[R] Running R under Sun Grid Engine with OpenMPI tight integration

Rainer M Krug r.m.krug at gmail.com
Thu Dec 4 11:21:35 CET 2008

Did you make any progress in using R in the SGE / OpenMPI environment?
I am asking, because I am struggling with the same problem. Using qsub
does not give me an interactive session which I can use (wherefore I
don't see a way of using RMPISNOW and getMPIcluster()) and the
spawning (makeMPIcluster()) when R is running only yields slave
processes on the node on which the master is running.
I have the feeling, that I am missing something really basic - but what is it...


On Thu, Oct 9, 2008 at 3:18 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> We have spent some time setting up Sun Grid Engine and OpenMPI on a
> group of linux boxes.  I have created a parallel environment and
> everything seems to be working.  I have Rmpi 0.5.5-5 installed on all
> machines.  I would like to start an interactive R session using, say,
> 8 processors and then start the Rmpi cluster.  I haven't been able to
> find what needs to be done in order to accomplish this task.  Is
> anyone using R in such an environment that can point me in the right
> direction?
> Thanks,
> Sean
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Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Faculty of Science
Natural Sciences Building
Private Bag X1
University of Stellenbosch
Matieland 7602
South Africa

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