[R-sig-hpc] [R] torque/psb & snow library

Markus Schmidberger schmidb at ibe.med.uni-muenchen.de
Wed Oct 22 17:57:47 CEST 2008

Hi Javier,

there is a new mailing list for R and HPC: r-sig-hpc at r-project.org
This is probably a better list for your question.

I never tried torque with socket. We use torque and mpi or pvm (and R)
and it is working very well.
Why do you use socket as communication layer?
MPI was especially developed for communication between nodes in a
computer cluster. And there you can specify which nodes and the number
of processors per node you want use. Therfore I would strongly recommend
to use MPI. This will be faster in every condition!


jgarcia at ija.csic.es wrote:
> Hello all;
> I'm trying to execute parallel jobs trough library snow on a cluster built
> through torque/PSB. I'm succesfully obtaining the cluster with:
>> system("cat $PBS_NODEFILE > cluster.txt")
>> mycluster <- scan(file="cluster.txt",what="character")
>> cl <- makeSOCKcluster(mycluster)
> The only problem, at the moment, is that if I use processors in nodes
> other that the one in which I'm running R, the communication is extremely
> slow. If all processor are in the "master" computer there not seems ti be
> any problem.
> Has anyone got any experience with this and any advice? Perhaps snow() s
> not adequate for this kind of clusters?
> Thanks and best regards,
> Javier
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Dipl.-Tech. Math. Markus Schmidberger

Ludwig-Maximilians-Universität München
IBE - Institut für medizinische Informationsverarbeitung,
Biometrie und Epidemiologie
Marchioninistr. 15, D-81377 Muenchen
URL: http://www.ibe.med.uni-muenchen.de
Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de
Tel: +49 (089) 7095 - 4599

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