Install Rmpi as a user of HPC

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Installing Rmpi is tricky. I don't know about RHEL/CentOS/Scientific
Linux, but I had to write a special script to get it to work on
openSUSE 12.1:

https://github.com/znmeb/Computational-Journalism-Server/tree/master/HighPerformanceComputing

Note in particular that I had to set up a configuration file for
OpenMPI as 'root' and I had to install Rmpi using "R CMD install"
after downloading the package from CRAN.
Hi all,

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.

When searching the web, I saw that before installing Rmpi, I should modify
LD_LIBRARY_PATH  to include the path to the Open MPI libraries. I checked
/usr/lib64 folder of the hpc. There is no folder called openmpi. So I think
that there is no default link to OpenMPI libraries on the system.

If admins run *Idconfig /usr/lib64/openmpi/lib/*, could I install Rmpi
properly after indicating the path to openmpi lib?

Moreover, there are many other users who are working on the system and
using openmpi. Will this command run affect them?

Also I have to say that almost everything (Linux, HPC, parallel R...) is
new to me. I hope that my questions and thoughts aren't nonsense.

Thanks in advance for any advice.

Semra

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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,
Bj?rn-Helge Mevik, dr. scient,
Research Computing Services, University of Oslo
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