Your message dated Tue, 15 Feb 2022 20:46:50 +0000
with message-id <[email protected]>
and subject line Bug#1003079: fixed in scotch 7.0.1-1exp1
has caused the Debian Bug report #1003079,
regarding scotch v7 MPI dgord dgpart tests fail
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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--
1003079: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1003079
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: scotch
Version: 7.0.0-1exp1
Severity: normal
autopkgtest fails for the new scotch v7 package on the MPI tests of
dgord and dgpart (check_prog_dgord and check_prog_dgpart rules in
src/check/Makefile)
The failure is intermittent, usually fails with
$ mpirun -n 3 --oversubscribe /usr/bin/dgord data/bump.grf /dev/null -Cu -vt
*** Process received signal ***
Signal: Segmentation fault (11)
Signal code: Address not mapped (1)
Failing at address: 0x55aa224dfee0
[ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3c910)[0x7f7bcf819910]
[ 1]
/usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_vader.so(mca_btl_vader_poll_handle_frag+0x154)[0x7f7bccb93be4]
[ 2]
/usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_btl_vader.so(+0x4fc1)[0x7f7bccb93fc1]
[ 3] /lib/x86_64-linux-gnu/libopen-pal.so.40(opal_progress+0x2c)[0x7f7bcf4d596c]
[ 4]
/lib/x86_64-linux-gnu/libmpi.so.40(ompi_request_default_wait+0x55)[0x7f7bcf9f8075]
[ 5]
/lib/x86_64-linux-gnu/libmpi.so.40(ompi_coll_base_sendrecv_actual+0xcf)[0x7f7bcfa5174f]
[ 6]
/lib/x86_64-linux-gnu/libmpi.so.40(ompi_coll_base_allgather_intra_bruck+0x140)[0x7f7bcfa4f9b0]
[ 7]
/usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi3/mca_coll_tuned.so(ompi_coll_tuned_allgather_intra_dec_fixed+0x4a)[0x7f7bcc554aca]
[ 8] /lib/x86_64-linux-gnu/libmpi.so.40(MPI_Allgather+0x121)[0x7f7bcfa0be61]
[ 9]
/lib/x86_64-linux-gnu/libptscotch-7.0.so(_SCOTCHhdgraphInduceList+0x22f)[0x7f7bcfb307ff]
[10] /lib/x86_64-linux-gnu/libptscotch-7.0.so(+0x49e02)[0x7f7bcfb30e02]
[11] /lib/x86_64-linux-gnu/libptscotch-7.0.so(+0x4a6f8)[0x7f7bcfb316f8]
[12] /lib/x86_64-linux-gnu/libptscotch-7.0.so(+0x6597b)[0x7f7bcfb4c97b]
[13] /lib/x86_64-linux-gnu/libpthread.so.0(+0x8d80)[0x7f7bcf765d80]
[14] /lib/x86_64-linux-gnu/libc.so.6(clone+0x3f)[0x7f7bcf8d9b6f]
*** End of error message ***
but sometimes passes.
The unreliability of the failure suggests a race condition, likely
related to the new dynamic thread management in v7. Perhaps we need a
different set of scotch PTHREAD flags when compiling?
Review further once v7 has passed the NEW queue to experimental.
-- System Information:
Debian Release: bookworm/sid
APT prefers unstable
APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 5.15.0-2-amd64 (SMP w/8 CPU threads)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages scotch depends on:
ii libc6 2.33-1
ii libscotch-7.0 7.0.0-1exp1
scotch recommends no packages.
scotch suggests no packages.
-- no debconf information
--- End Message ---
--- Begin Message ---
Source: scotch
Source-Version: 7.0.1-1exp1
Done: Drew Parsons <[email protected]>
We believe that the bug you reported is fixed in the latest version of
scotch, 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.
Drew Parsons <[email protected]> (supplier of updated scotch 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: SHA256
Format: 1.8
Date: Tue, 15 Feb 2022 18:38:13 +0100
Source: scotch
Architecture: source
Version: 7.0.1-1exp1
Distribution: experimental
Urgency: medium
Maintainer: Debian Science Maintainers
<[email protected]>
Changed-By: Drew Parsons <[email protected]>
Closes: 1003079
Changes:
scotch (7.0.1-1exp1) experimental; urgency=medium
.
* Team upload.
* New upstream release.
- drops scotchparmetisv5 (it was added to 7.0.0 by mistake)
Only scotchparmetisv3 is provided for parmetis emulation.
- now provides cmake build, so override dh_auto_configure
to keep existing direct Makefile builds with Makefile.inc
* use "set -e" in debian/tests to catch segfaults in tests
* add -DSCOTCH_PTHREAD_MPI to build flags, as recommended upstream
Closes: #1003079.
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6933ef40ac71fc83d0922a00ed85fc52 5551476 math optional scotch_7.0.1.orig.tar.xz
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scotch_7.0.1-1exp1.debian.tar.xz
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--- End Message ---
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