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 > ------------------------------------------------------ > > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > 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 https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.