Which version of R are you using, please?
I had that problem with some earlier versions of R.
On Thu, Oct 30, 2008 at 3:59 PM, Cahill, Joshua
<Joshua.Cahill at sdstate.edu> wrote:> 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
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
Erin Hodgess
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: erinm.hodgess at gmail.com