New docker image based on pure ubuntu and gracefully handle services #6080

unkcpz · 2023-07-10T10:09:39Z

Supercede #6072

Details are described in aiidateam/AEP#39
I commend on the PR for some technical details and the link to s6 toolkit.

The PR is from aiidateam directly so the push to ghcr.io can be triggered. I also set the arm64 test only triggered from PR from aiidateam to prevent the cost from malicious PRs from the forked repository.

CI tests
Clean up the environment variable pass to the s6-overlay startup scripts.
iron-up
Update the documentation of using docker to run aiida.

codecov · 2023-07-10T10:37:15Z

Codecov Report

Patch coverage has no change and project coverage change: +0.07% 🎉

Comparison is base (4e0e7d8) 79.64% compared to head (a399e21) 79.71%.
Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #6080      +/-   ##
==========================================
+ Coverage   79.64%   79.71%   +0.07%     
==========================================
  Files         546      546              
  Lines       39811    39987     +176     
==========================================
+ Hits        31704    31870     +166     
- Misses       8107     8117      +10

see 4 files with indirect coverage changes

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unkcpz · 2023-07-10T16:00:14Z

I push the image to ghcr.io, to test the PR image, just run:

docker run -it ghcr.io/aiidateam/aiida-core:pr-6080 bash

pyproject.toml

.github/workflows/docker.yml

unkcpz · 2023-07-16T21:14:26Z

.docker/README.md

+All commands `build`, `tests`, and `up` will use the locally detected platform and use a version tag based on the state of the local git repository.
+However, you can also specify a custom platform or version with the `--platform` and `--version` parameters, example: `doit build --arch=amd64 --version=my-version`.
+
+You can specify target stacks to build with `--target`, example: `doit build --target base --target base`.


The doit not only used for local build and test, but it is the command run on the CI action directly.

To see how it works in CI, you can run this command locally from .docker folder.

.docker/base-with-services/Dockerfile

unkcpz · 2023-07-16T21:16:30Z

.docker/base-with-services/Dockerfile

+
+RUN mamba install --yes \
+     --channel conda-forge \
+     postgresql=${PGSQL_VERSION} && \


postgresql is installed from conda forge to avoid the version may not exist from apt repo.

unkcpz · 2023-07-16T21:18:49Z

.docker/base-with-services/Dockerfile

+# Install erlang.
+RUN apt-get update --yes && \
+     apt-get install --yes --no-install-recommends \
+     erlang \


It is tricky to install the correct RMQ version because the erlang version needs to compatible with the final rabbitmq version as shown in https://www.rabbitmq.com/which-erlang.html

.docker/base-with-services/s6-assets/init/postgresql-prepare.sh

.docker/base/Dockerfile

.docker/dodo.py

unkcpz · 2023-07-16T21:36:20Z

Hi @sphuber, I update the AEP with the details. Let me know if any more information is needed.

sphuber · 2023-09-04T10:02:13Z

Is this fully ready for final review @unkcpz . I notice the tests are not yet passing?

unkcpz · 2023-09-04T12:08:40Z

Is this fully ready for final review @unkcpz . I notice the tests are not yet passing?

Hi @sphuber, yes it is ready to review. I also rebase the commits to every commit are specific to one task.
The failed tests were from rabbitmq test, the changes have nothing to do with it, I rebased so should all be fine now.

Edit: now the test failed for install CI test and seems caused by pymatgen?

sphuber · 2023-09-04T12:43:54Z

The test-install tests still fail. Two out of three failures seem to be due to a new pymatgen version released two days ago.

The third failure is not (necessarily) related to that. I have seen it before in my branch where I am introducing the pydantic dependency. Somehow, this affects the test that tries to unload the profile, which now somehow holds on to a reference of the backend. I have no clue what is causing this or how to fix it. I have lost many an hour trying to debug this already...

sphuber · 2023-09-04T13:24:58Z

Here is the culprit: materialsproject/pymatgen@118c245
Apparently, properties was deprecated for Specie.

sphuber · 2023-09-04T14:10:44Z

@unkcpz I have a tentative fix for the pymatgen problems in #6109. Could you please squash your commits on this branch into one and then rebase on that branch to see if it fixes the tests. In my PR I don't think the relevant workflow is triggered.

unkcpz · 2023-09-04T15:24:36Z

Could you please squash your commits on this branch into one and then rebase on that branch to see if it fixes the tests. In my PR I don't think the relevant workflow is triggered.

Yes, done! But seems #6109 still fails with those three tests.

sphuber · 2023-09-05T06:33:12Z

Yes, done! But seems #6109 still fails with those three tests.

No, there is just one test remaining. The two related to pymatgen are fixed, but as I already explained above, the third one is not related and I have no clue what causes it.

unkcpz · 2023-09-05T08:56:51Z

I see. But it is strange to me why pre-commit CI in #6109 is not failed but failed in this PR? It also has the old pymatgen version installed (python3.9).

sphuber · 2023-09-05T10:22:32Z

But it is strange to me why pre-commit CI in #6109 is not failed but failed in this PR?

It also failed in my PR originally, but I fixed it. The problem is that since we are now using API of two different versions, pylint will complain for the syntax of the version that is not installed. So we need to add disable statements for both versions of the API.

sphuber

Thanks @unkcpz . I have added some initial comments. I have also commented on the AEP with a question on the image names. Let's discuss that there first, before we start changing it here.

.github/workflows/docker-push.yml

.github/workflows/docker-merge-tags.yml

.github/workflows/docker-build-test-upload.yml

.github/actions/load-image/action.yml

.github/actions/create-dev-env/action.yml

.github/workflows/docker.yml

docs/source/intro/run_docker.rst

.github/workflows/docker-build-test-upload.yml

Minimal working version of the basic docker image build locally base image can run First working with-service stack adapt dodo script to build for correct arch Use mamba image back again workable s6-overlay solution Properly tear down the aiida daemon Fixes CI test pass locally fix env variable in s6 scripts suppress dev version warning [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci push ghcr only when it is pull request form org upload artifact which is time consuming only for PR from org Add a CI action only for container build not run some container action from fork Add doc for the docker build and how to use the new docker stack Fixes the package permission pre-commit fix - pg log to home folder Fixes CI errors [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Update pyproject.toml Update .github/workflows/docker.yml exclude .docker files from yapf and pylint Update .docker/dodo.py With git, vim, ssh client pre-installed more doc on how to start the exist container Add .local/bin to PATH for packages install by user Pin PyYAML<5.3 Looks like the particular issue is caused by a new release of Cython which breaks PyYAML builds. yaml/pyyaml#724 yaml/pyyaml#724 Pinning PyYAML to earlier version seems to do the trick for now... Remove doit but use docker baked directly Rename image to aiida-core-base and aiida-core-with-services

.docker/aiida-core-with-services/Dockerfile

sphuber

Great stuff, thanks a lot @unkcpz

The current Docker image provided with `aiida-core` depends on `aiida-prerequisites` as a base image. This image is maintained outside of the `aiida-core` repo, making it additional maintenance to keep it up to date when a new `aiida-core` version is released. In addition, the `aiida-prerequisites` image is no longer maintained because the AiiDAlab stack now depends on another base image. Finally, the `aiida-prerequisites` design had shortcomings as to how the required services, PostgreSQL and RabbitMQ, are handled. They had to be started manually and were not cleanly stopped on container shutdown. An AEP was submitted to add two Docker images to `aiida-core` that simplifies their maintenance and that improve the usability by properly and automatically handling the services. See the AEP for more details: https://aep.readthedocs.io/en/latest/009_improved_docker_images/readme.html Cherry-pick: 9e80834

unkcpz changed the title ~~Docker stack~~ New docker image based on pure ubuntu and gracefully handle services Jul 10, 2023

unkcpz marked this pull request as draft July 10, 2023 10:10

unkcpz mentioned this pull request Jul 10, 2023

New docker image based on pure ubuntu and gracefully handle services #6072

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unkcpz force-pushed the docker-stack branch 5 times, most recently from d4f6c9d to 564c2c0 Compare July 10, 2023 15:49

unkcpz marked this pull request as ready for review July 10, 2023 16:00

unkcpz force-pushed the docker-stack branch from 38485c0 to 12b59cc Compare July 10, 2023 19:12

unkcpz commented Jul 10, 2023

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unkcpz force-pushed the docker-stack branch from 16d0e2f to fea9398 Compare July 10, 2023 21:48

unkcpz mentioned this pull request Jul 11, 2023

Improve documentation on how to customize the user environment aiidalab/aiidalab-docker-stack#250

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unkcpz commented Jul 16, 2023

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unkcpz requested a review from sphuber July 16, 2023 21:36

unkcpz mentioned this pull request Aug 14, 2023

Shutdown verdi daemon gracefully upon container shutdown aiidalab/aiidalab-launch#180

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unkcpz force-pushed the docker-stack branch 7 times, most recently from 7b2976a to cd02a89 Compare September 4, 2023 11:55

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unkcpz force-pushed the docker-stack branch 2 times, most recently from a9191d2 to df6aece Compare September 6, 2023 11:49

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unkcpz force-pushed the docker-stack branch from 25f58e2 to 9357153 Compare September 7, 2023 19:23

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sphuber self-requested a review September 8, 2023 09:33

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sphuber merged commit 9e80834 into main Sep 8, 2023
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sphuber deleted the docker-stack branch September 8, 2023 09:34

unkcpz mentioned this pull request Sep 27, 2023

DevOps: devcontainer update to use new docker stack #6139

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unkcpz mentioned this pull request Oct 16, 2023

Remove build and publish base and base-with-services to registry aiidalab/aiidalab-docker-stack#412

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New docker image based on pure ubuntu and gracefully handle services #6080

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New docker image based on pure ubuntu and gracefully handle services #6080

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