RE: https://fediscience.org/@snakemake/116295568336688286

This is a big step forward: The SLURM plugin for Snakemake now supports so-called job arrays. These are cluster jobs, with ~ equal resource requirements in terms of memory and compute resources.

The change in itself was big: The purpose of a workflow system is to make use of the vast resources of an HPC cluster. Hence, jobs are submitted to run concurrently. However, for a job array, we have to "wait" for all eligible jobs to be ready. And then we submit.

To preserve concurrent execution of other jobs which are ready to be executed, a thread pool has been introduced. In itself, I do not see job arrays as such a big feature: The LSF system profited much more from arrays than the rather lean SLURM implementation does.

BUT: the new code base will ease further development to pooling many shared memory tasks (applications which support no parallel execution or are confined to one computer by "only" supporting threading). Until then, there is more work to do.

#HPC #SLURM #Snakemake #SnakemakeHackathon2026 #ReproducibleComputing #OpenScience

Techies: with IPv6, we'll never run out of addresses!

Also techies:

You've already eaten, kitty!