Gaussian Tutorial

Gaussian

How To launch Guassian jobs at VPAC on trifid

Launching Gaussian03 jobs at VPAC on the trifid cluster is straightforward, requiring just changing a few lines in a pbs script and reflecting those changes in your input files.

An example job can be found at /usr/local/examples/gaussian To run the example job, first copy the job to your home directory on trifid.

cd
cp -r /common/examples/gaussian .

(note there is a space and then a dot at the end of that second line.)

This job is a simple geometry optimization of a molecule running on 4 cpus. To launch the job, change into the job directory and launch with qsub.

cd gaussian
qsub pbs_script_gaussian


For each job you launch, it is good practice to create separate folders and launch the job withing that folder. The example job is running on 4 CPUs. To change that to 2 CPUs change the "#PBS -l nodes" line to read:

#PBS -l nodes=1:ppn=2

make sure to also your input file to reflect the changes in the first few lines:

%nproc=2
%mem=8GB

On trifid, your Gaussian jobs may have up to 8 cpus, and 4GB of memory is the default for each cpu. So for nproc=2 mem = 2x4= 8GB, for nproc=4 mem = 4x4=16GB, etc.

The pbs_script_gaussian copies the relevant files to the /tmp directory for better Gaussian performance and then copies the data back to the users job directory at the completion of the job.

IMPORTANT! - make sure to have enough walltime to cover the length of your job as defined in the line:

#PBS -l walltime=24:0:0

in the pbs script. If the job takes longer than the walltime data may be lost! If you think you need more walltime after you have already submitted a job, please email help@vpac.org and quote the job number.

Checkpoint / Restart

Some Gaussian jobs continue from a restart or checkpoint files. In order to continue jobs from checkpoint files make sure to define the OPT_FILES="" line in the pbs script to the name of your .chk file. ie):

OPT_FILE="gaussian_restart_file.chk"

In this case, the restart checkpoint file must then be located in your job directory.

Also, if you are saving a checkpoint file as defined in your input file, it is not necessary to define the path, as the checkpoint file will be copied back to your job directory. ie):

%chk=gaussian_example_input_opt.chk
(this works!)

%chk=/home/joeblogg/jobname010203/gaussian_example_input_opt.chk
(this does not work!)

Please report any problems you have to help@vpac.org.

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