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:
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 184.108.40.206:0 /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.
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.
To start GaussView, enter the following command:
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.
If the screens do not appear, resubmit the GaussView command and include the -soft option:
/usr/common/gv gview -soft
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.
To stop your GaussView job, click Exit in the dropdown File menu
To terminate the interactive session, enter the word exit in the command line.
Error: Nothing appears on my screen
Some things to check:
September 24, 2012