Job dependencies

Introduction

Job dependencies are a way to specify dependencies between jobs. The most common use is to launch a job only after a previous job has completed successfully. But other kinds of dependencies are also possible.

Basic example

Dependencies are specified with the --dependency=DEPENDENCY_LIST option. E.g. --dependency=afterok:123:124 means that the job can only start after job ID’s 123 and 124 have both completed successfully.

Automating job dependencies

A common problem with job dependencies is that you want job B to start only after job A finishes successfully. However, you cannot know the job ID of job A before it has been submitted. One solution is to catch the job id of job A when submitting it and store it as a shell variable, and using the stored value when submitting job B. Like:

idA=$(sbatch jobA.sh | awk '{print $4}')
sbatch --dependency=afterok:${idA} jobB.sh

Exercises

Dependencies-1: read the docs

Look at man sbatch and investigate the --dependency parameter.

Dependencies-2: Chain of jobs

Create a chain of jobs A -> B -> C each depending on the successful completion of the previous job. In each job run e.g. sleep 60 to give you time to investigate the status of the queue.

Dependencies-3: First job fails

Continuing from the previous exercise, what happens if at the end of the job A script you put exit 1. What does it mean?