Literature DB >> 25431538

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

Thomas J Hoffmann1.   

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.

Entities:  

Keywords:  R; batch; cluster; command line arguments; parallel

Year:  2011        PMID: 25431538      PMCID: PMC4243301          DOI: 10.18637/jss.v039.c01

Source DB:  PubMed          Journal:  J Stat Softw        ISSN: 1548-7660            Impact factor:   6.440


  1 in total

1.  Parallel biocomputing.

Authors:  Kenneth S Kompass; Thomas J Hoffmann; John S Witte
Journal:  Source Code Biol Med       Date:  2011-03-18
  1 in total

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