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Running Gaussian on the ORC Clusters

Gaussian16 is available on the ORC clusters. Due to licensing restrictions, only the ORC users in the Gaussian user group are able to use it.

Getting Added to the Gaussian User group

All users on the ORC clusters who want to use Gaussian16 need to sign a user agreement form as per the University Counsel office. Contact the ORC through orchelp@gmu.edu to get a copy of the Gaussian License T&C. You will also be sent the User Agreement to sign and will be added to the Gaussian User Group after the ORC gets back the signed form.

To check the installed versions:

module avail gaussian
This will list the currently installed Gaussian versions.

------------------------------------------------------------------------------------------------
  gaussian:
------------------------------------------------------------------------------------------------
     Versions:
        gaussian/09
        gaussian/16-c01

------------------------------------------------------------------------------------------------
  For detailed information about a specific "gaussian" package (including how to load the modules) use the module's full name.
  Note that names that have a trailing (E) are extensions provided by other modules.
  For example:

     $ module spider gaussian/16-c01
------------------------------------------------------------------------------------------------

and add it to your environment with:

module load  gaussian/16-c01

Running Gaussian with SLURM

To set up a gaussian run on the cluster, create a directory and add input file and slurm script to it:

mkdir g16-test-cpu

cd g16-test-cpu
The contents of your directory should appear as below:

./g16-test-cpu
├── [g16-test-cpu.com](g16_files/g16-test-cpu.com)
└── [g16-test-cpu.slurm](g16_files/g16-test-cpu.slurm)

0 directories, 2 files

Example input file g16-test-cpu.com

The example input file show below can be downloaded to your directory from the terminal with

wget http://wiki.orc.gmu.edu/mkdocs/g16_files/g16-test-cpu.com
%nproc=24
%mem=80gb
%chk=jneutral-opt.chk
#T b3lyp/6-31+G* integral=UltraFine opt(maxstep=10,maxcycles=200)

4-BMC-optimization

0 1
O          0.00000        0.00000        0.00000
C          0.00000        0.00000        3.50600
C          0.00000        0.97000        2.28000
C          1.45100       -0.52200        3.25200
C          1.30800        1.79400        2.51700
C          2.28200        0.79500        3.22500
C          1.35400       -0.96600        1.80900
C          0.38700       -0.00800        1.16800
C         -0.16600        0.70700        4.85600
C         -1.05600       -1.10900        3.39800
C         -1.24100        1.79300        1.99500
H          1.79700       -1.29000        3.96000
H          1.08000        2.66500        3.15200
H          1.71000        2.17800        1.56600
H          3.22200        0.66500        2.66700
H          2.53700        1.12700        4.24400
H          0.51000        1.56400        4.98600
H          0.02600       -0.00500        5.67600
H         -1.20100        1.07300        4.96800
H         -0.91900       -1.84200        4.21200
H         -1.00000       -1.65300        2.44100
H         -2.06900       -0.68600        3.49300
H         -1.09900        2.38900        1.07900
H         -1.45400        2.48200        2.82900
H         -2.11800        1.14600        1.83500
C          1.93800       -1.98700        1.12200
H          2.25200       -2.85000        1.72600
C          2.22300       -2.03300       -0.31600
C          1.45800       -1.31800       -1.27000
C          3.28700       -2.84400       -0.78300
C          1.77600       -1.38900       -2.63700
H          0.59000       -0.73900       -0.94700
C          3.60200       -2.90100       -2.14900
H          3.87200       -3.42400       -0.06100
C          2.85600       -2.17000       -3.10000
H          1.16500       -0.83800       -3.36000
H          4.43500       -3.52900       -2.48500
C          3.20900       -2.23400       -4.56900
H          3.26000       -3.27800       -4.91800
H          2.46300       -1.70300       -5.18000
H          4.19300       -1.77200       -4.75600

Example SLURM script g16-test-cpu.slurm

This example slurm script can be downloaded to your directory from the terminal with

wget http://wiki.orc.gmu.edu/mkdocs/g16_files/g16-test-cpu.slurm
#!/bin/bash
#SBATCH -p normal
#SBATCH -J g16-test-cpu
#SBATCH -o g16-test-cpu-%j-%N.out
#SBATCH -e g16-test-cpu-%j-%N.err
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=24
#SBATCH --mem-per-cpu=3500MB
#SBATCH --export=ALL
#SBATCH -t 00:30:00

set echo

umask 0027
echo $SLURM_SUBMIT_DIR
module load gaussian/16-c01
module list

# default scratch location is /scratch/$USER/gaussian. Users can change it using
# export GAUSS_SCRDIR=<NEW_SCRATCH_LOCATION>
which g16

g16 < g16-test-cpu.com > g16-test-cpu.log

Submitting the job

Once you have the files, submit the job to the cluster with:

sbatch g16-test-cpu.slurm
This will create additional files in your directory

./g16-test-cpu
├── g16-test-cpu-66631-hop049.err
├── g16-test-cpu-66631-hop049.out
├── g16-test-cpu.com
├── g16-test-cpu.log
├── g16-test-cpu.slurm
└── jneutral-opt.chk

To monitor the job and check on its status, you can use the slurm command

sacct -X --format=jobid,jobname,partition,state

       JobID    JobName  Partition      State
------------ ---------- ---------- ----------
66631        g16-test-+     normal  COMPLETED

Using GaussView on the Open OnDemand Server

NOTE: Tutorials on using GaussView for different processes can be found on these Gaussian Pages

To use GaussView on Hopper, you need to start an Open OnDemand (OOD)session. In your browser, go to ondemand.orc.gmu.edu. You will need to authenticate with your Mason credentials before you can access the dashboard.

  • Once you authenticate, you should be directed to the OOD dashboard.

  • You'll need to click on the "Interactive Apps icon to see the apps that are available.

  • Select the Hopper Desktop and set your configuration (number of hours upto 12 and number of cores upto 12). You'll see the launch option once the resources become available.

  • After launching the session, you'll get connected to a node on Hopper with a desktop environment from where you can now start the terminal (using the highlighted 'terminal emulator' icon)

  • From the launched shell session, load the gaussian module with

module load gaussian
and start GaussView with

gv

  • The GaussView window should now appear