Thank you very much Edward and Bjørn-Helge...

I've figured out how linking the path of mpi.h files to rmpi in our system;
as,

install.packages("Rmpi",
                 configure.args =

c("--with-Rmpi-include=/usr/mpi/intel/openmpi-1.2.8/include/",

"--with-Rmpi-libpath=/usr/mpi/intel/openmpi-1.2.8/lib64/",
                   "--with-Rmpi-type=OPENMPI"))

This code works, but the locked memory size prevents to complete the
initialisation. Now I am waiting the admin to increase it.

Regards,

Semra







On Mon, Sep 24, 2012 at 1:57 PM, Bjørn-Helge Mevik <b.h.mevik@usit.uio.no>wrote:

> semra yalcin <semra.yalcin@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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