Difference between revisions of "R/Batch"

From ScientificComputing
Jump to: navigation, search
(Created page with "Small tests, pre- and post-processing with R may be run in an interactive sessions on the login nodes. All other R jobs have to be submitted through the batch system. An R job...")
 
(4 intermediate revisions by the same user not shown)
Line 1: Line 1:
Small tests, pre- and post-processing with R may be run in an interactive sessions on the login nodes. All other R jobs have to be submitted through the batch system. An R job (inputfile.R) in batch mode can be started with the following command:
+
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 ''[LSF options]'' needs to be replaced with LSF parameters for the resource requirements of the job. A documentation about the parameters of bsub can be found on the corresponding wiki page about the 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".
 +
 
 +
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