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Gaussian

Gaussian is available on Aoraki as a module. To make it available in your shell, load it with:

Terminal

module load gaussian/16

This will add the g16 command to your path and set up the required environment variables.

Interactive session

An interactive session is useful for quick tests and debugging. The following command requests 4 CPUs, 32 GB of memory, and 1 hour of wall time on the aoraki partition:

Terminal

srun --partition=aoraki --cpus-per-task=4 --mem=32G --time=01:00:00 --pty bash

Once connected to the compute node:

Terminal

module load gaussian/16

g16 water.gjf > water.log

If Gaussian writes a checkpoint file to scratch, copy it back:

!!!! terminal

```bash
cp -p "$GAUSS_SCRDIR/water.chk" .
```

SLURM batch job

For longer calculations, use a SLURM batch job. Create a Gaussian input file (e.g., water.gjf) with your desired calculation settings. Make sure to include the following lines in your input file to set the number of processors and memory: 

%nprocshared=4
%mem=32GB

This matches the resources requested in the SLURM job script.

To submit a batch job, create a SLURM script (e.g., gaussian_job.slurm) with the following content:

Terminal

#!/bin/bash
#SBATCH --job-name=g16_water
#SBATCH --partition=aoraki
#SBATCH --cpus-per-task=4
#SBATCH --mem=32G
#SBATCH --time=02:00:00
#SBATCH --output=%x-%j.out
#SBATCH --error=%x-%j.err

set -euo pipefail
module purge
module load gaussian/16

export GAUSS_SCRDIR=/weka/scratch/gaussian/$USER
mkdir -p "$GAUSS_SCRDIR"
ulimit -s unlimited

g16 water.gjf > water.log

# Copy checkpoint file back if it exists
if [ -f "$GAUSS_SCRDIR/water.chk" ]; then
    cp -p "$GAUSS_SCRDIR/water.chk" .
fi

Submit the job with:

Terminal

sbatch gaussian_job.slurm

Check the job status with:

Terminal

squeue -u $USER

After submission, the job will run in the background.

  • You can monitor its progress using the SLURM commands like squeue or sacct.
  • The output and error logs will be saved in the files specified by --output and --error in the SLURM script.

After the job completes, the output will be in water.log, and any checkpoint files will be copied back to your current directory. You can view the output and error logs with:

Terminal

less water.log

Best practices

  • Match resources: Set %nprocshared in your .gjf file to match --cpus-per-task in your SLURM script.
  • Memory settings: Set %mem in the input file slightly below your SLURM --mem to avoid oversubscription.
  • Batch for production: Use batch jobs for large calculations for better scheduling and reliability.
  • Checkpoint files: If your job generates checkpoint files, ensure they are copied back to your working directory after the job completes.

See also

  • Gaussian website: https://gaussian.com/