On Mon, Oct 19, 2009 at 7:51 AM, sebastian.rohrer@basf.com <
sebastian.rohrer@basf.com> wrote:

> Hello,
>
> since I work on large datasets I would like to use R with on our linux
> cluster, however I am no cluster administrator and quite ignorant about
> HPC on a technical level.
>
> I know that our cluster is managed with the Sun Grid Engine. Can R be used
> with an SGE and how (roughly) would this have to be configured?
>
>
I think you will want to look at using mpi under SGE.  You would submit a
parallel job to SGE and have an mpi environment be established (how this
happens depends on the SGE/mpi setup) and run Rmpi in this mpi environment.
If you go this route, you will want to look at integrating MPI with SGE.
Alternatively, you could submit a parallel job to SGE, but configure the job
to run on a single multi-core node, and then use the various packages
available for R that take advantage of multi-core processing.  The latter is
less involved, but ties you to a single node.  In any case, if you are
unfamiliar with SGE, it is probably worth talking to your system
administrator about the possibilities given your local setup.

Of course, others may have other ideas about how to do this.

Sean

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