Create Containerfile

Tools/machines/perlmutter-nersc/Containerfile

@@ -0,0 +1,151 @@
+# Base System and Essential Tools Installation
+FROM nvidia/cuda:12.6.0-devel-ubuntu22.04 AS base
+
+# Set up environment variables
+ENV DEBIAN_FRONTEND=noninteractive \
+    SW_DIR=/opt/software \
+    FORCE_UNSAFE_CONFIGURE=1
+
+# Install essential system dependencies including MPI libraries
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    autoconf \
+    build-essential \
+    ca-certificates \
+    coreutils \
+    curl \
+    environment-modules \
+    gfortran \
+    git \
+    openssh-server \
+    python3 \
+    python3-pip \
+    python3-dev \
+    python3-venv \
+    unzip \
+    vim \
+    libmpich-dev \
+    cmake \
+    libblas-dev \
+    liblapack-dev \
+    g++ \
+    cuda-toolkit-12-2 \
+    pkg-config \
+    libbz2-dev \
+    zlib1g-dev \
+    libpng-dev \
+    libzstd-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install c-blosc from source
+FROM base AS c-blosc
+
+RUN git clone -b v1.21.1 https://github.com/Blosc/c-blosc.git /tmp/c-blosc && \
+    cd /tmp/c-blosc && \
+    mkdir build && cd build && \
+    cmake -DCMAKE_INSTALL_PREFIX=/usr .. && \
+    make -j$(nproc) && \
+    make install && \
+    rm -rf /tmp/c-blosc
+
+# Install ADIOS2 from source
+FROM base AS adios2
+
+# Ensure c-blosc is installed before ADIOS2
+COPY --from=c-blosc /usr /usr
+
+# Verify the location of Blosc library
+RUN find /usr -name 'libblosc*'
+
+# Ensure Blosc library paths are correctly configured
+ENV BLOSC_LIBRARY=/usr/lib/libblosc.so.1.21.1
+ENV BLOSC_INCLUDE_DIR=/usr/include
+
+# Install ADIOS2
+RUN git clone -b v2.8.3 https://github.com/ornladios/ADIOS2.git /tmp/adios2 && \
+    cd /tmp/adios2 && \
+    mkdir build && cd build && \
+    cmake -DADIOS2_USE_Blosc=ON \
+          -DBLOSC_LIBRARY=${BLOSC_LIBRARY} \
+          -DBLOSC_INCLUDE_DIR=${BLOSC_INCLUDE_DIR} \
+          -DADIOS2_USE_Fortran=OFF \
+          -DADIOS2_USE_Python=OFF \
+          -DADIOS2_USE_ZeroMQ=OFF \
+          -DADIOS2_USE_BZip2=ON \
+          -DADIOS2_USE_ZFP=OFF \
+          -DADIOS2_USE_SZ=OFF \
+          -DADIOS2_USE_MGARD=OFF \
+  -DADIOS2_USE_PNG=ON \
+          -DCMAKE_INSTALL_PREFIX=/usr .. && \
+    make -j$(nproc) && \
+    make install && \
+    rm -rf /tmp/adios2
+
+# Install BLAS++ and LAPACK++
+FROM base AS blaspp_lapackpp
+
+RUN git clone -b v2024.05.31 https://github.com/icl-utk-edu/blaspp.git /tmp/blaspp && \
+    cd /tmp/blaspp && \
+    mkdir build && cd build && \
+    cmake -Duse_openmp=OFF -Dgpu_backend=cuda -DCMAKE_CXX_STANDARD=17 -DCMAKE_INSTALL_PREFIX=/usr -DBLAS_LIBRARIES=/usr/lib/x86_64-linux-gnu/libblas.so -DLAPACK_LIBRARIES=/usr/lib/x86_64-linux-gnu/liblapack.so .. && \
+    make -j$(nproc) && \
+    make install && \
+    rm -rf /tmp/blaspp
+
+RUN git clone -b v2024.05.31 https://github.com/icl-utk-edu/lapackpp.git /tmp/lapackpp && \
+    cd /tmp/lapackpp && \
+    mkdir build && cd build && \
+    cmake -DCMAKE_CXX_STANDARD=17 -Dbuild_tests=OFF -DCMAKE_INSTALL_PREFIX=/usr -DLAPACK_LIBRARIES=/usr/lib/x86_64-linux-gnu/liblapack.so .. && \
+    make -j$(nproc) && \
+    make install && \
+    rm -rf /tmp/lapackpp
+
+# Install heFFTe
+FROM base AS heffte
+
+RUN git clone -b v2.4.0 https://github.com/icl-utk-edu/heffte.git /tmp/heffte #&& \
+   # cd /tmp/heffte && \
+    #mkdir build && cd build && \
+    # Disable LTO for CUDA builds
+ #   CXXFLAGS="-fno-lto" CFLAGS="-fno-lto"
+  #  cmake -DBUILD_SHARED_LIBS=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_STANDARD=17 -DHeffte_ENABLE_CUDA=ON -DCMAKE_INSTALL_PREFIX=/usr .. && \
+   # make -j$(nproc) && \
+    #make install && \
+       #rm -rf /tmp/heffte
+
+# Final Image
+FROM base AS final
+
+# Copy installed software from previous stages
+COPY --from=c-blosc /usr /usr
+COPY --from=adios2 /usr /usr
+COPY --from=blaspp_lapackpp /usr /usr
+#COPY --from=heffte /usr /usr
+
+# Create and activate Python virtual environment
+RUN python3 -m venv /opt/venv && \
+    /opt/venv/bin/pip install --no-cache-dir \
+    wheel \
+    numpy \
+    pandas \
+    scipy \
+    matplotlib \
+    jupyter \
+    scikit-learn \
+    openpmd-api \
+    yt \
+    cupy-cuda12x \
+    torch \
+    optimas[all] \
+    cython \
+    packaging \
+    build \
+    setuptools
+
+# Set up the environment for the virtual environment
+ENV PATH="/opt/venv/bin:${PATH}"
+
+# Set up entrypoint
+ENTRYPOINT ["/bin/bash", "-c"]
+
+# Default command
+CMD ["/bin/bash"]