Your message dated Mon, 02 Jul 2018 09:49:36 +0000
with message-id <[email protected]>
and subject line Bug#902848: fixed in examl 3.0.21-2
has caused the Debian Bug report #902848,
regarding examl: flaky autopkgtest: oversubscription
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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--
902848: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=902848
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: examl
Version: 3.0.20-1
Severity: important
User: [email protected]
Usertags: flaky
While inspecting regressions in autopkgtest results¹, I noticed that
your package failed multiple times without apparent changes and
passed later again. Your package is using openmpi, so it needs an update
for changes in openmpi3 regarding oversubscription (see below). The last
regression was involved in delaying the migration of openmpi.
Quote from (please help improve that wiki page if it isn't clear):
https://wiki.debian.org/ContinuousIntegration/TriagingTips/openmpi3-oversubscription
'''
The solution is to add the following (or equivalent) to the test script.
export OMPI_MCA_rmaps_base_oversubscribe=1
'''
Recent discussion of gating migration by autopkgtests on debian-devel²
noted that if this is going to work, and in particular if we are going
to *block* migration when it causes autopkgtest regressions rather than
merely delaying it, intermittent autopkgtest failures are likely to have
to be considered RC due to their impact on the tested package's
dependencies; for now I've filed it as important.
Paul
¹ https://ci.debian.net/packages/e/examl/testing/amd64
² https://lists.debian.org/debian-devel/2018/05/msg00061.html
https://ci.debian.net/data/autopkgtest/testing/amd64/e/examl/541415/log.gz
Run MPI on 2 of 2 available processors
Use examl with AVX support and 2 processors
--------------------------------------------------------------------------
There are not enough slots available in the system to satisfy the 2 slots
that were requested by the application:
/usr/lib/examl/bin/examl-AVX
Either request fewer slots for your application, or make more slots
available
for use.
--------------------------------------------------------------------------
signature.asc
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: examl
Source-Version: 3.0.21-2
We believe that the bug you reported is fixed in the latest version of
examl, 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.
Andreas Tille <[email protected]> (supplier of updated examl 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: Mon, 02 Jul 2018 11:32:28 +0200
Source: examl
Binary: examl
Architecture: source
Version: 3.0.21-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
examl - Exascale Maximum Likelihood (ExaML) code for phylogenetic inferen
Closes: 902848
Changes:
examl (3.0.21-2) unstable; urgency=medium
.
* export OMPI_MCA_rmaps_base_oversubscribe=1 in autopkgtest script
Closes: #902848
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