I doubt that it is a problem with your script and suspect that there is some weird interaction with scancel on interactive jobs. If you wanted to get to the bottom of that I’d suggest disabling the prolog and test by manually cancelling some interactive jobs.
Another suggestion is to try a completely different approach to solve your problem. Why wait until the job starts to do the check? You can use a submit filter and it will alert the user as soon as they try to submit. That will prevent them from potentially having to wait in the queue if the cluster is busy and gets around having to cancel a running job. There is a description and simple example at the bottom of this page: https://slurm.schedmd.com/resource_limits.html
Mike
From: slurm-users <slurm-users-bounces at lists.schedmd.com> on behalf of Ratnasamy, Fritz <fritz.ratnasamy at chicagobooth.edu>
Date: Tuesday, August 24, 2021 at 21:00
To: slurm-users at lists.schedmd.com <slurm-users at lists.schedmd.com>
Subject: [External] [slurm-users] scancel gpu jobs when gpu is not requested
CAUTION: This email originated from outside of the Colorado School of Mines organization. Do not click on links or open attachments unless you recognize the sender and know the content is safe.
Hello,
I have written a script in my prolog.sh that cancels any slurm job if the parameter gres=gpu is not present. This is the script i added to my prolog.sh
if [ $SLURM_JOB_PARTITION == "gpu" ]; then
if [ ! -z "${GPU_DEVICE_ORDINAL}" ]; then
echo "GPU ID used is ID: $GPU_DEVICE_ORDINAL "
list_gpu=$(echo "$GPU_DEVICE_ORDINAL" | sed -e "s/,//g")
Ngpu=$(expr length $list_gpu)
else
echo "No GPU selected"
Ngpu=0
fi
# if 0 gpus were allocated, cancel the job
if [ "$Ngpu" -eq "0" ]; then
scancel ${SLURM_JOB_ID} fi
fi
What the code does is look at the number of gpus allocated, and if it is 0, cancel the job ID. It working fine if a user use sbatch submit.sh (and the submit.sh do not have the value --gres=gpu:1). However, when requesting an interactive session without gpus, the job is getting killed and the job hangs for 5-6 mins before getting killed.
jlo at mfe01:~ $ srun --partition=gpu --pty bash --login
srun: job 4631872 queued and waiting for resources
srun: job 4631872 has been allocated resources
srun: Force Terminated job 4631872 ...the killing hangs for 5-6minutes
Is there anything wrong with my script? Why only when scancel an interactive session, I am seeing this hanging. I would like to remove the hanging
Thanks
Fritz Ratnasamy
Data Scientist
Information Technology
The University of Chicago
Booth School of Business
5807 S. Woodlawn
Chicago, Illinois 60637
Phone: +(1) 773-834-4556
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