UsingRUnderCondor < DistributedComputing

DistributedComputing Web>Condor>UsingRUnderCondor (24 Jan 2006, DavidReitter) (raw view)EditAttach

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-- 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>

Topic revision: r1 - 24 Jan 2006 - 23:17:29 - DavidReitter

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