I strongly suggest to use the BatchJobs package [http://cran.r-project.org/web/packages/BatchJobs] for this. It is easy to install and cross platform and does not rely on external software such as perl. It allows you develop your script running sequentially/interactively on your local machine/laptop, the via *a single configuration file* (./.BatchJobs.R) you can use the exact same script to distribute the jobs to separate R sessions either on multiple cores on the same machine or on a cluster (most common cluster types are supported). The learning curve is not that step - as with most parallel computations you have to move away from using for loops to using lapply() and then you're almost done.
/Henrik On Sun, Sep 29, 2013 at 10:22 AM, Chee Chen <chee.c...@yahoo.com> wrote: > Dear All, > I have spent almost 2 days but did not succeed yet. > > Problem description: I have 3 parameters, p1, p2 and p3, for which p1 take 1 > of 5 possible distributions (e.g., normal, laplace), p2 takes 1 of 3 possible > distributions, and p3 takes 1 of 5 possible distribution. These 3 parameters > create 75 settings, and these 3 parameters are arguments of a function F; and > F is part of simulation codes. To summarize: different value of the ordered > triple (p1,p2,p3) means different setting and this is the only difference in > the simulation codes. > > Target to achieve: instead of loop through each of the 75 settings one after > another, I would like to concurrently run all 75 settings on the cluster. > > My attempts: via loops, I used Perl to create 75 files, each for a different > triple (p1,p2,p3), and Perl uses "system(R ..)" to execute this setting once > it is created. The Perl codes are submitted to cluster correctly. But when I > looked into the log file, the cluster still executes it one setting after > another setting. > > Request: any help is appreciated! It is because of the loops of Perl that > executes a setting once it is created? > > Have a nice day! > Chee > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
