[R-sig-hpc] snowfall: missing MPI node

Mario Valle mvalle at cscs.ch
Mon Nov 23 11:45:13 CET 2009

I don't know if the question pertains to Rmpi, snow or snowfall.

I run my job on Linux by:

    mpirun -np N -hostfile $PBS_NODEFILE RMPISNOW -f my-script.r --slave

First thing the script load Rmpi and snowfall.

Then in the snowfall sfInit call I have to specify one less CPU respect to
the mpirun call:

    sfInit(parallel=TRUE, cpus=N-1, type="MPI")

otherwise I receive an error similar to: "cluster size N-1 already
running" (sorry I don't remember the exact message)

Is this normal? If yes and I want to call my script with --cpus
option I have to resort to inelegant shell scripting to obtain N-1 from
the -mp argument.
Another alternative could be to obtain in the script the number of
processes (-np #) requested to mpirun. Is it possible?

Thanks for your time!

Ing. Mario Valle
Data Analysis and Visualization Group            | http://www.cscs.ch/~mvalle
Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91) 610.82.60
v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91) 610.82.82

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