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ARUP-NGS / BMFtools

Barcoded Molecular Families
MIT License
22 stars 8 forks source link

Multi-threading creates multiple threads, but processes these on a single core #32

Closed progee closed 8 years ago

progee commented 9 years ago

When the bmftools "threads" option is set to an integer > 1, bmftools will spin off as many subprocesses as requested in multiple threads as desired. These threads, however, are limited to one CPU core. It would be nice to have each thread spin off on a separate CPU, if available on the machine. For example, if I set threads to 12 on a machine with 24 cores, bmftools will spin off 12 threads on the same core (maxed to 100%) leaving 23 idle cores.

dnbaker commented 9 years ago

So Brett claims it worked for him on AR, but that was outside of the queueing/job management environment of the CHPC. That is concerning... New tag for the issue.

Let's revisit Monday.

dnbaker commented 8 years ago

Solved. Parallelization handled by OpenMP.