Thanks Kevin, Allan & Dirk.

With your help & comments, I think I've installed it correctly!

take care.

On Tue, Mar 15, 2011 at 7:30 PM, <Kevin.Buckley@ecs.vuw.ac.nz> wrote:

> > Sorry, if this appears to be a naive question! I was trying
> > to set up a parallel R working environment on my account on
> > hpc (running SGE). I tried to install Rmpi, but wasn't successful.
> > What do I need to get this going ?
>
> Hey Brian,
>
> a few things around and about this:
>
> In terms of building the package, look for a thread entitled:
>
>  "Trouble using Rmpi after successful installation"
>
> from April last year (2010), and one entitled
>
>  "trouble installing Rmpi"
>
> from November last year (2010), which contain some info about
> the way I got similar stuff going, especially in directing the
> R build process to use the OpenMPI compiler wrappers.
>
>
> And as someone else has already suggested: LAM has been pretty much
> absorbed into OpenMPI.
>
>
> Within an SGE/OpenMPI environment, I got things going by taking
> a wrapper from the RmpiSNOW package and tailoring that for
> invoking plain Rmpi scripts.
>
> This allowed an SGE submission, into an SGE parallel environment,
> to contain a line akin to:
>
> mpirun -np $NSLOTS /usr/local/bin/RMPI -f /some/path/to/an/Rmpi_script.R
> --args 2 5
>
> where that "/usr/local/bin/RMPI" wrapper sets up the various paths
> and, eg, Rlibs env var, for your actual script, whilst "$NSLOTS" gets
> set by the SGE when the parallel queue gets requested, eg.
>
>  qsub -pe pe_mpi 2 qsub_script.sh
>
> This has even worked for Rmpi scripts submitted via a Globus
> grid gateway into an SGE grid.
>
> Kevin
>
> PS
> You'll find that the RmpiSNOW packages script has a stanza
> that mentions ${LAMRANK} and "LAM-MPI's mpirun", but ignore
> it and go with OpenMPI!
>
> --
> Kevin M. Buckley                                  Room:  CO327
> School of Engineering and                         Phone: +64 4 463 5971
>  Computer Science
> Victoria University of Wellington
> New Zealand
>
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