Hello all,

I've seen multiple posts on this subject, but haven't clearly been able to
understand the issue. There must be something small.

I am trying to get Rmpi, foreach and snow working on a beowulf cluster,
using debian.

I have succeeded in installing Rmpi, changing the paths, etc.

However, i remain the with my original problem, when

cl<-makeCluster(4,type="MPI")

spawns slaves, they are always on the same node!

There are two processor per node on my cluster. What i need is a way to
spawn slaves across all nodes i've requested in my qsub script.

export PATH=$PATH:/usr/local/pkg/openmpi-1.4.4/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/pkg/openmpi-1.4.4/lib
#!/bin/bash
#PBS -o 'qsub.out'
#PBS -e 'qsub.err'
#PBS -l nodes=4:ppn=1
#PBS -m bea
$PBS_NODEFILE
$hostname

cd $PBS_O_WORKDIR

# Run an R script
R --vanilla < /nfs/user08/bw4sz/Files/Seawulf.R > output.Rout

I have tried using mpirun -np 4 in front of the R - call, but this just
fails without message.

In my R script, i call (alot of things, just the meat shown below).

cl <- makeCluster(4, type = "MPI")
print(clusterCall(cl,function() Sys.info()[c("nodename","machine")])) #This
always gives me the same nodenames, just on of the nodes in the Pbs
nodefile (and no, not the head node).

registerDoSNOW(cl)
print(getDoParWorkers())
system.time(five.ten <- rbind.fill(foreach(j=1:times ) %dopar%
drop.shuffle(j,iterations))) # Parameters are defined elsewhere, this is
not the issue.
stopCluster(cl)


My dream scenerio is to use both processors on each node, and pass
information between nodes in separate workflows.

I appreciate any suggestions

There is nothing wrong with my R script in terms of code, it works great
using doMC and foreach, with 8 cores on my desktop. However, i have not
been able to register the correct cores when using the University Cluster.

I am new at this, please forgive my lack of precise terms.

Best,

Ben Weinstein
-- 
Ben Weinstein
Graduate Student
Ecology and Evolution
Stony Brook University

http://life.bio.sunysb.edu/~bweinste/index.html

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