[GE users] [OT] Running R under SGE and OpenMPI

Sean Davis sdavis2 at mail.nih.gov
Fri Oct 17 13:29:36 BST 2008


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On Fri, Oct 17, 2008 at 8:15 AM, Davide Cittaro
<davide.cittaro at ifom-ieo-campus.it> wrote:
> @Sean
> Have you been able to run R+OpenMPI+SGE?
>
> I have OpenMPI running in batch jobs.
> Interactive jobs work only if I specify a hostfile.
> I'm still playing with R, trying to understand the right options for mpirun
> and mpi.spawn.Rslaves

mpirun -np 1 R --vanilla # just start the master

mpi.spawn.Rslaves() # will start as many processes as possible

If I run on a single machine, then it works.  I think I have some
issues with spawning processes across hosts under openMPI, but I
haven't sorted them out yet.

Sean

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