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

[Hao Yu]

Try
R CMD ldd path_to_Rmpi.so

to see if Rmpi can find libs in /usr/lib64/openmpi/1.3.2-gcc/lib.
Otherwise you have to modify env LD_LIBRARY_PATH or modify R script to add
at third line

LD_LIBRARY_PATH=/usr/lib64/openmpi/1.3.2-gcc/lib

Hao

Paul Geeleher wrote:
> Hi guys,
>
> 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:
>
>> library(Rmpi)
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared library '/usr/lib64/R/library/Rmpi/libs/Rmpi.so':
>  libmpi.so.0: cannot open shared object file: No such file or directory
> 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 '/usr/lib64/R/library/Rmpi/libs/Rmpi.so' was not
> loaded
>
> I wonder does anybody have an ideas as to what might be wrong here?
>
> It seemed to install just fine on my master node by the way.
>
> Thanks,
>
> Paul.
>
>
> --
> Paul Geeleher
> School of Mathematics, Statistics and Applied Mathematics
> National University of Ireland
> Galway
> Ireland
> --
> www.bioinformaticstutorials.com
>
> --
> Paul Geeleher
> School of Mathematics, Statistics and Applied Mathematics
> National University of Ireland
> Galway
> Ireland
> --
> www.bioinformaticstutorials.com
>
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> R-sig-hpc mailing list
> R-sig-hpc at r-project.org
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>


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