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

Stephen Weston stephen.b.weston at gmail.com
Thu Aug 11 23:02:40 CEST 2011

Hi Jonathan,

I think this is normal.  Consider the following script rmpi.R:


If I run this using:

  % R --slave -f rmpi.R
  [1] 1

the universe size is 1.  I also see this if I run the script

Specifying three hosts using orterun:

  % orterun -H localhost,localhost,localhost R --slave -f rmpi.R
  [1] 3
  [1] 3
  [1] 3

In this case, the script is execute three times, and each instance
sees a universe size of 3, since I specified three hosts.

If I use orterun to run the script only once, using "-n 1", as you
would for a spawned cluster:

  % orterun -n 1 -H localhost,localhost,localhost R --slave -f rmpi.R
  [1] 3

you see that one copy of the script is executed, and the universe size
is still 3.

In other words, if you don't use orterun (or mpirun, mpiexec, etc) the
universe size is always 1, at least as far as I've been able to discover.

- Steve

On Thu, Aug 11, 2011 at 4:39 PM, Jonathan Greenberg
<greenberg at ucdavis.edu> wrote:
> R-sig-hpc'ers:
> 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:
> require("snow")
> cl <- makeCluster(4, type = "MPI")
> # look at top/gkrellm or run some stuff, only 1 CPU lights up.
>> mpi.universe.size()
> [1] 1
> stopCluster(cl)
> 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?
> Thanks!
> --j
> --
> 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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