Upgrade HOOMD-blue and OpenMM in Colab (#341) #4
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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 |