[R-sig-hpc] multicore with functions calling an exe/.sh file
Mauricio Zambrano-Bigiarini
mauricio.zambrano at jrc.ec.europa.eu
Fri Jun 24 11:12:33 CEST 2011
Dear List,
I'm just doing my first trials with HPC, and I would like to ask your
opinion regarding the following issue.
In R 2.13.0, I have an optimization algorithm for hydrological models,
which internally runs the .exe/.sh file of the model, and then computes
and writes into a file the results of different parameter values.
So far this algorithm runs only in a sequential mode, i.e., trying
different parameter values one after another, and I would like to
parallelize it.
My first attempt was using the multicore library, and changing the
existing 'lapply' loop for an 'mclapply' one. However, when I run the
optimization algorithm, I got several error messages:
forrtl: Sharing violation
forrtl: Sharing violation
forrtl: Sharing violation
forrtl: severe (30): open failure, unit 1, file
Z:\home\zambrhe\S090-test\file.cio
which are due to the fact that all the 4 process are trying to access
the same .exe/.sh file and to modify the same input files at the same time.
Is there any way to use multicore for parallelizing this type of
optimization function or should I move to some master/slave option ?
Thanks in advance for any help.
Mauricio Zambrano-Bigiarini
PS,
SesionInfo():
R version 2.13.0 (2011-04-13)
Platform: i386-redhat-linux-gnu (32-bit)
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