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Starting up Gaussian on the Chemistry Cluster for a Mac User

If you are a member of the Chemistry Department, get an account on the computer cluster, ted, by emailing Margaret Doll. She will set up your account so that the variables necessary to run Gaussian have been defined for your account.

If you have not transferred your .com file from your Mac, see the Mac User documentation.

After your files have been transferred or created to ted, ssh into ted. The login process takes about a minute, so be patient.

If you are using a Mac, start up Terminal.app which is found in the Utilities folder.

In the terminal window following the example below where you must

  • type the words that appear in bold type as is and
  • substitute words appropriate to your setup for the words that appear in Bold-Italic.
  • Standard and standard italic typed words indicate the system's output.

ssh youraccount@ted.chem.brown.edu
youraccount@ted's password: yourpassword
Last login: ...
...
(a listing of the software on the system)
...
Profile built ...

To see the files in your directory, type ls at the prompt.

To run your Gaussian calculation, you must follow the instructions on submitting Gaussian jobs on ted.

A filename.chk and filename.log will be created by the run. The results of the calculations will be in filename.log.

Example:

ls
test1.chk test1.com test1.log

To view the contents of the log file, type more followed by the name of the log file. Example:

more test1.log
Entering Gaussian Sysstem, Ling 0=g03
...(lots of stuff about the Gaussian Program)...
test1
----
Symbolic Z-matrix:
Charge = 0 Multiplicity = 1
...

A page of the log file will appear on your screen. To advance down the file to a new page, hit the Space Bar. To advance down the page a line at a time, hit the Return key. Hit q to quit.

To transfer the log file back to your mac, open another terminal window on your mac. Assuming that you want to put the log file on your Mac Desktop, type the following in the new terminal window,

  • type the words that appear in bold type as is and
  • substitute words appropriate to your setup for the words that appear in Bold-Italic.
  • Standard and standard italic typed words indicate the system's output.

cd Desktop
sftp youraccountname@ted.chem.brown.edu
Connecting to ted ...
youraccountname@ted's password: yourpassword
sftp> get yourfile.log
Downloading yourfile.log to /home/youraccountname/yourfile.log
yourfile.log 100% ...
sftp>exit

If you are going to setup some other calculations on GaussView, you may want to convert your .chk file to and .fchk file and sftp the .fchk to your mac as well.


To end your ssh session on ted, type exit twice. The first exit gets you to the head node; the second exit ends the session on ted.


Margaret Doll 12-04-07