Dealing with job submission limits

Question

I am running slurm job arrays with --array, and I would like to run about 2000 tasks/array items. However this is beyond the cluster's job submission limit of ~500 at a time.

Are there any tips/best practices for splitting this up? I'd like to submit it all at once and still be able to pass the array id arguments 1-2000 to my programs if possible. I think something like waiting to submit pieces of the array might be helpful but I'm not sure how to do this at the moment.

Answer 1

If the limit is on the size of an array:

You will have to split the array into several job arrays. The --array parameter accepts values of the form <START>-<END> so you can submit four jobs:

sbatch --array=1-500 ...
sbatch --array=501-1000 ...
sbatch --array=1001-1500 ...
sbatch --array=1501-200 ...

This way you will bypass the 500-limit and still keep the SLURM_ARRAY_TASK_ID ranging from 1 to 2000.

To ease things a bit, you can write this all in one line like this:

paste -d- <(seq 1 500 2000) <(seq 500 500 2000) | xargs -I {} sbatch --array={} ... 

If the limit is on the number of submitted jobs:

Then one option is to have the last job of the array submit the following chunk.

#!/bin/bash
#SBATCH ...
...
...
if [[ $((SLURM_ARRAY_TASK_ID % 500)) == 0 ]] ; then 
    sbatch --array=$((SLURM_ARRAY_TASK_ID+1))-$((SLURM_ARRAY_TASK_ID+500)) $0
fi

Note that ideally, the last running job of the array should submit the job, and it may or may not be the one with the highest TASK ID, but this has worked for all practical purposes in many situations.

Another options is to setup a cron job to monitor the queue and submit each chunk when possible, or to use a workflow manager that will that for you.