ALIs

kommt noch

GAMESS

The General Atomic and Molecular Electronic Structure System (GAMESS) is an ab-initio quantum chemistry code.

General

Description, License

GAMESS is an ab initio quantum mechanics program, which provides many methods for computation of the properties of molecular systems using standard quantum chemical methods, many of them updated for parallel execution.
For a detailed description, please look at the GAMESS home page or at the program description in $GAMESS_DOCUMENTATION, which is available after executing "module load gamess ".
 
  GAMESS should be cited as:

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.J.Su, T.L.Windus, M.Dupuis, J.A.Montgomery, J.Comput.Chem.  14, 1347-1363(1993).

Gamess in LRZ has been updated since November 2009

The new installed versions which contain the Coupled-Cluster approaches, the Density Functional Theory approximation, as well as the Fragment Molecular Orbital (FMO) method which includes now the 3-body MP2 computations and the pair interaction energy decomposition analysis (PIEDA) are available in our parallel machines.


Gamess versions

Itanium-Cluster

(Ia64)

Linux-Cluster (X86_64)

Altix 4700 (HLRB-II)

2007

2009

Available

Available

 

Not available

Not available

 

 Available

 Available

 

How to run GAMESS on the Linux-Cluster and HLRB-II

Before running GAMESS job interactively, please think first if you wish to check your input file via: EXETYP=CHECK.

After login to the system please load the module environment appropriate via:

    module load gamess

or   for a specific version of GAMESS:

    module load gamess/2007


The execution of gamess can be done with

   gamess [-n  N]  inputfilename >& outputfilename.log
    N: number of processors

where the input file in this example would be named "inputfilename.inp", and output file outputfilename.log.

Restart files are written to the files given by the following environment variables:

 IRCDATA=/ntmp/$USER/$JOB.irc
 PUNCH=/ntmp/$USER/$JOB.dat

If you do not change these defaults for IRCDATA and PUNCH, the files will not be deleted. All other files (except your output file, of course) will be deleted, as long as you do not set:

   -K on gamess command

before starting GAMESS. All scratch files will reside on “SCR = $OPT_TMP― on the respective computer and will be deleted after the job finished.

Running serial-GAMESS on the Linux-Cluster and HLRB-II

After login to the system, you should use a job script like this:

Linux-Cluster (Itanium-Cluster)

HLRB-II, Altix 4700

 
 #!/bin/ksh
 #$-o $HOME/gamess/gamess-seq.out -j y
 #$-l march=ia64
 #$-N gamess-seq
 #$-l h_rt=10:00:00
 #$-M <your email address>
     . /etc/profile.d/modules.sh
 cd  mydire
 module load gamess/2007
 gamess -n 1 my-job.inp 

 #!/bin/ksh
 #PBS -o $HOME/gamess/gamess-seq.out -j y
 #PBS -N gamess-seq
 #PBS -l walltime=10:00:00
 #PBS -M <your email address>
    . /etc/profile.d/modules.sh
 cd mydire
 module load gamess/2007
 gamess -n 1 my-job.inp

Running Parallel-GAMESS on the Linux-Cluster and HLRB-II

After login to the system, you should use a job script like this:

Linux-Cluster (Itanium-Cluster)

HLRB-II

 
 #!/bin/ksh
 #$ -o $HOME/gamess/gamess.out -j y
 #$ -l march=ia64
 #$ -N gamess-par 
 #$ -l h_rt=10:00:00
 #$ -M <your email address>
 #$ -pe mpi_pe 8
    . /etc/profile
 cd mydire
 module load gamess
 gamess -n 16 my-job.inp >& my-job.out
 #twice the number of processors

 #!/bin/ksh
 #PBS -o $HOME/gamess/gamess.out -j y
 #PBS -N gamess.altix or gamess.shmem
 #PBS -l walltime=10:00:00
 #PBS -M <your email address>
 #PBS -l select=8
   . /etc/profile.d/modules.sh
 cd  mydire
 module load gamess
 gamess -n 8 my-job.inp >& my-job.out

So always use twice the number of processors which you have allocates, expect for the shared memory version on the Altix-system, here use the same.

To use the gamess.shmem version, please switch the modules mpi.altix or mpi.parastation to mpi.shmem in hlrb2 or linux-cluster respectively.

Documentation

  • After execution of "module load gamess", the environment variable documentation points to a directory containing the GAMESS documentation as it comes with the source code:

         ls -C  $GAMESS_DOC

  • Other format of the documentation and more information may be found on the GAMESS Home Page.

Examples

After execution of "module load gamess", the environment variable EXAMPLES points to the GAMESS examples:

       ls -C $GAMESS_EXAMPLES

FAQ - Frequently asked questions 

Number of used processors in parallel GAMESS jobs

Q: I requested 8 processors but GAMESS tells me:
 PARALLEL VERSION RUNNING WITH   4 PROCESSORS

A: This is OK! You may find a detailed description of how GAMESS distributes its work and data around the processors in the documentation, Section 5 - Programmer's Reference (PROG.DOC): the first half processors computes (compute processes), the second half serves as data servers.

Support

If you have any questions or problems with GAMESS installed on the different LRZ platforms, please don't hesitate to contact Dr. M. Brehm, (brehm_at_lrz.de) or Dr. M. Allalen: allalen_at_lrz.de.