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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]]. | |||
The following Modules files should be loaded for this package: | |||
<pre> | |||
module load R/R-2.7.2 | |||
</pre> | |||
For other versions, simply replace the version number | |||
<pre> | |||
module load R/R-2.11.1 | |||
</pre> | |||
The following libraries are available, additional libraries should be installed by the user under ~/R_exlibs | |||
* /share/apps/R/R-<font color="red">X.X.X</font>/gnu/lib/R/library | |||
** The default libraries that come with R | |||
** Rmpi | |||
** Snow | |||
* /share/apps/R/R-<font color="red">X.X.X</font>/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 | |||
<pre> | |||
#!/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 | |||
</pre> | |||
Revision as of 15:42, 15 March 2012
This page is a Generic stub.
You can help by expanding this page..
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