Quick Reference

 

Connecting to the Cluster

Open Terminal (Mac/*nix) or puTTY (Windows)

$ ssh i.p._address

$ password 

 

Interactive Jobs

$ interactive

         Processors: [1]

      Memory (GB): [1]

       Time (hours): [2]

$ exit (when finished)

 

Writing Submit Scripts

$ nano filename

Opens filename in a text editor                                                                        

#!/bin/bash

Identifies the file as a bash script

#PBS –N name

Names the job

PBS –l walltime=00:10:00

Sets time limit required by the job (10 minutes in this example)

#PBS –l nodes=1:ppn=12

Sets the number of nodes and processors per node (1 node and 12 processors in this example)

#PBS –l vmem=10gb

Sets amount of virtual memory required by the job (10 gigabytes in this example)

set –o nounset

Treats undefined variables as errors in the script
set -o errexit Treats errors in this script as fatal (stops processing the script and exits)

module load module_name

Loads the named module

cd ${PBS_O_WORKDIR}

Changes the script's  working directory to the directory from where the script was submitted.

 

Running Jobs

$ qsub script_name

Submits job to the queue 

$ qstat

Displays status of jobs in the queue

   

Commonly Used Module Commands

$ module avail

Lists all module packages available

module load module_name

Adds module to a script or session

$ module whatis module_name

Provides module description

$ module unload

Removes module from script or session

$ module list

Lists modules already loaded

 

Checking and Modifying Job Results

$ cd /directory/

Changes your working directory to /directory/

$ ls

Lists the contents of your working directory

$ less filename.e######

Displays Standard output file (error)

$ less filename.o######

Displays Standard output file (output)