[R-sig-hpc] Installing Rmpi on hpc

Kevin.Buckley at ecs.vuw.ac.nz Kevin.Buckley at ecs.vuw.ac.nz
Wed Sep 14 03:14:24 CEST 2011

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 \

or similarly, on a different system, like so

$ cat ~/.R/Makevars
$ 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 \

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

(Hope this provides pointers useful for your particular circumstances)

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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