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/msg04091.html> https://www.mail-archive.com/slurm-users@lists.schedmd.com/msg04091.html and <https://www.mail-archive.com/slurm-users@lists.schedmd.com/msg04190.html> https://www.mail-archive.com/slurm-users@lists.schedmd.com/msg04190.html or <https://bugs.schedmd.com/show_bug.cgi?id=3216> 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: CgroupAutomount=yes ConstrainCores=yes ConstrainDevices=yes ConstrainKmemSpace=no ConstrainRAMSpace=yes ConstrainSwapSpace=yes MaxSwapPercent=10 TaskAffinity=no Relevant bits from slurm.conf: SelectTypeParameters=CR_Core_Memory,CR_ONE_TASK_PER_CORE SelectType=select/cons_tres GresTypes=gpu,mps,bandwidth Very simple example: #!/bin/bash # multalloc.sh - each line is a very simple cpp program that allocates a 8Gb vector and fills it with random floats echo one ./alloc8Gb echo two ./alloc8Gb echo three ./alloc8Gb echo done. This is submitted as follows: sbatch --mem=1G ./multalloc.sh The log is : one ./multalloc.sh: line 4: 231155 Killed ./alloc8Gb two ./multalloc.sh: line 6: 231181 Killed ./alloc8Gb three ./multalloc.sh: line 8: 231263 Killed ./alloc8Gb done. 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, Arthur ------------------------------------------------------------- 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 www.helmholtz-muenchen.de 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
