Gaussian
Gaussian requires membership in a specific POSIX group to function. Before you can run Gaussian you will need to email
muitrss@missouri.eduto be added to the group.Gaussian 16 is the latest in the Gaussian series of programs. It provides state-of-the-art capabilities for electronic structure modeling. Gaussian 16 is licensed for a wide variety of computer systems. All versions of Gaussian 16 contain every scientific/modeling feature, and none imposes any artificial limitations on calculations other than your computing resources and patience.
- Software URL: http://gaussian.com/
- Documentation: http://gaussian.com/gaussian16/
Usage
To run this example you will need the following SBATCH file and input file
in a folder called /data/${USER}/gauss_test.
mkdir /data/${USER}/gauss_test
cd /data/${USER}/gauss_test
Your results should look like this:
[jgotberg@lewis4-r710-login-node223 ~]$ mkdir /data/${USER}/gauss_test
[jgotberg@lewis4-r710-login-node223 ~]$ cd /data/${USER}/gauss_test
[jgotberg@lewis4-r710-login-node223 gauss_test]$ pwd
/data/jgotberg/gauss_test
Gaussian Input File
Now create the SBATCH file using a text editor. In the example below the
gauss_job.sh file assumes that h20.com has the path
/data/${USER}/gauss_test/. You will want to make sure to replace the
placeholders X.Y in the module load gaussian/gaussian-X.Y line with the
latest version. If you want to receive the email notifications replace
user@missouri.edu with your email address.
You will need to replace
X.Ywith the specific Gaussian module you want to load
gauss_job.sh:
#!/bin/bash -
#-------------------------------------------------------------------------------
# SBATCH CONFIG
#-------------------------------------------------------------------------------
## resources
#SBATCH -N1 # nodes
#SBATCH -n4 # tasks (cores)
#SBATCH --ntasks-per-node=4 # how many tasks per node
#SBATCH --mem-per-cpu=4G # memory required per core
#SBATCH -t 0-02:00 # time (days-hours:minutes)
#
## housekeeping
#SBATCH -p General # partition (which set of nodes to run on)
#SBATCH -o gauss_h2o-%j.out # filename for the output from this job (%j is the job#)
#SBATCH -J gauss_h2o # job name - shows up in sacct and squeue
#
## notifications
#SBATCH --mail-user=user@missouri.edu
#SBATCH --mail-type=END,FAIL
#
#-------------------------------------------------------------------------------
## Load the Gaussian Module
module load gaussian/gaussian-16-A.03
module list
## Run Gaussian
echo "### Starting Gaussian ###"
g16 < /data/${USER}/gauss_test/h2o.com
echo "### All Done ###"
Gaussian input file
Now create the following Gaussian input file. The number of cores in the SBATCH
file (-n 4) must match the number of cores in the Gaussian input file (%NProcShared=4).
You will also need a blank space at the end of the h20.com file for it to work
in all cases.
h2o.com:
%Chk=water
%NProcShared=4
%mem=9GB
#RHF/6-31G(d)
water energy
0 1
O
H 1 1.0
H 1 1.0 2 105.0
Be sure to have an empty line at the end of the file or you will receive an error in the output file
Submitting the job
Once we have the SBATCH and Gaussian input files created we can start the test.
sbatch gauss_job.sh
Sample output
[jgotberg@lewis4-r710-login-node223 gaussian]$ sbatch gauss_job.sh
Submitted batch job 254952
[jgotberg@lewis4-r710-login-node223 gaussian]$ sacct
JobID JobName Partition Account AllocCPUS State ExitCode
------------ ---------- ---------- ---------- ---------- ---------- --------
...
254952 gauss_h2o General engineeri+ 4 COMPLETED 0:0
254952.batch batch engineeri+ 4 COMPLETED 0:0
[jgotberg@lewis4-r710-login-node223 gaussian]$ cat gauss_h2o-254952.out
Currently Loaded Modulefiles:
1) gaussian/gaussian-D.01
### Starting Gaussian ###
Entering Gaussian System, Link 0=g09
Initial command:
/cluster/software/gaussian/gaussian-16-A.03/avx2/g16/l1.exe "/local/scratch/jgotberg/Gau-10173.inp" -scrdir="/local/scratch/jgotberg/"
Entering Link 1 = /cluster/software/gaussian/gaussian-16-A.03/avx2/g16/l1.exe.exe PID= 10174.
Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2009,2013,
Gaussian, Inc. All Rights Reserved.
...
lots of output here
...
Job cpu time: 0 days 0 hours 0 minutes 4.4 seconds.
File lengths (MBytes): RWF= 5 Int= 0 D2E= 0 Chk= 2 Scr= 1
Normal termination of Gaussian 09 at Fri Dec 9 10:13:16 2016.
All Done
GaussView
From http://gaussian.com/gaussview6/. "GaussView 6 is the latest iteration of a graphical interface used with Gaussian. It aids in the creation of Gaussian input files, enables the user to run Gaussian calculations from a graphical interface without the need for using a command line instruction, and helps in the interpretation of Gaussian output (e.g., you can use it to plot properties, animate vibrations, visualize computed spectra, etc.)."
To use GaussView, first load your chosen Gaussian module, then run gview.sh.
In the following example, we will use gaussian/gaussian-16-A.03.
Command:
module load gaussian/gaussian-16-A.03
gview.sh
Output:
[quinnm@lewis4-r630-hpc3-node242 ~]$ module load gaussian/gaussian-16-A.03
[quinnm@lewis4-r630-hpc3-node242 ~]$ gview.sh
Xlib: extension "SYNC" missing on display "10.46.70.241:15.0".
...
NOTE
If you get a window that states "OpenGL is not available", run
export USE_MESAGL=1before runninggview.sh
