http://www.r-project.org/

We installed the libraries Rmpi, doMPI and foreach and their dependencies on VSC2 and VSC3. These libraries give you the possibility to parallelize loops over more nodes with MPI using the foreach function which is very similar to a for loop.

Given a simple for loop:

for (i in 1:50) {mean(rnorm(1e+07))}

Sequential execution on VSC3 leads to an execution time [s] of:

/opt/sw/R/current/bin/R
> system.time(for (i in 1:50) { mean(rnorm(1e+07))})
   user  system elapsed 
 83.690   1.013  84.721 

The R-code may be parallelized in the following form:

• berk-rmpi.R

# basic example with foreach
# start R as usual:'R'or via a batch job
library (Rmpi)
library (doMPI)
cl <- startMPIcluster ()
registerDoMPI (cl)

result <- foreach (i = 1:50) %dopar% {
mean(rnorm(1e+07))
}

closeCluster(cl)
mpi.finalize()

using this script on VSC2:

#$ -N rstat
#$ -V
#$ -pe mpich 16
#$ -l h_rt=01:00:00
echo $NSLOTS
mpirun -machinefile $TMPDIR/machines -np 16 ~/sw/rstat/bin/R CMD BATCH berk-rmpi.R

using this script on VSC3:

#!/bin/sh
#SBATCH -J rstat
#SBATCH -N 1
#SBATCH --tasks-per-node=16

module unload intel-mpi/5
module load intel-mpi/4.1.3.048
module load R

export I_MPI_FABRICS=shm:tcp

mpirun R CMD BATCH berk-rmpi.R

takes on VSC2:

> proc.time()
   user  system elapsed 
  8.495   0.264   9.616