Job Dependencies

Slurm supports dependencies between jobs, allowing users to define simple workflows and pipelines. To create a depenency, you can use the following sbatch flag:

-d, --dependency=<dependency_list>

where dependency_list specifies which jobs to depend on and what kind of dependency it is. This is an example of a simple dependency:

sbatch --dependency=afterok:11536887

This will submit a job, which can only start once the job with the ID 11536887 finished successfully.

A list of possible dependency types can be found in the following table and in the sbatch man-page.

Multiple jobs can be specified by appending with a colon as delimiter, e.g. -d after:123:124:125.

Manually creating complex job dependencies on the command line can be cumbersome and error-prone. It is advised to set up scripts to do this task for you. sbatch has the --parsable flag to make this task easier: When using this flag, only the job ID will be returned and it can be used to capture the job ID into a variable.

Capture sbatch output into variable and use it in the next job:

# submit a first job, extract job id
jobid=$(sbatch --parsable job1.sbatch)
 
# submit a second job with dependency: starts only if the previous job terminates successfully)
jobid=$(sbatch --parsable --dependency=afterok:$jobid job2.sbatch)
 
# submit a third job with dependency: starts only if the previous job terminates successfully)
jobid=$(sbatch --parsable --dependency=afterok:$jobid job3.sbatch)

Submit scripts, each with a with dependency on the previous one:

sub_dep.sh

#!/bin/bash
 
ID=$(sbatch --parsable $1)
shift
for script in "$@"; do
  ID=$(sbatch --parsable --dependency=afterany:${ID} $script)
done

Usage: ./sub_dep.sh scriptA.sh scriptB.sh scriptC.sh scriptD.sh