[Debian-med-packaging] Bug#992052: cd-hit: autopkgtest fails on very powerful CI workers

[Paul Gevers]

Source: cd-hit
Version: 4.8.1-3
Severity: serious
X-Debbugs-CC: debian-ci at lists.debian.org
Tags: sid bookworm
User: debian-ci at 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: -----------------------]

-------------- next part --------------
A non-text attachment was scrubbed...
Name: OpenPGP_signature
Type: application/pgp-signature
Size: 495 bytes
Desc: OpenPGP digital signature
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20210810/bebe023e/attachment.sig>