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EBI-Metagenomics / genomes-catalogue-pipeline

MGnify genome analysis pipeline
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SanntiS floods CPUs #85

Closed lam-c closed 6 months ago

lam-c commented 10 months ago

Hi, developers

I got a warning on CPU usage on process:SANNTIS, which flooding CPUs regardless the process cpu (1) assigned in config.

I checked the scripts and found that execution command of sanntis lacking cpu params. I did some modification like this and reran this step.

image

However, The cpus still ran out of limits. I reported this issue to Sanntis too https://github.com/Finn-Lab/SanntiS/issues/6, but not quite sure how to fix it. I wonder if there any options we could skip Sanntis temporarily?

Environment:

System: Red Hat 8.5.0-10
Singularity-ce: version 3.10.2-1.el8
Linux Cgroups v1  # thus cannot limit cpus when creating container
Nextflow: version 23.10.0 build 5889
Container: "quay.io/microbiome-informatics/sanntis:0.9.3.2"

Execution scripts and log files: logfiles.zip

mberacochea commented 10 months ago

Hey,

@lam-c thanks for the bug report. The PR #86 adds the --cpu flag but doesn't fix the underlying issue with SanntiS. I'll close this one when https://github.com/Finn-Lab/SanntiS/issues/6 is fixed

Cheers