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

[Sklyar, Oleg (London)]

I had the same problem with RHEL5 and the main problem was the lack of
documentation. What you might want is to look into
/etc/openmpi-default-hostfile, which in my case had to be populated
with:

mynode1 slots=7
mynode2 slots=7 

etc. You might also want to try and create a local user-specific
hostfile if default OpenMPI configuration on Debian supports that,
pretty much with the same contents located in ~/.openmpi/hostfile

Both worked for me. However Rmpi still reports that the universe size is
1, i.e. in conctrast to LAM I could not rely on that value to get the
number of CPUs I can use w/o LB.

Dr Oleg Sklyar
Research Technologist
AHL / Man Investments Ltd
+44 (0)20 7144 3107
osklyar at maninvestments.com 

> -----Original Message-----
> From: r-sig-hpc-bounces at r-project.org 
> [mailto:r-sig-hpc-bounces at r-project.org] On Behalf Of Ingeborg Schmidt
> Sent: 11 February 2009 13:33
> To: r-sig-hpc at r-project.org
> Subject: [R-sig-hpc] Rmpi with Open MPI on Debian
> 
> 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.pd
> f ) 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
> 
> 
> 
> 
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