Slurm: Best Practise

Shellcheck

shellcheck.net is very useful to highlight problems with your shell scripts! You can use it to check and improve your job scripts.

Other Best Practise

Every job submission in Slurm introduces some overhead to the batch system. If you have many short jobs of the same kind, e.g. 2000 x 30 minutes, you should combine your workload in fewer submission scripts or consider using Slurms job arrays (check our example job). This way you bundle all of these jobs in a single job submission, but still can treat the items individually as job steps.

Please try to estimate a maximum execution time and set your job time limits accordingly.

• Specify it with -t, shorter than the partitions maximum time
• This will also increase the likelihood of your job starting early!
• For longer job times than three days, if your program regularly saves states/snapshots:
  • Schedule a first job to the normal partition
  • Use sbatch -d <jobid> to set a job dependency to the original job, to continue processing
• As an exception, the long partition allows for longer jobs, but there are a couple of risks involved:
  • Jobs naturally have to wait longer to start, since other (long) jobs may block the partition resources
  • A power or cooling failure might kill your jobs prematurely, wasting all of the computation and energy up to that point
  • Planned maintenance has to wait longer until your jobs are finished. In case of critical security interventions we might be even forced to kill you jobs.
  • All issues are mitigated if your programs have some form of checkpointing to save intermediate states. In this case, use the normal partition as described above.

Coming from SGE

Previously, we used SGE to submit batch jobs.
Since many concepts are similar between these kind of tools, you just have to look up the new tool names in many cases. This rosetta stone, provided by SchedMD is a good starting point.