Sheffield High Performance Computing Documentation

This is the source for the documentation of Bessemer and ShARC, The University of Sheffield's High Performance Computing clusters.

It is written in the reStructuredText (rst) format and the Sphinx tool is used to convert this to a set of HTML pages.

For a guide on the rst file format see this document.

Rendered Documentation

This website is currently automatically built from this repository: each push to the master branch causes the ReadTheDocs service to build and serve the documentation.

The ReadTheDocs build configuration is stored in the .readthedocs.yaml file with the Python version pinned to 3.7 and the Pip requirements file. The requirements file is requirements.txt.

Please note that the use of the .readthedocs.yaml file will also override certain web UI settings set in the ReadTheDocs administrative panel.

How to Contribute

To contribute to this documentation, first you have to fork it on GitHub and clone it to your machine, see Fork a Repo for the GitHub documentation on this process.

Once you have the git repository locally on your computer, you will need to ensure you have Python and the Tox build tool installed.

Once you have made your changes and updated your Fork on GitHub you will need to Open a Pull Request. All changes to the repository should be made through Pull Requests, including those made by the people with direct push access.

Building the documentation on a local Windows machine

1. Install Python 3 on your machine by downloading and running the Miniconda installer:

   • Install for just you;
   • Install to the default location (e.g. C:\Users\myusername\Miniconda3);
   • Do not add Anaconda to your PATH environment variable;
   • Do not register Anaconda as your default Python 3.

2. Click Start -> Anaconda3 (64-bit) -> Anaconda Prompt to open a terminal window.

3. Create a new conda environment for building the documentation by running the following from this window:

   conda create --name sheffield_hpc python=3.7
   conda activate sheffield_hpc        # . activate sheffield_hpc on older versions of conda
   pip install tox
   

4. To build the HTML documentation run:

   tox -e py37
   

The output should be written to ./_build/html.

Building the documentation on a local Linux machine

1. Ensure one of Python 3.9 or 3.7 are installed.

2. Ensure the Tox build tool is installed and can be used/seen by your chosen Python interpreter.

3. Run Tox to create an isolated Python virtual environment then build documentation:

   tox -e py37  # OR
   tox -e py39
   

The output should be written to ./_build/html.

Building the documentation on a local Mac machine

1. Ensure Python 3 is installed. If you do not already have a python distribution installed, we recommend you install :ref:`Miniconda <Miniconda installer>`.

2. Install the Python packages needed to build the HTML documentation. If you are using (mini)conda create a new conda environment for building the documentation by running:

   export PATH=${HOME}/miniconda3/bin:$PATH
   conda create -n sheffield_hpc python=3.7
   conda activate sheffield_hpc        # . activate sheffield_hpc on older versions of conda
   pip install tox
   

3. To build the HTML documentation run:

   tox -e py37
   

The output should be written to ./_build/html.

Check external links

Do this with:

tox -e py37-linkcheck

Continuous build and serve

Build and serve the site and automatically rebuild when source files change:

tox -e py37-livehtml

Testing the building of the documentation

The validity of the reStructuredText in this repo and the ability to convert that to HTML with Sphinx can be tested in three ways:

• Locally by contributors when they run e.g. tox -e py37-livehtml
• By a [GitHub Actions](https://github.com/rcgsheffield/sheffield_hpc/actions/) Workflow each time a contributor creates or updates a Pull Request.
• By ReadTheDocs on each push to the master branch.

Important files / folders

• conf.py - Sphinx configuration file.
• requirements.txt - Main requirements file.
• setuptoolsrequirements.txt - Initial requirements file set in order to first pin setuptools to version 57.5.0 to retain support for the current theme.
• tox.ini - Tox configuration file.
• .readthedocs.yaml - ReadTheDocs configuration file (must match the PIP requirements.)
• Makefile
• global.rst - A globally included file (goes into all pages) which is excluded from direct building using exclude_patterns in conf.py.
• referenceinfo/imports - sub-folder tree of files to be included by not directly built. This is excluded from direct building using exclude_patterns in conf.py.
• _static/css/custom.css - custom CSS overrides for the theme.

(Re)-generating PNG images from Mermaid.js diagram definitions

Some diagrams, such as images/hpcgateway-sequence-diag.png have been generated with mermaid-cli and Mermaid.js diagram definitions such as images/hpcgateway-sequence-diag.mmd. How to install mermaid-cli and regenerate one of these diagrams:

yarn add @mermaid-js/mermaid-cli
./node_modules/.bin/mmdc -i images/hpcgateway-sequence-diag.mmd -o images/hpcgateway-sequence-diag.png