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Welcome to the Documentation of HPC Submit Scripts (hpcss)

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Date

pre-commit pre-commit.ci status Test Status CodeQL Status Documentation Status MIT License Made with Bash Made with Python Code style black Made with Sphinx Style NumPy

Site Contents

Introduction

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 (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 ("Paralleles Linux-System für Münsteraner Anwender") HPC cluster of the University of Münster and on the HPC cluster of the . However, it should be easy to adopt them to any other HPC system that runs Slurm if needed.

Note

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 .

Warning

The scripts and functions are not (extensively) tested!

doc_pages/general/installation doc_pages/general/usage doc_pages/general/config_file doc_pages/general/sbatch_options doc_pages/general/hpc_terminology doc_pages/submit_scripts doc_pages/pymodules doc_pages/dev_guide/dev_guide

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-label section. The basic usage of the scripts is described in the usage-label section.

Support

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

Contributing

If you want to contribute to the project, please read the .

Source Code

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

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

License

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

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

Indices and Tables

  • genindex
  • modindex
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