R-MPI

Introduction

This page is intended to help you with writing and running parallel R codes using the Rmpi package, the MPI interface for R, on the Odyssey cluster. Currently, Rmpi is available with the software moduleR/3.5.1-fasrc03 with OpenMPI MPI libraries, compiled with both Intel version and GNU compilers. In order to use the Rmpi package, first you need to load an appropriate set of software modules in your user environment, Example:
module load gcc/7.1.0-fasrc01 openmpi/2.1.0-fasrc02 R/3.5.1-fasrc03

Other versions may be available. Please see the modules search page for R for a list: Portal Modules Page

Example Rmpi code

Below is an example R code using Rmpi:
# Load the R MPI package if it is not already loaded.
if (!is.loaded("mpi_initialize")) {
library("Rmpi")
}
print(mpi.universe.size())
ns <- mpi.universe.size() - 1
mpi.spawn.Rslaves(nslaves=ns)
#
# In case R exits unexpectedly, have it automatically clean up
# resources taken up by Rmpi (slaves, memory, etc...)
.Last <- function(){
if (is.loaded("mpi_initialize")){
if (mpi.comm.size(1) > 0){
print("Please use mpi.close.Rslaves() to close slaves.")
mpi.close.Rslaves()
}
print("Please use mpi.quit() to quit R")
.Call("mpi_finalize")
}
}
# Tell all slaves to return a message identifying themselves
mpi.remote.exec(paste("I am",mpi.comm.rank(),"of",mpi.comm.size(),system("hostname",intern=T)))
# Test computations
x <- 5
x <- mpi.remote.exec(rnorm, x)
length(x)
x
# Tell all slaves to close down, and exit the program
mpi.close.Rslaves()
If you name this code mpi_test.R, for instance, it is submitted to the queue with the following batch-job submission script:

Assuming the batch-job submission script is named mpi_test.run, the job is submitted to the queue by typing in

Upon completion the job output is in the file mpi_test.Rout which has the below contents

Resources

• CRAN – Package Rmpi
• Rmpi manual