R help - Apr 2011 - R and multithread

Hello,
Sorry if this question has been posted before but could't find out 
exactly an answer to the question....

I'm doing bioinformatics and doing small RNA sequencing that make use of 
packages such as DESeq and EDGE. For those familiar with this data you 
will notice that you end up having large matrices with millions of 
entries. So i guess many people might be facing the same problem of 
dealing with so big matrices. and vectors.

I've heard of people using other math libraries (since the default R 
math lib is single core). to compile R and make it use several procs on 
the server. I'm not familiar with the different math libs availables 
(BLAS,..)

Can i use faster math libraries so that R uses the full procs capacities 
of my server ?

I'm running 2.12.2 on an  linux server (16cpu with 32Gb ram).

thanks for your tips,
david

How about googling it?!!

"R multithread"
" R Parallel processing"

both got numerous apprently relevant hits.

Also please familiarize yourself with CRAN's task views, where you
will find HighPerformanceComputing.

-- Bert

On Wed, Apr 6, 2011 at 5:27 AM, David martin <vilanew at gmail.com>
wrote:
> Hello,
> Sorry if this question has been posted before but could't find out
exactly
> an answer to the question....
>
> I'm doing bioinformatics and doing small RNA sequencing that make use
of
> packages such as DESeq and EDGE. For those familiar with this data you will
> notice that you end up having large matrices with millions of entries. So i
> guess many people might be facing the same problem of dealing with so big
> matrices. and vectors.
>
> I've heard of people using other math libraries (since the default R
math
> lib is single core). to compile R and make it use several procs on the
> server. I'm not familiar with the different math libs availables
(BLAS,..)
>
> Can i use faster math libraries so that R uses the full procs capacities of
> my server ?
>
> I'm running 2.12.2 on an ?linux server (16cpu with 32Gb ram).
>
> thanks for your tips,
> david
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>


-- 
"Men by nature long to get on to the ultimate truths, and will often
be impatient with elementary studies or fight shy of them. If it were
possible to reach the ultimate truths without the elementary studies
usually prefixed to them, these would not be preparatory studies but
superfluous diversions."

-- Maimonides (1135-1204)

Bert Gunter
Genentech Nonclinical Biostatistics