[R-sig-hpc] [R] Problem about spawn nodes with Rmpi

Markus Schmidberger schmidb at ibe.med.uni-muenchen.de
Wed Oct 22 18:05:30 CEST 2008

Hi Marce,

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.

Probably Rmpi does not find the correct Rmpi implementation. Have you
installed a second mpi implementation (lammpi)?
How do you have installed Rmpi?
Did you compiled it to the mpi libraries?
R CMD INSTALL --configure-args="--with-mpi=MPIPATH" Rmpi


Marce wrote:
> Hi all,
> now I'm testing R in a "virtual cluster", made it with VirtualBox. This one
> has 3 nodes, running CentOS 5 and OpenMPI 1.2.8, and the principal node
> (called "server") exports the /home to other nodes.
> I have installed R and OpenMPI in /home, in fact, it seems work OK. Editing
> the openmpi-default-hostfile and run "mpirun -np 3 hostname" I can see the
> hostname of all nodes in my cluster.
> But my problem comes when I want to spawn several nodes in R. I have
> installed R 2.6.1 and Rmpi 0.5.5. When I run mpi.spawn.Rslaves(nslaves=3)
> for example, it only spawn 3 processors in the same node, in fact, the local
> node.
> How I can tell to Rmpi that there are 2 o more nodes in the cluster? This
> problem can be solved passing a hostfile like an argument?
> Thanks for all
> 	[[alternative HTML version deleted]]
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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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