How do I run Gaussview on Argo?

GaussView is a graphical user interface (GUI) that helps you prepare input for submission to Gaussian and permits you to graphically examine the output. GaussView allows you to rapidly sketch in large molecules and then rotate, translate, and zoom in on the molecules using mouse operations. It makes it easy to set up many types of Gaussian calculations, and lets you examine the results of Gaussian calculations.

GaussView is installed and runs on Argo, you don't install it on your local computer. Since GaussView is a GUI, requires X-server software on the computer which you use to connect to Argo. If your computer's operating system is Windows, then there are two X-server packages you can use:

Running GaussView with X11 Forwarding

Without X11 Forwarding, you start a GaussView job by means of the qsub command and a script. For example:

qsub -V gaussview-script

where gaussview-script is a file containing something like the following:

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

With X11 Forwarding, you don't use a script. Initiating GaussView is a two-step process: Start an interactive, X11 forwarding job and then start GaussView.

Start an interactive, X11 forwarding job

The first step is initiating an interactive session with X11 Forwarding. To do so, you use both the -I option (for interactive) and the -X option (for X11 Forwarding) on the qsub command:

qsub -I -X-V -q the-name-of-the-queue

Notice that there is no script file; that's how it's supposed to be. All options that might have been included in the script, like the name of the queue, must be specified on the command line. Examples:

qsub -I -X -V -l nodes=1 -q student_short
qsub -I -X -V -l nodes=1 -q staff

FYI: It is always best to include the -V option. Once you submit the command, you will see something like the following:

qsub: waiting for job 13555.argo.cc.uic.edu to start
qsub: job 13555.argo.cc.uic.edu ready

Obviously, your job will have an different id (not 13555). There may be a pause between the appearance of the first line (qsub: wating...) and the appearance of the second (qsub: job...). But, once you see the second line, you are ready for the second step.

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 the qsub command. 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.

Start GaussView

To start GaussView, enter the following command:

/usr/common/gv/gview

It may take a couple of seconds and you may again be asked to confirm connections from 127.0.0.1 but the main GaussView screens will appear.

gaussview-startpage

If the screens do not appear, resubmit the GaussView command and include the -soft option:

/usr/common/gv gview -soft

Terminating your GaussView job

Just like starting a GaussView job, terminating a GaussView job is also a two step process: Stopping GaussView and terminating the interactive, X11 Forwarding session.

Stop GaussView

To stop your GaussView job, click Exit in the dropdown File menu

gaussview-exit

Terminating X11 Forwarding session

To terminate the interactive session, enter the word exit in the command line.

Troubleshooting

Error: 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.

xming-taskbar

  • You changed the DISPLAY variable!  You should never alter the setting of the DISPLAY variable when using X11 Forwarding. The ssh client will set the DISPLAY variable.
  • Did you tell ssh to use X11 Forwarding? If you didn't tell your SSH client (the command or the GUI) to use X11 Forwarding, then your DISPLAY variable will most likely contain nothing and GaussView will not know where to display its screens. Please refer to these configuring X11 Forwarding instructions for more detail to fix the problem.

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Last updated: 

September 24, 2012

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