ACCC Home Page ACADEMIC COMPUTING and COMMUNICATIONS CENTER
Accounts / Passwords Email Labs / Classrooms Telecom Network Security Software Computing and Network Services Education / Teaching Getting Help
 

GAUSSVIEW

   
 
     
Introduction
 

GaussView is a (G)raphical (U)ser (I)nterface that helps you prepare input for submission to Gaussian and permits you to graphically examine the output. GaussView provides three benefits:

  • Allows you to rapidly sketch in large molecules and then rotate, translate, and zoom in on the molecules using mouse operations
  • Makes it easy to set up many types of Gaussian calculations, and
  • Lets you examine the results of Gaussian calculations.
 
     
Setup
  GaussView is a GUI and therefore requires an X-server on the machine from which you will interact with the software (your desktop PC, for example).
  • If your desktop machine is Windows, then the appropriate X-server emulation package is X-Win32
  • If your desktop machine is some variant of UNIX (Linux, for example), then the standard X-server will suffice.

My PC runs Windows

    X-Win32 is not available from E-sales; instead, systems will place the software (a file called x-win81-1122s.exe) in your argo home directory. You should download it, using sftp, to your PC for installation.

    Installing X-Win32

    • Download the X-server software (x-win81-1122s.exe) to the C:\ directory of your PC (use sftp)
    • Install the software on your PC (done once and then you will not have to do it again)
      • Click on Start and then Run
      • In the resulting Open box, enter C:\x-win81-1122s.exe
      • Choose Setup Language screen
        • Use the default selection, English (United States)
        • Click on the OK button
      • X-Win32 8.1 InstallShield Wizard screen
        • Click Next box
      • License Agreement screen
        • Click on the radio button corresponding to the option I accept the terms in the license agreement
        • Click Next box
      • Customer Infromation screen
        • Enter your netid for User Name
        • Enter UIC in the organization box
        • Use the default selection Install this application for Anyone who uses this computer (all users)
        • Click Next box
      • Destination Folder screen
        • Use the default selection (C:\program Files\StarNet\X-Win32 8.1
        • Click Next box
      • Setup Type screen
        • Use the default selection Complete
        • Click Next box
      • Ready to Installl the Program screen
        • Click Next box
      • InstallShield Wizard Completed screen
        • Click Next box

    Configuring X-Win32)

    • Click on Start, Programs, X-Win32 8 1, X-Config
      • Click on Window tab on the task bar of the X-Win32 Configuration screen
      • Make the following changes:
        • Put a X in the OpenGL Software rendering box
        • Remove the X from the Display splash screen on startup
        • Click OK box
      • Click on Security tab on the task bar of the X-Win32 Confgiuration screen
      • Make the following changes:
        • Click on the radio button Only allow these host addresses box
        • Click on the Add box
          As a result of the above action, a new screen appears asking you to Please enter a host name
          • Enter argo-new.cc.uic.edu
          • Click on the OK button
      • Click on the OK button

    Starting the X server

    • Click on Start, Programs, X-Win32 8 1, X-Win32

    • Important: The X server must be done each time you reboot the local machine, power cycle it, or shutdown the X-Win32 program)

My PC runs Unix

    Configuring X

    • On your machine, enter the following command:
        xauth list

        Generic output:
          the_host_name_of_your_local_machine:0 MIT-MAGIC-COOKIE-1 string_of_characters_and_digits

          For example:
            jsmith.cc.uic.edu:0 MIT-MAGIC-COOKIE-1 0bbf41ac1a5d33b1162fd5ec38d032fa

    • On your argo account, enter the xauth add command with the output from YOUR run of the xauth list as the operand:

      • xauth add jsmith.cc.uic.edu:0MIT-MAGIC-COOKIE-1 0bbf41ac1a5d33b1162fd5ec38d032fa

      TWO important points:
      • Don't cut-and-paste what appears above; it will not work. USE the output of YOUR xauth list command.
      • If you power off your local machine OR if you shutdown the X server on the local machine, then you will have to repeat the configuration procedure.
 
     
Running GaussView
 

Step 1: Get the IP address of the machine that contains your running X server.

    Enter the following command on argo, replacing xxxxx with your netid:

    who -u | grep xxxxx

    The resulting output, what appears in parenthesis, is the fully-qualified domain name of your PC (the X server). Convert the name to an IP address. Assume the output is jsmith.cc.uic.edu. To convert it, use the nslookup command:

    nslookup jsmith.cc.uic.edu

    In the resulting output, the line that contains what you want starts with the word Address:

    Name: jsmith.cc.uic.edu
    Address: 128.248.5.192

Step 2: Create a script like the following (name it whatever you want; in the example, it is called gaussview-script)

      #! /bin/csh
      setenv DISPLAY xxx.xxx.xxx.xxx:0
      /usr/common/gv/gview

      Two IMPORTANT points:
      • Replace the xxx.xxx.xxx.xxx with the IP address that you acquired following the commands given in step two. Do not use the fully-qualified domain name.
      • Remember to include the colon zero combination :0.

      #! /bin/csh
      setenv DISPLAY 128.248.5.192:0
      /usr/common/gv/gview

Step 3: Submit your script for execution

      Use the following command to submit the script, replacing the xxxx with the compute node you want to use:

      qsub -l nodes=xxxx gaussview-script

      For example, to run the script on argo16-4:

      qsub -l nodes=argo16-4 gaussview-script

      Instead of including the particular node on the qsub statement, you may identify the node in the script. For example:

        #! /bin/csh
        #PBS -l nodes=argo16-4
        setenv DISPLAY 128.248.5.192:0
        /usr/common/gv/gview

      Now, the format of the submit statement is:
        qsub gaussview-script

      If several screens appear on your monitor, then success; you are now in GaussView.

      For a detailed presentation of what you can do in GaussView, see the GaussView manual by clicking here

Step 4: Terminating your gaussview job

      There are three basic GaussView screens:
      • GaussView 3.09
      • Select Element
      • Gview

      To terminate your Gaussview job, do the following:
      • Click on the File option in the GaussView 3.09 screen
      • Click on the Exit option in the File dropdown menu
 
     
Additional Help
   
     
Troubleshooting
 
  • Nothing appears on my screen: Some things to check:

    • Did you start the web server on your local machine?

      If you are running a Windows machine, there should be an X icon in the lower right. On the bottom right corner of the X, there should be a very small monitor icon. If you don't have the X icon, then the server is not running.

      Though the server is not running, that is not cause for your program not to start; it will start to execute though you will see nothing on your screen and it will eventually time out. To see if this is the case, run the qstat -an command:

        30528.argo-new. batch gaussview.script 10588 1 -- -- 999:0 R 00:00 argo16-4/0

      Nothing is on the screen though the job is running. To fix the situation:

      • Terminate the job using the qdel command (for example: qdel 30528)
      • Start the X server on your PC, and
      • Submit your gaussview.script job (qsub gaussview.script).

    • You put the word DISPLAY in lower case; it must be CAPITALIZED:

        WRONG: setenv display 128.248.5.192:0
        RIGHT: setenv DISPLAY 128.248.5.192:0

    • Did you put the valid IP address in the gaussview.script? If you put in the fully-qualified domain name, the screens will not appear:

        WRONG: setenv DISPLAY jsmith.cc.uic.edu:0
        RIGHT: setenv DISPLAY 128.248.5.192:0

    • You forgot the trailing colon and zero digit after the IP address in the setenv statement:

        WRONG: setenv DISPLAY 128.248.5.192__
        RIGHT: setenv DISPLAY 128.248.5.192:0

 


2007-11-13  ACCC Systems Group
UIC Home Page Search UIC Pages Contact UIC