How to install Rmpi on a Scientific Unix Cluster

load the right modules

1. module add openmpi/gcc
2. module add r

This loads the most recent version of R, which is probably what you want. If you want a specific version x.y, load r/x.y.

install Rmpi

this is very easy. start R on the hpc console (type R). then do

install.packages("Rmpi",configure.args=c("--with-Rmpi-include=/cm/shared/apps/openmpi/gcc/64/1.4.5/include",
                                         "--with-Rmpi-libpath=/cm/shared/apps/openmpi/gcc/64/1.4.5/lib64",
                                         "--with-Rmpi-type=OPENMPI"))

you will be asked if you want to install to a personal library. say yes.

install snow

install.packages('snow')

run a test

if you have git

clone the git test repository with git clone git@github.com:floswald/mpitest.git on the hpc.

alternatively download the repository

to a folder on the hpc.

1. go to mpitest/R/singleThread/flos-test/ and
2. type make and hit enter.
3. if everything was installed correctly a test will use 3 nodes and do some things.
4. check the file exp.Rout for correct output.