MPI Apply on Biowulf

simRun.bat

#!/bin/bash

# navigate to directory

cd Simulation

# Get OpenMPI in our PATH.  openmpi_ipath and openmpi_ib

module load R
# module load openmpi/1.4.4/gnu/eth loaded above so not needed anymore
`which mpirun` -n 1 -machinefile $PBS_NODEFILE R --vanilla >Run1.out<<EOF

# begin R code

library(Rmpi)
# load stuff if necessary
# source("mysims.R")

mpi.spawn.Rslaves(nslaves=$np)

onerun<-function(number){
set.seed(number+14)

# do something
boots <- rnorm(100)

# return something
return(boots)
}

results <- Rmpi::mpi.applyLB(1:1000, onerun)
finishedout <- do.call(rbind, results)

write.csv(finishedout, "Run.csv", row.names=FALSE)

mpi.close.Rslaves()
mpi.quit()

EOF

Submit to biowulf

qsub -v np=52 -l walltime=424:00:00, nodes=26 simRun.bat

np should be 2 times the number of nodes, because the default nodes each have 2 processors.