TORQUE/PBS Quick Start Guide

Start using Torque/PBS now! Let Torque/PBS choose any available node for your job, and you can work on bioservx as usual.

  • Use it like ssh:
    1. The easiest way to use Torque/PBS is to use it in interactive mode. In a terminal window, type:
      qsub -I and hit return.
    2. Torque/PBS will find a node for you, and you can just start working in the new node as if you ssh to the node.
    3. Even easier if you create an alias: e.g., add: alias que 'qsub -I'
      in your .tcshrc (if you are using tcsh).
    4. Now you can just type: que
    5. NOTE: When your job is finished, don't forget to exit the node to release it.
  • Run a simple batch job without creating a script file.
    1. Type: qsub
      and hit return.
    2. Now write a command or commands, and finish your inputs with ctrl-D. For example, if you have a test.fas file in the "test" directory, type:
      cd test
      linsi test.fas > test.aln
    3. This example changes your working directory to "test", and runs LINSi (a MAFFT multiple alignment program) with the "test.fas" file including sequences in FASTA format as the input. The alignment output for STDOUT is redirected to the "test.aln" file.
  • Use "qstat" to check the status of your job. Use "man qstat" to read the manual to find out many userful options for qstat.
  • Use "qdel job_ID" to kill your Torque/PBS job. The "job_ID" can be found by using qstat.
  • For more options and script usage, read PBS FAQ.

E. M. (June/2018)