Discussion

I want to reach out: I have this pending release for the SLURM executor (https://github.com/snakemake/snakemake-executor-plugin-slurm/pull/412 ). It implements better error feedback (in case of hardware failures and otherwise). It would need some thorough checking, and I cannot provoke too many hardware failures. Is anyone working on an older cluster? 😉

Feedback (as issues) would be appreciated. Also nice, if you tell me it is working, here.

#Snakemake #HPC #SLURM #ReproducibleComputing

Christian Meesters

@rupdecat@fediscience.org · last week

On a similar note: there is another (draft) PR. The #SLURM executor plugin for #Snakemake is capable of respecting partition definitions since v. 2.

I had the notion, that this is rather difficult to set this up manually and wrote a little command line helper. It queries the SLURM config and writes out a preliminary partition configuration template. This still requires manual adaptation, I'm afraid.

A small step forward as it requires both an understanding of Snakemake and your local SLURM setup. The world is as is it is, the phantasy of admin teams is unlimited and a one-fits-all solution is not on the horizon.

Still, if you want to try it out and provide feedback, this would be very much appreciated! All suggestions are welcome!

Christian Meesters

@rupdecat@fediscience.org · last week

I actually forgot the link in the last note: https://github.com/snakemake/snakemake-executor-plugin-slurm/pull/410

Meanwhile, it is not a draft PR any more. It is just a PR. And there is some more work to do. Think, I will merge it relatively soon into the main branch for a release.

The other features merit some more testing, though.