mlp w/ glu style gating #1043

Workflow file for this run

.github/workflows/docker_action.yml at c19fc43

	# docker_action.yml
	name: Docker-ubuntu-build

	on:
	push:
	branches:
	- '*'
	tags:
	- '*'
	pull_request:
	branches:
	- 'main'
	- 'develop'
	- 'releases/**'
	- 'release/**'
	- 'release'

	# only allow one copy of this workflow to run at a time (the group specified by workflow name)
	# cancel current workflows if they are running, so that we just run the latest queue'd.
	concurrency:
	group: ${{ github.workflow }}-${{ github.ref }}
	cancel-in-progress: true

	env:
	REGISTRY: ghcr.io
	IMAGE_NAME: ${{ github.repository }} # github.repository as <account>/<repo> "abcucberkeley/opticalaberrations"
	DO_SIGNING: ${{ false }}
	BRANCH: ${{ github.head_ref \|\| github.ref_name }} # 'latest-tf' or 'develop'
	PYTEST: python -m pytest --cache-clear -vvv --color=yes --disable-warnings

	jobs:
	cleanup-job:
	runs-on: self-hosted
	container:
	image: ghcr.io/catthehacker/ubuntu:act-22.04
	defaults:
	run:
	shell: bash
	steps:
	- name: 'Cleanup build folder'
	run: \|
	ls -la ./
	rm -rf ./* \|\| true
	rm -rf ./.??* \|\| true
	ls -la ./

	build-docker:
	needs: cleanup-job
	if: always()
	name: docker_image_build
	runs-on: self-hosted
	strategy:
	matrix:
	include:
	- CUDA_VERSION: "Torch_CUDA_12_3"
	- CUDA_VERSION: "TF_CUDA_12_3"
	steps:
	- name: Dump GitHub context
	env:
	GITHUB_CONTEXT: ${{ toJson(github) }}
	run: echo "$GITHUB_CONTEXT"
	- name: Dump job context
	env:
	JOB_CONTEXT: ${{ toJson(job) }}
	run: echo "$JOB_CONTEXT"
	- name: Dump steps context
	env:
	STEPS_CONTEXT: ${{ toJson(steps) }}
	run: echo "$STEPS_CONTEXT"
	- name: Dump runner context
	env:
	RUNNER_CONTEXT: ${{ toJson(runner) }}
	run: echo "$RUNNER_CONTEXT"

	- name: Show default environment variables
	run: \|
	echo "The job_id is: $GITHUB_JOB" # reference the default environment variables
	echo "The id of this action is: $GITHUB_ACTION" # reference the default environment variables
	echo "The run id is: $GITHUB_RUN_ID"
	echo "The GitHub Actor's username is: $GITHUB_ACTOR"
	echo "GitHub SHA: $GITHUB_SHA"

	# The repo gets volume mapped into the container automatically in test-docker
	- name: Checkout whole repo
	uses: actions/checkout@v4
	with:
	lfs: 'true'
	submodules: 'recursive'

	- name: List files in the repository
	run: \|
	ls -lhXR ${{ github.workspace }}

	- name: Set file permissions in the repository
	run: \|
	chmod -R 777 ${{ github.workspace }}
	ls -lhXR ${{ github.workspace }}

	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v3
	with:
	driver: docker

	# Login against a Docker registry except on PR
	# https://github.com/docker/login-action
	- name: Log into registry ${{ env.REGISTRY }}
	if: github.event_name != 'pull_request'
	uses: docker/login-action@v3
	with:
	registry: ${{ env.REGISTRY }} # aka ghcr.io
	username: ${{ github.actor }}
	password: ${{ secrets.GITHUB_TOKEN }}

	# Extract metadata (tags, labels) for Docker
	# https://github.com/docker/metadata-action
	- name: Extract Docker metadata
	id: meta
	uses: docker/metadata-action@v5
	with:
	images: ${{ env.REGISTRY }}/${{ github.repository }}
	labels: \|
	org.opencontainers.image.title=OpticalNet_ubuntu
	org.opencontainers.image.description=Docker image for a transformer network to perform sensorless detection of aberrations in adaptive optics. https://github.com/abcucberkeley/opticalaberrations
	org.opencontainers.image.vendor=Advanced Bioimaging Center at UC Berkeley and Janelia Research Campus
	tags: \|
	type=schedule
	type=ref,suffix=_${{ matrix.CUDA_VERSION }},event=branch
	type=ref,suffix=_${{ matrix.CUDA_VERSION }},event=tag
	type=ref,suffix=_${{ matrix.CUDA_VERSION }},event=pr

	- name: Build and push Docker image
	id: build-and-push
	uses: docker/build-push-action@v5
	with:
	context: .
	file: ./Dockerfile
	push: ${{ github.event_name != 'pull_request' }}
	tags: ${{ steps.meta.outputs.tags }}
	labels: ${{ steps.meta.outputs.labels }}
	build-args: \|
	BRANCH_NAME=${{ env.BRANCH }}
	target: ${{ matrix.CUDA_VERSION }}

	build-apptainer:
	needs: build-docker
	runs-on: self-hosted
	strategy:
	matrix:
	include:
	- CUDA_VERSION: "Torch_CUDA_12_3"
	- CUDA_VERSION: "TF_CUDA_12_3"
	steps:
	- name: List files in the directory
	run: \|
	ls -lhXR

	# Login against a Docker registry except on PR
	# https://github.com/docker/login-action
	- name: Log into registry ${{ env.REGISTRY }}
	if: github.event_name != 'pull_request'
	uses: docker/login-action@v3
	with:
	registry: ${{ env.REGISTRY }} # aka ghcr.io
	username: ${{ github.actor }}
	password: ${{ secrets.GITHUB_TOKEN }}

	- name: Pull latest docker
	run: \|
	docker pull ghcr.io/${{ github.repository }}:${{ github.head_ref \|\| github.ref_name }}_${{ matrix.CUDA_VERSION }}

	- name: Build Apptainer from local docker image we just pulled to a local .sif
	run: \|
	apptainer build --nv --force ${{ github.workspace }}/${{ github.head_ref \|\| github.ref_name }}_${{ matrix.CUDA_VERSION }}.sif docker-daemon:ghcr.io/${{ github.repository }}:${{ github.head_ref \|\| github.ref_name }}_${{ matrix.CUDA_VERSION }}

	- name: Login and Push Apptainer SIF to github
	run: \|
	ls .si
	apptainer remote login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io
	apptainer push ${{ github.workspace }}/${{ github.head_ref \|\| github.ref_name }}_${{ matrix.CUDA_VERSION }}.sif oras://ghcr.io/${{ github.repository }}:${{ github.head_ref \|\| github.ref_name }}_${{ matrix.CUDA_VERSION }}_sif

	# singularity push container.sif oras://ghcr.io/abcucberkeley/opticalaberrations:develop_sif
	# singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://${{ env.REGISTRY }}
	# apptainer pull --force --disable-cache develop.sif oras://ghcr.io/abcucberkeley/opticalaberrations:develop_sif

	test-apptainer:
	needs: build-apptainer
	runs-on: self-hosted
	strategy:
	matrix:
	include:
	- CUDA_VERSION: "TF_CUDA_12_3"
	test_framework: "tensorflow"
	- CUDA_VERSION: "Torch_CUDA_12_3"
	test_framework: "pytorch"
	fail-fast: false # do the other tests in the matrix even if one of them fails
	env:
	APPTAINER_RUN: apptainer exec --nv ${{ github.workspace }}/${{ github.head_ref \|\| github.ref_name }}_${{ matrix.CUDA_VERSION }}.sif
	steps:
	- name: investigate
	run: \|
	pwd
	id
	id -u
	ls -lhXR

	- name: pip list
	run: ${{ env.APPTAINER_RUN }} pip list

	- name: Test NVIDIA-SMI
	run: ${{ env.APPTAINER_RUN }} nvidia-smi

	- name: Test ${{ matrix.test_framework }}
	run: ${{ env.APPTAINER_RUN }} ${{ env.PYTEST }} ${{ github.workspace }}/tests/test_${{ matrix.test_framework }}.py

	- name: Test Cupy
	run: ${{ env.APPTAINER_RUN }} ${{ env.PYTEST }} ${{ github.workspace }}/tests/test_cupy.py

	- name: Test IO
	run: ${{ env.APPTAINER_RUN }} ${{ env.PYTEST }} ${{ github.workspace }}/tests/test_io.py

	- name: Test preprocessing
	run: ${{ env.APPTAINER_RUN }} ${{ env.PYTEST }} ${{ github.workspace }}/tests/test_preprocessing.py

	- name: Test embeddings
	run: ${{ env.APPTAINER_RUN }} ${{ env.PYTEST }} ${{ github.workspace }}/tests/test_embeddings.py

	- name: Test synthetic datasets
	run: ${{ env.APPTAINER_RUN }} ${{ env.PYTEST }} ${{ github.workspace }}/tests/test_datasets.py

	- name: Test AO # requires test data generated by previous step: Test synthetic datasets. Seems to fail on aggregate_rois plotting. Try this in a separate call.
	run: ${{ env.APPTAINER_RUN }} ${{ env.PYTEST }} --deselect=tests/test_ao.py::test_aggregate_rois ${{ github.workspace }}/tests/test_ao.py

	- name: Test aggregate_rois
	run: ${{ env.APPTAINER_RUN }} ${{ env.PYTEST }} ${{ github.workspace }}/tests/test_ao.py::test_aggregate_rois

	test_train-apptainer:
	strategy:
	matrix:
	include:
	- CUDA_VERSION: "TF_CUDA_12_3"
	- CUDA_VERSION: "Torch_CUDA_12_3"
	needs: test-apptainer # need to wait for test-docker to finish otherwise GPU will be utilized.
	runs-on: self-hosted
	env:
	APPTAINER_RUN: apptainer exec --nv ${{ github.workspace }}/${{ github.head_ref \|\| github.ref_name }}_${{ matrix.CUDA_VERSION }}.sif
	steps:
	- name: Test training
	run: ${{ env.APPTAINER_RUN }} ${{ env.PYTEST }} ${{ github.workspace }}/tests/test_train.py

	# cleanup-job2:
	# runs-on: self-hosted
	# needs: test_train-apptainer # needs to run after apptainer because this is going to write root files.
	# container:
	# image: ghcr.io/catthehacker/ubuntu:act-22.04
	# defaults:
	# run:
	# shell: bash
	# steps:
	# - name: 'Cleanup build folder'
	# run: \|
	# ls -la ./
	# rm -rf ./* \|\| true
	# rm -rf ./.??* \|\| true
	# ls -la ./

	# setup-job2:
	# needs: cleanup-job2
	# runs-on: self-hosted
	# steps:
	# # The repo gets volume mapped into the container automatically in test-docker
	# - name: Checkout whole repo
	# uses: actions/checkout@v4
	# with:
	# lfs: 'true'
	# submodules: 'recursive'

	# - name: List files in the repository
	# run: \|
	# ls -lhXR ${{ github.workspace }}

	# - name: Set file permissions in the repository
	# run: \|
	# chmod -R 777 ${{ github.workspace }}
	# ls -lhXR ${{ github.workspace }}

	# test-docker:
	# needs: setup-job2 # needs to run after apptainer because this is going to write root files.
	# runs-on: self-hosted
	# strategy:
	# matrix:
	# include:
	# - CUDA_VERSION: "TF_CUDA_12_3"
	# container:
	# image: ghcr.io/${{ github.repository }}:${{ github.head_ref \|\| github.ref_name }}_${{ matrix.CUDA_VERSION }} # pull image 'latest-tf' or 'develop' that we just built
	# credentials:
	# username: ${{ github.actor }}
	# password: ${{ secrets.GITHUB_TOKEN }}
	# ports:
	# - 80
	# options: --gpus all --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 # --user 1000 Needs to run as 'root' not 'vscode' for cupy cache to work.
	# defaults:
	# run:
	# shell: bash
	# steps:
	# - name: investigate
	# run: \|
	# pwd
	# id
	# id -u
	# ls -lhXR

	# - name: pip list
	# run: pip list

	# - name: Test NVIDIA-SMI
	# run: nvidia-smi

	# - name: Test TensorFlow
	# run: ${{ env.PYTEST }} tests/test_tensorflow.py

	# - name: Test Cupy
	# run: ${{ env.PYTEST }} tests/test_cupy.py

	# - name: Test IO
	# run: ${{ env.PYTEST }} tests/test_io.py

	# - name: Test preprocessing
	# run: ${{ env.PYTEST }} tests/test_preprocessing.py

	# - name: Test embeddings
	# run: ${{ env.PYTEST }} tests/test_embeddings.py

	# - name: Test synthetic datasets
	# run: ${{ env.PYTEST }} tests/test_datasets.py

	# - name: Test AO # requires test data generated by previous step: Test synthetic datasets
	# run: ${{ env.PYTEST }} tests/test_ao.py

	# test_train-docker:
	# needs: test-docker
	# runs-on: self-hosted
	# strategy:
	# matrix:
	# include:
	# - CUDA_VERSION: "TF_CUDA_12_3"
	# container:
	# image: ghcr.io/${{ github.repository }}:${{ github.head_ref \|\| github.ref_name }}_${{ matrix.CUDA_VERSION }} # pull image 'latest-tf' or 'develop' that we just built
	# credentials:
	# username: ${{ github.actor }}
	# password: ${{ secrets.GITHUB_TOKEN }}
	# ports:
	# - 80
	# options: --gpus all --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 # --user 1000 Needs to run as 'root' not 'vscode' for cupy cache to work.
	# defaults:
	# run:
	# shell: bash
	# steps:
	# - name: Test training
	# run: ${{ env.PYTEST }} tests/test_train.py


	# build-native-apptainer:
	# needs: build-docker
	# if: always()
	# runs-on: self-hosted
	# strategy:
	# matrix:
	# include:
	# - CUDA_VERSION: "TF_CUDA_12_3"
	# steps:
	# # Login against a Docker registry except on PR
	# # https://github.com/docker/login-action
	# - name: Log into registry ${{ env.REGISTRY }}
	# if: github.event_name != 'pull_request'
	# uses: docker/login-action@v3
	# with:
	# registry: ${{ env.REGISTRY }} # aka ghcr.io
	# username: ${{ github.actor }}
	# password: ${{ secrets.GITHUB_TOKEN }}

	# - name: Build Apptainer from Recipe to a local .sif
	# run: \|
	# apptainer build --nv --force --build-arg BRANCH_NAME=${{ env.BRANCH }} ${{ github.workspace }}/${{ github.head_ref \|\| github.ref_name }}_${{ matrix.CUDA_VERSION }}_native.sif Apptainerfile_${{ matrix.CUDA_VERSION }}

	# - name: Login and Push Apptainer SIF to github
	# run: \|
	# ls .si
	# apptainer remote login --username ${{ github.actor }} --password ${{ secrets.GITHUB_TOKEN }} oras://ghcr.io
	# apptainer push ${{ github.workspace }}/${{ github.head_ref \|\| github.ref_name }}_${{ matrix.CUDA_VERSION }}_native.sif oras://ghcr.io/${{ github.repository }}:${{ github.head_ref \|\| github.ref_name }}_${{ matrix.CUDA_VERSION }}_native_sif

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

mlp w/ glu style gating #1043

Workflow file

mlp w/ glu style gating #1043

Jobs

Run details

Workflow file for this run