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An example of how to install Rmpi using the module openmpi/gcc/64/1.10.7 can be found below. Note that, the package snow has to be installed as well.
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module load r/4.2.1 module load openmpi/gcc/64/4.1.10.74 R .libPaths("~/rlibs") # assuming you are installing your # packages at the ~/rlibs folder install.packages("Rmpi", lib = "~/rlibs", repo = "https://cloud.r-project.org/", configure.args = "--with-mpi=/gpfs/cm/sharedsharedfs1/admin/hpc2.0/apps/openmpi/gcc/64/4.1.10.74/") install.packages("snow", lib = "~/rlibs", repo = "https://cloud.r-project.org/") |
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#!/bin/bash #SBATCH -p general #SBATCH -n 30 source /etc/profile.d/modules.sh module purge module load r/4.2.1 mpi/openmpi/gcc/64/4.1.10.74 # If MPI tells you that forking is bad uncomment the line below # export OMPI_MCA_mpi_warn_on_fork=0 Rscript mpi.R |
Now create the mpi.R script:
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library(parallel)
.libPaths("~/rlibs")
hello_world <- function() {
## Print the hostname and MPI worker rank.
paste(Sys.info()["nodename"],Rmpi::mpi.comm.rank(), sep = ":")
}
cl <- makeCluster(Sys.getenv()["SLURM_NTASKS"], type = "MPI")
clusterCall(cl, hello_world)
stopCluster(cl) |
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