[R-sig-hpc] [R] Running R under Sun Grid Engine with OpenMPI tight integration
schmidb at ibe.med.uni-muenchen.de
Wed Jan 28 09:54:25 CET 2009
in Munich we use SGE with Lam/MPI and Rmpi (latest version). It is
working very well now. There were only some small changes to the SGE
Attached a document form REvolution Computing for using SGE with
OpenMPI. It is a nice installation guide. Thanks to REvolution for
providing this document to the R community.
Rainer M Krug schrieb:
> On Tue, Jan 27, 2009 at 11:04 AM, Marce <marcemb at gmail.com> wrote:
>> 2009/1/27 Rainer M Krug <r.m.krug at gmail.com>:
>>> On Tue, Jan 27, 2009 at 2:30 AM, Peter Waltman <peter.waltman at gmail.com> wrote:
>>>> Hi -
>>>> I saw your posting on the R-help mailing list. Were you ever able to get
>>>> this working? did you end up switching to use the rsge library?
>>> Yes - that is exactly what I did - I am using rsge or, which is in
>>> most cases sufficient for me, starting several instances of R and run
>>> the whole simulation (array processing).
>>> But I would still like to know how I can use the Rmpi and snow on the
>>> Sun Grid Engine.
>>> Please keep me posted,
>>>> I'm trying to do the same, and not having very much luck getting it going.
>>>> Peter Waltman
>>> 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
>>> R-help at r-project.org mailing list
>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>> Hi all,
>> I have been installed R in SGE but with LAM tight integration, I don't
>> k now if this help you :s . The problem I had with OpenMPI was that
>> the load in all nodes waiting for a job and with an instance of R.
>> Their load up to 100 %, and there isn't a job running on them.
>> Even so, I will try to configure it with OpenMPI..when I have results
>> I will post them ok?
> Yes please - could you please provide some info (and a small example)
> on how you managed this with LAM?
> I think we should move this thread to r-sig-hpc, as it is more
> appropriate there. I CC'd it to there - please respond there and not
> on r-help.
>> R-help at r-project.org mailing list
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
Dipl.-Tech. Math. Markus Schmidberger
IBE - Institut für medizinische Informationsverarbeitung,
Biometrie und Epidemiologie
Marchioninistr. 15, D-81377 Muenchen
Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de
Tel: +49 (089) 7095 - 4497
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