[R-sig-hpc] R Cluster

[Jonathan Olmsted]

Hi, Elias.

This is a shot in the dark since I've not tried it out on my own end, but
does the problem persist if the setting of the environmental variables
happens prior to the starting of R?

So, in a world where you were using BASH, you might define LD_LIBRARY_PATH
in "~/.bashrc".

If that does not work, have you confirmed that MPI is working as you'd
expect with a standard MPI "hello world" example? Not suggesting you come
up with one yourself, but I'll link one only if you don't already know what
I'm talking about.


-Jonathan


On Sun, Jun 7, 2015 at 9:24 PM, Elias Carvalho <ecacarva at gmail.com> wrote:

> Hello Guys
>
> I installed a Cluster with OpenMPI with support to TORQUE in a CENTOS 6,
> tested it with 1 master and two slaves and cluster works fine.
>
> Installed R and RStudio and executed the code below, an error occurred when
> trying to load package, somebody can help, please ?
>
> *# Clean environment*
> *closeAllConnections()*
> *rm(list=ls())*
>
> *# Adjust environment variables*
>
> *Sys.setenv(PATH="/usr/local/openmpi-1.4.5-tm/bin:/usr/local/openmpi-1.4.5-tm/include:/usr/lib64/qt-3.3/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin:/usr/local/maui/sbin:/usr/local/maui/bin")*
>
> *Sys.setenv(LD_LIBRARY_PATH="/usr/lib64/R/lib:/lib:/usr/local/lib64:/usr/lib/jvm/jre/lib/amd64/server:/usr/lib/jvm/jre/lib/amd64:/usr/lib/jvm/java/lib/amd64:/usr/java/packages/lib/amd64:/lib:/usr/lib:/usr/local/openmpi-1.4.5-tm/lib/:/usr/local/opemmpi-1.4.5/lib:")*
> *Sys.setenv(LD_PRELOAD="/usr/lib64/libutil.so")*
>
> *# Install Package*
> *install.packages("Rmpi", configure.args = c*
> *                 (*
> *
> "--with-Rmpi-include=/usr/local/openmpi-1.4.5-tm/include/",*
> *                  "--with-Rmpi-libpath=/usr/local/openmpi-1.4.5-tm/lib/",
> *
> *                  "--with-Rmpi-type=OPENMPI",*
> *                  "--with-mpi=/usr/local/openmpi-1.4.5-tm/"*
> *                 )*
> *                )*
>
> *# Load Package*
> *library(Rmpi)*
>
> The package installed without problems, but when loading it the error below
> occursr:
>
> *** building package indices
> ** testing if installed package can be loaded
> * DONE (Rmpi)
>
> The downloaded source packages are in ‘/tmp/RtmpVk8euT/downloaded_packages’
> > # Load Package
> > library(Rmpi)
> Error : .onLoad failed in loadNamespace() to 'Rmpi', details:
>   call: dyn.load(file, DLLpath = DLLpath, ...)
>   error: impossíble load object shared
> '/home/hpc/R/x86_64-redhat-linux-gnu-library/3.2/Rmpi/libs/Rmpi.so':
>   libmpi.so.0: cannot open shared object file: file or directory not found
> Erro: package or namespace load failed for ‘Rmpi’*
>
>
>
>
> *-- *
> *Best regards... 8^)*
>
> “*A mente que se abre a novas ideias jamais voltará *
> *a seu tamanho original*”  *Albert Einstein*
>
>
> _____________________________________________
> Prof. Elias César Araújo de Carvalho
> CV: http://lattes.cnpq.br/4248328961021251
>
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>
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-- 

J.P. Olmsted
j.p.olmsted at gmail.com
olmjo.com

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