[R] Parallel computing in R for dummies--how to optimize an external model?

From: Waichler, Scott R <Scott.Waichler_at_pnl.gov>
Date: Tue 14 Feb 2006 - 16:11:28 EST

I am trying to use the optimizing function genoud() with the snow package on a couple of i686 machines running Redhat Linux WS4 . I don't know anything about PVM or MPI, so I just followed the directions in snow and rgenoud for the simplest method and started a socket cluster. My function fn for genoud involves updating an input file for a separate numerical model with the latest parameter set from the optimizer, running the (compiled) model on the input file with system(), and processing the output including calculation of objective function. The whole process works on the localhost machine in one cpu, and I can see that an R session is created in the second, non-localhost machine, but it doesn't seem to be doing anything. All of the model runs generated by the application of genoud take place in the cpu. What am I missing? I can see where there would be a conflict in having multiple processors trying to access the same system model input file at once, but I don't see any indication of that type of problem.

Grateful for any help,

Scott Waichler
Pacific Northwest National Laboratory

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