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{{Generic_stub}} | {{Generic_stub}} | ||
R is a free software environment for statistical computing and graphics. | R is a free software environment for statistical computing and graphics. | ||
==SGE module files== | |||
The following Modules files should be loaded for this package: | The following Modules files should be loaded for this package: | ||
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** BioConductor libraries (default package set using getBioC) | ** BioConductor libraries (default package set using getBioC) | ||
==SGE Job script == | |||
'''Sample R Grid Engine Job Script''' | '''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 | 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 | ||
Revision as of 15:51, 15 March 2012
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R is a free software environment for statistical computing and graphics.
SGE module files
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)
SGE Job script
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