Update container infrastructure

.github/workflows/container.yml

@@ -7,60 +7,46 @@ on:
       - pegasus
   workflow_dispatch:
 
+env:
+  REGISTRY: docker.io
+  IMAGE_NAME: earthquakesuc/workflow-bootstrap
+
 jobs:
   build-test-upload:
     runs-on: ubuntu-latest
-
-    env:
-      COMMIT_HASH: ${{ github.sha }}
-      CONTAINER_NAME: runner-${{ github.sha }}.sif
-
     steps:
-    - name: Configure rclone for Dropbox
-      run: |
-        mkdir -p ~/.config/rclone
-        cat <<EOF > ~/.config/rclone/rclone.conf
-        [dropbox]
-        type = dropbox
-        client_id =
-        client_secret =
-        token = ${{ secrets.RCLONE_CONFIG }}
-        EOF
-
-    - name: Set up SSH for deploy key
-      run: |
-        mkdir -p ~/.ssh
-        echo "${{ secrets.DEPLOY_KEY }}" > ~/.ssh/id_rsa
-        chmod 600 ~/.ssh/id_rsa
-        ssh-keyscan github.com >> ~/.ssh/known_hosts
-
-    - name: Clone private repo
-      env:
-         TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      run: |
-         git clone git@github.com:ucgmsim/EMOD3D.git /tmp/EMOD3D
-
-    - name: Checkout repository
-      uses: actions/checkout@v3
-
-    - name: Install dependencies
-      run: |
-        sudo apt update
-        sudo apt install -y squashfuse e2fsprogs runc rclone
-        wget --quiet https://github.com/apptainer/apptainer/releases/download/v1.4.0/apptainer_1.4.0_amd64.deb -O /tmp/apptainer_1.4.0_amd64.deb
-        sudo apt install -y /tmp/apptainer_1.4.0_amd64.deb
-
-    - name: Build Apptainer container
-      run: |
-        apptainer build $CONTAINER_NAME container/runner.def
-
-    - name: Run pytest inside container
-      run: |
-        apptainer exec \
-          --bind $PWD:/mnt \
-          $CONTAINER_NAME \
-          bash -c "cd /mnt && pytest tests/"
-
-    - name: Upload container to Dropbox
-      run: |
-        rclone copy $CONTAINER_NAME dropbox:/QuakeCoRE/Containers
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: earthquakesuc
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Extract metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            type=sha,format=long
+            type=ref,event=branch
+            type=raw,value=latest
+
+      - name: Build and push
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: ./container/Dockerfile
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+
+      - name: Run pytest
+        run: |
+          # Use the long SHA tag generated by the meta step
+          docker run --rm \
+            -v ${{ github.workspace }}:/mnt \
+            ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:sha-${{ github.sha }} \
+            bash -c "pytest /mnt/tests"

container/Dockerfile

@@ -0,0 +1,78 @@
+# Bootstrap Dockerfile
+FROM ubuntu:latest
+
+# Set noninteractive mode for apt
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Update package lists and install build dependencies
+RUN apt-get update && apt-get install -y \
+        build-essential \
+        cmake \
+        curl \
+        gfortran \
+        git \
+        pkg-config \
+        libfftw3-dev \
+        libpapi-dev \
+        libopenmpi-dev \
+        openmpi-bin \
+        openmpi-common \
+        libopenblas-openmp-dev \
+        libhdf5-dev \
+        libssl-dev \
+        zlib1g-dev \
+        libbz2-dev \
+        libreadline-dev \
+        libsqlite3-dev \
+        libffi-dev \
+        liblzma-dev \
+        libexpat1-dev \
+        libgdbm-dev \
+        libgdbm-compat-dev \
+        libncurses5-dev \
+        libncursesw5-dev \
+        uuid-dev \
+        libnss3-dev \
+        libedit-dev \
+        libuuid1 \
+        libdb5.3-dev \
+        lzma \
+        tcl-dev \
+        gdb \
+        lcov \
+        ca-certificates \
+    && rm -rf /var/lib/apt/lists/*
+
+# Create software directories (removed uv directory)
+RUN mkdir -p /sw/cargo /sw/rust /sw/python /sw/venv
+
+# Python installation
+ARG PYTHON_VERSION=3.13.12
+RUN curl -o /tmp/Python-${PYTHON_VERSION}.tar.xz \
+        https://www.python.org/ftp/python/${PYTHON_VERSION}/Python-${PYTHON_VERSION}.tar.xz && \
+    cd /tmp && \
+    tar xf Python-${PYTHON_VERSION}.tar.xz && \
+    cd Python-${PYTHON_VERSION} && \
+    ./configure --prefix=/sw/python --enable-optimizations && \
+    make -j$(nproc) && \
+    make install && \
+    cd /tmp && \
+    rm -rf Python-${PYTHON_VERSION}*
+
+# Set Environment Paths
+ENV RUSTUP_HOME=/sw/rust
+ENV CARGO_HOME=/sw/cargo
+ENV VIRTUAL_ENV="/sw/venv"
+# Added /sw/python/bin to path early to ensure we use the compiled python
+ENV PATH="$VIRTUAL_ENV/bin:/sw/python/bin:/sw/cargo/bin:$PATH"
+ENV LD_LIBRARY_PATH="/usr/local/lib:$LD_LIBRARY_PATH"
+
+# Install Rust
+RUN curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+
+# Setup Virtual Environment and Install via pip
+ARG WORKFLOW_BRANCH=pegasus
+RUN python3 -m venv $VIRTUAL_ENV && \
+    pip install --no-cache-dir --upgrade pip setuptools wheel && \
+    pip install --no-cache-dir "git+https://github.com/ucgmsim/workflow@${WORKFLOW_BRANCH}" --no-binary=h5py && \
+    chmod -R a+rX /sw

container/runner.def

@@ -1,56 +1,23 @@
 Bootstrap: docker
-From: ubuntu:latest
-
-%setup
-    [ -d /tmp/EMOD3D ] || git clone --depth 1 git@github.com:ucgmsim/EMOD3D.git /tmp/EMOD3D
+From: earthquakesuc/workflow-bootstrap:latest
 
 %files
-    /tmp/EMOD3D /EMOD3D
+    EMOD3D /EMOD3D
 
 %post
-    apt-get update && apt-get install -y \
-                      build-essential \
-                      cmake \
-                      gdal-bin \
-                      gfortran \
-                      ghostscript \
-                      git \
-                      gmt \
-                      libgmt-dev \
-                      gmt-dcw \
-                      gmt-gshhg \
-                      graphicsmagick \
-                      libfftw3-dev \
-                      libopenmpi-dev \
-                      libpapi-dev \
-                      python-is-python3 \
-                      python3-pip \
-                      sqlite3 \
-                      wget
-
-    wget "https://www.dropbox.com/scl/fi/b4m9g32x1j70ti69zyybq/genslip_velocity_model.vmod?rlkey=yxurhrdn8uvqh33hsb0inhsq0&st=o77aaccp&dl=0" -O /genslip_velocity_model.vmod
-    wget "https://www.dropbox.com/scl/fi/qakchhg6qu23aclcb02ye/Cant1D_v2-midQ_leer.1d?rlkey=wn1a6nnol2eaf5n6qsy5t1nym&st=8yahw7id&dl=0" -O /Cant1D_v2-midQ_leer.1d
-    wget "https://www.dropbox.com/scl/fi/tw1m15owloi0eo8h3u1kw/geoNet_stats-2023-06-28.vs30?rlkey=plu90zg0ti4lc2nvf51zu9xmg&st=iz8c2ls3&dl=0" -O /stations.vs30
-    wget "https://www.dropbox.com/scl/fi/bb852b1f0rly6cfvs9p9b/geoNet_stats-2023-06-28.ll?rlkey=3y8k5qviy52nbksfdkm1n92yh&st=605h60u6&dl=0" -O /stations.ll
-
     cd /EMOD3D && \
-    mkdir build && \
-    cd build && \
-    cmake .. && \
-    make -j $(nproc) genslip_v5.6.2 srf2stoch hb_high_binmod_v6.0.3 hb_high_binmod_v5.4.5
-
-    # Remove all folders in EMOD3D except the tools folder
-    find /EMOD3D -mindepth 1 -maxdepth 1 ! -name "tools" -exec rm -rf \{\} \;
-
-
-    git clone --depth 1 https://github.com/ucgmsim/Velocity-Model.git /Velocity-Model && \
-    cd /Velocity-Model && \
-    mkdir build && \
-    cd build && \
-    cmake ../ -DCMAKE_C_FLAGS="-fopenmp" -DCMAKE_CXX_FLAGS="-fopenmp" && \
-    make -j $(nproc)
+      mkdir build && cd build && \
+      cmake -DHF_TIME_WINDOW=off -DUSE_FFTW=on -DCMAKE_C_FLAGS="-march=x86-64 -mtune=generic" .. && \
+      make -j $(nproc) genslip_v5.6.2 srf2stoch generic_slip2srf \
+                      hb_high_binmod_v6.0.3
 
-    pip install "git+https://github.com/ucgmsim/workflow@pegasus" --break-system-packages
+    cd /
+    # Keep only the EMOD3D tools folder and compiled binaries
+    find /EMOD3D -mindepth 1 -maxdepth 1 ! -name "tools" -exec rm -rf {} \;
 
 %environment
-    export PATH="$PATH:/EMOD3D/tools:/Velocity-Model"
+    export RUSTUP_HOME=/sw/rust
+    export CARGO_HOME=/sw/cargo
+    export PATH="/sw/venv/bin:/EMOD3D/tools:/sw/cargo/bin:/sw/python/bin:$PATH"
+    export VIRTUAL_ENV="/sw/venv"
+    export LD_LIBRARY_PATH="/usr/local/lib:$LD_LIBRARY_PATH"