GAUSSVIEW

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.

• 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.

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

• GaussView Manual
• Gaussian web site

• 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