Welcome to the Documentation of HPC Submit Scripts (hpcss)




Apr 16, 2024

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This project contains job and submit scripts to run and analyze Molecular Dynamics (MD) simulations on High Performance Computing (HPC) clusters. Most of the scripts are job scripts for the Slurm (Simple Linux Utility for Resource Management) Workload Manager.

This project only contains batch scripts and Python scripts that submit these batch scripts to Slurm. It does not contain the actual simulation and analysis software that is evoked in the batch scripts!

The scripts of this project are designed to run on the Palma2 (“Paralleles Linux-System für Münsteraner Anwender”) HPC cluster of the University of Münster and on the Bagheera HPC cluster of the research group of Professor Heuer. However, it should be easy to adopt them to any other HPC system that runs Slurm if needed.


Currently, this project is mainly intended for my personal use and will evolve according to my personal needs. However, everybody is welcome to use it and to contribute to it and to write scripts for his/her own purposes. If you want to contribute, please read the Developer’s Guide.


The scripts and functions are not (extensively) tested!

Why Using hpcss?

Benefits of hpcss:

  • Automatically resubmit MD simulations that take longer than the maximum allowed time limit by Slurm.

  • Submit many (or even all) analysis tasks at once while respecting their interconnections and dependencies.

  • Check for required input files before submitting jobs to Slurm so that jobs will not fail anymore because of missing input files.

  • Have all your Slurm job scripts at one place instead of having them scattered around in your different project directories.

  • Automatically adapt the Slurm job scripts to other systems or simulation settings. No need to manually change file names in Slurm job scripts anymore.

Getting Started

Installation instructions are given in the Installation section. The basic usage of the scripts is described in the Usage section.


If you have any questions, feel free to use the Question&Answer forum on GitHub. If you encounter a bug or want to request a new feature, please open a new Issue.


If you want to contribute to the project, please read the Developer’s Guide.

Source Code

Source code is available from https://github.com/andthum/hpc_submit_scripts under the MIT License. You can download or clone the repository with Git:

git clone https://github.com/andthum/hpc_submit_scripts.git


hpcss is free software: you can redistribute it and/or modify it under the terms of the MIT License.

hpcss is distributed in the hope that it will be useful, but WITHOUT WARRANTY OF ANY KIND. See the MIT License for more details.

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