[Rd] Rmpi_0.5-4 and OpenMPI questions

From: Dirk Eddelbuettel <edd_at_debian.org>
Date: Wed, 3 Oct 2007 20:55:54 -0500

Many thanks to Dr Yu for updating Rmpi for R 2.6.0, and for starting to make the changes to support Open MPI.

I have just built the updated Debian package of Rmpi (i.e. r-cran-rmpi) under R 2.6.0 but I cannot convince myself yet whether it works or not. Simple tests work. E.g. on my Debian testing box, with Rmpi installed directly using Open Mpi 1.2.3-2 (from Debian) and using 'r' from littler:

edd_at_ron:~> orterun -np 3 r -e 'library(Rmpi); print(mpi.comm.rank(0))'

[1] 0
[1] 1
[1] 2


but I basically cannot get anything more complicated to work yet. R / Rmpi just seem to hang, in particular snow and and getMPIcluster() just sit there:

> cl <- makeSOCKcluster(c("localhost", "localhost"))
> stopCluster(cl)
> library(Rmpi)
> cl <- makeMPIcluster(n=3)

Error in makeMPIcluster(n = 3) : no nodes available.

I may be overlooking something simple here, in particular the launching of apps appears to be different for Open MPI than it was with LAM/MPI (or maybe I am just confused because I also look at LLNL's slurm for use with Open MPI ?)

Has anybody gotten Open MPI and Rmpi to work on simple demos? Similarly, is anybody using snow with Rmpi and Open MPI yet?

Also, the Open MPI FAQ is pretty clear on their preference for using mpicc for compiling/linking to keep control of the compiler and linker options and switches. Note that e.g. on my Debian system

edd_at_ron:~> mpicc --showme:link
-pthread -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl

whereas Rmpi built with just the default from R CMD:

gcc-4.2 -std=gnu99 -shared -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/lib -lmpi -lpthread -fPIC -L/usr/lib/R/lib -lR

Don't we need libopen-rte and libopen-pal as the MPI FAQ suggests?

Many thanks, Dirk

Three out of two people have difficulties with fractions.

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Received on Thu 04 Oct 2007 - 01:59:00 GMT

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