Gaussian¶

Gaussian Status¶

Gaussian 16 is installed and available for use on the HPC.

Gaussian Overview¶

Gaussian 16 is the latest in the Gaussian series of programs. It provides state-of-the-art capabilities for electronic structure modelling. Gaussian 16 is licensed for a wide variety of computer systems. All versions of Gaussian 16 contain every scientific/modelling feature, and none imposes any artificial limitations on calculations other than your computing resources and patience.

Gaussian Program Quick List¶

The main binary for Gaussian is g16.

Running Gaussian SLURM Jobs¶

Gaussian can be somewhat tricky to ensure that it runs in parallel under SLURM. Below are some starting points for you to fine-tune your Guassian runs. Please remember that not all Gaussian algorithms scale well across multiple nodes. There are also several variables to you will want to set, or your job will almost certainly crash!

The below options are known to work well as a starting point for general options. These must be before the call to g16:

export GAUSS_SCRDIR=$BGFS
export GAUSS_RDEF=”Maxdisk=-1”
export GAUSS_MDEF=$(($SLURM_CPUS_PER_TASK*$SLURM_MEM_PER_CPU-512))MB

Single-Node Parallelism¶

The -c CLI Option or the GAUSS_CDEF=”” environment variable are what must be set for Gaussian to use >1 CPU Core.

Gaussian expects a list of hardware CPU ID’s. You can obtain this within any job launched via SLURM with the following:

CPUS_ALLOCATED=`cat /sys/fs/cgroup/cpuset/slurm/uid_$UID/job_$SLURM_JOB_ID/cpuset.cpus

You can then either:

export GAUSS_CDEF=$CPUS_ALLOCATED; # Must be before your call to g16
g16 -c=$CPUS_ALLOCATED

Multi-Node Parallelism: Linda Workers¶

Linda is the mechanism for Multi-Node parallelism for Gaussian. As not all algorithms in Gaussian scale well beyond a single node, each job will need testing to identify if MPI-Enabled jobs gain you any significant speedup.

The following SLURM Snippet is a starting point for Multi-Node execution of Gaussian16:

## Guassian16 may benefit from >1 CPU/Task.
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=<Memery needed per CPU>
#SBATCH --ntasks=<Total Number of Tasks Wanted"
# 1 Day Runtime, alter as needed
#SBATCH --time=1-0
# Will write to the $SLURM_SUBMIT_DIR, which is wherever you call sbatch <file>
#SBATCH --output=%x-%j.out
#SBATCH --error=%x-%j.err

module load gaussian
#SLURM sets this for us, but just in case.
export OMP_NUM_THREADS=1
# Make sure LINDA Workers are more talkative
export GAUSS_LFLAGS="-v"
# G16 Scratch is in /cluster/jobs/<FAN>/JOBID/
export GAUSS_SCRDIR=$BGFS
# Generate the Linda Parallel hosts file
# If you need >1 CPU/Task, this will need alteration, to append each-nodes CPUSet as well as the node-name
for n in `scontrol show hostname | sort -u`; do
echo ${n}
done | paste -s -d, > g.nodes.$SLURM_JOBID

# Datestamp Start of G16 run in the SLURM Output file
date
g16 -w=`cat g.nodes.$SLURM_JOBID` <INPUT FILE>
# Datestamp End of G16 run in the SLURM Output file
date

# remove the par-nodes file
rm g.nodes.$SLURM_JOBID