[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 

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

R version 2.13.0 (2011-04-13)
Platform: i386-redhat-linux-gnu (32-bit)

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