Running R under Sun Grid Engine with OpenMPI tight integration
On Wed, Jan 28, 2009 at 10:54 AM, Markus Schmidberger
<schmidb at ibe.med.uni-muenchen.de> wrote:
Hi, 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 configuration required. 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.
Thanks a lot for the document and the info - that sounds fantastic, and I will try it out very soon. Could you provide the link to the original document from Revolution, so that I can check for updates on the document? Cheers Rainer
Best Markus 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, Rainer
I'm trying to do the same, and not having very much luck getting it going. Thanks! 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 https://stat.ethz.ch/mailman/listinfo/r-help 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. Thanks Rainer
Saludos
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help 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 Ludwig-Maximilians-Universit?t M?nchen IBE - Institut f?r medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D-81377 Muenchen URL: http://www.ibe.med.uni-muenchen.de Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de Tel: +49 (089) 7095 - 4497
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