Re: [R] rmpi/snow/sge/openmpi help

From: Markus Schmidberger <schmidb_at_ibe.med.uni-muenchen.de>
Date: Fri, 07 Nov 2008 11:54:06 -0800

Hi,

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. Do not forgett, first of all you have to register: https://stat.ethz.ch/mailman/listinfo/r-sig-hpc

Did you tried to run openmpi and R without SGE? Like this: "orterun -n 1 R --no-save"

I think openmpi / orterun do not get the correct hostfile. Therefore it starts with a default hostfile and this is only for the local machine! So all nodes are at the same machine.
It normally works like this that SGE creates a hostfile and puts the path of the hostfile to a special (environment) variable. Now you have to make sure that the correct hostfile will be used. So SGE should call something like this:
"ortrun -n 1 --hostfile $PATH_TO_HOSTFILE R --so-save"

Best
Markus

jk jk wrote:
> Forgive the spam. Let me try that e-mail again.
>
>
> I'm trying to get snow working with openmpi and sge. Everything
> appears to work, except the program only runs on 1 node. If i tell
> snow to run on 5 nodes, it spawns 5 processes on a single node, 6
> nodes = 6 procs on 1 node and so on. I'm at a loss for ideas. Any
> help would be appreciated.
>
> Setup: Rocks Cluster, OpenMPI, R 2.8.0, Snow, Rmpi.
>
>
> Please ask for specifics. Thanks in advance.
>
> ______________________________________________
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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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Received on Fri 07 Nov 2008 - 20:02:19 GMT

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