GaussView

GaussView

Note:  As of 2016, if you are having trouble with Gaussview starting, with errors about X11 or "OpenGL is not available", try to type this first.

export USE_MESAGL=1

 

These are general instructions for using GaussView on the cluster - the detailed instructions from Gaussian are here.

To use GaussView on the cluster (note you must be logged in for a graphical interface), simply type

gv

or  

gv  myfile.com  

to open a particular com file.You can use the 'Builder' to build, or modify your molecule

(note, again if you have problems with starting from a Mac, you can either set the USE_MESAGL variable, or start it with 'gv -soft', or 'gv -mesagl')

To submit a job, you need to create a job file, but then you will submit it with 'subg09', and not the 'submit' within Gaussview.  However, you create the job file by starting (but not completing) the submit process.

Click on the Calculate menu and choose 'Gaussian Calculation Setup' and you'll get a window like this

 

There are only a few tabs across the top that you need to worry about.  They are:

  • Job Type tab - there's a pull down menu where you select what you want (energy, optimization, etc.)
  • Method tab - which ab initio method you want to use (HF, DFT, etc.)
  • Title tab - give your job a title/name
  • Link0 tab - here you turn on to save a checkpoint file for later analysis.  You also set the number of processors.  Gaussian can run in parallel - it can be up to 12 on knot, or 4 on QSR.   More cores will make it run faster, but might take longer to start up in the queue
  • Additional Keywords (on bottom, it's not a tab).  If you are transfering the checkpoint files back and forth to a PC, put the word 'FORMCHECK' in that line so that the files are readable by both Linux and Windows.

A sample window is below with pertinent items circled (tabs in yellow, important items on Link0 tab in red)

 

After everything is set, click the 'submit' button.  It will ask you to save the file, say OK, and give it some name that makes sense to you, e.g.  Fragment7.com (note - avoid using spaces in your filenames, uses dashes or underscores instead).  After saving the file a diaglog box will come up saying "Submit the following file to Gaussian" - here you click 'Cancel', and you can then also close the calculation setup window.

Now go back to your terminal window and type

subg09  Fragment7.com

Answer the questions (Related to time, memory, etc.) and it will submit your job.  When you're first testing out your calculation (to see that you set it up correctly)  you should give it a 1 hour time limit (1:00:00) as this will submit to a fast queue to immediately run it - this way if it immediately fails you can fix the problem.  If it starts up and keeps running, delete the job (qdel  JOBID) and then resubmit with a longer time limit.

An example is below

subg09 Fragment7.com

...answer questions.....
343495.node96
Job Submitted...cleaning up temporary setup files

qstat -u pcw 

(will show files I'm running)

Job ID               Username Queue    Jobname          SessID NDS   TSK Memory Time  S Time
-------------------- -------- -------- ---------------- ------ ----- --- ------ ----- - -----
343498.node96        pcw      short    AlSiOH.job         5383     1   1    --  01:00 C 00:00
343500.node96        pcw      batch    AlSiOH.job         2556     1   1    --  24:00 R   --

The next to last column tells you the status (i.e. C=Completed, R=running, Q=queued)

You can see the output of interest in the log file (AlSiOH.log in this case if I just used defaults in subg09)