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From UABgrid Documentation

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R is a free software environment for statistical computing and graphics. Please refer to the following page for additional instructions for running R on Cheaha [[R-userinfo|Running R Jobs on a Rocks Cluster]].
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The following Modules files should be loaded for this package:
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<pre>
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module load R/R-2.7.2
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</pre>
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For other versions, simply replace the version number
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<pre>
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module load R/R-2.11.1
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</pre>
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The following libraries are available, additional libraries should be installed by the user under ~/R_exlibs
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* /share/apps/R/R-<font color="red">X.X.X</font>/gnu/lib/R/library
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** The default libraries that come with R
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** Rmpi
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** Snow
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* /share/apps/R/R-<font color="red">X.X.X</font>/gnu/lib/R/bioc
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** BioConductor libraries (default package set using getBioC)
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'''Sample R Grid Engine Job Script'''
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This is an example of a serial (i.e. non parallel) R job that has a 2 hour run time limit requesting 256M of RAM
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<pre>
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#!/bin/bash
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#$ -S /bin/bash
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#$ -cwd
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#
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#$ -j y
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#$ -N rtestjob
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# Use '#$ -m n' instead to disable all email for this job
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#$ -m eas
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#$ -M YOUR_EMAIL_ADDRESS
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#$ -l h_rt=2:00:00,s_rt=1:55:00
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#$ -l vf=256M
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. /etc/profile.d/modules.sh
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module load R/R-2.7.2
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#$ -v PATH,R_HOME,R_LIBS,LD_LIBRARY_PATH,CWD
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R CMD BATCH rscript.R
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</pre>

Revision as of 10:42, 15 March 2012

This page is a Generic stub.

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R is a free software environment for statistical computing and graphics. Please refer to the following page for additional instructions for running R on Cheaha Running R Jobs on a Rocks Cluster.

The following Modules files should be loaded for this package:

module load R/R-2.7.2

For other versions, simply replace the version number

module load R/R-2.11.1

The following libraries are available, additional libraries should be installed by the user under ~/R_exlibs

  • /share/apps/R/R-X.X.X/gnu/lib/R/library
    • The default libraries that come with R
    • Rmpi
    • Snow
  • /share/apps/R/R-X.X.X/gnu/lib/R/bioc
    • BioConductor libraries (default package set using getBioC)

Sample R Grid Engine Job Script This is an example of a serial (i.e. non parallel) R job that has a 2 hour run time limit requesting 256M of RAM

#!/bin/bash
#$ -S /bin/bash
#$ -cwd
#
#$ -j y
#$ -N rtestjob
# Use '#$ -m n' instead to disable all email for this job
#$ -m eas
#$ -M YOUR_EMAIL_ADDRESS
#$ -l h_rt=2:00:00,s_rt=1:55:00
#$ -l vf=256M
. /etc/profile.d/modules.sh
module load R/R-2.7.2

#$ -v PATH,R_HOME,R_LIBS,LD_LIBRARY_PATH,CWD

R CMD BATCH rscript.R