Build alphafold3 container

.github/workflows/github_actions.yml

@@ -11,7 +11,7 @@ on:
 
 jobs:
   build-and-test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
@@ -132,6 +132,38 @@ jobs:
           tags: ${{ secrets.DOCKER_USERNAME }}/alphalink:${{ github.event.release.tag_name }}
           ssh: default
 
+  build-alphafold3-container:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: webfactory/[email protected]
+        with:
+          ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}
+      - uses: actions/checkout@v4
+      - run: rm -rf /opt/hostedtoolcache
+      - uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+      - uses: docker/setup-buildx-action@v3
+      - name: Build and push alphafold3 container
+        if: github.event_name == 'push'
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: ./docker/alphafold3.dockerfile
+          push: true
+          tags: ${{ secrets.DOCKER_USERNAME }}/alphafold3:latest
+          ssh: default
+      - name: Build and push alphafold3 container with version
+        if: github.event_name == 'release' && github.event.action == 'published'
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: ./docker/alphafold3.dockerfile
+          push: true
+          tags: ${{ secrets.DOCKER_USERNAME }}/alphafold3:${{ github.event.release.tag_name }}
+          ssh: default
+
   build-analysis-container:
     runs-on: ubuntu-latest
     steps:

docker/alphafold3.dockerfile

@@ -0,0 +1,86 @@
+FROM nvidia/cuda:12.6.0-base-ubuntu22.04
+
+# ---------------------------------------------------------
+# 1. System Packages Installation
+# ---------------------------------------------------------
+RUN apt-get update -q && \
+    DEBIAN_FRONTEND=noninteractive apt-get install -y -q --no-install-recommends \
+      software-properties-common \
+      git \
+      wget \
+      gcc \
+      g++ \
+      make \
+      zlib1g-dev \
+      zstd \
+    && rm -rf /var/lib/apt/lists/*
+
+# ---------------------------------------------------------
+# 2. Miniforge Installation
+# ---------------------------------------------------------
+RUN wget -q -P /tmp https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh && \
+    bash /tmp/Miniforge3-Linux-x86_64.sh -b -p /opt/conda && \
+    rm /tmp/Miniforge3-Linux-x86_64.sh
+ENV PATH="/opt/conda/bin:$PATH"
+ENV LD_LIBRARY_PATH="/opt/conda/lib:$LD_LIBRARY_PATH"
+
+# ---------------------------------------------------------
+# 3. Conda + Mamba Environment
+# ---------------------------------------------------------
+RUN conda install --solver=classic -y \
+    conda-forge::conda-libmamba-solver \
+    conda-forge::libmamba \
+    conda-forge::libmambapy \
+    conda-forge::libarchive \
+    conda-forge::git && \
+    mamba install -y -c conda-forge -c bioconda -c omnia --solver classic \
+      openmm==8.0 \
+      pdbfixer==1.9 \
+      kalign2 \
+      modelcif \
+      pip \
+      hmmer \
+      hhsuite \
+      python=3.11 && \
+    conda clean --all --force-pkgs-dirs --yes
+
+# ---------------------------------------------------------
+# 4. SSH and GitHub Known Host
+# ---------------------------------------------------------
+RUN mkdir -p /root/.ssh && chmod 700 /root/.ssh
+RUN ssh-keyscan github.com >> /root/.ssh/known_hosts
+
+# ---------------------------------------------------------
+# 5. Clone AlphaPulldown & Install
+# ---------------------------------------------------------
+RUN --mount=type=ssh git clone --recurse-submodules [email protected]:KosinskiLab/AlphaPulldown.git
+WORKDIR /AlphaPulldown
+RUN pip3 install .
+
+# ---------------------------------------------------------
+# 6. Additional Python Tools
+# ---------------------------------------------------------
+RUN pip3 install --upgrade pip --no-cache-dir && \
+    pip3 install --upgrade --no-cache-dir \
+      pytest \
+      "jax[cuda12]" && \
+    chmod u+s /sbin/ldconfig.real
+
+# ---------------------------------------------------------
+# 7. AlphaFold 3 Source & Dependencies
+# ---------------------------------------------------------
+COPY . /app/alphafold
+WORKDIR /app/alphafold
+RUN pip3 install -r dev-requirements.txt && \
+    pip3 install --no-deps . && \
+    build_data
+
+# ---------------------------------------------------------
+# 8. Environment for XLA
+# ---------------------------------------------------------
+# For GPUs < 8.0 compute capability, see note in Dockerfile
+ENV XLA_FLAGS="--xla_gpu_enable_triton_gemm=false"
+ENV XLA_PYTHON_CLIENT_PREALLOCATE=true
+ENV XLA_CLIENT_MEM_FRACTION=0.95
+
+ENTRYPOINT ["bash"]