Running R under Sun Grid Engine with OpenMPI tight integration
On Fri, Dec 5, 2008 at 12:11 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
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.
Thanks - I'll keep you and the list posted when I find something out. I found the package Rsge which looks promising, and I'll try to get it to work. I'll go to the R-sig-hpc mailing list for this topic. Rainer
Sean
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
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