OpenMPI vs MPICH2 on debian system

That sounds strange. ?Rmpi or Open MPI would have to go
out of its way to restrict processes from being scheduled on
different cores of the CPU using numactl, or something like that,
which seems unlikely.

Does "top" say each of the four workers is getting 25% of a
CPU rather than about 100%?

- Steve


On Thu, Aug 11, 2011 at 5:06 PM, Jonathan Greenberg
<greenberg at ucdavis.edu> wrote:

Stephen:

Thanks! ?I guess the issue is that I'm seeing the slaves only spawn to
a single CPU on a 4-core system, which makes me think that the problem
is more significant, but I can't tell if its part of the openmpi
install or the Rmpi call. ?I don't recall having this problem on my
other debian system, but I unfortunately forgot to document how I set
it up on that system (also, I had root access to the original system
but now I'm trying to get this installed via my sysadmin).

--j

On Thu, Aug 11, 2011 at 2:02 PM, Stephen Weston
<stephen.b.weston at gmail.com> wrote:

Hi Jonathan,

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

library(Rmpi)
print(mpi.universe.size())
mpi.quit()

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
interactively.

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

--
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