From ripley at stats.ox.ac.uk  Tue Nov 18 18:35:38 2014
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Tue, 18 Nov 2014 17:35:38 +0000
Subject: [Rd] ShortRead::FastqStreamer and parallelization
In-Reply-To: <D4772401B9D976478C0895769BE3E7920F27A42C@MBSRV02.sgc.loc>
References: <D4772401B9D976478C0895769BE3E7920F27A42C@MBSRV02.sgc.loc>
Message-ID: <546B836A.1060008@stats.ox.ac.uk>

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



[Rd] ShortRead::FastqStreamer and parallelization
Prof Brian Ripley