add resources for using slurm with snakemake

[shannonekj]

Add what resources: options are available

[ctb]

from slack,

shannonekj:national_park: 2:35 PM Is there a place that lists all of the resources: options?? I can find mem_mb , attempt and runtime via @bluegenes helpful guide but I’m failing to know how to find a list of all available.

bluegenes:feet: 2:51 PM the only info I found was here: https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#resources

bluegenes:feet: 2:52 PM I only found out that runtime existed thanks to a twitter answer from Johannes Koster

camille_codon:snake: 2:52 PM most of the sbtch options will work: https://slurm.schedmd.com/sbatch.html#lbAG :+1: 2

2:53 if you’re using --profile every resource option is converted directly to flag and passed to sbatch or scontrol

[SichongP]

There is a slurm profile that supports basically everything sbatch takes in.

You can also just make your own profile. In that case you can use whatever keywords for resources as long as you define them in your profile. I personally have a slurm profile set up to only count resources towards constraint when a job is submitted to bmm or bmh so most of my jobs on bml can go wild :) I don't think that preset slurm profile can do this yet but I could be wrong.

[ctb]

see https://bluegenes.github.io/Using-Snakemake_Profiles/

[ctb]

for some of the inspiration for this thread