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About cluster-computing : How-to-hold-up-a-script-until-a-slurm-job-start-with-srun-is-completely-finished

Question Detail

I am running a job array with SLURM, with the following job array script (that I run with sbatch job_array_script.sh [args]:

#!/bin/bash

#SBATCH ... other options ...

#SBATCH --array=0-1000%200

srun ./job_slurm_script.py $1 $2 $3 $4

echo 'open' > status_file.txt

To explain, I want job_slurm_script.py to be run as an array job 1000 times with 200 tasks maximum in parallel. And when all of those are done, I want to write ‘open’ to status_file.txt. This is because in reality I have more than 10,000 jobs, and this is above my cluster’s MaxSubmissionLimit, so I need to split it into smaller chunks (at 1000-element job arrays) and run them one after the other (only when the previous one is finished).

However, for this to work, the echo statement can only trigger once the entire job array is finished (outside of this, I have a loop which checks status_file.txt so see if the job is finished, i.e when the contents are the string ‘open’).

Up to now I thought that srun holds the script up until the whole job array is finished. However, sometimes srun “returns” and the script goes to the echo statement before the jobs are finished, so all the subsequent jobs bounce off the cluster since it goes above the submission limit.

So how do I make srun “hold up” until the whole job array is finished?

Question Answer

You can add the flag --wait to sbatch.

Check the manual page of sbatch for information about --wait.

You can use --wait option in sbatch in combination with wait in bash to send jobs off to the cluster, pause script execution until those are complete, and then continue. E.g.

#!/bin/bash
set -e
date

for((i=0; i<5; i++)); do
    sbatch -W --wrap='echo "hello from $SLURM_ARRAY_TASK_ID"; sleep 10' &
done;
wait

date
echo "I am finished"

You can use the wait bash command. It will wait until whatever lines of code above are finished. Thus you script should look like this:

#!/bin/bash

#SBATCH ... other options ...

#SBATCH --array=0-1000%200

srun ./job_slurm_script.py $1 $2 $3 $4

wait

echo 'open' > status_file.txt

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