Difference between revisions of "R/Batch"

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For small tests, pre- and post-processing with R, you can start an interactive sessions on the login nodes. All other R jobs have to be submitted through the batch system. You can start an R job (inputfile.R) in batch mode with the following command:
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For small tests, pre- and post-processing with R, you can start an interactive sessions on the login nodes. All other R jobs have to be submitted through the batch system. You can submit an R job (inputfile.R) in batch mode with the following command:
  
 
  bsub [LSF options] "R --vanilla --slave < inputfile.R > outputfile"
 
  bsub [LSF options] "R --vanilla --slave < inputfile.R > outputfile"
  
 
Here you need to replace ''[LSF options]'' with LSF parameters for the resource requirements of the job. Please find a documentation about the parameters of <tt>bsub</tt>  on the wiki page about the [[Using_the_batch_system|batch system]]. In this case, stdout is redirected into "outputfile".
 
Here you need to replace ''[LSF options]'' with LSF parameters for the resource requirements of the job. Please find a documentation about the parameters of <tt>bsub</tt>  on the wiki page about the [[Using_the_batch_system|batch system]]. In this case, stdout is redirected into "outputfile".

Revision as of 11:58, 30 September 2016

For small tests, pre- and post-processing with R, you can start an interactive sessions on the login nodes. All other R jobs have to be submitted through the batch system. You can submit an R job (inputfile.R) in batch mode with the following command:

bsub [LSF options] "R --vanilla --slave < inputfile.R > outputfile"

Here you need to replace [LSF options] with LSF parameters for the resource requirements of the job. Please find a documentation about the parameters of bsub on the wiki page about the batch system. In this case, stdout is redirected into "outputfile".