Your message dated Wed, 29 Jul 2020 15:36:13 +0000 with message-id <[email protected]> and subject line Bug#966175: fixed in openblas 0.3.10+ds-2 has caused the Debian Bug report #966175, regarding libopenblas0-pthread: segfault in scipy tests: calls Haswell to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 966175: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=966175 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: libopenblas0-pthread Version: 0.3.10+ds-1 Severity: normal Two (or at least 2) tests in scipy are segfaulting specifically with libopenblas0-pthread. If I configure alternatives to set libblas.so.3-x86_64-linux-gnu and liblapack.so.3-x86_64-linux-gnu to generic reference blas then the tests pass. The libblas.so segfault occurs with both scipy 1.4.1-2 (unstable) and 1.5.2-1 (experimental). The liblapack.so segfault occurs with scipy 1.5.2-1 but passes in 1.4.1-2 The segfaults can be reproduced manually (with python3-scipy installed and blas/lapack configured to libopenblas0-pthread): python3 -m pytest /usr/lib/python3/dist-packages/scipy/cluster/tests/test_vq.py -k "krandinit" -v python3 -m pytest /usr/lib/python3/dist-packages/scipy/linalg/tests/test_decomp.py -v (the second test here is the one that fails with scipy 1.5.2-1 in test_orth_memory_efficiency, passes with 1.4.1-2. It also passes when run on its own with -k "test_orth_memory_efficiency") gdb backtraces show libopenblas0-pthread is inculpated: $ gdb python3 > run -m pytest /usr/lib/python3/dist-packages/scipy/cluster/tests/test_vq.py > -k "krandinit" -v ../../../../../../usr/lib/python3/dist-packages/scipy/cluster/tests/test_vq.py::TestKMean::test_krandinit Thread 2 "python3" received signal SIGSEGV, Segmentation fault. [Switching to Thread 0x7ffff4b6a700 (LWP 1589273)] 0x00007ffff5c8d284 in dgemm_oncopy_HASWELL () from /lib/x86_64-linux-gnu/libblas.so.3 (gdb) bt #0 0x00007ffff5c8d284 in dgemm_oncopy_HASWELL () from /lib/x86_64-linux-gnu/libblas.so.3 #1 0x00007ffff4d2a7c5 in ?? () from /lib/x86_64-linux-gnu/libblas.so.3 #2 0x00007ffff4e3098d in ?? () from /lib/x86_64-linux-gnu/libblas.so.3 #3 0x00007ffff7f62ea7 in start_thread (arg=<optimized out>) at pthread_create.c:477 #4 0x00007ffff7cf7daf in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:95 $ gdb python3 > run -m pytest > /usr/lib/python3/dist-packages/scipy/linalg/tests/test_decomp.py -v ... ../../../../../../usr/lib/python3/dist-packages/scipy/linalg/tests/test_decomp.py::TestOverwrite::test_svd PASSED [ 92%] ../../../../../../usr/lib/python3/dist-packages/scipy/linalg/tests/test_decomp.py::TestOverwrite::test_svdvals PASSED [ 92%] ../../../../../../usr/lib/python3/dist-packages/scipy/linalg/tests/test_decomp.py::test_orth_memory_efficiency Thread 9 "python3" received signal SIGSEGV, Segmentation fault. [Switching to Thread 0x7fffe0e10700 (LWP 1589405)] 0x00007fffe27cc284 in dgemm_oncopy_HASWELL () from /lib/x86_64-linux-gnu/liblapack.so.3 (gdb) bt #0 0x00007fffe27cc284 in dgemm_oncopy_HASWELL () from /lib/x86_64-linux-gnu/liblapack.so.3 #1 0x00007fffe18aeb62 in ?? () from /lib/x86_64-linux-gnu/liblapack.so.3 #2 0x00007fffe1943c4d in ?? () from /lib/x86_64-linux-gnu/liblapack.so.3 #3 0x00007ffff7f62ea7 in start_thread (arg=<optimized out>) at pthread_create.c:477 #4 0x00007ffff7cf7daf in clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:95 In both cases the segfault happens at dgemm_oncopy_HASWELL. Probably worth mentioned I'm not using a haswell system: $ cat /proc/cpuinfo | grep 'model name' | uniq model name : Intel(R) Core(TM) i5-8365U CPU @ 1.60GHz So looks like the bug is that libopenblas0-pthread is invoking haswell code on non-haswell systems. cpu.userbenchmark.com tells me that i5-8365U is Whiskey Lake not Haswell For completeness I tested other BLAS: openblas-openmp: FAIL (calls dgemm_oncopy_HASWELL) openblas-serial: PASS blis-pthread: PASS blis-openmp: PASS atlas: PASS -- System Information: Debian Release: bullseye/sid APT prefers unstable APT policy: (500, 'unstable'), (1, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.7.0-1-amd64 (SMP w/8 CPU threads) Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8), LANGUAGE=en_AU:en Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages libopenblas0-pthread depends on: ii libc6 2.31-2 ii libgfortran5 10.1.0-6 libopenblas0-pthread recommends no packages. libopenblas0-pthread suggests no packages. -- no debconf information
--- End Message ---
--- Begin Message ---Source: openblas Source-Version: 0.3.10+ds-2 Done: =?utf-8?q?S=C3=A9bastien_Villemot?= <[email protected]> We believe that the bug you reported is fixed in the latest version of openblas, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Sébastien Villemot <[email protected]> (supplier of updated openblas package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Wed, 29 Jul 2020 14:51:22 +0200 Source: openblas Architecture: source Version: 0.3.10+ds-2 Distribution: unstable Urgency: medium Maintainer: Debian Science Team <[email protected]> Changed-By: Sébastien Villemot <[email protected]> Closes: 960728 966175 Changes: openblas (0.3.10+ds-2) unstable; urgency=medium . * lib{blas,lapack}.so.3 are again dynamically linked against libopenblas.so.0. This restores the pre-multi-flavour behaviour. Incidentally, this brings back the possibility of checking at runtime for the presence of openblas_get_config symbol. (Closes: #960728) * fix-dynamic-arch-gemm-crashes.patch: new patch (Closes: #966175) * Add debian/upstream/metadata Checksums-Sha1: a8b13939b35b3c3f2ad8ffca5657de44bf0799e3 4891 openblas_0.3.10+ds-2.dsc 58654a22697a2e0519c7e0879d8640c1b5d15d21 22020 openblas_0.3.10+ds-2.debian.tar.xz a936c87fc0f8a38ad9e1f2643234d7d31f34d83a 13624 openblas_0.3.10+ds-2_amd64.buildinfo Checksums-Sha256: a34004c52181237410c4b6539f22cb6b633496c9afb1f5b56f20ba382f122415 4891 openblas_0.3.10+ds-2.dsc 972cfedfde62900db2b835be3e1be8b08dd9b9260f0f79e19c31f4472e0af017 22020 openblas_0.3.10+ds-2.debian.tar.xz d458f8c246e17ca509a68337f46ad238fb3d3d34064a841f6fd444d9ce3aba2a 13624 openblas_0.3.10+ds-2_amd64.buildinfo Files: bd0e58991df3ff258f09510972b798d0 4891 devel optional openblas_0.3.10+ds-2.dsc b1b622a6304ca310b3e67a473f2e5208 22020 devel optional openblas_0.3.10+ds-2.debian.tar.xz bc0fff6d10da9a31ea4551ff1a7f442a 13624 devel optional openblas_0.3.10+ds-2_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEU5UdlScuDFuCvoxKLOzpNQ7OvkoFAl8hkmkACgkQLOzpNQ7O vkrD9g/6AqoL7+FIxFti0Jk7F1dr4tx3e7CmdrUKNZt0WdvYD7yiwI014bjVoIJI okM7lY+c2uIKMjNivIW7Eze83e9v+y98x16O3WQ7Ate5G171SL96rSv7V96+KbOk QYhj3L5+dZJaCHJnxROhJum8OVEEjBJBdOXUhC73heAjLJ01H61qJunfqxQE9z0D F1dGJJpbxYvmDr5ZIzKBZNNRMY6qUGEoCD441eRt94YwpoysZNBAp/dfNukrgWlL ROcFVJ1pb26Kvsh1JR9iU0nsL2dVTXkiwpk5qVJ9b5C32T+bGfG4z5HrwqaND+g1 VabEVl//AqDzvAUz8zQLBDQMQHCKoGb32M+OKmNd1ZDqr7/uR6rZCc5ELAu5i7R3 pWGEBwDBTrmBzJxNfAStyzsLMzx66RGSZTEM3yWIiUSZko5mzyoEal985MvshbHt PnuFfYk1gF6noFNOBLxNa6pBM5UVIMTVGxIOuGLYqM3vJOZgSEw11Y0hOKYflV0J gbSjvH0OLfbubiYqPbcLQwUjZhoVy+Y/x749JH1CNpoVG7ksrqsX+ENIv607poJF vh9dJJOc1KV9Vau5RVrWOsB07JkjIJhzPPrxw1wz15wJWlqcN9wW6pm7wgVUtawz wvOMQgaR+pvenL926Cdpps/Z0GoxwD3v0ije/FW+axiKi/0vZgE= =ZCO8 -----END PGP SIGNATURE-----
--- End Message ---
-- debian-science-maintainers mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-science-maintainers
