[R-sig-hpc] OpenMPI vs MPICH2 on debian system

Jonathan Greenberg greenberg at ucdavis.edu
Thu Aug 11 22:39:21 CEST 2011


I'm a big fan of the snow/Rmpi package, and we've recently tried to
get it running on a new debian system in our lab.  My sysadmin is not
too keen on non-debian package installs (you know, ./configure, make,
make install), although I can convince him to do an apt-get -b source
/ dpkg install.  We tried a straightforward binary install of
openmpi-dev, but it appears to be spawning the threads only on one cpu
(the same one the master is running on) when doing a:

cl <- makeCluster(4, type = "MPI")
# look at top/gkrellm or run some stuff, only 1 CPU lights up.
> mpi.universe.size()
[1] 1

Does this have to do with something within Rmpi/snow, or is this a
"bad" install of openmpi?  Would doing an apt-get -b source
openmpi-dev/dpkg install solve this?  Would mpich2 (or another mpi
flavor) be a better choice?



Jonathan A. Greenberg, PhD
Assistant Project Scientist
Center for Spatial Technologies and Remote Sensing (CSTARS)
Department of Land, Air and Water Resources
University of California, Davis
One Shields Avenue
Davis, CA 95616
Phone: 415-763-5476
AIM: jgrn307, MSN: jgrn307 at hotmail.com, Gchat: jgrn307

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