Containerisation of NEMO Employing Singularity (CoNES)

Getting Started

The CoNES repository was templated from Singularity Deploy

To generate a NEMO/XIOS Singularity Container please read the documentaion. What follows is a simplified quick-start guide:

If building locally is not an option then it is also possible to build and release Singularity containers using GitHub Actions. Singularity Deploy developed by Vanessa Sochat has been modified to allow users to fork the GitHub CoNES repository and, using GitHub Actions, build and release a bespoke NEMO singularity container.

The CoNES repository has been set up such that:

• the container is updated/developed via a branch
• the container build will be tested on a pull request
• a release will be triggered on merge into main

This workflow can easily be modified by altering:

• .github/workflows/test.yml for the testing of builds
• .github/workflows/builder.yml for the container release

An individual NEMO SIF build can be created using the following steps:

1. Fork the CoNES repository under USER account (main branch only is fine)
   Under the Actions tab enable workflows
   Under the Settings tab click through actions -> general and set workflow permissions to r+w and save
   Return to the code tab
2. Create a new branch
3. Edit the VERSION file to something approprate (e.g. 0.0.3)
   [Optional] Edit the inputs/NEMO_in namelist for NEMO version number, MPI choice etc.
4. Create a Pull Request from that branch to main. Make sure this is from USER/branch to USER/main and not to NOC-MSM/main.
   At this point a test build will be triggered, which can take ~15 minutes per MPI build requested
5. If successful the merge will be available. Click merge and ...
6. A NEMO SIF will be built and released under the version specified (again this can take ~15 minutes per MPI build requested).
7. The NEMO SIF and asscoiated assets will appear under the Releases tab.

The branch can now either be deleted or held open for further changes to NEMO_in and subsequent releases.

Note:

If the tag in the VERSION file is not incremented then a new release is not built.

To download the released NEMO SIF either use:

    wget -c https://github.com/MY_CoNES/releases/download/$VERSION/MY_CoNES.nemo.sif -o nemo.sif

or Singularity can also pull just knowing the URL. For example:

    singularity pull https://github.com/MY_CONES/releases/download/$VERSION/MY_CONES.nemo.sif