[Rd] ShortRead::FastqStreamer and parallelization

Prof Brian Ripley ripley at stats.ox.ac.uk
Tue Nov 18 18:35:38 CET 2014

What does this have to do with this (or any R) list?

Bioconductor has its own support arrangements.

On 18/11/2014 17:00, Cook, Malcolm wrote:
> Hi,
> I understand ShortRead::FastqStreamer will read chunks in parallel depending on the value of ShortRead:::.set_omp_threads
> I see this discussed here:  https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004355.html and nowhere else.
> It probably should be documented in ShortRead.
> Possibly this has already changed for I am using still R 3.1.0.   I thought I'd check.
> Oh, and, in my hands/hardware, the value of this FastqStreamer's use of srapply's parallelization is negligible, at least if the consumer of successive yields is in the main process.  I see that the new bpiterate appears to take advantage of yielding in forked processes, which sounds promising.  Is that the idea?
> Looking forward....
> Malcolm Cook
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Brian D. Ripley,                  ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
1 South Parks Road, Oxford OX1 3TG, UK

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