Rmpi
From FarmShare
Rmpi
Rmpi is R with mpi support. On the barley this means OpenMPI. Rmpi can be installed from CRAN packages if you wish. It is installed on the barley in /mnt/glusterfs/apps/R as a convenience.
setup
grid engine submit script (rmpi.submit)
#
#$ -cwd
#$ -j y
#$ -S /bin/bash
#$ -N rmpi32
#$ -pe orte 32
tmphosts=`mktemp` awk '{ for (i=0; i < $2; ++i) { print $1} }' $PE_HOSTFILE > $tmphosts
echo "Got $NSLOTS slots" echo "jobid $JOB_ID"
cat $PE_HOSTFILE
mpirun -np $NSLOTS -machinefile $tmphosts R --no-save -q < ~/Rmpitest.R
- This R profile can be used when a cluster does not allow spawning or a job
- scheduler is required to launch any parallel jobs. Saving this file as
- .Rprofile in the working directory or root directory. For unix platform, run
- mpirexec -n [cpu numbers] R --no-save -q
- For windows platform with mpich2, use mpiexec wrapper and specify a working
- directory where .Rprofile is inside.
- Cannot be used as Rprofile.site because it will not work
- Following system libraries are not loaded automatically. So manual loads are
- needed.
.libPaths(c("/mnt/glusterfs/apps/R", "/usr/lib/R/library"))
library(utils) library(stats) library(datasets) library(grDevices) library(graphics) library(methods)
if (!invisible(library(Rmpi,logical.return = TRUE))){
warning("Rmpi cannot be loaded")
q(save = "no")
}
options(error=quote(assign(".mpi.err", FALSE, env = .GlobalEnv)))
if (mpi.comm.size(0) > 1)
invisible(mpi.comm.dup(0,1))
if (mpi.comm.rank(0) >0){
#sys.load.image(".RData",TRUE)
options(echo=FALSE)
.comm <- 1
mpi.barrier(0)
repeat
try(eval(mpi.bcast.cmd(rank=0,comm=.comm)),TRUE) #try(eval(mpi.bcast.cmd(rank=0,comm=.comm),env=sys.parent()),TRUE)
#mpi.barrier(.comm)
if (is.loaded("mpi_comm_disconnect"))
mpi.comm.disconnect(.comm)
else mpi.comm.free(.comm)
mpi.quit()
}
if (mpi.comm.rank(0)==0) {
#options(echo=TRUE)
mpi.barrier(0)
if(mpi.comm.size(0) > 1)
slave.hostinfo(1)
}
.Last <- function(){
if (is.loaded("mpi_initialize")){
if (mpi.comm.size(1) > 1){
print("Please use mpi.close.Rslaves() to close slaves")
mpi.close.Rslaves(comm=1)
}
}
print("Please use mpi.quit() to quit R")
mpi.quit()
}
- Tell all slaves to return a message identifying themselves
mpi.remote.exec(paste("I am",mpi.comm.rank(),"of",mpi.comm.size()))
- Tell all slaves to close down, and exit the program
mpi.close.Rslaves() mpi.quit()
