Running CarveMe on HPC cluster about carveme

[cdanielmachado]

The -r option uses the multiprocessing module (https://docs.python.org/2/library/multiprocessing.html), which is not very sophisticated, it simply launches multiple processes at once (as many as possible I suppose).

We don't have any support for specific cluster systems. I have experience running CarveMe with LSF and Slurm (and migrating between the two).

The most efficient way to run CarveMe on a cluster is to submit your jobs as a job array (most cluster systems support job arrays), instead of using the -r option. That will allow the cluster system to efficiently allocate each job, and manage the number of running jobs at any given time. Just use the job index in the environment variables to select the genome file each job will use.

[rdmtinez]

Thanks for that info!