Setup docker compose to construct end-to-end container workflow

[glemieux]

Ideally we would like to have the users (and developers) simply run a single command to set up both the fates container, the jupyter container, and connect the two. Automating this with docker compose would help us avoid issues during setup due to users conducting operations out of order manually.

Tasks

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1. docker-compose.yml
2. run compose up and down test
3. How do I keep the elm-fates container running?
4. Address Figure out why jupyter only launches from the http://127.0.0.1:8888 option tutorial-containers#4 (comment)
5. How do I launch jupyter if docker compose is run in detached mode?
6. test sharing output across data volume
7. Update elm-fates container to contain cime
8. Restructure where the docker compose scripts will be mounted relative to the tutorial and container repos
9. Add case scripts to the container (via COPY or WGET)
10. Update jupyter dockerfile to connect to shared volumes #23
    +0
11. Determine why container notebook saves to local host with a weird user id and group (linux only) #29
    OS: Linux permissions +2
12. Develop workflow and documentation for jupyter token tutorial-containers#5
    +0
13. (Optional) setup development container: https://containers.dev/overview
14. Develop script to launch jupyter lab #43
    3 of 3
    enhancement +1

Current process is as follows:

1. Update env-template file with local folders and rename to .env
2. docker compose up -d: use compose to start both containers in detached mode
3. docker exec tutorial-notebook jupyter server list to expose the jupyter url to enable launching it
4. docker exec -it elm-fates /bin/bash to enter interactive shell with the host land model and fates

[glemieux]

The initial docker compose up test successfully started the containers, so I have the formatting correct currently. That said the following issues need to be addressed (added to tasks above):

• The elm-fates container doesn't stay running. I think I need to set an attribute to make sure it stays up.
• Figure out why jupyter only launches from the http://127.0.0.1:8888 option tutorial-containers#4 (comment) is presenting itself as a problem.

[glemieux]

I needed to add tty to keep the elm-fates container running. I haven't found a definitive answer, but it has been suggested that stdin_open: true is also necessary, although rudimentary tests seems to suggest this isn't necessarily true.

[glemieux]

Currently, I'm launching jupyter after running docker compose in detached mode by grabbing the last few lines of the docker log:

docker logs --tail 3 tutorial-notebook

This works as the url is being populated with the necessary token. It is possible to simply enter http://localhost:8888/ to launch, but then I need to enter the token. It is also possible to simply click on the docker desktop port link:

New issue created to address tokens: NGEET/tutorial-containers#5

[glemieux]

During discussions with @JessicaNeedham I realized that we could move the docker compose files into the fates-tutorial repo. This will allow the users to simply download or clone the just the repo that is most relevant to them, i.e. the fates-tutorial repo. The docker compose file move is updated via #27.

[glemieux]

Added helper script launch_jupyter for windows and mac/linux machines per #43. There are still some outstanding issues, but the workflow is operational as is.