Difference between revisions of "NAMD/Batch"

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(Created page with "All NAMD calculations should be submitted as a batch job to the batch system. To run a simulation with an input file <tt>input.in</tt> use the following command: bsub [LSF op...")
 
 
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All NAMD calculations should be submitted as a batch job to the batch system. To run a simulation with an input file <tt>input.in</tt> use the following command:
+
You need to submit your NAMD calculations in batch mode, through the batch system. To run a simulation with an input file <tt>input.in</tt> use the following command:
 +
 
 
  bsub [LSF options] "namd2 input.in"
 
  bsub [LSF options] "namd2 input.in"
By default the output will be found in the <tt>lsf.oXXXXXXX</tt> output file where XXXXXXX corresponds to the job ID of the job.
+
 
The <tt>[LSF options]</tt> needs to be replaced with LSF parameters for the resource requirements of the job. For example,
+
By default you can find the output in the <tt>lsf.oXXXXXXX</tt> output file where XXXXXXX corresponds to the job ID of the job. 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]]. For example,
 +
 
 
  bsub -W 12:00 -R "rusage[mem=500]" "namd2 input.in"
 
  bsub -W 12:00 -R "rusage[mem=500]" "namd2 input.in"
 +
 
will request a runtime of up to 12 hours and only 500&nbsp;MB of RAM.
 
will request a runtime of up to 12 hours and only 500&nbsp;MB of RAM.
  
 
Jobs that can run on a single node (24 cores) can be submitted in a similar way:
 
Jobs that can run on a single node (24 cores) can be submitted in a similar way:
 +
 
  bsub [LSF options] -n N "charmrun +p N +isomalloc_sync namd2 input.in"
 
  bsub [LSF options] -n N "charmrun +p N +isomalloc_sync namd2 input.in"

Latest revision as of 11:19, 29 August 2016

You need to submit your NAMD calculations in batch mode, through the batch system. To run a simulation with an input file input.in use the following command:

bsub [LSF options] "namd2 input.in"

By default you can find the output in the lsf.oXXXXXXX output file where XXXXXXX corresponds to the job ID of the job. 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. For example,

bsub -W 12:00 -R "rusage[mem=500]" "namd2 input.in"

will request a runtime of up to 12 hours and only 500 MB of RAM.

Jobs that can run on a single node (24 cores) can be submitted in a similar way:

bsub [LSF options] -n N "charmrun +p N +isomalloc_sync namd2 input.in"