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This addresses functions summarizeOverlaps in GenomicAlignments and
tallyVariants in VariantTools, and perhaps others, not BiocParallel,
really, but only one CC: is available on this form.
Those two functions invoke BiocParallel capabilities to use multiple
cores when appropriate, much like mclapply in the parallel package.
Like mclapply they identify and utilize all available cores by
default. On a multi-user system that is frowned on.
The tallyVariants argument list includes BPPARAM, I learned how to use
that to specify the number of cores used (see code below).
The help for summarizeOverlaps says "control parallel evaluation using
the register interface in the
BiocParallel package." I looked into that, but not long enough to be
able to set core number. BPPARAM is not in the argument list.
Controlling the number of cores used in an R session is important in
my work environment. Functions invoking multiple cores should be clear
about it in their help pages and provide an obvious way to control
worker number.
I don't think that's done with these two functions. Apologies if I'm
not up to speed with developments, on asking for uniform specification
of BiocParallel parameters in the argument list of functions using
that package.
-- output of sessionInfo():
BPPARAM=MulticoreParam(workers=5)
--
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