R devel - Nov 2014 - ShortRead::FastqStreamer and parallelization

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

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
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
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