Batch System PBSPro (Hunter)

Introduction

The only way to start a job (parallel or single node) on the compute nodes of this system is to use the batch system. The installed batch system is PBSPro.

Writing a submission script is typically the most convenient way to submit your job to the batch system. You generally interact with the batch system in two ways: through options specified in job submission scripts (these are detailed below in the examples) and by using PBSPro commands on the login nodes. There are three key commands used to interact with PBSPro:

• qsub
• qstat
• qdel

Check the man page of PBSPro for more advanced commands and options with

man pbs_professional

Requesting Resources with the batch system

Resources are allocated to jobs both by explicitly requesting them and by applying specified defaults.
Jobs explicitly request resources either at the host level in chunks defined in a selection statement, or in job-wide resource requests.

Format:

• job wide request:
  qsub ... -l <resource name>=<value>

  The only resources that can be in a job-wide request are server-level or queue-level resources, such as walltime.

• selection statement:
  qsub ... -l select=<chunks>

  The only resources that can be requested in chunks are host-level resources, such as mem and ncpus. A chunk is the smallest set of resources that will be allocated to a job. The select It is one or more resource_name=value statements separated by a colon, e.g.:

  ncpus=2:mem=128GB

  A selection statement is of the form:

  -l select=[N:]chunk[+[N:]chunk ...]

  Note: If N is not specified, it is taken to be 1. No spaces are allowed between chunks.

  
  

Warning: all requested cluster nodes will be exclusively allocated by 1 job. The default nodes can not be shared by multiple jobs. The allocated nodes of your job will be accounted completely, even though your job uses the allocated nodes only partial