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

Sean Davis sdavis2 at mail.nih.gov
Thu Dec 4 23:11:13 CET 2008

On Thu, Dec 4, 2008 at 5:21 AM, Rainer M Krug <r.m.krug at gmail.com> wrote:
> 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...

No, I haven't gotten things to work.  Even under openmpi without SGE,
I have R crashes on a regular basis when using Rmpi-0.5.5, so I
haven't really pursued it further.


> 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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>> and provide commented, minimal, self-contained, reproducible code.
> --
> 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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