Docker ci build

[TomMelt]

Nextsim CI **now with added Docker**

This PR mainly pertains to the ubuntu build of the code.

Previously the CI workflow built nextsim using a GitHub VM instance that would apt install basic dependencies required for the build process.

However, with the addition of xios (#496 ) this is no longer a tractable solution. Furthermore, it would take ~15 mins just to build xios before then going on to build nextsim.

Now I have created a Dockerfile and associated pre-built image (currently on my Dockerhub: tommelt/nextsimdg-dev-env:with-xios) which contains all the prerequisites to build and test the code for our typical CI workflow.

In theory it could also be repurposed by developers as a dev environment (although I personally don't love this).

more about the dockerfile

The Dockerfile is based on a spack environment file (spack.yaml) was generated originally using the following command:

spack containerize > Dockerfile

However, I needed to make some manual adjustments to the Dockerfile (necessary for installing xios and some other dependencies).

Dockerfiles/Dockerfile is the one that was used to generate the docker image tommelt/nextsimdg-dev-env:with-xios.

The image is 2.41GB and contains all prerequisites for MPI and XIOS. When uploaded to dockerhub (docker push tommelt/nextsimdg-dev-env:with-xios) it is compressed to 625.97 MB.

benefits of Docker in CI

• It's fast
  • only takes 45s to download the image and then 150s to build nextsim :fire:
  • a full CI (for ubuntu) is now less than 4 minutes -- building XIOS alone used to take ~15 minutes
• It's reproducible
  • one of the problems of github CI is it's hard to debug when things don't work
  • you can now pull the docker image (docker pull tommelt/nextsimdg-dev-env:with-xios) and test stuff locally
• It's easy
  • nextsim is necessarily adding complexity, which increases the required dependencies
  • the docker image can be built with all dependencies ready-to-go

Changes to the parallel (MPI) test naming convention

• There was only one existing MPI test before I added the xios one (testRectGrid_MPI).
• I think it would be sensible to name all MPI tests something like testname_MPIX where X = the number of ranks the test should be run with
• This is required because doctest specifies minimum/maximum numbers of procs for the test to run. A test that requires 2 procs to run, run with 1 MPI proc instead will "pass" but with a message like "test skipped". This is not a situation we want to end up i.e., thinking our tests pass when they have actually not been run.

To Do:

• [x] TM to add docker image to github container registry
• [x] ~@timspainNERSC to fix MacOS build.~ I tried to fix MPI/xios build on mac (using tmate plugin to debug github action live) but the fix requires a lot of effort. (Compiling most/all dependencies from source) and it may not be worth it. We could consider not running the MPI/xios tests on mac? For now I have simply disabled MPI and XIOS on the mac build. One other work around would be create a dedicated spack build cache. (decided to not run tests for MPI/XIOS build on mac)
• [x] add instructions to build the docker image (docker build .)
• [x] add documentation around new docker image
• [x] rebase to include Kacpers latest changes and Tim's fix of mac build
• [x] ~should we keep existing docker images? or "rebase" them? or just have one with all dependencies and users can build their own version of nextsim to meet their needs?~ dev environment build is sufficient for now.
• [x] move pre-built image to nextsim dockerhub repo (do we have a NextSim docker account yet?)