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Gaussian 09

Description

Gaussian 09 is a connected series of programs for performing semi-empirical, density functional theory and ab initio molecular orbital calculations. Starting from the fundamental laws of quantum mechanics, Gaussian 09 predicts the energies, molecular structures, vibrational frequencies and molecular properties of molecules and reactions in a wide variety of chemical environments. Gaussian 09’s models can be applied to both stable species and compounds which are difficult or impossible to observe experimentally (e.g., short-lived intermediates and transition structures).

How to Access Gaussian 09

NERSC uses modules to manage access to software. Gaussian is available at NERSC only on the Carver system. To use the default version of Gaussian 09, type

% module load g09

Access Restrictions

Gaussian is available to the general user community at NERSC subject to the License To Use Agreement between the U.C. Regents, Lawrence Berkeley National Lab and Gaussian Inc. This agreement restricts use of the Gaussian software in that NERSC may only "provide to third parties who are not directly or indirectly engaged in competition with Gaussian access to the binary code of the Software."

You must certify that this condition is met by using the g09_register command. A NERSC consulting trouble ticket will be generated and you will be provided access in a timely manner.  The procedure for doing this is as follows:

  1. module load g09
  2. g09_register
  3. follow instructions
  4. wait for confirmation email from NERSC consultants

Note: If you already registered for Guassian 03 at NERSC then you don't have to register for Guassian 09 again. Gaussian 09 and Gaussian 03 share the same license agreement.

Using Gaussian 09 on Carver

Gaussian 09 is installed on Carver. To run it you must request compute node resources. After that, it can be run interactively using the command:

% g09 <input > output &

To submit a job to the batch scheduler, please refer to the following sample job script.

Sample batch job script for Carver:

For a serial job:

#!/bin/bash -l
#PBS -l nodes=1:ppn=1,walltime=06:00:00
#PBS -N t1
#PBS -j oe
#PBS -q regular
#PBS -V

mkdir -p $SCRATCH/g09/$PBS_JOBID
cd $SCRATCH/g09/$PBS_JOBID
module load g09
ulimit -Sv unlimited
g09 < $HOME/g_tests/T/t1.inx > $HOME/g_tests/T/t1.out
ls -l

For a parallel job, use the following form:

#!/bin/bash -l
#PBS -l nodes=2:ppn=8,walltime=06:00:00
#PBS -N t1
#PBS -j oe
#PBS -q regular
#PBS -V

mkdir -p $SCRATCH/g09/$PBS_JOBID
cd $SCRATCH/g09/$PBS_JOBID
module load g09
ulimit -Sv unlimited
g09l < $HOME/g_tests/T/t1.inx > $HOME/g_tests/T/t1.out
ls -l

Note: an alternative strategy to giving explicit paths for input and output is to copy input to $SCRATCH at the beginning of the run and then copy output to permanent storage at the end of the job.

Then submit the job script using the qsub command, e.g., assuming the job script name is test_g09.pbs:

% qsub  test_g09.pbs

Using Gaussian 09 on Hopper/Edison

G09 is installed on Hopper and Edison as well. As you may know, the Hopper and Edison compute nodes run a stripped down operating system, the Compute Node Linux (CNL), therefore some of the standard Linux services are not available on Hopper compute nodes. G09 couldn't run on Hopper due to missing the TCP/IP support on Hopper compute nodes in the past. Now with the Cray Cluster Compatibility Mode (CCM) which provides the standard Linux services on Hopper/Edison compute nodes,  G09 runs on Hopper. For more details about using CCM on Hopper, please visit our CCM website.

Please note that CCM doesn't support the native torque job launch mechanisms (a job launches from a mom node instead of the head compute node), some special care has to be taken in order to run g09 on Hopper/Edison compute nodes. It is important to follow the following steps exactly

To use g09 on Hopper/Edison, you need to follow the steps below:

1) Load g09 module in your shell startup file, eg., the .tcshrc.ext/.cshrc.ext for tcsh/csh users, and the .bashrc.ext for bash shell users. You can insert the following line in the if block for hopper:

module load g09

2) Submit a job to the ccm_queue. Here is a sample job script. Note, mppwidth of 48 corresponds to 2 Hopper nodes and 3 Edison nodes:

#PBS -S /bin/csh
#PBS -N g09_ccm
#PBS -q ccm_queue
#PBS -l mppwidth=48,walltime=48:00:00
#PBS -j oe

module load ccm
setenv CRAY_ROOTFS DSL

mkdir -p $SCRATCH/g09/$PBS_JOBID
cd $SCRATCH/g09/$PBS_JOBID
module load g09

ccmrun g09l < $HOME/g_tests/T/t1.inx > $HOME/g_tests/T/t1.out
ls -l

 

Notes on Memory and Storage:

Some jobs, especially MP2, may consume large memory and disk storage resources. Instead of running these kinds of jobs in distributed memory Linda-parallel mode it might be better to use a shared-memory parallel approach. For larger systems Gaussian09 also allows a mixed-mode approach using shared-memory-parallelism within nodes and Linda only between nodes.

Using shared memory parallel execution can save a lot of disk space usage (roughly eight times), since tasks on the same node will share a copy of the scratch file whereas each Linda-parallel task will create its own copy of the scratch data file. The savings of up to a factor of eight can be quite significant because the minimum disk required for MP2 frequencies is a multiple of N^4 (where N is the number of basis functions).

For a one-node job (eight cores) use, for example, something like:

%mem=16gb
%nprocshared=8

and for multiple nodes job (for example, two nodes), use something like:

%mem=16gb
%NProcShared=8
%NProcLinda=2

The parameter NProcLinda should equal the number of nodes used for your job. The total number of the processors used to run the g09 job is NProcLinda X NProcShared.

For very large jobs, you might consider setting two Gaussian09 parameters, %Mem and %MaxDisk, that affect the amount of memory and disk, respectively, in order to produce good general performance. For the types of calculations that obey %MaxDisk, the disk usage will be kept below this value. See the Gaussian Efficiency Considerations web page for details. There are some examples in the directory $g09root/g09/tests/com.

When using multiple processors with shared memory, a good estimate of the memory required is the amount of memory required for a single processor job times the number of cores used per node. In other words, %Mem represents the total memory requested for each node. For distributed memory calculations using Linda, the amount of memory specified in %Mem should be equal to or greater than the value for a single processor job.

Special Memory Notes for Carver:

We have set memory limits (soft limit 2.5Gb, hard 20Gb) on Carver compute nodes to protect the nodes from crashes due to using too much memory.  As a result, g09 jobs that request more than 2.5Gb memory through the %mem key word will fail. The error message you will see is "galloc: could not allocate memory."

The workaround, if you use bash or if your gaussian job script uses the bash shell, is to add the following in your batch script (submit file):

ulimit -v 20971520

If you use a csh job script, put the following in your batch script (submit file):

limit vmemoryuse unlimited

Make sure to put the above IF blocks after the NERSC_HOST is set in your dot files.

Documentation

Gaussian 09 Online Manual

Availability

PackagePlatformCategoryVersionModuleInstall DateDate Made Default
G09 carver applications/ chemistry b1 g09/b1 2010-12-21 2011-01-26
G09 carver applications/ chemistry c1 g09/c1 2012-01-21
G09 carver applications/ chemistry d1 g09/d1 2013-06-06
G09 edison applications/ chemistry c1 g09/c1 2013-02-08 2013-02-08
G09 edison applications/ chemistry d1 g09/d1 2013-06-12
G09 hopper applications/ chemistry b1 g09/b1 2012-01-21 2012-01-21
G09 hopper applications/ chemistry c1 g09/c1 2012-01-21 2012-01-21
G09 hopper applications/ chemistry d1 g09/d1 2013-06-06