Automating ORCA and Gaussian Submissions with Bash Scripting

Introduction

High-Performance Computing (HPC) clusters provide scientists and researchers with the computational power needed to tackle complex simulations and calculations. Tools like ORCA and Gaussian are widely used in computational chemistry, molecular modeling, and quantum mechanics studies. However, submitting jobs to an HPC cluster manually can be time-consuming and error-prone. In this blog post, we’ll learn how to create a bash script to streamline the process of submitting ORCA and Gaussian jobs via qsub to an HPC cluster, making your scientific computations more efficient and manageable.

Step 1: Configure Environment Variables

Before creating the bash script, you’ll need to set up environment variables to ensure that ORCA and Gaussian executables are accessible from any directory on the HPC cluster. Modify your .bashrc or .bash_profile file to include the necessary paths:

export ORCA_PATH=/path/to/your/orca_executable
export GAUSSIAN_PATH=/path/to/your/gaussian_executable

Step 2: Create the Bash Script

Now, let’s create a bash script that automates the job submission process for both ORCA and Gaussian.

#!/bin/bash
#PBS -l nodes=1:ppn=4           # Specify the number of nodes and cores per node
#PBS -l walltime=24:00:00       # Set the maximum walltime
#PBS -N Job_Name               # Name your job
#PBS -o output.log             # Output file
#PBS -e error.log              # Error file

# Load required modules
module load your_orca_module    # Replace 'your_orca_module' with the module name for ORCA
module load your_gaussian_module  # Replace 'your_gaussian_module' with the module name for Gaussian

# Navigate to your working directory
cd /path/to/your/working_directory

# Execute ORCA or Gaussian
your_orca_executable input_file.inp > output.log      # Replace 'your_orca_executable' with the ORCA executable name and provide the input file
your_gaussian_executable input_file.com > output.log  # Replace 'your_gaussian_executable' with the Gaussian executable name and provide the input file

Step 3: Submitting the Job

Now that you have your bash script ready, you can submit the ORCA or Gaussian job to the HPC cluster using the qsub command:

qsub your_bash_script.sh

Conclusion

By automating ORCA and Gaussian job submissions with a bash script, you can significantly simplify the process of running computational chemistry simulations on an HPC cluster. The script handles environment variable configurations, job specifications, and execution, saving you time and reducing the risk of errors.

With this automation in place, you can focus more on refining your scientific models and analyzing results, making the most of the powerful resources provided by the HPC cluster.