feat: Add Pixi Docker example #38

matthewfeickert · 2025-11-15T04:23:50Z

Resolves #36

Add example of using a Pixi environment distributed in a Docker container image.
- Link to 'Reproducible Machine Learning Workflows for Scientists' Carpentries Incubator lesson for CI/CD workflow example.
Add note in pixi/ example that the containers/pixi example provides a recommended approach.

Requires PR #37 to go in first.

matthewfeickert

High-level comments for reviewers.

matthewfeickert · 2025-11-15T07:29:47Z

containers/pixi/mnist_gpu.sh

+# As main.py is copied to the worker through transfer_input_files, it is not
+# located in the same directory as the Pixi manifest (/app/pixi.toml).
+# To avoid moving files around further or complicating the HTCondor submit
+# description file have the command written out here instead of using a Pixi
+# task.
+time pixi run python ./main.py --epochs 20 --save-model


This is just explaining why in the pixi/ example we can use the Pixi task runner system

templates-GPUs/pixi/mnist_gpu.sh

Line 33 in 8db14b2

time pixi run train

but here we give the command explicitly.

matthewfeickert · 2025-11-15T07:30:35Z

containers/pixi/mnist_gpu_docker.sub

+universe = container
+# To avoid excessive pulls, and potential rate limits, set as "missing" (default value)
+docker_pull_policy = missing
+container_image = docker://ghcr.io/<your github org>/templates-gpu:mnist-gpu-noble-cuda-12.9


I prepared such an image already, so if you want to test this you can use

container_image = docker://ghcr.io/matthewfeickert/templates-gpu:mnist-gpu-noble-cuda-12.9

containers/pixi/README.md

matthewfeickert · 2025-11-15T07:34:54Z

containers/pixi/README.md

+```
+
+Note that this manual build and publish process is slow.
+It is recommended to have this step be done through a continuous integration and continuous delivery (CI/CD) workflow.


I used the following GitHub Actions workflow to build my container image.

.github/workflows/docker.yml:

name: Docker Images on: push: branches: - main tags: - 'v*' paths: - 'containers/pixi/pixi.toml' - 'containers/pixi/pixi.lock' - 'containers/pixi/Dockerfile' - 'containers/pixi/.dockerignore' pull_request: paths: - 'containers/pixi/pixi.toml' - 'containers/pixi/pixi.lock' - 'containers/pixi/Dockerfile' - 'containers/pixi/.dockerignore' release: types: [published] workflow_dispatch: concurrency: group: ${{ github.workflow }}-${{ github.ref }} cancel-in-progress: true permissions: {} jobs: docker: name: Build and publish images runs-on: ubuntu-latest permissions: contents: read packages: write steps: - name: Free disk space uses: AdityaGarg8/remove-unwanted-software@v5 with: remove-android: 'true' remove-dotnet: 'true' remove-haskell: 'true' - name: Checkout uses: actions/checkout@v5 with: fetch-depth: 0 - name: Docker meta id: meta uses: docker/metadata-action@v5 with: # images: | # ghcr.io/chtc/templates-gpu images: | ghcr.io/matthewfeickert/templates-gpu # generate Docker tags based on the following events/attributes tags: | type=raw,value=mnist-gpu-noble-cuda-12.9 type=raw,value=latest type=semver,pattern={{version}} type=semver,pattern={{major}}.{{minor}} type=sha - name: Set up QEMU uses: docker/setup-qemu-action@v3 - name: Set up Docker Buildx uses: docker/setup-buildx-action@v3 - name: Login to GitHub Container Registry if: github.event_name != 'pull_request' uses: docker/login-action@v3 with: registry: ghcr.io username: ${{ github.repository_owner }} password: ${{ secrets.GITHUB_TOKEN }} - name: Test build id: docker_build_test uses: docker/build-push-action@v6 with: context: containers/pixi file: containers/pixi/Dockerfile tags: ${{ steps.meta.outputs.tags }} labels: ${{ steps.meta.outputs.labels }} pull: true - name: Deploy build id: docker_build_deploy uses: docker/build-push-action@v6 with: context: containers/pixi file: containers/pixi/Dockerfile tags: ${{ steps.meta.outputs.tags }} labels: ${{ steps.meta.outputs.labels }} pull: true push: ${{ github.event_name != 'pull_request' }}

I assumed that adding CI for this template repo isn't of interest, but if it is, I can add something.

Yeah, I think that it's beyond the scope of this repo, but I think linking out to an example setup or general documentation is fine to plant some seeds.

Do you want the readme to point to #38 (comment) to plant that seed?

@agitter I was going to point to https://carpentries-incubator.github.io/reproducible-ml-workflows/pixi-deployment.html#automation-with-github-actions-workflows. I have that staged, but haven't pushed yes as am waiting on clarification on #38 (comment).

Thoughts?

That would be a better pointer than this thread

matthewfeickert · 2025-11-15T07:35:22Z

pixi/README.md

 > While this approach does work, as there is no shared file system cache that Pixi can leverage it is less efficient than building a Linux container with the Pixi environment and using a `container` universe job.
 > Note also that as the jobs executable, `mnist_gpu.sh`, is installing all dependencies from a remote conda channel (conda-forge), multiple copies of the job should not be submitted to avoid intensive bandwidth demand.
+>
+> Look at the example in the [`containers/pixi`](https://github.com/CHTC/templates-GPUs/tree/master/containers/pixi) directory for the recommended approach for use of Pixi with HTCondor systems with no shared file system.


Noting now that there is a more recommended approach using Linux containers.

matthewfeickert · 2025-11-15T07:37:31Z

This is ready for review now. Following #37 (comment), @iross @ChristinaLK, if you have any questions or comments let me know. 👍

(CHTC Office hours have been a bit difficult for me to call into lately given conflicting meetings, but I can try to join them if it helps to discuss anything.)

containers/pixi/README.md

matthewfeickert · 2025-11-20T18:53:51Z

👋 Ping to @iross @ChristinaLK for review. Also happy to close this and move things to https://github.com/CHTC/recipes depending on feedback on CHTC/recipes#29.

matthewfeickert · 2025-12-03T18:06:33Z

(Rebase and force-push was from upgrading and relocking the environment — not necessary, but might as well keep this updated until merge.)

matthewfeickert · 2025-12-03T18:10:11Z

cc @xamberl given CHTC/recipes#29 (comment) (thanks!).

iross

The only thing I feel is really necessary before merge is an explanation of the entrypoint pieces with a beginner audience in mind.

iross · 2025-12-17T16:18:00Z

containers/pixi/Dockerfile

+
+FROM ghcr.io/prefix-dev/pixi:noble AS build
+
+# Redeclaring ARGS in a stage without a value inherits the global default


This tripped me up for longer than I'd like to admit on something I was working on earlier this week 😆

iross · 2025-12-17T16:30:23Z

containers/pixi/README.md

+```
+
+Note that this manual build and publish process is slow.
+It is recommended to have this step be done through a continuous integration and continuous delivery (CI/CD) workflow.


Yeah, I think that it's beyond the scope of this repo, but I think linking out to an example setup or general documentation is fine to plant some seeds.

containers/pixi/mnist_gpu_docker.sub

containers/pixi/README.md

containers/pixi/Dockerfile

* Add example of using a Pixi environment distributed in a Docker container image. - Link to 'Reproducible Machine Learning Workflows for Scientists' Carpentries Incubator lesson for CI/CD workflow example. * Add note in pixi/ example that the containers/pixi example provides a recommended approach.

matthewfeickert

Some high-level notes for @iross following his review feedback. 👍

containers/pixi/Dockerfile

containers/pixi/mnist_gpu_docker.sub

containers/pixi/README.md

matthewfeickert · 2026-01-05T19:45:01Z

@iross just bumping this in 2026 as I know that I have a plethora of emails and GitHub notifications that have piled up in the liminal weeks at the end of 2025, and I assume you do as well. :P

iross

👍

agitter mentioned this pull request Nov 15, 2025

chore: Rename 'docker' directory to 'containers' #37

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matthewfeickert force-pushed the feat/add-pixi-docker-example branch from e31a1aa to d7eb5f2 Compare November 15, 2025 07:27

matthewfeickert marked this pull request as ready for review November 15, 2025 07:27

matthewfeickert force-pushed the feat/add-pixi-docker-example branch 2 times, most recently from 0e49408 to 22ee4ca Compare November 15, 2025 07:31

matthewfeickert commented Nov 15, 2025

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This was referenced Nov 18, 2025

Target repositories for GPU based workflow recipes? CHTC/recipes#29

Closed

Add PyTorch recipes CHTC/recipes#28

Merged

Update conda-pytorch recipes CHTC/recipes#30

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matthewfeickert force-pushed the feat/add-pixi-docker-example branch from ffcadd4 to bd8dabe Compare December 3, 2025 18:05

iross self-requested a review December 12, 2025 02:50

iross self-assigned this Dec 12, 2025

iross reviewed Dec 17, 2025

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matthewfeickert mentioned this pull request Dec 17, 2025

fix: Correct repository name to 'templates-GPUs' #39

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matthewfeickert commented Dec 17, 2025

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matthewfeickert force-pushed the feat/add-pixi-docker-example branch from bd8dabe to 4800eaf Compare December 19, 2025 09:47

matthewfeickert commented Dec 19, 2025

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matthewfeickert requested a review from iross December 19, 2025 09:55

iross approved these changes Jan 5, 2026

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iross merged commit 80df2e3 into CHTC:master Jan 5, 2026

matthewfeickert deleted the feat/add-pixi-docker-example branch January 5, 2026 23:47

matthewfeickert mentioned this pull request Jan 6, 2026

feat: Add Pixi Apptainer example #40

Open


		FROM ghcr.io/prefix-dev/pixi:noble AS build

		# Redeclaring ARGS in a stage without a value inherits the global default

feat: Add Pixi Docker example #38

feat: Add Pixi Docker example #38

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