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Snakemake

Snakemake Profile for Running on AWS ParallelCluster with the Slurm Scheduler

This is a Snakemake profile for running on AWS ParallelCluster with the Slurm scheduler. It is heavily based on John Blischak's smk-simple-slurm profile and as such this repository uses the same license.

Default ParallelCluster Slurm installations have two peculiarities that make them differ from most other Slurm installations:

  • The --mem argument to sbatch is not supported, and if used sends nodes into the DRAINED state.
  • The sacct accounting system is not installed by default.

This profile accomodates these peculiarities.

Usage

Given a workflow my-workflow, copy the aws-parallelcluster-slurm directory to my-workflow/profiles. Make sure the status-scontrol.sh script is executable, and in config.yamlchange the parameter partition in section default-resources to the name of a queue in your cluster.

From my-workflow, execute Snakemake as snakemake --profile profiles/aws-parallelcluster-slurm.