Opened 10 months ago

Closed 10 months ago

Last modified 10 months ago

#1512 closed enhancement (fixed)

Limit the number of threads used by allelecounter

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.49.1
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

The default settings for the ASCAT analysis is to use 8 cores since that still performs well with allelecounter that can be parallelized. But it doesn't perform well at all when multiple jobs are running on the same node. The nodes have 64 cores which means up to 8 jobs all doing file copying. Unless we can configure Slurm with QoS or partitions to prevent too many ASCAT jobs from running at the same time I think we should let ASCAT jobs ask for maybe 16 cores, but only use 4 for the allelecounter step.

Change History (2)

comment:1 by Nicklas Nordborg, 10 months ago

Resolution: fixed
Status: newclosed

In 7320:

Fixes #1512: Limit the number of threads used by allelecounter

We now assign 16 cores to ASCAT jobs, but only let allelecounter use 4 cores.

comment:2 by Nicklas Nordborg, 10 months ago

In 7323:

References #1512: Limit the number of threads used by allelecounter

The progress output didn't match the actual number of threads used.

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