[GE dev] Rmpi and SGE: issues

ecs_vuw_kevin Kevin.Buckley at ecs.vuw.ac.nz
Tue May 18 04:40:31 BST 2010

Take a look at the R HPC SIG list, this gets discussed on there a lot.

As a result of following the info in threads on there,
I got Rmpi going, on SGE/OpenMPI, by following the
mechanism which R's SNOW packages uses.

SNOW comes with a wrapper for R called RMPISNOW

The wrapper overides the R_PROFILE variable
so that R loads the SNOW one.

Having flapped around for a good while with Rmpi, I shamelessly
copied that wrapper, calling it RMPI and edited it 
to point at my Rmpi installtion
(It'll be obvious when you see it)

I can now qsub a script containing this type of thing

mpirun -np $NSLOTS /some/path/to/RMPI
-f /some/path/to/scripts/script.R --args 1 2 3

I also needed to edit Rmpi's Rprofile so as to add a lib.loc="/path/to/R/libs"

Well, it worked for me (tm).

If you need more info, use the R HPC SIG list.

Kevin M. Buckley

e-Research Programmer
School of Engineering and Computer Science
Victoria University of Wellington
New Zealand


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