Tutorial: Submitting Gaussian G03 jobs for Execution

Submitting Gaussian G03 input files

Querying job status and downloading output files

Submitting Molecule for Gaussian Calculation

Submitting Gaussian G03 input files

Molecular Editor has a function to submit already prepared Gaussian input files for remote execution. Select File->Submit Input File->g03 in the Menu bar.

Programs opens "Submit Gaussian Script" Dialog

which consists of several panels. On the very top user should choose Task Provider and Scheduler. Task Provider defines a protocol which will be used for job submission, file transfer, and job status queries (ssh, globus, etc.).

Each Task Provider has its own Task Provider Panel. User should also specify required resources in the Resources Panel. Scheduler specific options should be set in the Scheduler Panel.

Gaussian G03 specific options are in the (Job Specifications) Program Panel.

As an example, we shall consider job submission using SSH (Secure Shell) Task Provider and pbs scheduler.

First, we need to specify remote host and login name (type or select in the combobox) in the "Remote Host" and "User Name" comboboxes, correspondingly:

To submit jobs to the National Facility at the ANU use ac.anu.edu.au or lc.anu.edu.au host names for the Altix and Linux clusters, correspondingly.

Check your connection by hitting "Connect" button:

In the case of successful connection a corresponding message will be shown (otherwise an error message):

Now download your Gaussian G03 input file:

After downloading a file programs automatically fills in fields in the "Job Specification " panel:

Next step is to specify working directory on the remote host ("Remote Directory" textfield). User can either type it

or to use "Browse" button to browse remote file system using in-built SFTP browser:

To go quickly to the working directory one needs to type its name in the editable combobox on the top of a dialog window and to press Enter:

SFTP browser will change a directory and show its contents:

To create new directory use corresponding button in the Tool bar:

and type name for the new folder:

A new folder will appear in the SFTP browser:

To enter it double click on it:

To confirm remote directory selection press "Confirm Selection" button:

Selected folder will appear in the "Remote Directory" textfield of the "Job Specification" Panel:

Now we can submit job for execution by pressing "Submit" button:

Now we can either download and submit another input file or exit dialog by pressing "Cancel" button:

Querying job status and downloading output files

To query the status of submitted jobs select Grid->Job Statuses in the Menu bar.

It will open "Job Status" dialog with statuses for all submitted jobs. Placing mouse cursor on a row will show popup panel with extended information about a job. To update job statuses press "Update" button:

During querying process a dialog with a progress bar will popup:

When submitted job becomes active an Extended Task Info panel shows computer resources used:

When submitted job finishes its "Submit Status" changes into "DONE", however the resulted output files are still on a remote computer. To download them one needs to select a row in the table (multiple rows could selected) by clicking on a row

and press "Download" button:

"Job Status" dialog provides fast method to inspect output files after their downloading. Pointing cursor on a row and right-button mouse clicking will popup Download menu. Selecting Gaussian output file from the list (phosphate.log in our case)

will cause the Editor to parse the file and in the case of geometry optimization it will show "Select Structure" dialog

which allows select the structure along the optimization pathway (by default the last structure is selected). Finally, molecular structure will be shown in the Main Window:

In the case of a standard output (error) file a text window will be opened:

Submitting Molecule for Gaussian Calculation

It is possible to generate Gaussian input file for a molecule in the Main Window and submit it for calculation. Select File->Submit Input File->g03 in the Menu bar.

Program opens a Simple Gaussian Editor:

Setup Gaussian options and press Submit button:

Program will ask to save Gaussian input file

and open "Submit Gaussian Script" Dialog

How to work with the "Submit Gaussian Script" Dialog was described earlier (see Submitting Gaussian G03 input files)

Send all questions, suggestions and comments to Vlad (vvv900@gmail.com)

Dr. Vladislav Vasilyev

Supercomputer Facility,

The Australian National University,

Canberra, ACT, 0200, Australia