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
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
Dipl.-Tech. Math. Markus Schmidberger
Ludwig-Maximilians-Universit?t M?nchen
IBE - Institut f?r 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