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PBS

Use PBS batch control system whenever it is possible.
If you're not familiar with PBS - please consider learning it, because it will make your use of the cluster more efficient and it will help to advocate fair use of the cluster among the users. ravanize command might be of help to get things running

Basic PBS commands

  • qsub to schedule a command to be ran. If you are not familiar with PBS, simply make use of ravanize to generate and run .pbs script for you.
  • qstat (qstat -f provides more information) - to see the status on the tasks scheduled within PBS
  • qdel to delete your scheduled/running task
  • pbsnodes know details about the nodes within PBS (of marginal use for a regular user)

Queues

There are different pbs queues set up, and you should use the one which fits your time requirements. You can mention default queue so pbs chooses the queue for you depending on the time requirement you provided in your pbs file:
  • small - up to 25 minutes (nice level 2)
  • medium - up to 6 hours (nice level 4)
  • long - up to 24 hours (nice level 6)
  • verylong - up to 528 hours (nice level 7)
  • directors - up to 4 hours of cpu time and 1000 hours of walltime (nice level 5): queue is intended for scripts which can span other PBS jobs and sleep waiting for their compition
  • default - will schedule your task to one of the queues depending on the time limit you requested

Rules

  • Time: Try to make sure that you have selected an appropriate queue since if your task does not complete in the allowed time slot, it gets killed. If you see that your job is going to exceed the original time you requested (ie for a specific queue) and it had been running already quite long time (ie it was scheduled for long or verylong queue) email SysAdmin to request the extension of allowed time
  • Memory: request sensible amount of RAM for your job to complete (-l mem=2GB option for ravanize or qsub command)