Your message dated Fri, 20 Aug 2021 09:03:35 +0000
with message-id <e1mh0r5-000gqk...@fasolo.debian.org>
and subject line Bug#992052: fixed in cd-hit 4.8.1-4
has caused the Debian Bug report #992052,
regarding cd-hit: autopkgtest fails on very powerful CI workers
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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--
992052: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=992052
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: cd-hit
Version: 4.8.1-3
Severity: serious
X-Debbugs-CC: debian...@lists.debian.org
Tags: sid bookworm
User: debian...@lists.debian.org
Control: affects -1 src:perl
Dear maintainer(s),
With a recent upload of perl the autopkgtest of cd-hit fails in testing
on armhf when that autopkgtest is run with the binary packages of perl
from unstable. Unlike usually, this is not a *regression* from the
package point of view, but the result of a change of the workers showing
that the current defaults in the test are too low for some of our workers.
I copied some of the output at the bottom of this report. It's ironical
that cd-hit complains about not enough memory when the worker this test
runs on has the biggest amount of memory we have in the ci.d.n worker
park: 250GB. If I read the output correctly, you assign the amount of
memory cd-hit is allowed to use and the required amount of memory also
depends on the amount of cores. This machine has 160 cores. I wonder if
the value for -M needs to be calculated instead of hard coded or that
you should limit the maximum amount of cores used or... But I leave it
up to you to find the appropriate solution.
Paul
https://ci.debian.net/data/autopkgtest/testing/amd64/c/cd-hit/14380008/log.gz
autopkgtest [03:24:50]: test run-unit-test: [-----------------------
==== CD_HIT ====
================================================================
Program: CD-HIT, V4.8.1 (+OpenMP), Nov 21 2020, 19:27:41
Command: cd-hit -i example.fa -o out -c 1.00 -n 5 -M 1000 -T 0
Started: Tue Aug 10 03:24:50 2021
================================================================
Output
----------------------------------------------------------------
total number of CPUs in the system is 160
Actual number of CPUs to be used: 160
total seq: 4
longest and shortest : 1132 and 149
Total letters: 2136
Sequences have been sorted
Approximated minimal memory consumption:
Sequence : 0M
Buffer : 160 X 10M = 1715M
Table : 2 X 49M = 98M
Miscellaneous : 0M
Total : 1813M
Fatal Error:
not enough memory, please set -M option greater than 1913
Program halted !!
autopkgtest [03:24:51]: test run-unit-test: -----------------------]
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: cd-hit
Source-Version: 4.8.1-4
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
cd-hit, 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 992...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@debian.org> (supplier of updated cd-hit 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: Fri, 20 Aug 2021 10:39:56 +0200
Source: cd-hit
Architecture: source
Version: 4.8.1-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 992052
Changes:
cd-hit (4.8.1-4) unstable; urgency=medium
.
* d/watch: fix broken link to github
* d/control: add myself to uploaders
* d/t/run-unit-test: disable memory limits in tests (Closes: #992052)
* Standards-Version: 4.6.0 (routine-update)
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