Running R under Sun Grid Engine with OpenMPI tight integration
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. 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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