Gaussian is an electronic structure modeling program that Atlas has licensed for its HPC clusters that support AVX2 set of instructions (currently Atlas). To see available versions of Gaussian on the cluster, run:
$ module spider Gaussian ----------------------- Gaussian: ----------------------- Versions: Gaussian/09 Gaussian/16 ----------------------- For detailed information about a specific Gaussian module (including how to load the modules) use the module's full name. For example: $ module spider Gaussian/16 -----------------------
However, before trying to run Gaussian, please, make sure your user belongs to either
g16 Unix group. If this is not the case, please, email us .
In most cases, the scratch storage location (set by the environment variable
GAUSS_SCRDIR) should be on the local parallel file system of the cluster (
/scratch) or the local lscratch filesystems (
/lscratch). In case you fail to define this variable within the batch script, the value of this variable will be the same as
$SLURM_SUBMIT_DIR, that is, the directory from which the job was submitted.
Before running Gaussian, you must set up a number of environment variables. This is accomplished most easily by loading the Gaussian module file using:
$ module load Gaussian/16
Example of a batch script that can be used as a template to submit Gaussian 16 jobs:
GAUSSIAN: batch script
#!/bin/bash #SBATCH --partition=regular #SBATCH --job-name=gaussian_job #SBATCH --cpus-per-task=1 #SBATCH --mem=75gb #SBATCH --nodes=1 #SBATCH --ntasks-per-node=1 #SBATCH --output=%x-%j.out #SBATCH --error=%x-%j.err # Load environment for Gaussian module load Gaussian/16 # Insert nodes and cores in the header of the input file echo -e "%NProcShared=$SLURM_NPROCS\n%LindaWorkers=$(scontrol show hostname | paste -d, -s)\n$(cat input.com)" > input.com g16 < input.com
Notice that you do not need to specify the number of cores and nodes in your input file if you use the example above as a template, because the script will take care of it.
If you want to write temporary files out of the working directory you would need to define the
GAUSS_SRCDIR environment variable.
Restarting Gaussian jobs¶
If your Gaussian jobs are stopped prematurely (due to a crash, due to the fact that reached the maximum walltime allowed for the job) you can restart said jobs. Please, take a look to the Gaussian Documentation to learn more about how to do it.
GaussView is a visualization program that can be used to open Gaussian output files and checkpoint files (
.chk) to display structures, molecular orbitals, normal modes, etc. You can also set up jobs and submit them directly.
GaussView 6 on Atlas¶
The GaussView version for Gaussian 16 is release 6. To load and run GaussView on Atlas, you first have to load the corresponding Gaussian module, and then call GaussView:
$ module load GAUSSIAN/16 $ gv
X11forwarding to be able to open a graphical window.