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UsingRUnderCondor
(24 Jan 2006,
DavidReitter
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<!-- This is a comment, in the HTML sense of the word, but Wiki directives still work, so you could put access control statements here to restrict access to your new topic, and they won't show up in the published page. Please think carefully when creating a new topic, and use a GoodWikiName --> -- Main.DavidReitter - 24 Jan 2006 R can only run in the Vanilla universe. Linking R against the Condor libraries is currently not going to be fruitful. (See also recent messages on the R mailing list.) Here is a simple sample job description which runs R out of a local installation in a home directory. Using the global installation should work fine as well provided its version is suitable. Note that the below example will start 10 different jobs, loading prepared datafiles (*.0 - .*.9) to do its job. <verbatim> Universe = vanilla Executable = /home/user/usr/bin/R Arguments = --no-save --no-restore --args --paraphrase=/home/user/PhD/paraphrase/paraphrase.data.250k.$(Process) --maptask=/home/user/PhD/maptask/maptask.data.250k.$(Process) Requirements = Memory >= 1500 Error = /home/user/PhD/stats/joined/250k.err.$(Process) Input = /home/user/PhD/stats/stats2.R Output = /home/user/PhD/stats/joined/250k.out.$(Process) Log = /home/user/PhD/stats/joined-500k.condor.log.$(Process) Initialdir = /home/user Queue 10 </verbatim> The S (R) code below (from stats2.R) reads a command line argument --maptask=<path> given to R and initializes a variable _file.mapt_ from it: <verbatim> file.mapt = sub('--maptask=','', grep("maptask=.*", commandArgs(), value=TRUE)) </verbatim>
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Topic revision: r1 - 24 Jan 2006 - 23:17:29 -
DavidReitter
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