memory 174s --no_parallel_disc_io (false) : Do NOT let parallel (MPI) processes access the disc simultaneously (use this option with NFS) 174s --preread_images (false) : Use this to let the leader process read all particles into memory. Be careful you have enough RAM for large data sets! 174s --scratch_dir () : If provided, particle stacks will be copied to this local scratch disk prior to refinement. 174s --keep_free_scratch (10) : Space available for copying particle stacks (in Gb) 174s --reuse_scratch (false) : Re-use data on scratchdir, instead of wiping it and re-copying all data. 174s --keep_scratch (false) : Don't remove scratch after convergence. Following jobs that use EXACTLY the same particles should use --reuse_scratch. 174s --fast_subsets (false) : Use faster optimisation by using subsets of the data in the first 15 iterations 174s --gpu (false) : Use available gpu resources for some calculations 174s --free_gpu_memory (0) : GPU device memory (in Mb) to leave free after allocation. 174s ====== Expert options ===== 174s --pad (2) : Oversampling factor for the Fourier transforms of the references 174s --ref_angpix (-1.) : Pixel size (in A) for the input reference (default is to read from header) 174s --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? 174s --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation 174s --verb (1) : Verbosity (1=normal, 0=silent) 174s --random_seed (-1) : Number for the random seed generator 174s --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach 174s --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling 174s --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) 174s --fix_sigma_noise (false) : Fix the experimental noise spectra? 174s --fix_sigma_offset (false) : Fix the stddev in the origin offsets? 174s --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement 174s --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit 174s --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit 174s --strict_highres_exp (-1) : High resolution limit (in Angstrom) to restrict probability calculations in the expectation step 174s --strict_lowres_exp (-1) : Low resolution limit (in Angstrom) to restrict probability calculations in the expectation step 174s --dont_check_norm (false) : Skip the check whether the images are normalised correctly 174s --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) 174s --solvent_correct_fsc (false) : Correct FSC curve for the effects of the solvent mask? 174s --skip_maximize (false) : Skip maximization step (only write out data.star file)? 174s --failsafe_threshold (40) : Maximum number of particles permitted to be handled by fail-safe mode, due to zero sum of weights, before exiting with an error (GPU only). 174s --external_reconstruct (false) : Perform the reconstruction step outside relion_refine, e.g. for learned priors?) 174s --auto_iter_max (999) : In auto-refinement, stop at this iteration. 174s --auto_ignore_angles (false) : In auto-refinement, update angular sampling regardless of changes in orientations for convergence. This makes convergence faster. 174s --auto_resol_angles (false) : In auto-refinement, update angular sampling based on resolution-based required sampling. This makes convergence faster. 174s --allow_coarser_sampling (false) : In 2D/3D classification, allow coarser angular and translational samplings if accuracies are bad (typically in earlier iterations. 174s --trust_ref_size (false) : Trust the pixel and box size of the input reference; by default the program will die if these are different from the first optics group of the data 174s --maxsig (-1) : Maximum number of poses & translations to consider 174s --skip_gridding (false) : Skip gridding in the M step 174s --version : Print RELION version and exit 175s autopkgtest [19:52:04]: test command1: -----------------------] 175s autopkgtest [19:52:04]: test command1: - - - - - - - - - - results - - - - - - - - - - 175s command1 PASS (superficial) 176s autopkgtest [19:52:05]: @@@@@@@@@@@@@@@@@@@@ summary 176s command1 PASS (superficial) 192s Creating nova instance adt-noble-ppc64el-relion-20240314-194909-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-ppc64el-server-20240314.img (UUID a031584c-aec8-4412-bff6-4238354f4d17)...