[R] rmpi/snow/sge/openmpi help

Markus Schmidberger schmidb at ibe.med.uni-muenchen.de
Fri Nov 7 20:54:06 CET 2008


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"


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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