[R] torque/psb & snow library

jgarcia at ija.csic.es jgarcia at ija.csic.es
Wed Oct 22 18:18:13 CEST 2008

Thanks you! I'll look at this new list!
Well, I'm not the system administrator, and my installation of Rmpi and/or
pvm libraries for R crashes. As this is the first time I parallelize some
jobs, snow appealed as a first approach because 1) it compiled correctly
and 2) the use of the library is very easy.

As you tell me MPI is faster, I'll retry Rmpi installation.
B. Regards,

> 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!
> Best
> Markus
> 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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