[R-sig-hpc] snowfall: missing MPI node
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
More information about the R-sig-hpc