[BioC] multicore processor

[Senthil Kumar Sundaram]

Thanks. I am going through the options suggested by different members.

Thanks,
Senthil Sundaram, MD
Assistant Professor of Pediatrics and Neurology
Wayne State University
PET Center
Children's Hospital of Michigan
3901 Beaubien Street
Detroit, MI 48201
Ph:  313-993-2870
Email: ssundaram at pet.wayne.edu






-----Original Message-----
From: Markus Schmidberger [mailto:schmidb at ibe.med.uni-muenchen.de] 
Sent: Thursday, October 16, 2008 4:41 PM
To: João Fadista
Cc: Senthil Kumar Sundaram; bioconductor at stat.math.ethz.ch;
r-sig-hpc at r-project.org
Subject: Re: [BioC] multicore processor

You also should have a look to Luke Tierney's website and his pnmath
code (using openMP):
http://www.cs.uiowa.edu/~luke/R/experimental/

And there is a new mailing list for HPC: R SIG on High-Performance
computing: r-sig-hpc at r-project.org.

And there is a lot of other stuff for parallelization in R and managing
big datasets: snow, Rmpi, affyPara, aroma.affymetrix, ...

And have a look to Dirks tutorial at the UseR2008. This should be a good
starting point for optimization in R:
http://www.statistik.uni-dortmund.de/useR-2008/tutorials/eddelbuettel.html

Best
Markus


João Fadista wrote:
> Check out this paper about R in parallel:
> http://www.biomedcentral.com/1471-2105/9/390
>  
> Regards,
> João
> 
> ________________________________
> 
> De: bioconductor-bounces at stat.math.ethz.ch em nome de Senthil Kumar
Sundaram
> Enviada: qui 16-10-2008 21:17
> Para: bioconductor at stat.math.ethz.ch
> Assunto: [BioC] multicore processor
> 
> 
> 
> Hi,
> 
>    I am new to using bioconductor. We have more than 200 CEL files to
> analyze and would like do it on a Linux(64 bit) system with 2 quadcore
Intel
> Xeon processors and 16GB RAM. We would like to utilize all 8 processors
> using Oligo package. But currently, it runs only on one processor. Can
> anyone help us to configure bioconductor to use all 8 processors?
> 
> 
> 
> Thanks,
> 
> 
> 
> Senthil Sundaram, MD
> Assistant Professor of Pediatrics and Neurology
> 
> Wayne State University
> PET Center
> Children's Hospital of Michigan
> 3901 Beaubien Street
> Detroit, MI 48201
> Ph:  313-993-2870
> Email: ssundaram at pet.wayne.edu
> 
> 
> 
> 
> 
> 
>         [[alternative HTML version deleted]]
> 
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-- 
Dipl.-Tech. Math. Markus Schmidberger

Ludwig-Maximilians-Universität München
IBE - Institut für medizinische Informationsverarbeitung,
Biometrie und Epidemiologie
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Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de
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