[R-sig-hpc] Installing Rmpi on hpc

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

Looks like you are building the package with the system compilers
and not the OpenMPI wrappers for them, hence missing some of the
libraries that the wrappers pull in.

I think you need to set things up for the build using R's
Makevars file and/or overwriting the compilers from the
command line.

I have had success building like so

$ /usr/bin/R CMD INSTALL \
   --library=/opt/Rlibs \
   /srv/global/work/buckleke/Srcs/R-parallel/Rmpi_0.5-9.tar.gz \
   --configure-args=--with-Rmpi-type=OPENMPI \
   --configure-args=--with-Rmpi-libpath=/usr/lib64/openmpi/1.4-gcc/lib \
   --configure-args=--with-Rmpi-include=/usr/lib64/openmpi/1.4-gcc/include

or similarly, on a different system, like so

$ cat ~/.R/Makevars
CC=mpicc
SHLIB_LD=mpicc
$ cd /local/scratch/kevin/Build/RMPI
$ gtar xf Rmpi_0.5-8.tar.gz
$ cd Rmpi
$ patch -Np1 -i ../Rmpi-ECS_NetBSD-patch.diff
$ cd ..
$ R CMD INSTALL --library=/vol/grid/pkg/R/Rlibs Rmpi \
  --configure-args=--with-Rmpi-type=OPENMPI \
  --configure-args=--with-Rmpi-libpath=/usr/pkg/lib/openmpi \
  --configure-args=--with-Rmpi-include=/usr/pkg/include


though I think this is probably all in the mailing list archives
somewhere !

HTPPUFYPC,
(Hope this provides pointers useful for your particular circumstances)
Kevin

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