Gaussian 09 Rev. A.02


Directory list:

VersionDescription
bdist Binary distribution of Gaussian 09 Rev. A.02

Level of support

Tier 1 NSC has at least one application expert on staff with knowledge about this software, and we will try to help you with any problems. We have also ran some internal tests to make sure that the program is working as intended. NSC also commits to installing updates to this program as they become available.

Please see the page describing our software support categories for more information.
You can also contact support@nsc.liu.se for further information.

How to run

Example batch script for running Gaussian 09:

#!/bin/bash 

#SBATCH --time=10:00:00                #Requested walltime 
#SBATCH --nodes=2                      #Number of compute nodes to allocate
#SBATCH --exclusive                    #Don't share compute nodes with other jobs (i.e. allocate complete nodes)
#SBATCH --account=liu-2012-00060-20    #Account string for the project that you wish to account the job to

job=jobname
WRKDIR=$(pwd)

#Trap SIGTERM and copy the chk file if the job hits the walltime limit 
trap 'if [ -f ${job}.chk ]; then cp ${job}.chk ${WRKDIR}; else echo "No named chk file"; fi; echo "SIGTERM was traped"' SIGTERM

#Load the relevant Gaussian module
module load gaussian/G09RevA.02-bdist
#If you want to run two Linda workers per compute node, then uncomment the line below
#export NSC_G_LW=2
. $g09root/g09/bsd/g09.profile 

cd $GAUSS_SCRDIR

if [ -f ${WRKDIR}/${job}.chk ]
then
    cp ${WRKDIR}/${job}.chk .
fi

(time g09 < ${WRKDIR}/${job}.com) > ${WRKDIR}/${job}.out &
wait

g_exit_status=$?

if [ -f ${job}.chk ]
then
    cp ${job}.chk ${WRKDIR}
fi

exit $g_exit_status
#END OF SCRIPT

Note that you must edit the jobname and the account string before submitting!

Important Link 0 commands

NOTE: NSC’s g09 wrapper will per default start one Linda worker per compute node!

%NProcLinda : The number of Linda workers to use for the job.
If NProcLinda is not specified, then the job will only run on one compute node!
The value of NProcLinda should, in general, be set to the number of compute nodes that you intend to use for the job.

One Linda worker per compute node (default):
#SBATCH --nodes=2
=> %NProcLinda=2

However, if you want to run more than one Linda worker per compute node, then you must adjust the value for NProcLinda accordingly. For example, if you want to run two Linda workers per compute node, then the value for NProcLinda must be twice the number of allocated compute nodes

Two Linda workers per compute node:
#SBATCH --nodes=2  
=> %NProcLinda=4  
Remember to also uncomment the #export NSC_G_LW=2 line in this case.

%NProcShared : The number of shared memory threads to use for a shared memory (only) parallel job.
Note that this value should never exceed the number of physical cores on the compute node (i.e. 16 in the case of Triolith).
OR
%NProcShared : The number of shared memory threads to use for each Linda worker in a Linda parallel job, if NProcLinda is also spefified.
Note that this value multiplied by the number of Linda workers per compute node should never exceed the number of physical cores on the compute node. For example, if you use the default of one Linda worker per compute node, then NProcShared can be set to the number of physical cores on the compute node (i.e. 16 in the case of Triolith). However, if you use two Linda workers per compute node, then NProcShared must be set to half the number of physical cores on the compute node (i.e. 8 in the case of Triolith).

%Mem : The amount of memory to allocate for the job.
Note that this value should never exceed the amount of physical memory available on the compute node.
OR
%Mem : The amount of memory to allocate per Linda worker for a Linda parallel job.
Note that this value multiplied by the number of Linda workers per compute node should never exceed the amount of physical memory available on the compute node.

Release notes

Changes between Gaussian 09 Revision A.01 and A.02:

  1. The logic for handling extra negative eigenvalues of the Hessian during minimizations has been improved.

  2. The combination of DFT and General SCF, automatically turned on if DFT is requested along with Int=DKHSO, does not work and is now rejected by the route generator.

  3. ONIOM input is now checked for divalent link atoms. The position of these atoms is ill-defined unless the distance scale factors are set to 1, and the model is usually poor if the scale factor is forced to be 1. Since this input is normally an error, it is now rejected by link 101. IOp 132 can be used to force acceptance of this input, but this is strongly discouraged.

  4. Semidirect integral transformation is the the default. This code parallelizes better than the fully direct or in-core algorithms and is similar in speed on a single processor.

  5. A bug which caused ONIOM=InputFiles to fail when PDB secondary structure information was included in the input has been fixed.

Disclaimer

NSC takes no responsibility for the correctness of results produced with the binaries! Hence, always evaluate the binaries against known results for the systems and properties you are investigating before using the binaries for production jobs.