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Passing in Command Line Arguments and Parallel Cluster/Multicore Batching in R with batch

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  • Hoffmann, Thomas J.

Abstract

It is often useful to rerun a command line R script with some slight change in the parameters used to run it - a new set of parameters for a simulation, a different dataset to process, etc. The R package batch provides a means to pass in multiple command line options, including vectors of values in the usual R format, easily into R. The same script can be setup to run things in parallel via different command line arguments. The R package batch also provides a means to simplify this parallel batching by allowing one to use R and an R-like syntax for arguments to spread a script across a cluster or local multicore/multiprocessor computer, with automated syntax for several popular cluster types. Finally it provides a means to aggregate the results together of multiple processes run on a cluster.

Suggested Citation

  • Hoffmann, Thomas J., 2011. "Passing in Command Line Arguments and Parallel Cluster/Multicore Batching in R with batch," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 39(c01).
    • Handle: RePEc:jss:jstsof:v:039:c01
    DOI: http://hdl.handle.net/10.18637/jss.v039.c01
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    Cited by:

    1. Bischl, Bernd & Lang, Michel & Mersmann, Olaf & Rahnenführer, Jörg & Weihs, Claus, 2015. "BatchJobs and BatchExperiments: Abstraction Mechanisms for Using R in Batch Environments," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 64(i11).

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