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  • #48

Closed
Open
Created Sep 16, 2021 by Susheel Busi@susheel.busi

Unexpected behavior: `ancient` keyword may trigger Snakemake scheduler issues

@valentina.galata and @anna.buschart

  • When running metaG samples through imp3 [commit ecead78b], I noticed the following message/warning in the SLURM log file:
Failed to solve scheduling problem with ILP solver in time (10s). Falling back to greedy solver.
  • While it doesn't cause any issue per se, I noticed that the jobs are taking longer to complete. I can't necessarily confirm this yet, and the sample is still running, but I've attached the SLURM log.

  • A little digging revealed an issue with snakemake when the keyword ancient is used. See here: https://github.com/snakemake/snakemake/issues/946

  • I noticed that imp3 uses this keyword in the function.definitions rule

Something to keep an eye on for the future ;)

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