Advanced tips and tricks

The universe of HPC clusters is extremely diverse, with different job schedulers, different configuration, different decisions (security, usage, etc…) made by each HPC cluster. An unfortunate consequence of this is that this is impossible for Dask-Jobqueue to cover all possible tiny edge cases of some HPC clusters.

This page is an attempt to document tips and tricks that are likely to be useful on some clusters (strictly more than one ideally although hard to be sure …).

Skipping unrecognised line in submission script with header_skip

On some clusters the submission script generated by Dask-Jobqueue (you can look at it with print(cluster.job_script())) may not work on your HPC cluster because on some configuration quirk of your HPC cluster. Probably there are some reasons behind this configuration quirk of course.

You’ll get an error when doing cluster.scale (i.e. where you actually submit some jobs) that will tell you your job scheduler is not happy with your job submission script (see examples below). The main parameter you can use to work-around this is header_skip:

# this will remove any line containing either '--mem' or
# 'another-string' from the job submission script
cluster = YourCluster(
    header_skip=['--mem', 'another-string'],
    **other_options_go_here)

An example of this problem is very well detailed in this blog post by Matthew Rocklin. In his case, the error was:

Command:
bsub /tmp/tmp4874eufw.sh
stdout:

Typical usage:
     bsub [LSF arguments] jobscript
     bsub [LSF arguments] -Is $SHELL
     bsub -h[elp] [options]
     bsub -V

NOTES:
 * All jobs must specify a walltime (-W) and project id (-P)
 * Standard jobs must specify a node count (-nnodes) or -ln_slots. These jobs cannot specify a resource string (-R).
 * Expert mode jobs (-csm y) must specify a resource string and cannot specify -nnodes or -ln_slots.

stderr:
ERROR: Resource strings (-R) are not supported in easy mode. Please resubmit without a resource string.
ERROR: -n is no longer supported. Please request nodes with -nnodes.
ERROR: No nodes requested. Please request nodes with -nnodes.

Another example of this issue is this github issue where --mem is not an accepted option on some SLURM clusters. The error was something like this:

$sbatch submit_slurm.sh
sbatch: error: Memory specification can not be satisfied
sbatch: error: Batch job submission failed: Requested node configuration is not available