[R-sig-hpc] Install Rmpi as a user of HPC
Bjørn-Helge Mevik
b.h.mevik at usit.uio.no
Mon Sep 24 12:57:37 CEST 2012
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
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