[BioC] memory bottleneck on Linux

[Tapan Mehta]

Thanks a lot for your reply. No ihaven't modified the
affy library for cluster because I thought 4 GB RAM
should suffice. Is there anything in particular
available for parallel computing in the Bioconductor
project.

Regards,

Tapan Mehta


--- "A.J. Rossini" <rossini at blindglobe.net> wrote:
> 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.
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> 
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