Tutorial Exercise 1: Run Gaussian

Owned by Suresh Marru
Last updated: Nov 02, 2015
3 min read

Goals of This tutorial:

  • Authenticate to SEAGrid using Community Authentication Workshop Accounts
  • Setup and run a simple Gaussian job
  • View the results
  • Download the Gaussian output file

Installation

See Desktop Client Installation for detailed instructions. The following is a summary.

  1. Go to http://seagrid.org/
  2. Click on the "Download Desktop App" link in the top right.
  3. Save the JNLP file to your computer.
  4. Double click the file to launch it.
  5. Choose "Open it with Java Web Start Launcher (JNLPFile) to launch the SEAGrid desktop client.

Sign In

  1. Click the "Sign In" button.
    1. After you click it, a new window will pop up with the title "Get Access to SEAGrid."
  2. Type in your workshop username (wrk###) and password.
  3. Click the LOGIN button.
  4. If you input your account information correctly, you will be authorized to use SEAGrid.

Submit a Gaussian Job

Now you are ready to use SEAGrid to submit jobs. Click on "X" button on the top right corner to close the My CCG window.

  1. Click the CREATE JOB button in the SEAGrid main window.
    1. A new window named "SEAGrid: Submit Jobs" will pop up.
    2. There may be some jobs already listed. If so, just ignore them and go to the next step.
  2. Click the CREATE NEW JOB button in the "Submit Jobs Panel: Submit Jobs" window, and another new window to edit/prepare a job will pop up.
  3. For this exercise, we will use the default water Gaussian input file that comes up in the "Input File Information" box with a name gaussian_sample0.inp
    1. Get this and other input files from Sample Application Input Files.
  4. Select comet in the "HPC System" box.
    1. Use the up or down arrows to move the desired system to the top
  5. Click "Submit". The "Submit Job Editor" window should disappear.
  6. In the "Submit Jobs" window, you will see your job in the "Queued Jobs" list.
  7. Select the job in the job list if it is not highlighted.
  8. Click the SUBMIT SELECTED JOBS TO QUEUE button to submit this job.
    1. A small "Progress" pop-up window indicating that your job is being submitted will appear.
    2. Once the job has been accepted, the "Progress" box will disappear and the job will move from the top box in the "Submit Jobs" window to the lower "Submitted Jobs" box, indicating that the job has been accepted by the scheduler.
  9. Click on the CLOSE button in the "Submit Jobs" window. The only SEAGrid window that should be up is the main SEAGrid window. 

Monitor Your Job

  1. Click on the "My CCG" button in the main SEAGrid window.
    1. A window will appear that contains a list of all of the jobs that you (the wrk### user) have submitted.
    2. The most recent job submission should be at the top of the list.
  2. The status of the job is shown in the "Status" column of the table.
    1. The window is freshed automatically to get the most updated information, but you may also want to click "Refresh Jobs" if you want to monitor the progress of all the jobs.
    2. You can also select a job from the list and click on "Get Job Status" to check on the status of that one job.
    3. The job status will be one of the following: SCHEDULED, RUNNING, FINISHED or ERROR.
  3. When the job has completed, you may check the job statistics by double clicking on the job row.
    1. You can also right click on that job and select "Get Job Status" from the pull-down menu.

Get Your Job's Output

  1. Once the job has completed, it is possible to look at the resulting output from the calculations.
  2. To view the data available graphically, click on the MONITOR OUTPUT button in the MyCCG window.
    1. The job that is highlighted in the left hand side of the window will be the job whose output is fetched and displayed.
  3. For the Gaussian job run here, four windows should appear after the data has been fetched.
    1. One is the Output Editor window for looking at the application (Gaussian in this example) raw output file.
    2. One is the NanoCAD application window for looking at the molecules.
    3. The other two windows are an X-Y chart of Energy vs. iteration and RMS Gradient vs. iteration. 

Clean Up and Log Out

  1. Click on the "X" icon in the upper right hand corner of the X-Y plot windows and the NanoCAD window to close them.
  2. Click the CLOSE button in the Output Editor window.
  3. Click the EXIT button in the main SEAGrid window to end the SEAGrid session.