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 bsub  on the wiki page about the [[Using_the_batch_system|batch system]]. In this case, stdout is redirected into "outputfile".
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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".
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Please note that from version 4.0.2 the command line option <tt>--slave</tt> has been renamed to <tt>--no-echo</tt>

Revision as of 09:59, 1 December 2020

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".

Please note that from version 4.0.2 the command line option --slave has been renamed to --no-echo