Update notebooks to work with latest version of the precompiled Colab environment #1547

Workflow file for this run

.github/workflows/docker-ci.yml at b746558

	name: Docker CI

	on:
	push:
	branches:
	- main
	- trunk-merge/**
	paths-ignore:
	- "README.md"
	- "docs/*"
	pull_request:
	branches:
	- main
	paths-ignore:
	- "README.md"
	- "docs/*"

	workflow_dispatch:

	jobs:
	build:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v3
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v2
	- name: Build and export
	uses: docker/build-push-action@v3
	with:
	context: .
	tags: pysages:latest
	outputs: type=docker,dest=/tmp/pysages.tar
	- name: Upload artifact
	uses: actions/upload-artifact@v3
	with:
	name: pysages
	path: /tmp/pysages.tar
	retention-days: 1

	forward-flux-sampling:
	runs-on: ubuntu-latest
	needs: build
	steps:
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v2
	- name: Download artifact
	uses: actions/download-artifact@v3
	with:
	name: pysages
	path: /tmp
	- name: Load and run test
	run: \|
	SCRIPT="cd PySAGES/examples/openmm &&"
	SCRIPT="${SCRIPT} python3 forward_flux_sampling.py "
	SCRIPT="${SCRIPT} --cv-start=80 --cv-distance=2 --window-number=2 --sampling-steps=50 --replicas=5"
	docker load --input /tmp/pysages.tar
	docker run -t pysages bash -c "${SCRIPT}"

	abf-alanine-dipeptide-openmm:
	runs-on: ubuntu-latest
	needs: build
	steps:
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v2
	- name: Download artifact
	uses: actions/download-artifact@v3
	with:
	name: pysages
	path: /tmp
	- name: Load and run test
	run: \|
	docker load --input /tmp/pysages.tar
	docker run -t pysages bash -c "cd PySAGES/examples/openmm/abf/ && python3 ./alanine-dipeptide_openmm.py"

	spectral-abf-alanine-dipeptide-openmm:
	runs-on: ubuntu-latest
	needs: build
	steps:
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v2
	- name: Download artifact
	uses: actions/download-artifact@v3
	with:
	name: pysages
	path: /tmp
	- name: Load and run test
	run: \|
	SCRIPT="cd PySAGES/examples/openmm/spectral_abf &&"
	SCRIPT="${SCRIPT} python3 ./alanine-dipeptide.py --time-steps=25"
	docker load --input /tmp/pysages.tar
	docker run -t pysages bash -c "${SCRIPT}"

	abf-tip3p-water-ase:
	runs-on: ubuntu-latest
	needs: build
	steps:
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v2
	- name: Download artifact
	uses: actions/download-artifact@v3
	with:
	name: pysages
	path: /tmp
	- name: Load and run test
	run: \|
	docker load --input /tmp/pysages.tar
	docker run -t pysages bash -c "cd PySAGES/examples/ase/abf/ && python3 ./water.py"

	metad-alanine-dipeptide-openmm:
	runs-on: ubuntu-latest
	needs: build
	steps:
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v2
	- name: Download artifact
	uses: actions/download-artifact@v3
	with:
	name: pysages
	path: /tmp
	- name: Load and run test
	run: \|
	docker load --input /tmp/pysages.tar
	docker run -t pysages bash -c "cd PySAGES/examples/openmm/metad/ && python3 ./alanine-dipeptide.py --time-steps=25"

	alanine-dipeptide-openmm-mpi:
	runs-on: ubuntu-latest
	needs: build
	steps:
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v2
	- name: Download artifact
	uses: actions/download-artifact@v3
	with:
	name: pysages
	path: /tmp
	- name: Load and run test
	run: \|
	SCRIPT="cd PySAGES/examples/openmm/umbrella_integration &&"
	SCRIPT="${SCRIPT} mpirun --allow-run-as-root --oversubscribe -n 6"
	SCRIPT="${SCRIPT} python3 -m mpi4py.futures"
	SCRIPT="${SCRIPT} integration.py --replicas=5 --time-steps=1000 --mpi"
	docker load --input /tmp/pysages.tar
	docker run --privileged -t pysages bash -c "${SCRIPT}"

	cv-pucker-openmm-unbiased:
	runs-on: ubuntu-latest
	needs: build
	steps:
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v2
	- name: Download artifact
	uses: actions/download-artifact@v3
	with:
	name: pysages
	path: /tmp
	- name: Load and run test
	run: \|
	docker load --input /tmp/pysages.tar
	docker run -t pysages bash -c "cd PySAGES/examples/openmm/cv_pucker && python3 ./unbiased.py && python3 ./check_pucker.py"

	cv-ermsd-openmm-unbiased:
	runs-on: ubuntu-latest
	needs: build
	steps:
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v2
	- name: Download artifact
	uses: actions/download-artifact@v3
	with:
	name: pysages
	path: /tmp
	- name: Load and run test
	run: \|
	docker load --input /tmp/pysages.tar
	docker run -t pysages bash -c "cd PySAGES/examples/openmm/cv_ermsd/ermsd && python3 ./unbiased.py && python3 ./check_ermsd.py"

	cv-ermsd-cg-openmm-unbiased:
	runs-on: ubuntu-latest
	needs: build
	steps:
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v2
	- name: Download artifact
	uses: actions/download-artifact@v3
	with:
	name: pysages
	path: /tmp
	- name: Load and run test
	run: \|
	docker load --input /tmp/pysages.tar
	docker run -t pysages bash -c "cd PySAGES/examples/openmm/cv_ermsd/ermsd_cg && python3 ./unbiased.py && python3 ./check_ermsd.py"

	alanine-dipeptide-string:
	runs-on: ubuntu-latest
	needs: build
	steps:
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v2
	- name: Download artifact
	uses: actions/download-artifact@v3
	with:
	name: pysages
	path: /tmp
	- name: Load and run test
	run: \|
	SCRIPT="cd PySAGES/examples/openmm/string &&"
	SCRIPT="${SCRIPT} mpirun --allow-run-as-root --oversubscribe -n 6"
	SCRIPT="${SCRIPT} python3 -m mpi4py.futures"
	SCRIPT="${SCRIPT} integration.py --replicas=5 --string-steps=2 --time-steps=1000 --mpi"
	docker load --input /tmp/pysages.tar
	docker run --privileged -t pysages bash -c "${SCRIPT}"

	openmm-nacl-metad-displacement:
	runs-on: ubuntu-latest
	needs: build
	steps:
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v2
	- name: Download artifact
	uses: actions/download-artifact@v3
	with:
	name: pysages
	path: /tmp
	- name: Load and run test
	run: \|
	SCRIPT="cd PySAGES/examples/openmm/metad/nacl &&"
	SCRIPT="${SCRIPT} python3 nacl-displacement.py --time-steps=500"
	docker load --input /tmp/pysages.tar
	docker run -v/tmp:/tmp -t pysages bash -c "${SCRIPT}"

	metad-hoomd:
	runs-on: ubuntu-latest
	needs: build
	steps:
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v2
	- name: Download artifact
	uses: actions/download-artifact@v3
	with:
	name: pysages
	path: /tmp
	- name: Load and run test
	run: \|
	docker load --input /tmp/pysages.tar
	docker run -v/tmp:/tmp -t pysages bash -c "cd PySAGES/examples/hoomd-blue/metad/ && python3 butane.py --use-grids=1 --time-steps=5000"

	funn-butane-hoomd:
	runs-on: ubuntu-latest
	needs: build
	steps:
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v2
	- name: Download artifact
	uses: actions/download-artifact@v3
	with:
	name: pysages
	path: /tmp
	- name: Load and run test
	run: \|
	SCRIPT="cd PySAGES/examples/hoomd-blue/funn/ &&"
	SCRIPT="${SCRIPT} python3 butane.py --train-freq=1000 --time-steps=1001"
	docker load --input /tmp/pysages.tar
	docker run -v/tmp:/tmp -t pysages bash -c "${SCRIPT}"

	cff-butane-hoomd:
	runs-on: ubuntu-latest
	needs: build
	steps:
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v2
	- name: Download artifact
	uses: actions/download-artifact@v3
	with:
	name: pysages
	path: /tmp
	- name: Load and run test
	run: \|
	SCRIPT="cd PySAGES/examples/hoomd-blue/cff/ &&"
	SCRIPT="${SCRIPT} python3 butane.py --train-freq=1000 --time-steps=1001"
	docker load --input /tmp/pysages.tar
	docker run -v/tmp:/tmp -t pysages bash -c "${SCRIPT}"

	harmonic-bias-hoomd:
	runs-on: ubuntu-latest
	needs: build
	steps:
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v2
	- name: Download artifact
	uses: actions/download-artifact@v3
	with:
	name: pysages
	path: /tmp
	- name: Load and run test
	run: \|
	docker load --input /tmp/pysages.tar
	docker run -v/tmp:/tmp -t pysages bash -c "cd PySAGES/examples/hoomd-blue/harmonic_bias/ && ./run.sh && mv hist.pdf /tmp/"
	- name: Upload artifact
	uses: actions/upload-artifact@v3
	with:
	name: harmonic-hist.pdf
	path: /tmp/hist.pdf
	retention-days: 7

	unbiased-hoomd:
	runs-on: ubuntu-latest
	needs: build
	steps:
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v2
	- name: Download artifact
	uses: actions/download-artifact@v3
	with:
	name: pysages
	path: /tmp
	- name: Load and run test
	run: \|
	docker load --input /tmp/pysages.tar
	docker run -v/tmp:/tmp -t pysages bash -c "cd PySAGES/examples/hoomd-blue/unbiased/ && ./run.sh"

	umbrella-integration-hoomd:
	runs-on: ubuntu-latest
	needs: build
	steps:
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v2
	- name: Download artifact
	uses: actions/download-artifact@v3
	with:
	name: pysages
	path: /tmp
	- name: Load and run test
	run: \|
	docker load --input /tmp/pysages.tar
	docker run -v /tmp:/tmp -t pysages bash -c "cd PySAGES/examples/hoomd-blue/umbrella_integration && python3 ./gen_gsd.py && python3 integration.py --replicas=5 --time-steps=1000 && mkdir /tmp/plots && mv *.pdf /tmp/plots/"
	- name: Upload artifacts
	uses: actions/upload-artifact@v3
	with:
	name: umbrella-integration-plots
	path: /tmp/plots
	retention-days: 1

	improved-string-hoomd:
	runs-on: ubuntu-latest
	needs: build
	steps:
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v2
	- name: Download artifact
	uses: actions/download-artifact@v3
	with:
	name: pysages
	path: /tmp
	- name: Load and run test
	run: \|
	docker load --input /tmp/pysages.tar
	docker run -v /tmp:/tmp -t pysages bash -c "cd PySAGES/examples/hoomd-blue/string && python3 ./gen_gsd.py && python3 spline_string.py --replicas=5 --time-steps=1000 --log-delay=0 --string-steps=2 && mkdir /tmp/plots && mv *.pdf /tmp/plots/"
	- name: Upload artifacts
	uses: actions/upload-artifact@v3
	with:
	name: spline-string-plots
	path: /tmp/plots
	retention-days: 1

	umbrella-integration-hoomd-mpi:
	runs-on: ubuntu-latest
	needs: build
	steps:
	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@v2
	- name: Download artifact
	uses: actions/download-artifact@v3
	with:
	name: pysages
	path: /tmp
	- name: Load and run test
	run: \|
	SCRIPT="cd PySAGES/examples/hoomd-blue/umbrella_integration &&"
	SCRIPT="${SCRIPT} python3 ./gen_gsd.py &&"
	SCRIPT="${SCRIPT} mpirun --allow-run-as-root --oversubscribe -n 2"
	SCRIPT="${SCRIPT} python3 -m mpi4py.futures"
	SCRIPT="${SCRIPT} integration.py --replicas=5 --time-steps=1000 --mpi &&"
	SCRIPT="${SCRIPT} mkdir /tmp/plots && mv *.pdf /tmp/plots/"
	docker load --input /tmp/pysages.tar
	docker run -v /tmp:/tmp -t pysages bash -c "${SCRIPT}"
	- name: Upload artifacts
	uses: actions/upload-artifact@v3
	with:
	name: umbrella-integration-mpi-plots
	path: /tmp/plots
	retention-days: 1

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Update notebooks to work with latest version of the precompiled Colab environment #1547

Workflow file

Update notebooks to work with latest version of the precompiled Colab environment #1547

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Workflow file for this run