[R-sig-hpc] Install Rmpi as a user of HPC

[Bjørn-Helge Mevik]

semra yalcin <semra.yalcin at gmail.com> writes:

> I have a problem with installation of Rmpi on my account at the hpc. I've
> tried to install Rmpi with different ways, but unfortunately I couldn't
> achieve it.
>
> OS of hpc is Scientific Linux v5.2 64 bit. Installed version of openMPI is
> 1.2.8. I have R 2.15.1 installed on my home folder. And I have no access to
> the root.

(OpenMPI 1.2.8 is quite old.  I think the current version is 1.6.1.)

I've just installed Rmpi on our cluster, running Rocks 6.0 (based on
CentOS 6.2).  We have installed OpenMPI in
/cluster/software/VERSIONS/openmpi-1.6.1.

I did the following to install Rmpi:

Make sure the following variables are set before installing Rmpi or
using it later on:

Add /cluster/software/VERSIONS/openmpi-1.6.1/bin to $PATH
Add /cluster/software/VERSIONS/openmpi-1.6.1/lib to $LD_LIBRARY_PATH
Add /cluster/software/VERSIONS/openmpi-1.6.1/share/man to $MANPATH
Add /cluster/software/VERSIONS/openmpi-1.6.1/include to $CPATH

(We use the Modules package for this.)

Then I started R and installed Rmpi with

install.packages("Rmpi", configure.args = "--with-mpi=/cluster/software/VERSIONS/openmpi-1.6.1")


-- 
Regards,
Bjørn-Helge Mevik, dr. scient,
Research Computing Services, University of Oslo