A python code to submit jobs to SLURM

[fdiblen]

About:

This pull request adds the preliminary version of a Python code to submit jobs to HPC.

Changes

• Added Messy Python class to submit jobs to a HPC system running SLURM.
• Added use_messy, an example script showing how the Messy class can be used.
• Added templates/netlogo_job.jinja, a jinja template which is rendered to create a script for the batch job.
• Added docs/HPCDocker.md, a document describing the steps to manually achieve the same goal as Messy class.
• Added requirements.txt for Messy class dependencies
• Added .gitignore
• Added test_folder to be used in examples.

Review instructions:

Requirements

• Docker 25.0.2 or newer
• Apptainer 1.2.5 or newer (https://apptainer.org/)
• Python 3.11.X or newer
• Bash shell

Instructions

1. Run a local SLURM service using a xenon docker image

   docker pull xenonmiddleware/slurm:latest

   Give it some time to start the services. If you need to ssh to the container the credentials are below. username: xenon password: javagat

2. Create a virtual environment and install the dependencies (run in Bash shell)

   python3 -m venv venv
   . ./venv/bin/activate
   pip install --upgrade pip wheel
   pip install -r requirements.txt

3. Test Messy class methods. You can find some examples in use_messy script.

Related issues:

• mess-nlesc/model#20
• mess-nlesc/mess#1
• mess-nlesc/model#36

[fdiblen]

Thank you for reviewing @recap! I created issues about the improvements you pointed to. Can you please review again and submit a review?

[fdiblen]

Thank you for the review @lyashevska. I updated the example. Can you have a look once again?

[lyashevska]

Thanks @fdiblen. All looks good.