[R-sig-hpc] Plain: R with Sun Grid Engine

[Rainer M Krug]

Check out the thread "Running R under Sun Grid Engine with OpenMPI
tight integration" some time ago - there was a pdf posted, which
outlined on how to use R with openMPI on an SGE.

There are some tricky bits, but it should work.

I am using single-thread simulations on our cluster, and it works
nicly - have not tried mpi yet as I did not have to.

Cheers,

Rainer


On Mon, Oct 19, 2009 at 2:20 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> On Mon, Oct 19, 2009 at 7:51 AM, sebastian.rohrer at basf.com <
> sebastian.rohrer at 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
>
>        [[alternative HTML version deleted]]
>
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-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

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