Edwin,
I'm not sure what you mean by "adapting"; other than installing
multicore, there is nothing else to set up. How and whether you could
then parallelise your code strongly depends on the specific problem you
are facing.
What have done in the past was to look at the source of the functions
from whatever package I was using that produced the bottleneck. If what
is taking the longest time is actually embarrassingly parallel,
mclapply() from package multicore can help. In the simplest case you
could simply replace lapply() in the with an appropriate mclapply().
Check out ?mclapply. But then again you might have to get a little more
creative, depending on exactly what in the code is taking so long to
run. If your problem is inherently sequential then even multicore won't
help.
Christian
On 09/14/2010 09:35 AM, Edwin Groot wrote:
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."<cedr...@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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PLEASE do read the posting guide
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Dr. Edwin Groot, postdoctoral associate
AG Laux
Institut fuer Biologie III
Schaenzlestr. 1
79104 Freiburg, Deutschland
+49 761-2032945
______________________________________________
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Christian Raschke
Department of Economics
and
ISDS Research Lab (HSRG)
Louisiana State University
Patrick Taylor Hall, Rm 2128
Baton Rouge, LA 70803
cras...@lsu.edu
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
