[slurm-users] EXTERNAL-Re: [External] scancel gpu jobs when gpu is not requested

Michael Robbert mrobbert at mines.edu
Thu Aug 26 14:18:06 UTC 2021

You need to set the following option in slurm.conf
A comma delimited list of job submission plugins to be used. The specified plugins will be executed in the order listed. These are intended to be site-specific plugins which can be used to set default job parameters and/or logging events. Sample plugins available in the distribution include "all_partitions", "defaults", "logging", "lua", and "partition". For examples of use, see the Slurm code in "src/plugins/job_submit" and "contribs/lua/job_submit*.lua" then modify the code to satisfy your needs. Slurm can be configured to use multiple job_submit plugins if desired, however the lua plugin will only execute one lua script named "job_submit.lua" located in the default script directory (typically the subdirectory "etc" of the installation directory). No job submission plugins are used by default.

Then as this documentation states, put the job_submit.lua into your script directory. Mine is in /etc/slurm/. You may want to make sure that you have the job_submit_lua.so library installed with your build of Slurm. I agree that finding complete documentation for this feature is a little difficult.


From: slurm-users <slurm-users-bounces at lists.schedmd.com> on behalf of Ratnasamy, Fritz <fritz.ratnasamy at chicagobooth.edu>
Date: Wednesday, August 25, 2021 at 23:13
To: Slurm User Community List <slurm-users at lists.schedmd.com>
Subject: Re: [slurm-users] EXTERNAL-Re: [External] scancel gpu jobs when gpu is not requested
Hi Michael,
Thanks for your message. Yes I was able to get all interactive sessions killed quickly when trying other partitions and deactivating the prolog. I read your example and I understand how it could possibly work (in the ex., maybe instead of looking if the gpu model is passed, we could look at the number of gpu passed?), but where do i set up that function and where do i call it?
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

On Wed, Aug 25, 2021 at 9:54 AM Michael Robbert <mrobbert at mines.edu<mailto:mrobbert at mines.edu>> wrote:
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<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fslurm.schedmd.com%2Fresource_limits.html&data=04%7C01%7Cmrobbert%40mines.edu%7C577fad20cd024e8f8d5a08d96850336c%7C997209e009b346239a4d76afa44a675c%7C0%7C0%7C637655515944014175%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=vnuQFWtAkvixWlJaLCVa%2Bcmt0Zt97RCWhStXO1VLoss%3D&reserved=0>


From: slurm-users <slurm-users-bounces at lists.schedmd.com<mailto:slurm-users-bounces at lists.schedmd.com>> on behalf of Ratnasamy, Fritz <fritz.ratnasamy at chicagobooth.edu<mailto:fritz.ratnasamy at chicagobooth.edu>>
Date: Tuesday, August 24, 2021 at 21:00
To: slurm-users at lists.schedmd.com<mailto:slurm-users at lists.schedmd.com> <slurm-users at lists.schedmd.com<mailto: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.


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)
                echo "No GPU selected"

       # if  0 gpus were allocated, cancel the job
        if [ "$Ngpu" -eq "0" ]; then
              scancel ${SLURM_JOB_ID}                                          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
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
CAUTION: This email has originated outside of University email systems. Please do not click links or open attachments unless you recognize the sender and trust the contents as safe.

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