Gaussian 03 on Sweetgum and Mimosa
The normal Gaussian 03 and 98 are installed on sweetgum
and the Lindaenabled Gaussian 03 is installed on mimosa.
Gaussian 03
Online Manual
Efficiency
Considerations with Gaussian 03
The following Gaussian calculations can be run in parallel on mimosa:
HartreeFock energies, geometry
optimizations and vibrational frequency calculations. HartreeFock
theory is the baselevel electronic structure method: it is the
least computationally intensive and is applicable to the widest
range of problem types. It is also frequently used as a starting
point for more accurate calculations.
Density functional theory (DFT)
energies, geometry optimization and vibrational frequency
calculations, using either pure or hybrid functionals. These methods
provide additional accuracy over HartreeFock theory for many
molecular systems by including some of the effects of electron
correlationthe way that individual electrons instantaneously affect
one anotherneglected by the less expensive method.
MP2 single point energy calculations and geometry
optimizations. MP2 theory is another method which attempts to
address the neglect of electron correlation of HartreeFock theory,
doing so via MøllerPlesset perturbation theory. It is more
expensive than Density Functional Theory but is more extensively
calibrated than the DFT methods and performs well for some types of
molecular systems with which they have trouble.
Note: CCSD problems are not sufficiently
parallelizable to approach linear speedup, and should not be
run across multiple cluster nodes.
For most jobs, running 2 processors has the best speedup and
performance. For MP2 jobs, you might want to use 6 processors.
This job naturally separates into a series of 6 batches of integral
computations. Remember, the more processors you use, the more
overhead you get.
To run a Gaussian 98 job on sweetgum,
please use this command or edit your own PBS script:
g98sub [t time] [m memory] jobs
To run a Gaussian 03 job on sweetgum,
please see the June 2003 ParallelOGram article about setting up your enviroment,
then use this command or edit your own PBS script:
g03sub [t time] [n nproc] [m memory] input_file
To run a Gaussian 03 job on mimosa: First,
make sure that the you have a file called .cshrc in your home
directory, and that it contains at least the following line:
setenv g03root /usr/local/apps
Also, make sure you have a file called .bashrc in your home directory
with the following line:
export g03root=/usr/local/apps
Then, please use the g03sub script located in the
/usr/local/apps/bin directory. To submit the job, please type:
g03sub [t time] [n nproc] [m memory] input_file
If you need to run a 2 node job with input file as test100.com,
the command line will be:
g03sub n 2 test100.com
If you need to run a 1 node job with input file as test100.com,
the command line will be:
g03sub n 1 test100.com
In your input file, please insert two lines denoting the number of
processors (or nodes, in this case) that the job will run on, and the
amount of memory it will require. The nprocl value should be the same
as the commandline parameter you use to invoke g03sub. For instance,
to run your job on two nodes and use 200MB of memory per node, you
would add the following two lines:
%nprocl=2
%mem=200MB
If you have any questions about running Gaussian 03 jobs, please
contact assist@mcsr.olemiss.edu
