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 (you are not required to use X-Win32; there are others)
• If your desktop machine is some variant of UNIX (Linux, for example), then the standard X-server software already installed with the OS will suffice.

My PC runs Windows

X-Win32 is not available from the Webstore; 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)
• Installing 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 Information 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 Install 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 Configuration 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.cc.uic.edu
    • Click on the OK button
    
    
    
    
• Click on the OK button

You've completed the installation and configuration of X-Win32. You don't have to do these two steps again.

Starting the X server

• Click on Start, Programs, X-Win32 8 1, X-Win32
  If you've successfully started the server, you will see the appropriate icon on the task bar in the lower right corner of your screen:
  
  
  
  

Important: An X server (be it X-Win or, if you elect to use some other product) must be started after you reboot your local machine, power cycle it, or shutdown the X-Win32 program. Without X-server running, the GaussView software will not appear on your local machine.

If you elect to use some other X-server, then that software must include the OpenGl software rendering capability.

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
  
  
• In your argo account session, 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). You have one of two choices. One, you may convert the fully-qualified domain name to an IP address. Or, two, you may use the fully-qualified domain name. Both will work; it's up to you to decide with which you are more comfortable. Some people prefer IP addresses; others, domain names. If you are the latter, go to step three. If, you prefer using an IP address,continue on.

Assume the output is jsmith.cc.uic.edu. To convert it, use the nslookup command:

nslookup jsmith.cc.uic.edu -server 128.248.2.50

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 or the fully-qualified domain name that you acquired following the commands given in the previous step.
  
  Samples:
  
  
  • IP address: 128.248.5.192
  • Fully-qualified domain name: jsmith.cc.uic.edu


• Remember to include the colon zero combination :0.


Sample using an IP address:


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


Sample using a fully-qualified domain name:


#! /bin/csh
setenv DISPLAY jsmith.cc.uic.edu:0
/usr/common/gv/gview


Using the ACCC VPN will not prevent you from running GaussView. The only difference is that the fully-qualified domain name will include gwvpn.cc.uic.edu.

Step 3: Submit your script for execution

Use the following command to submit the script, replacing the XXXXXXX with the name of the appropriate queue. If, for example, you are a student, then XXXXXX is either student_short or student_medium (which queue you should use depends on how long you will run GaussView); if faculty/staff, then staff:

qsub -V -l nodes=1 -q XXXXXXX gaussview-script

Examples::

qsub -V -l nodes=1 -q student_short gaussview-script
qsub -V -l nodes=1 -q student_medium gaussview-script


OR

qsub -V -l nodes=1 -q staff gaussview-script

Instead of including the number of nodes and the queue on the qsub statement, you may identify them in the script. For example:


#! /bin/csh
#PBS -l nodes=1
#PBS -q student_short
setenv DISPLAY 128.248.5.192:0
/usr/common/gv/gview


As a result, the format of the submit statement should be amended to just:


qsub -V gaussview-script

In fact, you may place the -V option in the script:

#! /bin/csh
#PBS -l nodes=1
#PBS -q student_short
#PBS -V
setenv DISPLAY 128.248.5.192:0
/usr/common/gv/gview


As a result, the qsub statement is now:

qsub gaussview-script

IMPORTANT POINT


GaussView, unlike Gaussian, is not distributive/parallel. That means it runs on ONLY one node and ONLY one processor on that node. Requesting more than a single node and/or a single processor does NOTHING to improve GaussView performance; it wastes resources that some other argo client could use. Do not specify a value for nodes greater than one; all of the following are examples of what not to do:


-l nodes=2
-l nodes=3
-l nodes=4
....
The same is true for the ppn value (don't include it):


-l nodes=2:ppn=2
-l nodes=2:ppn=3
-l nodes=2:ppn=4
-l nodes=3:ppn=2
....
In fact, there is no need to include a -l nodes=1 component on either the qsub statement or in the script. The default value, when -l nodes=1 is not given, is one. The same is true for ppn; when not specified, the system assumes one.


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





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

• Gaussian web site

• Nothing appears on my screen: Some things to check:
  
  
  • Did you start the X 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 batch gaussview.script 10588 1 -- -- 999:0 R 00:00 argo12-4/0
    
    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