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Using qgj/qg03

by Cristian V. Diaconu

qgj/qg03 can be found on almost all clusters in

/projects/guscus/software/util

I suggest users to create symlinks to the script or put the above directory in their path so that they can take advantage of the bug fixes asap.

Also, please report bugs asap to Cris Diaconu.

You only need the input file (and possibly the checkpoint file, or other files your job require), and qgj/qg03 takes care of the rest.

‘qgj -h’ or ‘qg03 -h’ gives a complete help, and here are some frequently used options:

qgj/qg03

If qgj is invoked as qg03 it runs Gaussian03 (revision D.01), if it is invoked as qgj or qgdv it runs Gaussian Development version (revision F.02).

-g gxx-rev

use specified branch and revision. Example: -g gdv-g1

-q queue

specify the queue instead of the default. On sugar, the default queue is commons, we also have guscus.

-t walltime

specify walltime, PBS format (seconds, or hours:mm:ss). Default on sugar is 24 hours for commons and 96 hours for guscus.

-x

submit the job. By default it only modifies the input file and produces the pbs file, which can subsequently be submitted with qsub.

-v

print a lot of information (useful when things don't work).

-ig igfile

use igfile for initial guess, it can be chk, fchk uncompressed or bzipped or gzipped.

-N jobname

use jobname for PBS job name, maximum 15 characters

-d dir

use dir as the parent gaussian directory. E.g.: -d $HOME/gaussian

-r | -raw

Use the raw input file. Prevents qgj from modifying the input file and making it a here-document in the PBS script. This also dissables initial guess, checkpoint file checks, automatic submission.

NOTES

• If you want qgj to run the created PBS do not forget to specify -x
• At this time qgj does not move files between home and shared scratch by itself, you need to do this manually
• qgj does not work with multi-step jobs out of the box. You can use 'qgj -raw' to produce a rough draft of a PBS script and then modify it to fit your needs

EXAMPLES

Example of running the above sugar-example using qgj:

$ qgj sugar-example.gjf -N example -t 10:00:00 -x

Here is an example with frequently used options (from 'qgj -h'):

$ qgj ex.gjf -N example -g gdv-e1 -d /my/path/to/gaussian -m 1GB -np 2 \
       -M 2000mb -q guscus -t 100:00:00 -ig ../other/example.fchk.bz2 -v -x

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