[GE dev] Rmpi and SGE: issues

myriad360 cblair at vandals.uidaho.edu
Thu Apr 1 18:04:23 BST 2010


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 I am having issues implementing Rmpi (for the R language) with SGE. Our SGE system is up and working well with OpenMPI, and programs compiled in C with mpicc spawn across all nodes after a qsub. So all that seems to be working as expected.

When running R straight off any node (via mpirun R < script.R --no-slave ), Rmpi spawns correctly, but of course only on that one node. When submitting to SGE via qsub with a submit script, the R program hangs on the Rmpi load in the R script (require (Rmpi)).

I was curious if any one can give me insight on why this is happening, and what I might need to do to get Rmpi working correctly with SGE.

Thanks everyone,

Colby



Contact Info:
Colby Blair
843 Travois Way
Moscow, ID 83843
Cell 1: 1.208.301.1576
Cell 2: 1.208.631.1059

IBEST Computing Core - www.ibest.uidaho.edu






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