Your message dated Wed, 29 Jul 2020 15:36:13 +0000
with message-id <e1k0o7p-0005kl...@fasolo.debian.org>
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.
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--
966175: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=966175
Debian Bug Tracking System
Contact ow...@bugs.debian.org 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?= <sebast...@debian.org>
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 966...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Sébastien Villemot <sebast...@debian.org> (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 ftpmas...@ftp-master.debian.org)
-----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
<debian-science-maintain...@lists.alioth.debian.org>
Changed-By: Sébastien Villemot <sebast...@debian.org>
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
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