[R-sig-hpc] Rmpi with Open MPI on Debian

[Ingeborg Schmidt]

Hello,
I wish to use Rmpi with Open MPI on Debian. Slaves should be spawned on serveral computers which should be able to communicate with a single master. However, there does not seem to be a default hostfile for Open MPI that is used. So when I use
library(Rmpi)
mpi.spawn.Rslaves()
it only spawns one slaves on the localhost instead of several thereads on all my computers. I am unable to find any useful documentation of Open MPI (yes, I checked the FAQ on open-mpi.org). Is there such a thing as a default hostfile that is used when calling mpi.spawn.Rslaves() ? Or is there any other way to use mpi.spawn.Rslaves() with Open MPI so that slaves are spawned across multiple computers?

I am unsure about calling R via orterun. The only tutorials regarding orterun and R I found (e.g. http://dirk.eddelbuettel.com/papers/bocDec2008introHPCwithR.pdf ) seemed to imply that there either is no master or the master identifies itself by looking at it's mpi.comm.rank() . Moreover running
paste("I am", mpi.comm.rank(), "of", mpi.comm.size())
via
orterun --hostfile MYHOSTFILE -n CPUNUMBER Rslaves.sh RTest.R testlog needlog /PATH/TO/R
results in
"I am 0 of 0"
on every node.
This is not what I want, I would like only the master to execute my R script and send relevant methods to the slaves via mpi.bcast.Robj2slave(). My code contains commands like mpi.remote.exec() which I would like to keep. I have not yet seen any examples that are able to combine calling R via orterun with communication between the slaves with mpi.remote.exec() etc.

By the way: Can you recommend a method to lower the thread priory of the R slaves so that other calculations done on the same computers are not disturbed? Is placing a nice (Linux command to lower thread priority) before R in the Rslaves.sh sufficient when using mpi.spawn.Rslaves()?

Cheers,
Ingeborg Schmidt