PBS Pro Quick STart GUIDE

How to prepare a batch job (PDF)

This section presents a few examples regarding jobs' submissions under the CERIT-SC infrastructure.

At first, let us summarize several fundamental principles and suggestions:

At first, check, whether the application you require is available in the CERIT-SC/MetaCentrum infrastructure (see the list of available applications being referenced in the Available Applications section)

Decide, where your job will read the input data from, and where it will save the working and output data

Submit the job via the Torque or PBS Pro submission systems (using the qsub command); do not forget to specify the requirements your job has -- the number of execution nodes, available memory, as well as available application licences.

Most probably, the job will wait for available nodes (or application license) after submission; the reason of job's waiting can be found using the following command, being run on any of the available frontends (see the comment section in the command's output):

$ qstat -f <jobid>
where <jobid> is your job's identifier (e.g.,  12345.wagap-pro.cerit-sc.cz)

The common waiting reasons are:

  • there is not enough nodes fitting the required properties; the job is waiting for another job to finish and to release the requested resources
  • the scheduling server's input queue limits the number of simultaneously running jobs of any user; if you have submitted more jobs than the limit is, the waiting job will be run once another (your) job finishes.

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