Gaussian
Gaussian is a general-purpose computational chemistry package.
Useful Links
Using Gaussian on Cirrus
Gaussian on Cirrus is only available to University of Edinburgh researchers through the University's site licence. Users from other institutions cannot access the version centrally-installed on Cirrus.
If you wish to have access to Gaussian on Cirrus please request access via SAFE
Gaussian cannot run across multiple nodes. This means that the maximum number of cores you can use for Gaussian jobs is 36 (the number of cores on a compute node). In reality, even large Gaussian jobs will not be able to make effective use of more than 8 cores. You should explore the scaling and performance of your calculations on the system before running production jobs.
Scratch Directories
You will typically add lines to your job submission script to create a scratch directory on the solid state storage for temporary Gaussian files. e.g.:
export GAUSS_SCRDIR="/scratch/space1/x01/auser/$SLURM_JOBID.tmp"
mkdir -p $GAUSS_SCRDIR
You should also add a line at the end of your job script to remove the scratch directory. e.g.:
rm -r $GAUSS_SCRDIR
Running serial Gaussian jobs
In many cases you will use Gaussian in serial mode. The following example script will run a serial Gaussian job on Cirrus (before using, ensure you have created a Gaussian scratch directory as outlined above).
#!/bin/bash
# job options (name, compute nodes, job time)
#SBATCH --job-name=G16_test
#SBATCH --ntasks=1
#SBATCH --time=0:20:0
# Replace [budget code] below with your project code (e.g. t01)
#SBATCH --account=[budget code]
# Replace [partition name] below with your partition name (e.g. standard,gpu)
#SBATCH --partition=[partition name]
# Replace [qos name] below with your qos name (e.g. standard,long,gpu)
#SBATCH --qos=[qos name]
# Load Gaussian module
module load gaussian
# Setup the Gaussian environment
source $g16root/g16/bsd/g16.profile
# Location of the scratch directory
export GAUSS_SCRDIR="/scratch/space1/x01/auser/$SLURM_JOBID.tmp"
mkdir -p $GAUSS_SCRDIR
# Run using input in "test0027.com"
g16 test0027
# Remove the temporary scratch directory
rm -r $GAUSS_SCRDIR
Running parallel Gaussian jobs
Gaussian on Cirrus can use shared memory parallelism through OpenMP by setting the OMP_NUM_THREADS environment variable. The number of cores requested in the job should also be modified to match.
For example, the following script will run a Gaussian job using 4 cores.
#!/bin/bash --login
# job options (name, compute nodes, job time)
#SBATCH --job-name=G16_test
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --time=0:20:0
# Replace [budget code] below with your project code (e.g. t01)
#SBATCH --account=[budget code]
# Replace [partition name] below with your partition name (e.g. standard,gpu)
#SBATCH --partition=[partition name]
# Replace [qos name] below with your qos name (e.g. standard,long,gpu)
#SBATCH --qos=[qos name]
# Load Gaussian module
module load gaussian
# Setup the Gaussian environment
source $g16root/g16/bsd/g16.profile
# Location of the scratch directory
export GAUSS_SCRDIR="/scratch/space1/x01/auser/$SLURM_JOBID.tmp"
mkdir -p $GAUSS_SCRDIR
# Run using input in "test0027.com"
export OMP_NUM_THREADS=4
g16 test0027
# Remove the temporary scratch directory
rm -r $GAUSS_SCRDIR