Use MulticoreParam under BatchtoolsParam
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@a9c5eb20
Last seen 9 days ago
United States

Hello,

Is it a good practice to use MulticoreParam on each of the cores/cpus requested by BatchtoolsParam?

Regards

BatchtoolsParam MulticoreParam BiocParallel • 220 views
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@martin-morgan-1513
Last seen 20 days ago
United States

Generally it is not a good idea to have nested parallel calls, because it is too easy to over-subscribe the compute nodes (e.g., on a six-core machine running six jobs, each job starts six more parallel jobs, so there are 36 jobs contending for only 6 cores). In batchtools it would be better to use slurm or other facilities for distributing appropriate numbers of tasks to each compute node.

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