[GE users] question concerning R on HPC

Dr. Rainer M Krug Rainer at krugs.de
Tue Nov 25 13:07:57 GMT 2008


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Hi

I want to use R on an HPC via MPI.

I managed to install Rmpi and to load it ionto R, but I get the
following errormessage when I try to create an MPI cluster and R hangs
(no response):

library(Rmpi)
[head001:15781] mca: base: component_find: unable to open osc pt2pt:
file not found (ignored)
> library(snow)
> cl <- makeCluster(2, type = "MPI")
Rscript execution error: No such file or directory
Rscript execution error: No such file or directory

I am using the following version:

> version
              _
platform       x86_64-unknown-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
status
major          2
minor          7.2
year           2008
month          08
day            25
svn rev        46428
language       R
version.string R version 2.7.2 (2008-08-25)
>

MPI version - the following implementations are installed:

OpenMPI 1.2.6 - compiled with GNU 4.2.1
/usr/local/openmpi_gnu/

OpenMPI 1.2.6 - compiled with SunStudio 12
/usr/local/openmpi_sun

MPICH2 1.0.8 - compile with GNU 4.2.1
/usr/local/mpich2-1.0.8_gnu

Rmpi was compiled against openmpi_sun.

I can compile the example C_MPI and it works, so MPI is working.


Any help welcome,

Rainer

- --
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Natural Sciences Building
Office Suite 2039
Stellenbosch University
Main Campus, Merriman Avenue
Stellenbosch
South Africa

Cell:		+27 - (0)83 9479 042
Fax:		+27 - (0)86 516 2782
Fax:		+49 - (0)721 151 334 888
email:		Rainer at krugs.de

Skype:		RMkrug
Google:		R.M.Krug at gmail.com

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