PBS system

What is PBS?

PBS or Portable Batch System is a job control system that manages the computing resources on a Linux/Unix cluster. It allows multiple users to submit tens of hundreds of computing jobs and run them in parallel without overloading the computing node machines. It can control the load levels of computing nodes and submit the jobs in the queues one after another. It is very good for bioinformatics computational problems where the same computing procedure is usually needed to be run on many data files, each such program-data file can be assigned as one job and then submitted to the PBS system to run in parallel.

What is the PBS system we are using?

We are using PBS Professional (PBS Pro), version Other PBS system can also be used but emdrunPX.pl and runmotif.sh need to be modified accordingly.

What are the frequently used PBS Commands?

qsub myjob.sh #submit a job (myjob.sh)
qstat .a .n #show all jobs and their running nodes in PBS system
qstat .q #show all job queues
qdel 1187 #delete a job

more at PBS User Guide

Useful Links

PBS wiki page
PBS Professional Homepage