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.ziervogel at 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
Andr?
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Dipl. Psych Andr? Ziervogel
andre.ziervogel at psychol.uni-giessen.de
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