[R] Multiple CPU HowTo in Linux?

[Edwin Groot]

Hello Cedrick,
Ah, yes, that looks like it would apply to my situation. I was
previously reading on snow, which is tailored for clusters, rather than
a single desktop computer.
Anyone with experience adapting multicore to an R-script?
I have to admit I know little about parallel processing,
multiprocessing and cluster processing.

Edwin

On Tue, 14 Sep 2010 10:15:42 -0400
 "Johnson, Cedrick W." <cedrick at cedrickjohnson.com> wrote:
>   ?multicore perhaps
> 
> On 09/14/2010 10:01 AM, Edwin Groot wrote:
> > Hello all,
> > I upgraded my R workstation, and to my dismay, only one core
> appears to
> > be used during intensive computation of a bioconductor function.
> > What I have now is two dual-core Xeon 5160 CPUs and 10 GB RAM. When
> I
> > fully load it, top reports about 25% user, 75% idle and 0.98
> short-term
> > load.
> > The archives gave nothing helpful besides mention of snow. I
> thought of
> > posting to HPC, but this system is fairly modest WRT processing
> power.
> > Any pointers of where to start?
> > ---
> > #Not running anything at the moment
> >> sessionInfo()
> > R version 2.11.1 (2010-05-31)
> > x86_64-pc-linux-gnu
> >
> > locale:
> >   [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
> >   [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
> >   [5] LC_MONETARY=C              LC_MESSAGES=en_GB.UTF-8
> >   [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
> >   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods
>   base
> >
> >
> > loaded via a namespace (and not attached):
> > [1] tools_2.11.1
> > ---
> > $ uname -a
> > Linux laux29 2.6.26-2-amd64 #1 SMP Sun Jun 20 20:16:30 UTC 2010
> x86_64
> > GNU/Linux
> > ---
> > Thanks for your help,
> > Edwin
> 
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Dr. Edwin Groot, postdoctoral associate
AG Laux
Institut fuer Biologie III
Schaenzlestr. 1
79104 Freiburg, Deutschland
+49 761-2032945