How to set -p (Slurm) - Githubissues

single-cell-genetics / cellsnp-lite

Efficient genotyping bi-allelic SNPs on single cells

https://cellsnp-lite.readthedocs.io

Apache License 2.0

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How to set -p (Slurm) #67

Closed flde closed 1 year ago

flde commented 1 year ago

Hi, many thanks for the great tool! I got a bit confused about the -p parameter. Should it be set to the number of available CPUs? I am asking because in the output it says [I::csp_fetch_core][Thread-1] and I would have multiple threads per CPU, right?

Highly appreciate you help.

All the best, Flo

flde commented 1 year ago

Okay, I think I got it. On the cluster the Slurm parameter --cpus-per-task actually referes to the number of threads on a node. So --cpus-per-task should equal -p. Quite basic I guess, sorry.