Rmpi
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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 <pre> # 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()