[R-sig-hpc] [R] Problem about spawn nodes with Rmpi

[Markus Schmidberger]

Hi Marce,

we have to be a little bit careful with cross postings :-)

You can try the new Rmpi version. To see your used MPI implementation.
http://www.stats.uwo.ca/faculty/yu/Rmpi/
Add C level function mpidist. .Call("mpidist",PACKAGE="Rmpi") returns 1
if it is OpenMPI; 2 if LAM and 3 if MPICH.

I am not a specialist in openMPI. I maily (still) use lammpi. But I
think there could be problems with your default hostfile.

Try to run R with openMPI like this:
orterun -n 1 --hostfile XXX R --no-save

Best
Markus

Marce wrote:
> 2008/10/22 Markus Schmidberger <schmidb at ibe.med.uni-muenchen.de>
>> Hi Marce,
>>
>> there is a new mailing list for R and HPC: r-sig-hpc at r-project.org
>> This is probably a better list for your question.
>>
>> Probably Rmpi does not find the correct Rmpi implementation. Have you
>> installed a second mpi implementation (lammpi)?
>> How do you have installed Rmpi?
>> Did you compiled it to the mpi libraries?
>> R CMD INSTALL --configure-args="--with-mpi=MPIPATH" Rmpi
>>
>> Best
>> Markus
>>
>> --
>> Dipl.-Tech. Math. Markus Schmidberger
>>
>> Ludwig-Maximilians-Universität München
>> IBE - Institut für medizinische Informationsverarbeitung,
>> Biometrie und Epidemiologie
>> Marchioninistr. 15, D-81377 Muenchen
>> URL: http://www.ibe.med.uni-muenchen.de
>> Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de
>> Tel: +49 (089) 7095 - 4599
> 
> Oh thanks, I don't know the existence of this mail list :p. I have
> just subscribe.
> 
> About your answer, I don't have more implementations of MPI, just
> OpenMPI. When I install Rmpi I did like you say: "/home/R/bin/R CMD
> INSTALL Rmpi.... --configure-args--with-mpi=/home/openmpi/.
> I think that installation went OK, after that in logs Rmpi recognize
> MPI directory..all OK.
> Now I'm not in my computer, tomorrow I'll do again to see more logs.
> 
> Thanks again for all Markus.
> 
> ((PD: I will send this post both list, sorry for the duplicated messages)
> 
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-- 
Dipl.-Tech. Math. Markus Schmidberger

Ludwig-Maximilians-Universität München
IBE - Institut für medizinische Informationsverarbeitung,
Biometrie und Epidemiologie
Marchioninistr. 15, D-81377 Muenchen
URL: http://www.ibe.med.uni-muenchen.de
Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de
Tel: +49 (089) 7095 - 4599