Automated Job Submission

The HPC Team has created an automated job submission system in order to systemize, simplify, and speed up your job submission.  This also eliminates syntax errors and misuse of SLURM command options in you job script.  The contents below explains how to use the command "run" and is displayed if you use "run -h".  Simply the run script takes the user's input and from a job script template creates a unique job script for you job and submits the job to the queue, and removes the script.  The run command and all job script templates are located in /usr/local/bin.

|          T A L O N 3 -  A U T O S U B M I S S I O N  -  R U N S C R I P T            |
                                                                          ctrl+c to quit

The script below was for the UGE batch system of Talon2, the SLURM version of this script is currently under construction, and this page will be updated to reflect any new information on the state of the script.

##    Last Update: 05.23.13
##    This RUN script prompts the user for variables to send to the jobs script templete
##    This script can be run in 3 ways
##    1.) Interactively menu driven by using simply the command "run"
##      2.) From the command-line with fixed fields, which arguments are taken in the following order:
##    [program] [input_file] [queue] [cores] [email] [extra_file1] [extra_file2] ...
##    Example: run matlab parallel.q 16
##      3.) With command-line options using following switches:

    -h      Show this message
    -p [program]   software program name
    -i [input]     input filename
    -q [queue]    queue
    -c [cores]     # computing cores (cpus)
    -n [nodes]     # of nodes
    -m [memory]    min memory (GB)
    -e [email]     email for notifications from queue (defaults to internal mail: root@hpc-02)
    -f [files]     auxilliary list of files in " "
    -j [.job]      absolute location of user's specified .job script template

    Example: run -p matlab -q parallel.q -c 16 -i -f "list.1 list.2 list.3"