Hi Ajad,

Amjad Syed via slurm-users slurm-users@lists.schedmd.com writes:

Hello

I have the following scenario: I need to submit a sequence of up to 400 jobs where the even jobs depend on the preceeding odd job to finish and every odd job depends on the presence of a file generated by the preceding even job (availability of the file for the first of those 400 jobs is guaranteed).

If I just submit all those jobs via a loop using dependencies, then I end up with a lot of pending jobs who might later not even run because no output file has been produced by the preceding jobs. Is there a way to pause the submission loop until the required file has been generated so that at most two jobs are submitted at the same time?

Here is a sample submission script showing what I want to achieve.

for i in {1..200}; do   FILE=GHM_paramset_${i}.dat # How can I pause the submission loop until the FILE has been created???? #if test -f "$FILE"; then jobid4=$(sbatch --parsable --dependency=afterok:$jobid3 job4_sub $i) jobid3=$(sbatch --parsable --dependency=afterok:$jobid4 job3_sub $i) #fi done

Any help will be appreciated

Amjad

You might find a job array useful for this (for any large number of jobs with identical resources, using a job array also helps backfilling to work efficiently, if you are using it).

With a job array you can specify how many jobs should run simultaneously with the '%' notation:

--array=1-200%2

Cheers,

Loris