Sun Grid Engine (SGE) and Rsge package

Thu, Dec 4, 2008 10:49 PM #

Hi

I just found the Rsge package which seems to suit my need to do
parallel processing on a cluster with SGE. I did not manage to use
Rmpi or snow (which would have been nice).

My only problem is, that I can't find any documentation on how to use
Rsge (apart from the one included in the source package) - it seems to
utilise several options which might be useful to set.
Does anybody has any experience with this package or can show me a way
of using snow or Rmpi in an environment where I have to use SGE (qsub
...)?

Thanks

Rainer

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

Markus Schmidberger

Fri, Dec 5, 2008 10:37 AM #

Hi,

we have a cluster with SGE, R, LAM/MPI, Rmpi and snow. And it is working
fine. But configuration of SGE was a long and stressful job.

I had a look to the Rsge job. I think first of all you need a working
SGE with MPI and R. The package will not help you to configure your SGE.

Best
Markus

Rainer M Krug wrote:

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 - 4599