[R-sig-hpc] mpirun and R

[Jonathan Greenberg]

R-sig-hpc'ers:

Our system (running openmpi) allows for an interactive session to be
created with N number of CPUs allotted to it (12 in my case).  Here's
the qsub command to get the interactive node running:

qsub -X -I -q [mygroup] -l nodes=1:ppn=12,walltime=48:00:00

If I boot R and then try some HPC R commands e.g.:

require(raster)
# Note this is just a wrapper for a snow call:
beginCluster()

I get:
> beginCluster()
Loading required package: snow
12 cores detected
cluster type: MPI
Loading required package: Rmpi
	12 slaves are spawned successfully. 0 failed.

If I "top" I see that I have 12 (13?) R spawns running.  The problem
is, they are all running on a SINGLE cpu, not distributed amongst all
12 cpus (even though it detected it).  My first question is: why is
this?  Is there a way to fix this from a standard "R" launch?

Now, I can SOMEWHAT fix this by:
`which mpirun` -n 1 -machinefile $PBS_NODEFILE R --vanilla

When I run the same commands, they distribute properly to all 12 cpus
BUT ANY error I make in typing will cause the entire system to "die":
> require(raster)
require(raster)
Loading required package: raster
Loading required package: sp
raster 1.9-92 (1-May-2012)
> beginCluster()
beginCluster()
Loading required package: snow
12 cores detected
cluster type: MPI
Loading required package: Rmpi
	12 slaves are spawned successfully. 0 failed.
> abc
Error: object 'abc' not found
Execution halted
--------------------------------------------------------------------------
mpirun has exited due to process rank 0 with PID 28932 on
node [mynode] exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------

Is there a way to allow me a "safer" mpirun launch that won't die if I
make a small typo?  This makes it REALLY hard to troubleshoot code if
any little error causes the quit.

--j


-- 
Jonathan A. Greenberg, PhD
Assistant Professor
Department of Geography and Geographic Information Science
University of Illinois at Urbana-Champaign
607 South Mathews Avenue, MC 150
Urbana, IL 61801
Phone: 415-763-5476
AIM: jgrn307, MSN: jgrn307 at hotmail.com, Gchat: jgrn307, Skype: jgrn3007
http://www.geog.illinois.edu/people/JonathanGreenberg.html