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ljwoods2ljwoods2
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Merge pull request #18 from Becksteinlab/develop
Remove NAMD
2 parents c15e014 + 29f59eb commit 7196755

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-226
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+4
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‎.github/workflows/ci.yaml‎

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@@ -89,44 +89,6 @@ jobs:
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build-args: |
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LMP_OPTS=${{ matrix.LMP_OPTS }}
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build-namd-image:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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arch: [amd64]
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tag_suffix: ["GPU"]
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# Sets the permissions granted to the `GITHUB_TOKEN` for the actions in this job.
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permissions:
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contents: read
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steps:
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- name: Free disk space
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uses: jlumbroso/free-disk-space@main
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with:
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android: true
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dotnet: true
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haskell: true
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large-packages: true
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swap-storage: true
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Convert compiler options to simple tag suffix
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id: NAMD_OPTS
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run: |
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if [[ "${{ matrix.tag_suffix }}" == "GPU" ]]; then
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echo NAMD_OPTS="--with-cuda" >> $GITHUB_ENV
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fi
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- name: Build and push Docker image
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uses: docker/build-push-action@v5
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with:
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context: ./docker/namd
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push: false
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build-args: |
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NAMD_OPTS=${{ matrix.NAMD_OPTS }}
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build-common-image:
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runs-on: ubuntu-latest
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strategy:
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id: option
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run: |
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if [ "${{ matrix.build }}" == "Common-CPU" ]; then
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echo NAMD_OPTS= >> $GITHUB_ENV
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echo GMX_OPTS= >> $GITHUB_ENV
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echo LMP_OPTS= >> $GITHUB_ENV
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echo DOCKERFILE="Dockerfile.cpu" >> $GITHUB_ENV
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else
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echo NAMD_OPTS="--with-cuda" >> $GITHUB_ENV
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echo GMX_OPTS="-DGMX_GPU=CUDA" >> $GITHUB_ENV
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echo LMP_OPTS="-DPKG_GPU=on -DGPU_API=cuda" >> $GITHUB_ENV
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echo DOCKERFILE="Dockerfile.gpu" >> $GITHUB_ENV
@@ -172,6 +132,5 @@ jobs:
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push: false
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file: ./docker/common/${{ env.DOCKERFILE }}
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build-args: |
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NAMD_OPTS=${{ env.NAMD_OPTS }}
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GMX_OPTS=${{ env.GMX_OPTS }}
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LMP_OPTS=${{ env.LMP_OPTS }}

‎.github/workflows/deploy_docker.yaml‎

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@@ -130,62 +130,6 @@ jobs:
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labels: ${{ steps.meta.outputs.labels }}
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build-args: |
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LMP_OPTS=${{ env.LMP_OPTS }}
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build-and-push-namd-image:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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arch: [amd64]
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tag_suffix: ["GPU"]
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# Sets the permissions granted to the `GITHUB_TOKEN` for the actions in this job.
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permissions:
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contents: read
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packages: write
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#
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steps:
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- name: Free disk space
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uses: jlumbroso/free-disk-space@main
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with:
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android: true
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dotnet: true
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haskell: true
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large-packages: true
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swap-storage: true
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- name: Checkout repository
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uses: actions/checkout@v4
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# Uses the `docker/login-action` action to log in to the Container registry registry using the account and password that will publish the packages. Once published, the packages are scoped to the account defined here.
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- name: Log in to the Container registry
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uses: docker/login-action@v3
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with:
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registry: ${{ env.REGISTRY }}
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Convert compiler options to simple tag suffix
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id: tag_suffix
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run: |
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if [[ "${{ matrix.tag_suffix }}" == "GPU" ]]; then
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echo NAMD_OPTS="--with-cuda" >> $GITHUB_ENV
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fi
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# This step uses [docker/metadata-action](https://github.com/docker/metadata-action#about) to extract tags and labels that will be applied to the specified image. The `id` "meta" allows the output of this step to be referenced in a subsequent step. The `images` value provides the base name for the tags and labels.
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- name: Extract metadata (tags, labels) for Docker
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id: meta
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uses: docker/metadata-action@v5
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with:
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images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
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# This step uses the `docker/build-push-action` action to build the image, based on your repository's `Dockerfile`. If the build succeeds, it pushes the image to GitHub Packages.
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# It uses the `context` parameter to define the build's context as the set of files located in the specified path. For more information, see "[Usage](https://github.com/docker/build-push-action#usage)" in the README of the `docker/build-push-action` repository.
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# It uses the `tags` and `labels` parameters to tag and label the image with the output from the "meta" step.
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- name: Build and push Docker image
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uses: docker/build-push-action@v5
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with:
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context: ./docker/namd
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push: true
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tags: ${{ steps.meta.outputs.tags }}-NAMD-${{ env.tag_suffix }}
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labels: ${{ steps.meta.outputs.labels }}
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build-args: |
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NAMD_OPTS=${{ env.NAMD_OPTS }}
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build-common-image:
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runs-on: ubuntu-latest
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id: option
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run: |
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if [ "${{ matrix.build }}" == "Common-CPU" ]; then
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echo NAMD_OPTS= >> $GITHUB_ENV
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echo GMX_OPTS= >> $GITHUB_ENV
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echo LMP_OPTS= >> $GITHUB_ENV
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echo DOCKERFILE="Dockerfile.cpu" >> $GITHUB_ENV
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else
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echo NAMD_OPTS="--with-cuda" >> $GITHUB_ENV
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echo GMX_OPTS="-DGMX_GPU=CUDA" >> $GITHUB_ENV
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echo LMP_OPTS="-DPKG_GPU=on -DGPU_API=cuda" >> $GITHUB_ENV
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echo DOCKERFILE="Dockerfile.gpu" >> $GITHUB_ENV
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tags: ${{ steps.meta.outputs.tags }}-${{ matrix.build }}
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labels: ${{ steps.meta.outputs.labels }}
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build-args: |
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NAMD_OPTS=${{ env.NAMD_OPTS }}
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GMX_OPTS=${{ env.GMX_OPTS }}
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LMP_OPTS=${{ env.LMP_OPTS }}

‎docker/common/Dockerfile.cpu‎

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@@ -3,13 +3,11 @@ FROM condaforge/linux-anvil-cuda:11.8 AS build
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ARG LMP_OPTS=""
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ARG GMX_OPTS=""
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ARG NAMD_OPTS=""
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COPY . .
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RUN source /opt/conda/etc/profile.d/conda.sh && conda env create --file env.yaml
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RUN source /opt/conda/etc/profile.d/conda.sh && conda activate env && ./install_lammps.sh "$LMP_OPTS"
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RUN source /opt/conda/etc/profile.d/conda.sh && conda activate env && ./install_gromacs.sh "$GMX_OPTS"
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RUN source /opt/conda/etc/profile.d/conda.sh && conda activate env && ./install_namd.sh "$NAMD_OPTS"
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# Delete the heavy environment but keep conda binaries
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RUN source /opt/conda/etc/profile.d/conda.sh && conda remove -n env --all -y
@@ -34,8 +32,6 @@ RUN ln -s /opt/gromacs_build/bin/gmx /bin/gmx
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COPY --from=build /opt/lammps_build /opt/lammps_build
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RUN ln -s /opt/lammps_build/bin/lmp /bin/lmp
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COPY --from=build /opt/namd-build /opt/namd-build
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RUN ln -s /opt/namd-build/namd3 /bin/namd3
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ENTRYPOINT [ "/opt/conda/bin/tini", "--", "/opt/docker/bin/entrypoint" ]
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CMD [ "/bin/bash" ]

‎docker/common/Dockerfile.gpu‎

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@@ -3,13 +3,11 @@ FROM condaforge/linux-anvil-cuda:11.8 AS build
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ARG LMP_OPTS=""
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ARG GMX_OPTS=""
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ARG NAMD_OPTS=""
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COPY . .
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RUN source /opt/conda/etc/profile.d/conda.sh && conda env create --file env.yaml
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RUN source /opt/conda/etc/profile.d/conda.sh && conda activate env && ./install_lammps.sh "$LMP_OPTS"
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RUN source /opt/conda/etc/profile.d/conda.sh && conda activate env && ./install_gromacs.sh "$GMX_OPTS"
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RUN source /opt/conda/etc/profile.d/conda.sh && conda activate env && ./install_namd.sh "$NAMD_OPTS"
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# Delete the heavy environment but keep conda binaries
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RUN source /opt/conda/etc/profile.d/conda.sh && conda remove -n env --all -y
@@ -34,8 +32,5 @@ RUN ln -s /opt/gromacs_build/bin/gmx /bin/gmx
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COPY --from=build /opt/lammps_build /opt/lammps_build
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RUN ln -s /opt/lammps_build/bin/lmp /bin/lmp
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COPY --from=build /opt/namd-build /opt/namd-build
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RUN ln -s /opt/namd-build/namd3 /bin/namd3
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ENTRYPOINT [ "/opt/conda/bin/tini", "--", "/opt/docker/bin/entrypoint" ]
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CMD [ "/bin/bash" ]

‎docker/common/env.yaml‎

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@@ -19,4 +19,5 @@ dependencies:
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- curl
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- openmp
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- openmpi
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- libacl
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‎docker/common/install_namd.sh‎

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‎docker/gromacs/env.yaml‎

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- curl
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- openmp
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- openmpi
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- libacl
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‎docker/gromacs/install_gromacs.sh‎

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#!/bin/bash
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export PATH="${PATH}:${CUDA_HOME}/bin"
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cd /opt/
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export HOME_DIR=${PWD}
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export NPROC=$(nproc)
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export LIBRARY_PATH=${CONDA_PREFIX}/lib
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export LD_LIBRARY_PATH=${CONDA_PREFIX}/lib
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git clone https://github.com/hcho38/gromacs.git
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cd gromacs
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git checkout imd-v3

‎docker/namd/Dockerfile‎

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‎docker/namd/env.yaml‎

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