[R-sig-hpc] R Cluster

[Elias Carvalho]

Thank you Jonathan

I executed the following commando with succes on OpemMPI:

mpirun -np 2 --hostfile myHosts hostname


I am thinking about try to install it on ubuntu server instead of centos,
it looks like to be more easy to install Rmpi

2015-06-07 23:18 GMT-03:00 Jonathan Olmsted <jpolmsted at gmail.com>:

> 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
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-hpc mailing list
>> R-sig-hpc at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>
>
>
>
> --
>
> J.P. Olmsted
> j.p.olmsted at gmail.com
> olmjo.com
>



-- 
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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