|Availability||bwUniCluster | BwForCluster_Chemistry|
|License||Site license for at no cost to academic and industrial users|
|Citing||As described in the manual|
|Included modules||compiler/intel/15.0 | mpi/ipenmpi/5.0.3-intel-15.0 | numlib/mkl/11.3|
- 1 Description
- 2 Versions and Availability
- 3 License
- 4 Usage
- 5 Examples
- 6 GAMESS-Specific Environments
- 7 Version-Specific Information
The General Atomic and Molecular Electronic Structure System (GAMESS)
is a general ab initio quantum chemistry package.
1.1 Summary of GAMESS' Capabilities
GAMESS is a program for ab initio molecular quantum chemistry. Briefly, GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Correlation corrections to these SCF wavefunctions include Configuration Interaction, second order perturbation Theory, and Coupled-Cluster approaches, as well as the Density Functional Theory approximation. Excited states can be computed by CI, EOM, or TD-DFT procedures. Nuclear gradients are available, for automatic geometry optimization, transition state searches, or reaction path following. Computation of the energy hessian permits prediction of vibrational frequencies, with IR or Raman intensities. Solvent effects may be modeled by the discrete Effective Fragment potentials, or continuum models such as the Polarizable Continuum Model. Numerous relativistic computations are available, including infinite order two component scalar relativity corrections, with various spin-orbit coupling options. The Fragment Molecular Orbital method permits use of many of these sophisticated treatments to be used on very large systems, by dividing the computation into small fragments. Nuclear wavefunctions can also be computed, in VSCF, or with explicit treatment of nuclear orbitals by the NEO code.
A variety of molecular properties, ranging from simple dipole moments to frequency dependent hyperpolarizabilities may be computed. Many basis sets are stored internally, together with effective core potentials or model core potentials, so that essentially the entire periodic table can be considered.
Most computations can be performed using direct techniques, or in parallel on appropriate hardware. Graphics programs, particularly the MacMolplt program (for Macintosh, Windows, or Linux desktops), are available for viewing of the final results, and the Avogadro program can assist with preparation of inputs.
For more information on features please visit Summary of GAMESS Capabilities web page.
2 Versions and Availability
A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the
On the command line interface of any bwHPC cluster you'll get a list of available versions by using the command 'module avail chem/gamess'.
$ module avail chem/gamess ------------------------ /opt/bwhpc/common/modulefiles ------------------------- chem/gamess/12052014
A site license for GAMESS is available at no cost to both academic and industrial users. You
will be asked to agree to this license during the process of downloading GAMESS.
The license acknowledges the Gordon group's exclusive distribution rights to GAMESS,
and also prohibits you from making copies of the GAMESS code for any purpose except
use at your own institution. Please note the distinction between "a site license at no cost"
and terms such as "public domain" or "freeware" or "open source".
In order to accept the license, register your name and address and so on, and then
obtain the password that will permit you to download the source code to GAMESS
(or one of the precompiled binaries).
After completing your registration, you will subsequently receive an E-mail containing the downloading password. Once you have the password you can download the source code's compressed tar file, or a pre-compiled binary, using any browser. Full details on how to do this will be sent in the E-mail mentioned above. Subsequent upgrades of GAMESS may be performed very quickly, provided you enter your same, previously registered E-mail address into the registration form.
4.1 Loading the module
You can load the default version of GAMESS with the command
$ module load chem/gamess
The module will try to load modules it needs to function (e.g. compiler, mpi, numlibs). If loading the module fails, check if you have already loaded one of those modules, but not in the version needed for Gamess. If you wish to load a specific (older) version (if available), you can do so using e.g. '$ module load chem/games/'version' to load the version you desires.
$ module avail chem/gamess ------------------------ /opt/bwhpc/common/modulefiles ------------------------- chem/gamess/12052014 $ module load chem/gamess/12052014 Please do not use this module if you do not own a valid GAMESS group license. Please cite GAMESS in your publications according to GAMESS documentation. Please read 'module help chem/gamess/12052014' before using GAMESS. $
4.2 Program Binaries
You can find the GAMESS binaries in the main folder of the GAMESS system.
After loading the GAMESS module (module load chem/gamess/'version') this path is
also set to the local $PATH- and $GAMESS_BIN_DIR environments.
$ ls -F $GAMESS_BIN_DIR auxdata/ gamess.01.x* libcchem/ object/ rungms-bwhpc/ bwhpc-examples/ gms-files.csh* lked* PROG.DOC rungms.old* bwhpc-install.log/ graphics/ machines/ qmnuc/ source/ comp* INPUT.DOC Makefile README tests/ compall* install.info Makefile.in REFS.DOC TESTS.DOC config* INTRO.DOC misc/ runall* tools/ ddi/ IRON.DOC modulefiles/ rungms* vb2000/
4.2.2 bwForCluster Justus
$ ls -F $GAMESS_BIN_DIR auxdata/ gamess.01.x* libcchem/ object/ source/ bwhpc-examples/ gms-files.csh* lked* PROG.DOC tests/ bwhpc-install.log/ graphics/ machines/ qmnuc/ TESTS.DOC comp* INPUT.DOC Makefile REFS.DOC tools/ compall* install.info Makefile.in runall* vb2000/ config* INTRO.DOC misc/ rungms* ddi/ IRON.DOC modulefiles/ rungms.old* $
A '/' at the end of a file name indicates a directory/folder. '*' is an executable.
4.3 Gamess RUNGMS-Script
We created an adapted version of the "rungms"-script for the bwUniCluster. You can find this on in the sub folder "rungms-bwhpc" and in the main folder. The rungms script included in chem/gamess was "replaced" by the one included in the "$GAMESS_BIN_DIR/rungms-bwhpc"-folder. So please use the adapted version. It's the default one.
$ echo $GAMESS_BIN_DIR/rungms-bwhpc /opt/bwhpc/common/chem/gamess/12052014/rungms-bwhpc $ ls -x /opt/bwhpc/common/chem/gamess/12052014/rungms-bwhpc/ README rungms
README: Instructions how to start an example Gamess simulation
rungms: the bwHPC-C5 accommodated version of the original startup script. Please use and modify this one for your own jobs. These scripts are included in the examples-folder, too ($GAMESS_EXA_DIR).
4.3.2 bwForCluster Justus
The main rungms start script is the adapted one and used as a default. You find it in $GAMESS_BIN_DIR. No extra rungms-bwhpc folder is present.
4.4 Disk Usage
Scratch files are written to the current directory by default. Please change to a local directory or to your local workspace (preferred) before starting your calculations.
'gamess_repo' is an example name of a repository you created by using the command 'ws_allocate'.
$ cd $(ws_find gamess_repo) ['your-id'-gamess_repo-0]$ pwd /work/workspace/scratch/'your-id'-gamess_repo-0 ['your-id'-gamess_repo-0]$
5.1 bwHPC examples
You can copy a simple interactive example to your workspace and run it, using 'msub'
$ cd $(ws_find gamess_repo) $ cp $GAMESS_EXA_DIR/* . $ cp bwunicluster-gamess-example.moab mygamessjob.moab § vi mygamessjob.moab # do your own modifications $ msub mygamessjob.moab # start job submission
5.2 Vendor examples/HowTo
A step-by-step example how to run Gamess jobs with the included testparams.
- Create a workspace
$ WS=$(ws_allocate gamess_repo 30) $ cd $WS
- Load chem/gamess module and copy test input files
$ module load chem/gamess ... $ cp -a $GAMESS_HOME/tests $WS
- Copy rungms script to workspace (be shure to use our adapted version of rungms)
$ cp $GAMESS_BIN_DIR/rungms-bwhpc/rungms $WS
- Create test job script gamess.moab or use the one we supplied in the $GAMESS_EXA_DIR.
$ cat gamess.moab # example only
cd $MOAB_SUBMITDIR module load chem/gamess JOB=exam01 ./rungms $JOB 01 $MOAB_PROCCOUNT $(($MOAB_PROCCOUNT/$MOAB_NODECOUNT)) >$JOB.log
- Submit test job to the nodes
$ msub -l nodes=2:ppn=8 -l walltime=5:00 gamess.moab
- Check log file exam01.log for correct execution.
The log file should indicate that the job has successfully run on multiple nodes.
6 GAMESS-Specific Environments
To see a list of all GAMESS environments set by the 'module load'-command use 'env | grep GAMESS'. Or use the command 'module display chem/gamess'.
$ env | grep GAMESS GAMESS_EXA_DIR=/opt/bwhpc/common/chem/gamess/12052014/bwhpc-examples GAMESS_HOME=/opt/bwhpc/common/chem/gamess/12052014 GAMESS_VERSION=12052014 GAMESS_BIN_DIR=/opt/bwhpc/common/chem/gamess/12052014 GAMESS_DOC_DIR=/opt/bwhpc/common/chem/gamess/12052014/machines $
7 Version-Specific Information
For a more detailed information specific to a specific GAMESS version, see the information available via the module system with the command 'module help chem/gamess/'version.
For a small abstract what GAMESS is about use the command 'module whatis chem/gamess/'version
$ module avail chem/gamess ------------------------ /opt/bwhpc/common/modulefiles ------------------------- chem/gamess/12052014 $ module whatis chem/gamess/12052014 chem/gamess/12052014 : General Atomic and Molecular Electronic Structure System (GAMESS, V.:12052014/impi) is a general ab initio quantum chemistry package. Command '/opt/bwhpc/common/chem/gamess/12052014/rungms' $ module help chem/gamess/12052014 ----------- Module Specific Help for 'chem/gamess/12052014' ------- # (excerpt) This module provides the quantum chemistry package GAMESS version 12052014 via command '/opt/bwhpc/common/chem/gamess/12052014/rungms'. Rungms is a script you should adapt to your own environment. The binary/palin gamess programm is called 'gamess.01.x'. This program was built with 'IMPI'. [...] Documentation: * Ames Laboratory/Iowa State University http://www.msg.ameslab.gov/gamess/documentation.html * Vendor-documentation (including 'run in MPI environment', 'cimshell') http://www.msg.chem.iastate.edu/gamess/GAMESS_Manual/refs.pdf See also: /opt/bwhpc/common/chem/gamess/12052014/machines/readme.unix * Vendor-test-examples (pdf format): http://www.msg.ameslab.gov/gamess/GAMESS_Manual/tests.pdf I M P O R T A N T * bwUniCluster-documentation /opt/bwhpc/common/chem/gamess/12052014/bwhpc-examples/README *** Explore the file 'README' in the bwhpc-examples folder! *** [...] $