I am working on a SLES 10 cluster with R available on it. To better use my
resources, I want to use Rmpi, but I am having a difficult time installing it.
I have set the $R_LIBS variable correctly.
The MPI libraries are available through the PGI compiler, but this R instance
was compiled with GCC.
The Rmpi package can be compiled and installed with
%R CMD INSTALL Rmpi_0.5-5.tar.gz --configure-args="CC=pgcc
--with-mpi=/shared/pgi725/linux86-64/7.2/mpi/mpich"
But when entering R and loading the library, I get
%R
> library(Rmpi)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '/home/<username>/.Rlib/Rmpi/libs/Rmpi.so':
/home/<username>/.Rlib/Rmpi/libs/Rmpi.so: undefined symbol: __pgdbg_stub
Error in library(Rmpi) : .First.lib failed for 'Rmpi'
Error in dyn.unload(file.path(libpath, "libs", paste("Rmpi",
.Platform$dynlib.ext, :
dynamic/shared library '/home/<username>/.Rlib/Rmpi/libs/Rmpi.so' was not
loaded
>
The undefined symbol is for the PGI debugger.
It doesn't matter if the $CC variable is gcc, pgcc, or mpicc, and all three do
show up in the make output during the configure process.
Thanks for your help,
Joshua
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