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.

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.

Temporary Directory
When running a PBS script you need to set up your GAUSS_SCRDIR (gaussian temp directory) variable to point to somewhere in your /lustre directory.
As all Trifid gaussian users issue "module load gaussian" they will get a brief message reminding them to set this variable .. it really has become that important.
EG: export GAUSS_SCRDIR=/lustre/
//temp

Note: The "export" line in your pbs scripts needs to be AFTER the "module load gaussian" line, as the gaussian module itself sets a GAUSS_SCRDIR to "/tmp" on the local node, overwriting your export.
Checkpoint and 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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