[BioC] memory bottleneck on Linux

[A.J. Rossini]

Tapan Mehta <tapmehta at yahoo.com> writes:

> I am trying to run a task of 100 CEL files each of 10
> MB on Linux based Bewoulf cluster with each node of  4
> GB. I am trying to use the mas5 method in the affy
> library. However I am unable to finish it gives memory
> problems. I am unable to increase the memory as the
> function of memory in R is only for Windows( as posted
> on the R mailing list). Please could anybody guide me
> in this problem? 

Have you modified the affy library to actually use the cluster?  

If not, why do you think the cluster will help?  I'm assuming that you
are simply running on a single node with 4Gb ram, which might not be
enough. 

best,
-tony


-- 
A.J. Rossini  /  rossini at u.washington.edu  /  rossini at scharp.org
http://software.biostat.washington.edu/ UNTIL IT MOVES IN JULY.
Biomedical and Health Informatics, University of Washington
Biostatistics, HVTN/SCHARP, Fred Hutchinson Cancer Research Center.
FHCRC: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email 

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