Hello,
In your email, you speak about foreach()%dopar%, but in your script,
it is foreach()%do%.
Best,
Pascal
On Thu, Aug 7, 2014 at 7:19 PM, André Ziervogel
andre.ziervo...@psychol.uni-giessen.de wrote:
Dear R people,
I’ve been doing some hpc using R and openmpi. Unfortunately I’ve encoutred a
major problem and it’s nature is hard to pin down:
Essentially I call mpirun Rscipt … as soon as the script reaches a
foreach()%dopar% it halts indefinitely. I’ve attached the qsub script:
#!/bin/bash
#$ -S /bin/bash
#$ -N test_14
#$ -cwd
#$ -V
#$ -o /fhgfs/g61570/Spectral Databases/log/test_14_$JOB_ID
#$ -j y
#$ -q regular
#$ -pe openmpi 8
#$ -l h_rt=00:15:00
#$ -l h_vmem=1.9G
#$ -m eas
#$ -M andre.ziervo...@psychol.uni-giessen.de
module add gcc
module add openmpi/gcc/64/1.6.5
module add R/gcc/3.0.1
date #log start time
echo Number of slots . $NSLOTS
mpirun Rscript /fhgfs/g61570/Spectral\ Databases/test_10.r
/fhgfs/g61570/Spectral\ Databases/log/test_14.Rout
date
exit
and the R file:
suppressMessages(library('doMPI'))
skylla.cluster - startMPIcluster()
registerDoMPI(skylla.cluster)
cat(paste(COMM SIZE: , mpi.comm.size(0), cluster size: ,
clusterSize(skylla.cluster), \n,sep = ))
tmp.time - proc.time()
sample - foreach(i=seq(from=0, to=1000, by =1),.combine='c',.inorder=TRUE)
%do%
{
r - sqrt(i^2 + i^2) + .Machine$double.eps * factorial(i)
sin(r) / r
}
cat(paste(Processing seriell time: , \n, sep = ))
print(proc.time() - tmp.time)
#print(sample)
tmp.time - proc.time()
sample - foreach(i=seq(from=0, to=1000, by =1),.combine='c',.inorder=TRUE)
%dopar%
{
r - sqrt(i^2 + i^2) + .Machine$double.eps * factorial(i)
sin(r) / r
}
cat(paste(Processing parallel time: , \n, sep = ))
print(proc.time() - tmp.time)
#print(sample)
closeCluster(skylla.cluster)
# mpi.close.Rslaves()
# mpi.exit()
mpi.quit(save='no‘)
Any suggestions would be highly appreciated! Thanks!
Best
André
--
Dipl. Psych André Ziervogel
andre.ziervo...@psychol.uni-giessen.de
--
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Pascal Oettli
Project Scientist
JAMSTEC
Yokohama, Japan
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
