reduce memory for meryl count to avoid crash #7074
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mahesh-panchal
approved these changes
Nov 25, 2024
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Is the same issue happening with MERFIN here? |
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No, it's also things like version strings are different between meryl conda ( doesn't have one ) and meryl singularity ( 1.4.1 ). |
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MERFIN_HIST is also failing, so might be as well as the other issues: |
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Avoid that meryl count crashes due to memory issues. It seems that meryl uses the complete buffer provided via
memory=SIZEfor the kmer counts, but meryl itself uses some memory too. When using meryl count within singularity containers and slurm, then usually slurm is killing meryl due to that overhead.Solution, reduce the meryl memory kmer buffer
task.memoryby 10%. This is potentially a bit to much as usually the memory overhead was around 2-4Gb, but it solved all my issues on 3 three different compute clusters (Uppmax rackham, PDC dardel, and nac).