[slurm-users] Kill job when child process gets OOM-killed

Arthur Gilly arthur.gilly at helmholtz-muenchen.de
Tue Jun 8 08:20:19 UTC 2021

Dear Slurm users,


I am looking for a SLURM setting that will kill a job immediately when any
subprocess of that job hits an OOM limit. Several posts have touched upon
that, e.g:
https://www.mail-archive.com/slurm-users@lists.schedmd.com/msg04190.html or
https://bugs.schedmd.com/show_bug.cgi?id=3216 but I cannot find an answer
that works in our setting.


The two options I have found are:

1.	Set shebang to #!/bin/bash -e, which we don't want to do as we'd
need to change this for hundreds of scripts from another cluster where we
had a different scheduler, AND it would kill tasks for other runtime errors
(e.g. if one command in the script doesn't find a file).
2.	Set KillOnBadExit=1. I am puzzled by this one. This is supposed to
be overridden by srun's -K option. Using the example below, srun -K --mem=1G
./multalloc.sh would be expected to kill the job at the first OOM. But it
doesn't, and happily keeps reporting 3 oom-kill events. So, will this work?


The reason we want this is that we have script that execute programs in
loops. These programs are slow and memory intensive. When the first one
crashes for OOM, the next iterations also crash. In the current setup, we
are wasting days executing loops where every iteration crashes after an hour
or so due to OOM.


We are using cgroups (and we want to keep them) with the following config:










Relevant bits from slurm.conf:






Very simple example:


# multalloc.sh - each line is a very simple cpp program that allocates a 8Gb
vector and fills it with random floats

echo one


echo two


echo three


echo done.


This is submitted as follows:


sbatch --mem=1G ./multalloc.sh


The log is :


./multalloc.sh: line 4: 231155 Killed                  ./alloc8Gb


./multalloc.sh: line 6: 231181 Killed                  ./alloc8Gb


./multalloc.sh: line 8: 231263 Killed                  ./alloc8Gb


slurmstepd: error: Detected 3 oom-kill event(s) in StepId=3130111.batch
cgroup. Some of your processes may have been killed by the cgroup
out-of-memory handler.


I am expecting an OOM job kill right before "two".


Any help appreciated.


Best regards,






Dr. Arthur Gilly

Head of Analytics

Institute of Translational Genomics

Helmholtz-Centre Munich (HMGU)



Helmholtz Zentrum Muenchen
Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)
Ingolstaedter Landstr. 1
85764 Neuherberg
Aufsichtsratsvorsitzende: MinDir.in Prof. Dr. Veronika von Messling
Geschaeftsfuehrung: Prof. Dr. med. Dr. h.c. Matthias Tschoep, Kerstin Guenther
Registergericht: Amtsgericht Muenchen HRB 6466
USt-IdNr: DE 129521671
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