This is an introduction to the usage of the electronic-structure code "Gamess" on the HPCVL clusters. It is meant as an initial pointer to more detailed information, and to get started. It does not replace study of the manual.
The "General Atomic and Molecular Electronic Structure System" (GAMESS) is a quantum chemistry software package that was assembled from various older codes (in particular, HONDO) by M. Dupuis, D. Spangler, and J. J. Wendoloski of the National Resources for Computations in Chemistry (NRCC). The code has undergone great changes since then and is maintained now by the Gordon Research Group at Iowa State University.
Gamess performs a great many of standard quantum chemical calculations. These include:
Gamess is described in General Atomic and Molecular Electronic Structure System; M.W.Schmidt, K.K.Baldridge, J.A.Boatz, S.T.Elbert, M.S.Gordon, J.H.Jensen, S.Koseki, N.Matsunaga, K.A.Nguyen, S.Su, T.L.Windus, M.Dupuis, J.A.Montgomery; J. Comput. Chem. 14, 1347-1363 (1993)
Advances in electronic structure theory: GAMESS a decade later; M.S.Gordon, M.W.Schmidt pp. 1167-1189 in Theory and Applications of Computational Chemistry: the first forty years; C.E.Dykstra, G.Frenking, K.S.Kim, G.E.Scuseria (editors), Elsevier, Amsterdam, 2005.
Location of the program and setup
The program resides in /opt/gamess and is called gamess.01.x. You also find some test examples in the program directory, which are useful to get an idea of the input format for the program. You are not allowed to copy the executable or any part of the distribution onto your local machine. However you can easily obtain the program yourself. See the GAMESS source code distribution page.Unlike other programs, no special setup is needed to run Gamess. All environment variables etc. are set with an execution script that will be described in the next section. However, it is a good idea to put the directory with the Gamess program into the path, i.e. set the PATH environment variable. This is best done through the usepackage utility, simply by typing
When you run Gamess a scratch space directory is set to /scratch/$USER and all temporary files and intermediate output will be placed in that directory. The program also requires a local temporary directory right below your home directory called $USER/scr. Make sure that you move files that you want to keep from there before running Gamess again with the same case_name. The second run requires that some temporary files be removed before re-run and will fail if they are still present in the scratch directory. For instance, if your username is "hpc9876", you will need "/scratch/hpc9876" and "/home/hpc9876/scr". Note that the former is automatically created when you obtain an account, but the latter has to be made by you explicitly.
Running Gamess from a command line
To run Gamess, a script file rungms is used. This file resides in the same directory as the gamess.00.x executable. Assuming that the home of the script file and executable is in your path, all you need to do is type
rungms case_name 01 n_procs
where case_name is the name of the input file (file extension is assumed to be .inp and must not be specified), and n_procs stands for the number of processes to be used in a parallel Gamess run. If n_procs=1 a serial run will be performed.
Note: It is absolutely essential to have a good idea about the size and complexity of your calculations before you start a Gamess job. Many of the methods have terrible scaling properties, i.e. the computational cost grows very quickly with the number of electrons, degrees of freedom, or number of basis functions used. We suggest you start with a small basis set and a cheap method, and then slowly increase those parameters.
Like most programs, Gamess requires an input (.inp) file that describes the system (usually a molecule) for which the calculation will be performed, specifies the level of calculation (eg, CISD), and provides other necessary information (starting orbitals, basis sets, required properties, etc). The format of the input is considerably more demanding than the one required for Gaussian (another widely used electronic-structure program), and much less information is hidden inside of defaults. This makes Gamess a very flexible program, but increases the risk of doing something wrong. Careful study of example input files and the documentation is required to run Gamess successfully. This is particularly true for CI or CAS-SCF calculations.
Once an input file is prepared, you will have to make the decision if you want to run Gamess in serial or in parallel mode. Gamess supports the use of multiple processors. However, the scaling (ie, the efficiency of parallel processing) varies with the type of calculation and the systems. We suggest you perform a small test calculation of the same type as your production calculation (eg, with a minimal basis set), and rerun it several times with a varying number of processors. Compare the timings and use the maximum number of processors that yield acceptable scaling for your production calculation.
Submitting (parallel) Gaussian jobs
If you want to run Gaussian on several processors on our machines, you have to include a line in your input file:
where we assume that you want to use 8 processors (cores, threads).
It is mandatory to submit a Gaussian job script through our scheduling software (see our Scheduler Help File for details).
Here is a "bare bones" sample of a Gaussian submission script:
#! /bin/bash #$ -S /bin/bash #$ -q abaqus.q #$ -l qname=abaqus.q #$ -cwd #$ -V #$ -M hpcXXXX@localhost #$ -m be #$ -o STD.out #$ -e STD.err #$ -pe shm.pe 8 g09 < sample.g09 > sample.log
The script (let's call it g09.sh) is submitted by the qsub command:
This must be done from the working directory, i.e. the directory that contains the input file and is supposed to contain the output. Also make sure that you have set up gaussian (use g09) before you submit a job.
Gaussian is a licensed program. The license held by the Centre for Advanced Computing is limited to our computers at our main site. That means that any of our users can use the program on our machines (but nowhere else), whether they are located at Queen's or not.
We require users of Gaussian to sign a statement in which they state that they are informed about the terms of the license to be included in the Gaussian user group named "g98". Please fax the completed statement to (613) 533-2015 or scan/email to firstname.lastname@example.org.
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