[R-sig-hpc] Trouble using Rmpi after successful installation

[Kevin.Buckley at ecs.vuw.ac.nz]

> I'm trying to install Rmpi on the slave nodes of my cluster. The
> installation seems to work with no errors or warnings using this
> command:
>
> R CMD INSTALL
> --configure-args="--with-Rmpi-include=/usr/lib64/openmpi/1.3.2-gcc/include
> --with-Rmpi-libpath=/usr/lib64/openmpi/1.3.2-gcc/lib
> --with-Rmpi-type=OPENMPI" Rmpi_0.5-8.tar.gz
>
> But when I attempt to load Rmpi I get the following error:

I appreciate that you say it compiled cleanly but are you sure that
the Rmpi library was actually compiled against the OpenMPI compiler
driver wrappers?

I found that I needed to explicity set the following in

~/.R/Makevars

before I ran the R CMD INSTALL upon my School's NetBSD platform:

$cat ~/.R/Makevars
CC=mpicc
SHLIB_LD=mpicc

I am now seeing other issues with invoking Rmpi (detailed elsewhere
on this list) but there was a point where I thought I had installed
the Rmpi.so correctly only to find that it was installed but not
seemingly linked against any OpenMPI libs.

Forcing the compiler and linker through the use of the ~/.R/Makevars
mechanism seemed to, at least, cure that issue - for some reason all
my other attempts pass stuff via the R command line did not seem to
percolate through to the actual build.


-- 
Kevin M. Buckley                                  Room:  CO327
School of Engineering and                         Phone: +64 4 463 5971
 Computer Science
Victoria University of Wellington
New Zealand