[R] Multiple CPU HowTo in Linux?

Edwin Groot edwin.groot at biologie.uni-freiburg.de
Tue Sep 14 16:01:25 CEST 2010


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
-- 
Dr. Edwin Groot, postdoctoral associate
AG Laux
Institut fuer Biologie III
Schaenzlestr. 1
79104 Freiburg, Deutschland
+49 761-2032945



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