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Plain: R with Sun Grid Engine
3 messages · sebastian.rohrer at basf.com, Sean Davis, Rainer M Krug
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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) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Cell: +27 - (0)83 9479 042 Fax: +27 - (0)86 516 2782 Fax: +49 - (0)721 151 334 888 email: Rainer at krugs.de Skype: RMkrug Google: R.M.Krug at gmail.com