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nemo-simsar🔗

Document your NEMO ocean model simulations and share them with others using git remote repositories.

This project is part of the IMMERSE Project funded by the EC.

1. Description🔗

Ocean model simulations that are based on the NEMO ocean modelling framework (nemo-ocean.eu) consists of several components:

  • The source code provided by NEMO and by the user (FORTRAN code)
  • Build settings (model components, compiler options)
  • Runtime parameters (FORTRAN and XML namelists)
  • Input data fIles (e.g. grid, bathymetry, boundary conditions, initialisation)

While the first two components define a certain "configuration", the latter two provide the details for a specific experiment with the said configuration. Both together form a simulation.

The recipes and the tools in this project allows users to create a package containing all the necessary information in order to share it with other users intending to reproduce the simulation or to start from this simulation with their own settings. See also the documentation in the doc/ folder for more details.

Features🔗

  • Interactive script in order to create a README file (Markdown format) giving an overview of the simulation's settings and providing instructions how to include it in your own NEMO framework.
  • Recipe to extract and upload a configuration from inside the NEMO framework into a remote git repository

2. Requirements🔗

Assuming you're working on a *nix like system you have to meet the following pre-requisits before running a tool or following a recipe from this project:

  • A working NEMO framework (see nemo-ocean.eu)
  • A NEMO simulation to share (=configuration + experiment details)
  • git client is installed and working
  • access to a remote git server
  • Python3 including these standard libraries: os, re, subprocess, pathlib, textwrap

  • The following additional Python3 packages must be installed (e.g. with pip or conda or through your favorite package manager):

    EXAMPLE: Install required Python3 packages

    pip3 install svn wget GitPython Jinja2 pycurl netCDF4

    Using the conda-forge channel:

    conda install --channel conda-forge python=3 svn wget gitpython jinja2 pycurl netcdf4

Terms of Use & License Agreement🔗

Before using this software, the user must agree to the license given by the LICENSE file in the project's repository.

This software can be used free of charge.

3. Download & Installation🔗

Then change to the directory where you want to keep your local copy of this project, e.g. your $HOME directory and clone it:

git clone git@github.com:immerse-project/nemo-simsar.git

In order to use the tools from the SIMSAR package, make sure, the full path to nemo-simsar/bin is part of your $PATH environment variable:

EXAMPLE: Prepending to $PATH

# bash-like shell:

export PATH=/path/to/nemo-simsar/bin:${PATH}

# or csh:

setenv PATH /path/to/nemo-simsar/bin:${PATH}

Updates🔗

Go into your local copy of the nemo-simsar repository and run git fetch and review any changes before merging manually. See the git documentation on git-fetch for details.

git fetch

Or, if you're inclined to merge any changes immediately into your local repository, just run a git pull (see git-pull manual):

git pull

4. Usage🔗

Please read the User Guide for further instructions how to use SIMSAR since it does not only consist of one single program but is a collection of recipes with a few tools to assist the user. The Introduction tells you about the background and how to use SIMSAR. The Getting Started section provides step-by-step instructions.

Testing🔗

Currently, there is no testing implemented.

5. Documentation🔗

See the User Guide in the docs/ folder of this project or visit the webpage nemo-simsar.

6. Support🔗

There is only a limited support during the introduction phase of this package. Please, use the issue reporting on GitHub.

7. Contributing🔗

Please use the collaboration tools provided for the GitHub project IMMERSE-project/nemo-simsar.