0s autopkgtest [00:31:41]: starting date: 2024-03-19 0s autopkgtest [00:31:41]: git checkout: d9c0295b adt_testbed.py: supress warnings from apt using a shell pipeline 0s autopkgtest [00:31:41]: host juju-7f2275-prod-proposed-migration-environment-4; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.7qkcp8ip/out --timeout-copy=6000 --setup-commands 'sed -i "s/ports.ubuntu.com/ftpmaster.internal/; s/ubuntu-ports/ubuntu/" /etc/apt/sources.list `ls /etc/apt/sources.list.d/*.list 2>/dev/null || true`; ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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\n" >> /etc/environment' --apt-pocket=proposed=src:openmpi,src:ampliconnoise,src:eztrace,src:gatb-core,src:gyoto,src:murasaki,src:pmix --apt-upgrade relion --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' -- lxd -r lxd-armhf-10.44.124.23 lxd-armhf-10.44.124.23:autopkgtest/ubuntu/noble/armhf 57s autopkgtest [00:32:38]: @@@@@@@@@@@@@@@@@@@@ test bed setup 60s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 61s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3736 kB] 65s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 65s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [485 kB] 65s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [52.0 kB] 65s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf Packages [585 kB] 65s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf c-n-f Metadata [2492 B] 65s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf Packages [1372 B] 65s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted armhf c-n-f Metadata [116 B] 65s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf Packages [3609 kB] 68s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf c-n-f Metadata [7776 B] 68s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf Packages [35.6 kB] 68s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse armhf c-n-f Metadata [116 B] 79s Fetched 8639 kB in 9s (993 kB/s) 82s Reading package lists... 101s tee: /proc/self/fd/2: Permission denied 134s Hit:1 http://ports.ubuntu.com/ubuntu-ports noble InRelease 134s Hit:2 http://ftpmaster.internal/ubuntu noble InRelease 134s Hit:3 http://ports.ubuntu.com/ubuntu-ports noble-updates InRelease 134s Hit:4 http://ftpmaster.internal/ubuntu noble-updates InRelease 134s Hit:5 http://ftpmaster.internal/ubuntu noble-security InRelease 134s Hit:6 http://ports.ubuntu.com/ubuntu-ports noble-backports InRelease 134s Hit:7 http://ftpmaster.internal/ubuntu noble-proposed InRelease 134s Hit:8 http://ports.ubuntu.com/ubuntu-ports noble-security InRelease 141s Reading package lists... 142s Reading package lists... 143s Building dependency tree... 143s Reading state information... 144s Calculating upgrade... 145s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 146s Reading package lists... 146s Building dependency tree... 146s Reading state information... 148s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 150s autopkgtest [00:34:11]: rebooting testbed after setup commands that affected boot 190s autopkgtest [00:34:51]: testbed running kernel: Linux 5.4.0-173-generic #191-Ubuntu SMP Fri Feb 2 13:54:37 UTC 2024 195s autopkgtest [00:34:56]: testbed dpkg architecture: armhf 214s autopkgtest [00:35:15]: @@@@@@@@@@@@@@@@@@@@ apt-source relion 226s Get:1 http://ftpmaster.internal/ubuntu noble/universe relion 3.1.3-3build1 (dsc) [2135 B] 226s Get:2 http://ftpmaster.internal/ubuntu noble/universe relion 3.1.3-3build1 (tar) [2345 kB] 226s Get:3 http://ftpmaster.internal/ubuntu noble/universe relion 3.1.3-3build1 (diff) [12.0 kB] 227s gpgv: Signature made Sat Feb 4 12:33:57 2023 UTC 227s gpgv: using RSA key 4D0BE12F0E4776D8AACE9696E66C775AEBFE6C7D 227s gpgv: Can't check signature: No public key 227s dpkg-source: warning: cannot verify inline signature for ./relion_3.1.3-3build1.dsc: no acceptable signature found 229s autopkgtest [00:35:30]: testing package relion version 3.1.3-3build1 229s autopkgtest [00:35:30]: build not needed 238s autopkgtest [00:35:39]: test command1: preparing testbed 259s Reading package lists... 260s Building dependency tree... 260s Reading state information... 261s Correcting dependencies...Starting pkgProblemResolver with broken count: 2 262s Starting 2 pkgProblemResolver with broken count: 2 262s Investigating (0) libpmix2t64:armhf < none -> 5.0.1-4.1 @un uN Ib > 262s Broken libpmix2t64:armhf Breaks on libpmix2:armhf < none -> 5.0.1-4 @un uN > (< 5.0.1-4.1) 262s Considering libpmix2:armhf -1 as a solution to libpmix2t64:armhf 0 262s Added libpmix2:armhf to the remove list 262s Fixing libpmix2t64:armhf via keep of libpmix2:armhf 262s Investigating (0) libopenmpi3t64:armhf < none -> 4.1.6-7ubuntu1 @un uN Ib > 262s Broken libopenmpi3t64:armhf Breaks on libopenmpi3:armhf < none -> 4.1.6-5ubuntu1 @un uN Ib > (< 4.1.6-7ubuntu1) 262s Considering libopenmpi3:armhf -1 as a solution to libopenmpi3t64:armhf 0 262s Added libopenmpi3:armhf to the remove list 262s Fixing libopenmpi3t64:armhf via keep of libopenmpi3:armhf 262s Investigating (1) relion:armhf < none -> 3.1.3-3build1 @un uN Ib > 262s Broken relion:armhf Depends on libopenmpi3:armhf < none | 4.1.6-5ubuntu1 @un uH > (>= 4.1.4) 262s Considering libopenmpi3:armhf -1 as a solution to relion:armhf 0 262s Holding Back relion:armhf rather than change libopenmpi3:armhf 262s Investigating (1) autopkgtest-satdep:armhf < 0 @iU K Nb Ib > 262s Broken autopkgtest-satdep:armhf Depends on relion:armhf < none | 3.1.3-3build1 @un uH > 262s Considering relion:armhf 0 as a solution to autopkgtest-satdep:armhf -2 262s Removing autopkgtest-satdep:armhf rather than change relion:armhf 262s Done 263s Done 264s Starting pkgProblemResolver with broken count: 0 264s Starting 2 pkgProblemResolver with broken count: 0 264s Done 266s The following packages will be REMOVED: 266s autopkgtest-satdep 267s 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. 267s 1 not fully installed or removed. 267s After this operation, 0 B of additional disk space will be used. 267s (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 ... 58620 files and directories currently installed.) 267s Removing autopkgtest-satdep (0) ... 273s autopkgtest: WARNING: package relion is not installed though it should be 276s autopkgtest: WARNING: Test dependencies are unsatisfiable with using apt pinning. Retrying with using all packages from noble-proposed 287s Reading package lists... 288s Building dependency tree... 288s Reading state information... 289s Correcting dependencies...Starting pkgProblemResolver with broken count: 0 290s Starting 2 pkgProblemResolver with broken count: 0 290s Done 291s Done 292s Starting pkgProblemResolver with broken count: 0 292s Starting 2 pkgProblemResolver with broken count: 0 292s Done 294s The following additional packages will be installed: 294s gcc-14-base libdeflate0 libevent-core-2.1-7 libevent-pthreads-2.1-7 294s libfabric1 libfftw3-double3 libfftw3-single3 libgcc-s1 libgomp1 294s libhwloc-plugins libhwloc15 libjbig0 libjpeg-turbo8 libjpeg8 liblerc4 294s libmunge2 libopenmpi3t64 libpciaccess0 libpmix2t64 librdmacm1t64 294s libsharpyuv0 libstdc++6 libtiff6 libwebp7 libxnvctrl0 ocl-icd-libopencl1 294s openmpi-bin openmpi-common relion 294s Suggested packages: 294s libfftw3-bin libfftw3-dev opencl-icd gfortran | fortran-compiler 294s The following NEW packages will be installed: 294s libdeflate0 libevent-pthreads-2.1-7 libfabric1 libfftw3-double3 294s libfftw3-single3 libgomp1 libhwloc-plugins libhwloc15 libjbig0 294s libjpeg-turbo8 libjpeg8 liblerc4 libmunge2 libopenmpi3t64 libpciaccess0 294s libpmix2t64 librdmacm1t64 libsharpyuv0 libtiff6 libwebp7 libxnvctrl0 294s ocl-icd-libopencl1 openmpi-bin openmpi-common relion 294s The following packages will be upgraded: 294s gcc-14-base libevent-core-2.1-7 libgcc-s1 libstdc++6 295s 4 upgraded, 25 newly installed, 0 to remove and 223 not upgraded. 295s 1 not fully installed or removed. 295s Need to get 17.7 MB of archives. 295s After this operation, 73.7 MB of additional disk space will be used. 295s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-9build1 [82.3 kB] 295s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-9build1 [7370 B] 295s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main armhf librdmacm1t64 armhf 50.0-2build1 [63.0 kB] 295s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libfabric1 armhf 1.17.0-3build1 [419 kB] 295s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/main armhf gcc-14-base armhf 14-20240315-1ubuntu1 [47.0 kB] 296s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgcc-s1 armhf 14-20240315-1ubuntu1 [41.5 kB] 296s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libstdc++6 armhf 14-20240315-1ubuntu1 [714 kB] 296s Get:8 http://ftpmaster.internal/ubuntu noble/universe armhf libhwloc15 armhf 2.10.0-1 [145 kB] 296s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libmunge2 armhf 0.5.15-4 [17.1 kB] 296s Get:10 http://ftpmaster.internal/ubuntu noble/main armhf libpciaccess0 armhf 0.17-3 [16.3 kB] 296s Get:11 http://ftpmaster.internal/ubuntu noble/main armhf libxnvctrl0 armhf 510.47.03-0ubuntu1 [10.4 kB] 296s Get:12 http://ftpmaster.internal/ubuntu noble/universe armhf ocl-icd-libopencl1 armhf 2.3.2-1 [34.4 kB] 296s Get:13 http://ftpmaster.internal/ubuntu noble/universe armhf libhwloc-plugins armhf 2.10.0-1 [13.7 kB] 296s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libpmix2t64 armhf 5.0.1-4.1 [616 kB] 297s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf libopenmpi3t64 armhf 4.1.6-7ubuntu1 [2041 kB] 297s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf openmpi-common all 4.1.6-7ubuntu1 [170 kB] 297s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf openmpi-bin armhf 4.1.6-7ubuntu1 [83.2 kB] 298s Get:18 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libgomp1 armhf 14-20240315-1ubuntu1 [125 kB] 298s Get:19 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfftw3-double3 armhf 3.3.10-1ubuntu2 [366 kB] 298s Get:20 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libfftw3-single3 armhf 3.3.10-1ubuntu2 [374 kB] 298s Get:21 http://ftpmaster.internal/ubuntu noble/main armhf libdeflate0 armhf 1.19-1 [41.3 kB] 298s Get:22 http://ftpmaster.internal/ubuntu noble/main armhf libjbig0 armhf 2.1-6.1ubuntu1 [24.9 kB] 298s Get:23 http://ftpmaster.internal/ubuntu noble/main armhf libjpeg-turbo8 armhf 2.1.5-2ubuntu1 [123 kB] 298s Get:24 http://ftpmaster.internal/ubuntu noble/main armhf libjpeg8 armhf 8c-2ubuntu11 [2148 B] 298s Get:25 http://ftpmaster.internal/ubuntu noble/main armhf liblerc4 armhf 4.0.0+ds-4ubuntu1 [152 kB] 298s Get:26 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libsharpyuv0 armhf 1.3.2-0.4build1 [13.5 kB] 298s Get:27 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libwebp7 armhf 1.3.2-0.4build1 [183 kB] 298s Get:28 http://ftpmaster.internal/ubuntu noble-proposed/main armhf libtiff6 armhf 4.5.1+git230720-4ubuntu1 [178 kB] 298s Get:29 http://ftpmaster.internal/ubuntu noble-proposed/universe armhf relion armhf 3.1.3-3build2 [11.6 MB] 302s Fetched 17.7 MB in 6s (2891 kB/s) 302s (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 ... 58620 files and directories currently installed.) 302s Preparing to unpack .../libevent-core-2.1-7_2.1.12-stable-9build1_armhf.deb ... 302s Unpacking libevent-core-2.1-7:armhf (2.1.12-stable-9build1) over (2.1.12-stable-9) ... 302s Selecting previously unselected package libevent-pthreads-2.1-7:armhf. 302s Preparing to unpack .../libevent-pthreads-2.1-7_2.1.12-stable-9build1_armhf.deb ... 302s Unpacking libevent-pthreads-2.1-7:armhf (2.1.12-stable-9build1) ... 302s Selecting previously unselected package librdmacm1t64:armhf. 302s Preparing to unpack .../librdmacm1t64_50.0-2build1_armhf.deb ... 302s Unpacking librdmacm1t64:armhf (50.0-2build1) ... 302s Selecting previously unselected package libfabric1:armhf. 302s Preparing to unpack .../libfabric1_1.17.0-3build1_armhf.deb ... 302s Unpacking libfabric1:armhf (1.17.0-3build1) ... 302s Preparing to unpack .../gcc-14-base_14-20240315-1ubuntu1_armhf.deb ... 302s Unpacking gcc-14-base:armhf (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 303s Setting up gcc-14-base:armhf (14-20240315-1ubuntu1) ... 303s (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 ... 58645 files and directories currently installed.) 303s Preparing to unpack .../libgcc-s1_14-20240315-1ubuntu1_armhf.deb ... 303s Unpacking libgcc-s1:armhf (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 303s Setting up libgcc-s1:armhf (14-20240315-1ubuntu1) ... 303s (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 ... 58645 files and directories currently installed.) 303s Preparing to unpack .../libstdc++6_14-20240315-1ubuntu1_armhf.deb ... 303s Unpacking libstdc++6:armhf (14-20240315-1ubuntu1) over (14-20240303-1ubuntu1) ... 303s Setting up libstdc++6:armhf (14-20240315-1ubuntu1) ... 304s Selecting previously unselected package libhwloc15:armhf. 304s (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 ... 58645 files and directories currently installed.) 304s Preparing to unpack .../00-libhwloc15_2.10.0-1_armhf.deb ... 304s Unpacking libhwloc15:armhf (2.10.0-1) ... 304s Selecting previously unselected package libmunge2:armhf. 304s Preparing to unpack .../01-libmunge2_0.5.15-4_armhf.deb ... 304s Unpacking libmunge2:armhf (0.5.15-4) ... 304s Selecting previously unselected package libpciaccess0:armhf. 304s Preparing to unpack .../02-libpciaccess0_0.17-3_armhf.deb ... 304s Unpacking libpciaccess0:armhf (0.17-3) ... 304s Selecting previously unselected package libxnvctrl0:armhf. 304s Preparing to unpack .../03-libxnvctrl0_510.47.03-0ubuntu1_armhf.deb ... 304s Unpacking libxnvctrl0:armhf (510.47.03-0ubuntu1) ... 304s Selecting previously unselected package ocl-icd-libopencl1:armhf. 304s Preparing to unpack .../04-ocl-icd-libopencl1_2.3.2-1_armhf.deb ... 304s Unpacking ocl-icd-libopencl1:armhf (2.3.2-1) ... 304s Selecting previously unselected package libhwloc-plugins:armhf. 304s Preparing to unpack .../05-libhwloc-plugins_2.10.0-1_armhf.deb ... 304s Unpacking libhwloc-plugins:armhf (2.10.0-1) ... 304s Selecting previously unselected package libpmix2t64:armhf. 304s Preparing to unpack .../06-libpmix2t64_5.0.1-4.1_armhf.deb ... 304s Unpacking libpmix2t64:armhf (5.0.1-4.1) ... 305s Selecting previously unselected package libopenmpi3t64:armhf. 305s Preparing to unpack .../07-libopenmpi3t64_4.1.6-7ubuntu1_armhf.deb ... 305s Unpacking libopenmpi3t64:armhf (4.1.6-7ubuntu1) ... 305s Selecting previously unselected package openmpi-common. 305s Preparing to unpack .../08-openmpi-common_4.1.6-7ubuntu1_all.deb ... 305s Unpacking openmpi-common (4.1.6-7ubuntu1) ... 305s Selecting previously unselected package openmpi-bin. 305s Preparing to unpack .../09-openmpi-bin_4.1.6-7ubuntu1_armhf.deb ... 305s Unpacking openmpi-bin (4.1.6-7ubuntu1) ... 305s Selecting previously unselected package libgomp1:armhf. 305s Preparing to unpack .../10-libgomp1_14-20240315-1ubuntu1_armhf.deb ... 305s Unpacking libgomp1:armhf (14-20240315-1ubuntu1) ... 305s Selecting previously unselected package libfftw3-double3:armhf. 305s Preparing to unpack .../11-libfftw3-double3_3.3.10-1ubuntu2_armhf.deb ... 305s Unpacking libfftw3-double3:armhf (3.3.10-1ubuntu2) ... 305s Selecting previously unselected package libfftw3-single3:armhf. 305s Preparing to unpack .../12-libfftw3-single3_3.3.10-1ubuntu2_armhf.deb ... 305s Unpacking libfftw3-single3:armhf (3.3.10-1ubuntu2) ... 305s Selecting previously unselected package libdeflate0:armhf. 306s Preparing to unpack .../13-libdeflate0_1.19-1_armhf.deb ... 306s Unpacking libdeflate0:armhf (1.19-1) ... 306s Selecting previously unselected package libjbig0:armhf. 306s Preparing to unpack .../14-libjbig0_2.1-6.1ubuntu1_armhf.deb ... 306s Unpacking libjbig0:armhf (2.1-6.1ubuntu1) ... 306s Selecting previously unselected package libjpeg-turbo8:armhf. 306s Preparing to unpack .../15-libjpeg-turbo8_2.1.5-2ubuntu1_armhf.deb ... 306s Unpacking libjpeg-turbo8:armhf (2.1.5-2ubuntu1) ... 306s Selecting previously unselected package libjpeg8:armhf. 306s Preparing to unpack .../16-libjpeg8_8c-2ubuntu11_armhf.deb ... 306s Unpacking libjpeg8:armhf (8c-2ubuntu11) ... 306s Selecting previously unselected package liblerc4:armhf. 306s Preparing to unpack .../17-liblerc4_4.0.0+ds-4ubuntu1_armhf.deb ... 306s Unpacking liblerc4:armhf (4.0.0+ds-4ubuntu1) ... 306s Selecting previously unselected package libsharpyuv0:armhf. 306s Preparing to unpack .../18-libsharpyuv0_1.3.2-0.4build1_armhf.deb ... 306s Unpacking libsharpyuv0:armhf (1.3.2-0.4build1) ... 306s Selecting previously unselected package libwebp7:armhf. 306s Preparing to unpack .../19-libwebp7_1.3.2-0.4build1_armhf.deb ... 306s Unpacking libwebp7:armhf (1.3.2-0.4build1) ... 306s Selecting previously unselected package libtiff6:armhf. 306s Preparing to unpack .../20-libtiff6_4.5.1+git230720-4ubuntu1_armhf.deb ... 306s Unpacking libtiff6:armhf (4.5.1+git230720-4ubuntu1) ... 307s Selecting previously unselected package relion. 307s Preparing to unpack .../21-relion_3.1.3-3build2_armhf.deb ... 307s Unpacking relion (3.1.3-3build2) ... 308s Setting up libsharpyuv0:armhf (1.3.2-0.4build1) ... 308s Setting up libpciaccess0:armhf (0.17-3) ... 308s Setting up liblerc4:armhf (4.0.0+ds-4ubuntu1) ... 308s Setting up libdeflate0:armhf (1.19-1) ... 308s Setting up libgomp1:armhf (14-20240315-1ubuntu1) ... 308s Setting up libjbig0:armhf (2.1-6.1ubuntu1) ... 308s Setting up libxnvctrl0:armhf (510.47.03-0ubuntu1) ... 308s Setting up libmunge2:armhf (0.5.15-4) ... 308s Setting up libhwloc15:armhf (2.10.0-1) ... 308s Setting up libevent-core-2.1-7:armhf (2.1.12-stable-9build1) ... 308s Setting up libjpeg-turbo8:armhf (2.1.5-2ubuntu1) ... 308s Setting up libfftw3-double3:armhf (3.3.10-1ubuntu2) ... 308s Setting up libwebp7:armhf (1.3.2-0.4build1) ... 308s Setting up ocl-icd-libopencl1:armhf (2.3.2-1) ... 308s Setting up openmpi-common (4.1.6-7ubuntu1) ... 308s Setting up librdmacm1t64:armhf (50.0-2build1) ... 308s Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-9build1) ... 308s Setting up libjpeg8:armhf (8c-2ubuntu11) ... 308s Setting up libfabric1:armhf (1.17.0-3build1) ... 308s Setting up libfftw3-single3:armhf (3.3.10-1ubuntu2) ... 308s Setting up libhwloc-plugins:armhf (2.10.0-1) ... 308s Setting up libpmix2t64:armhf (5.0.1-4.1) ... 308s Setting up libopenmpi3t64:armhf (4.1.6-7ubuntu1) ... 308s Setting up libtiff6:armhf (4.5.1+git230720-4ubuntu1) ... 308s Setting up openmpi-bin (4.1.6-7ubuntu1) ... 308s update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode 308s update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode 308s Setting up relion (3.1.3-3build2) ... 308s Setting up autopkgtest-satdep (0) ... 308s Processing triggers for man-db (2.12.0-3) ... 311s Processing triggers for libc-bin (2.39-0ubuntu2) ... 335s (Reading database ... 59187 files and directories currently installed.) 335s Removing autopkgtest-satdep (0) ... 348s autopkgtest [00:37:29]: test command1: /usr/bin/relion_refine 348s autopkgtest [00:37:29]: test command1: [----------------------- 351s +++ RELION: command line arguments (with defaults for optional ones between parentheses) +++ 351s ====== General options ===== 351s --i () : Input images (in a star-file) 351s --o () : Output rootname 351s --iter (50) : Maximum number of iterations to perform 351s --tau2_fudge (1) : Regularisation parameter (values higher than 1 give more weight to the data) 351s --K (1) : Number of references to be refined 351s --particle_diameter (-1) : Diameter of the circular mask that will be applied to the experimental images (in Angstroms) 351s --zero_mask (false) : Mask surrounding background in particles to zero (by default the solvent area is filled with random noise) 351s --flatten_solvent (false) : Perform masking on the references as well? 351s --solvent_mask (None) : User-provided mask for the references (default is to use spherical mask with particle_diameter) 351s --solvent_mask2 (None) : User-provided secondary mask (with its own average density) 351s --lowpass_mask (None) : User-provided mask for low-pass filtering 351s --lowpass (0) : User-provided cutoff for region specified above 351s --tau (None) : STAR file with input tau2-spectrum (to be kept constant) 351s --local_symmetry (None) : Local symmetry description file containing list of masks and their operators 351s --split_random_halves (false) : Refine two random halves of the data completely separately 351s --low_resol_join_halves (-1) : Resolution (in Angstrom) up to which the two random half-reconstructions will not be independent to prevent diverging orientations 351s ====== Initialisation ===== 351s --ref (None) : Image, stack or star-file with the reference(s). (Compulsory for 3D refinement!) 351s --denovo_3dref (false) : Make an initial 3D model from randomly oriented 2D particles 351s --offset (10) : Initial estimated stddev for the origin offsets (in Angstroms) 351s --firstiter_cc (false) : Perform CC-calculation in the first iteration (use this if references are not on the absolute intensity scale) 351s --ini_high (-1) : Resolution (in Angstroms) to which to limit refinement in the first iteration 351s ====== Orientations ===== 351s --oversampling (1) : Adaptive oversampling order to speed-up calculations (0=no oversampling, 1=2x, 2=4x, etc) 351s --healpix_order (2) : Healpix order for the angular sampling (before oversampling) on the (3D) sphere: hp2=15deg, hp3=7.5deg, etc 351s --psi_step (-1) : Sampling rate (before oversampling) for the in-plane angle (default=10deg for 2D, hp sampling for 3D) 351s --limit_tilt (-91) : Limited tilt angle: positive for keeping side views, negative for keeping top views 351s --sym (c1) : Symmetry group 351s --relax_sym () : Symmetry to be relaxed 351s --offset_range (6) : Search range for origin offsets (in pixels) 351s --offset_step (2) : Sampling rate (before oversampling) for origin offsets (in pixels) 351s --helical_offset_step (-1) : Sampling rate (before oversampling) for offsets along helical axis (in Angstroms) 351s --perturb (0.5) : Perturbation factor for the angular sampling (0=no perturb; 0.5=perturb) 351s --auto_refine (false) : Perform 3D auto-refine procedure? 351s --auto_local_healpix_order (4) : Minimum healpix order (before oversampling) from which autosampling procedure will use local searches 351s --sigma_ang (-1) : Stddev on all three Euler angles for local angular searches (of +/- 3 stddev) 351s --sigma_rot (-1) : Stddev on the first Euler angle for local angular searches (of +/- 3 stddev) 351s --sigma_tilt (-1) : Stddev on the second Euler angle for local angular searches (of +/- 3 stddev) 351s --sigma_psi (-1) : Stddev on the in-plane angle for local angular searches (of +/- 3 stddev) 351s --skip_align (false) : Skip orientational assignment (only classify)? 351s --skip_rotate (false) : Skip rotational assignment (only translate and classify)? 351s --bimodal_psi (false) : Do bimodal searches of psi angle? 351s ====== Helical reconstruction (in development...) ===== 351s --helix (false) : Perform 3D classification or refinement for helices? 351s --ignore_helical_symmetry (false) : Ignore helical symmetry? 351s --helical_nr_asu (1) : Number of new helical asymmetric units (asu) per box (1 means no helical symmetry is present) 351s --helical_twist_initial (0.) : Helical twist (in degrees, positive values for right-handedness) 351s --helical_twist_min (0.) : Minimum helical twist (in degrees, positive values for right-handedness) 351s --helical_twist_max (0.) : Maximum helical twist (in degrees, positive values for right-handedness) 351s --helical_twist_inistep (0.) : Initial step of helical twist search (in degrees) 351s --helical_rise_initial (0.) : Helical rise (in Angstroms) 351s --helical_rise_min (0.) : Minimum helical rise (in Angstroms) 351s --helical_rise_max (0.) : Maximum helical rise (in Angstroms) 351s --helical_rise_inistep (0.) : Initial step of helical rise search (in Angstroms) 351s --helical_nstart (1) : N-number for the N-start helix (only useful for rotational priors) 351s --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 351s --helical_inner_diameter (-1.) : Inner diameter of helical tubes in Angstroms (for masks of helical references and particles) 351s --helical_outer_diameter (-1.) : Outer diameter of helical tubes in Angstroms (for masks of helical references and particles) 351s --helical_symmetry_search (false) : Perform local refinement of helical symmetry? 351s --helical_sigma_distance (-1.) : Sigma of distance along the helical tracks 351s --helical_keep_tilt_prior_fixed (false) : Keep helical tilt priors fixed (at 90 degrees) in global angular searches? 351s --helical_exclude_resols () : Resolutions (in A) along helical axis to exclude from refinement (comma-separated pairs, e.g. 50-5) 351s --fourier_mask (None) : Originally-sized, FFTW-centred image with Fourier mask for Projector 351s ====== Corrections ===== 351s --ctf (false) : Perform CTF correction? 351s --pad_ctf (false) : Perform CTF padding to treat CTF aliaising better? 351s --ctf_intact_first_peak (false) : Ignore CTFs until their first peak? 351s --ctf_corrected_ref (false) : Have the input references been CTF-amplitude corrected? 351s --ctf_phase_flipped (false) : Have the data been CTF phase-flipped? 351s --only_flip_phases (false) : Only perform CTF phase-flipping? (default is full amplitude-correction) 351s --norm (false) : Perform normalisation-error correction? 351s --scale (false) : Perform intensity-scale corrections on image groups? 351s --no_norm (false) : Switch off normalisation-error correction? 351s --no_scale (false) : Switch off intensity-scale corrections on image groups? 351s ====== Stochastic Gradient Descent ===== 351s --sgd (false) : Perform stochastic gradient descent instead of default expectation-maximization 351s --stochastic_em (false) : Perform stochastic EM instead of SGD to avoid patent problems for initial model generation by commercial users 351s --sgd_ini_iter (50) : Number of initial SGD iterations 351s --sgd_fin_iter (50) : Number of final SGD iterations 351s --sgd_inbetween_iter (200) : Number of SGD iterations between the initial and final ones 351s --sgd_ini_resol (35) : Resolution cutoff during the initial SGD iterations (A) 351s --sgd_fin_resol (15) : Resolution cutoff during the final SGD iterations (A) 351s --sgd_ini_subset (100) : Mini-batch size during the initial SGD iterations 351s --sgd_fin_subset (500) : Mini-batch size during the final SGD iterations 351s --mu (0.9) : Momentum parameter for SGD updates 351s --sgd_stepsize (0.5) : Step size parameter for SGD updates 351s --sgd_sigma2fudge_initial (8) : Initial factor by which the noise variance will be multiplied for SGD (not used if halftime is negative) 351s --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) 351s --sgd_skip_anneal (false) : By default, multiple references are annealed during the in_between iterations. Use this option to switch annealing off 351s --sgd_write_iter (1) : Write out model every so many iterations in SGD (default is writing out all iters) 351s ====== Computation ===== 351s --pool (1) : Number of images to pool for each thread task 351s --j (1) : Number of threads to run in parallel (only useful on multi-core machines) 351s --dont_combine_weights_via_disc (false) : Send the large arrays of summed weights through the MPI network, instead of writing large files to disc 351s --onthefly_shifts (false) : Calculate shifted images on-the-fly, do not store precalculated ones in memory 351s --no_parallel_disc_io (false) : Do NOT let parallel (MPI) processes access the disc simultaneously (use this option with NFS) 351s --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! 351s --scratch_dir () : If provided, particle stacks will be copied to this local scratch disk prior to refinement. 351s --keep_free_scratch (10) : Space available for copying particle stacks (in Gb) 351s --reuse_scratch (false) : Re-use data on scratchdir, instead of wiping it and re-copying all data. 351s --keep_scratch (false) : Don't remove scratch after convergence. Following jobs that use EXACTLY the same particles should use --reuse_scratch. 351s --fast_subsets (false) : Use faster optimisation by using subsets of the data in the first 15 iterations 351s --gpu (false) : Use available gpu resources for some calculations 351s --free_gpu_memory (0) : GPU device memory (in Mb) to leave free after allocation. 351s ====== Expert options ===== 351s --pad (2) : Oversampling factor for the Fourier transforms of the references 351s --ref_angpix (-1.) : Pixel size (in A) for the input reference (default is to read from header) 351s --NN (false) : Perform nearest-neighbour instead of linear Fourier-space interpolation? 351s --r_min_nn (10) : Minimum number of Fourier shells to perform linear Fourier-space interpolation 351s --verb (1) : Verbosity (1=normal, 0=silent) 351s --random_seed (-1) : Number for the random seed generator 351s --coarse_size (-1) : Maximum image size for the first pass of the adaptive sampling approach 351s --adaptive_fraction (0.999) : Fraction of the weights to be considered in the first pass of adaptive oversampling 351s --maskedge (5) : Width of the soft edge of the spherical mask (in pixels) 351s --fix_sigma_noise (false) : Fix the experimental noise spectra? 351s --fix_sigma_offset (false) : Fix the stddev in the origin offsets? 351s --incr_size (10) : Number of Fourier shells beyond the current resolution to be included in refinement 351s --print_metadata_labels (false) : Print a table with definitions of all metadata labels, and exit 351s --print_symmetry_ops (false) : Print all symmetry transformation matrices, and exit 351s --strict_highres_exp (-1) : High resolution limit (in Angstrom) to restrict probability calculations in the expectation step 351s --strict_lowres_exp (-1) : Low resolution limit (in Angstrom) to restrict probability calculations in the expectation step 351s --dont_check_norm (false) : Skip the check whether the images are normalised correctly 351s --always_cc (false) : Perform CC-calculation in all iterations (useful for faster denovo model generation?) 351s --solvent_correct_fsc (false) : Correct FSC curve for the effects of the solvent mask? 351s --skip_maximize (false) : Skip maximization step (only write out data.star file)? 351s --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). 351s --external_reconstruct (false) : Perform the reconstruction step outside relion_refine, e.g. for learned priors?) 351s --auto_iter_max (999) : In auto-refinement, stop at this iteration. 351s --auto_ignore_angles (false) : In auto-refinement, update angular sampling regardless of changes in orientations for convergence. This makes convergence faster. 351s --auto_resol_angles (false) : In auto-refinement, update angular sampling based on resolution-based required sampling. This makes convergence faster. 351s --allow_coarser_sampling (false) : In 2D/3D classification, allow coarser angular and translational samplings if accuracies are bad (typically in earlier iterations. 351s --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 351s --maxsig (-1) : Maximum number of poses & translations to consider 351s --skip_gridding (false) : Skip gridding in the M step 351s --version : Print RELION version and exit 352s autopkgtest [00:37:33]: test command1: -----------------------] 356s command1 PASS (superficial) 356s autopkgtest [00:37:37]: test command1: - - - - - - - - - - results - - - - - - - - - - 362s autopkgtest [00:37:43]: @@@@@@@@@@@@@@@@@@@@ summary 362s command1 PASS (superficial)