Adds DataSpaces 2 support and GitHub CI #30
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| name: Compilation and Basic Run Testing for A4MD | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| build-and-test-a4md: | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| flux: [ 0.52.0 ] | |
| os: [ ubuntu-20.04 ] | |
| compiler: [ gcc ] | |
| gcc_version: [ 10 ] | |
| mercury_connection_str: [ "ucx+tcp" ] | |
| name: ${{ matrix.os }}-${{ matrix.compiler }}-${{ matrix.gcc_version }}-${{ matrix.flux }} | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| FLUX_VERSION: ${{ matrix.flux }} | |
| CC: gcc-${{ matrix.gcc_version }} | |
| CXX: g++-${{ matrix.gcc_version }} | |
| MERCURY_CONNECTION_STRING: ${{ matrix.mercury_connection_str }} | |
| PYTHON_PREFIX_PATH: "/opt/hostedtoolcache/Python/3.10.12/x64" | |
| SPACK_DIR: "/home/runner/work/spack" | |
| DSPACES_SPACK_REPO_DIR: "/home/runner/work/dspaces-spack" | |
| A4MD_INSTALL_PREFIX: "/home/runner/work/a4md/install" | |
| steps: | |
| - name: Checkout push | |
| if: github.event_name == 'push' | |
| uses: actions/checkout@v3 | |
| - name: Checkout PR | |
| if: github.event_name == 'pull_request' | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ github.event.pull_request.head.sha }} | |
| - name: Setup GCC | |
| uses: egor-tensin/setup-gcc@v1 | |
| with: | |
| version: ${{ matrix.gcc_version }} | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y --no-install-recommends \ | |
| gcc g++ gfortran \ | |
| cmake \ | |
| autoconf \ | |
| automake \ | |
| libtool \ | |
| libtool-bin \ | |
| openmpi-bin \ | |
| libopenmpi-dev \ | |
| libarchive-dev \ | |
| ncurses-bin \ | |
| hwloc \ | |
| lua5.3 liblua5.3-dev \ | |
| libczmq-dev \ | |
| lua-posix-dev \ | |
| lz4 \ | |
| pkgconf \ | |
| libzmq5 \ | |
| sqlite | |
| # sudo chmod 777 /usr -R | |
| # sudo chmod 777 ${PYTHON_PREFIX_PATH} -R | |
| - name: Setup Python 3.10 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10.12' | |
| - name: Install Python dependencies | |
| run: | | |
| python3 -m pip install jsonschema==4.17.3 cffi==1.15.1 ply==3.11 pyyaml==6.0.1 numpy | |
| - name: Check Python packages | |
| run: | | |
| python3 -m pip list | |
| ls ${PYTHON_PREFIX_PATH}/lib | |
| ls ${PYTHON_PREFIX_PATH}/include/python3.10 | |
| - name: Install Spack | |
| run: | | |
| git clone https://github.com/spack/spack.git ${SPACK_DIR} | |
| - name: Register system dependencies with Spack | |
| run: | | |
| . ${SPACK_DIR}/share/spack/setup-env.sh | |
| mkdir -p /home/runner/.spack | |
| GCC_VERSION="9.3.0" | |
| if [[ $CC == 'gcc-10' ]]; then | |
| GCC_VERSION="10.3.0" | |
| fi | |
| cat > /home/runner/.spack/packages.yaml <<EOF | |
| packages: | |
| all: | |
| target: [x86_64] | |
| providers: | |
| mpi: [openmpi] | |
| python: | |
| buildable: False | |
| externals: | |
| - spec: "[email protected]" | |
| prefix: ${PYTHON_PREFIX_PATH} | |
| py-cffi: | |
| buildable: False | |
| externals: | |
| - spec: "[email protected]" | |
| prefix: ${PYTHON_PREFIX_PATH} | |
| py-jsonschema: | |
| buildable: False | |
| externals: | |
| - spec: "[email protected]" | |
| prefix: ${PYTHON_PREFIX_PATH} | |
| py-ply: | |
| buildable: False | |
| externals: | |
| - spec: "[email protected]" | |
| prefix: ${PYTHON_PREFIX_PATH} | |
| py-pyyaml: | |
| buildable: False | |
| externals: | |
| - spec: "[email protected]" | |
| prefix: ${PYTHON_PREFIX_PATH} | |
| czmq: | |
| buildable: False | |
| externals: | |
| - spec: "[email protected]" | |
| prefix: /usr | |
| sqlite: | |
| buildable: False | |
| externals: | |
| - spec: "[email protected]" | |
| prefix: /usr | |
| libzmq: | |
| buildable: False | |
| externals: | |
| - spec: "[email protected]" | |
| prefix: /usr | |
| lua: | |
| buildable: False | |
| externals: | |
| - spec: "[email protected]" | |
| prefix: /usr | |
| lua-luaposix: | |
| buildable: False | |
| externals: | |
| - spec: "[email protected]" | |
| prefix: /usr | |
| lz4: | |
| buildable: False | |
| externals: | |
| - spec: "[email protected]" | |
| prefix: /usr | |
| ncurses: | |
| buildable: False | |
| externals: | |
| - spec: "[email protected]" | |
| prefix: /usr | |
| pkgconf: | |
| buildable: False | |
| externals: | |
| - spec: "[email protected]" | |
| prefix: /usr | |
| hwloc: | |
| buildable: False | |
| externals: | |
| - spec: "[email protected]" | |
| prefix: /usr | |
| libarchive: | |
| buildable: False | |
| externals: | |
| - spec: "[email protected]" | |
| prefix: /usr | |
| autoconf: | |
| buildable: False | |
| externals: | |
| - spec: "[email protected]" | |
| prefix: /usr | |
| automake: | |
| buildable: False | |
| externals: | |
| - spec: "[email protected]" | |
| prefix: /usr | |
| libtool: | |
| buildable: False | |
| externals: | |
| - spec: "[email protected]" | |
| prefix: /usr | |
| m4: | |
| buildable: False | |
| externals: | |
| - spec: "[email protected]" | |
| prefix: /usr | |
| openmpi: | |
| buildable: False | |
| externals: | |
| - spec: "[email protected]" | |
| prefix: /usr | |
| openssl: | |
| buildable: False | |
| externals: | |
| - spec: "[email protected]" | |
| prefix: /usr | |
| pkg-config: | |
| buildable: False | |
| externals: | |
| - spec: "[email protected]" | |
| prefix: /usr | |
| gcc: | |
| externals: | |
| - spec: gcc@${GCC_VERSION} languages=c,c++ | |
| prefix: /usr | |
| extra_attributes: | |
| compilers: | |
| c: ${CC} | |
| cxx: ${CXX} | |
| buildable: False | |
| EOF | |
| echo "-------------------------------" | |
| cat /home/runner/.spack/packages.yaml | |
| echo "-------------------------------" | |
| spack compiler find --scope=user | |
| if [[ $CC == 'gcc-10' ]]; then | |
| spack config add "packages:all:compiler:[[email protected]]" | |
| else | |
| spack config add "packages:all:compiler:[[email protected]]" | |
| fi | |
| spack external find | |
| spack spec flux-core@${FLUX_VERSION} | |
| # spack spec [email protected] | |
| # spack spec [email protected] fabrics=sockets,tcp,udp,shm | |
| # spack spec mercury+mpi+ofi+sm+ucx ^[email protected] ^[email protected] fabrics=sockets,tcp,udp,shm | |
| - name: Setup DataSpaces' Spack repo | |
| run: | | |
| git clone https://github.com/Analytics4MD/dspaces-spack.git ${DSPACES_SPACK_REPO_DIR} | |
| curr_dir=$(pwd) | |
| cd ${DSPACES_SPACK_REPO_DIR} | |
| git checkout dspaces_2.2.0_upgrade | |
| cd $curr_dir | |
| . ${SPACK_DIR}/share/spack/setup-env.sh | |
| spack repo add ${DSPACES_SPACK_REPO_DIR} | |
| # Have to use master here because the actual DataSpaces 2 releases are not yet in the repo | |
| spack spec [email protected]~pybind \ | |
| ^mercury+mpi+ofi+sm+ucx \ | |
| ^[email protected] \ | |
| ^[email protected] fabrics=sockets,tcp,udp,shm \ | |
| ^boost+iostreams+serialization | |
| - name: Install dependencies | |
| run: | | |
| mkdir -p ${A4MD_INSTALL_PREFIX} | |
| python3 -m venv ${A4MD_INSTALL_PREFIX} | |
| . ${SPACK_DIR}/share/spack/setup-env.sh | |
| spack install -j4 flux-core@${FLUX_VERSION} | |
| # spack install -j4 [email protected] | |
| # spack install -j4 [email protected] fabrics=sockets,tcp,udp,shm | |
| # spack install -j4 mercury+mpi+ofi+sm+ucx ^[email protected] ^[email protected] fabrics=sockets,tcp,udp,shm | |
| spack install -j4 [email protected]~pybind \ | |
| ^mercury+mpi+ofi+sm+ucx \ | |
| ^[email protected] \ | |
| ^[email protected] fabrics=sockets,tcp,udp,shm \ | |
| ^boost+iostreams+serialization | |
| spack view --verbose symlink ${A4MD_INSTALL_PREFIX} \ | |
| flux-core@${FLUX_VERSION} \ | |
| [email protected] \ | |
| [email protected] fabrics=sockets,tcp,udp,shm \ | |
| boost+iostreams+serialization \ | |
| mercury+mpi+ofi+sm+ucx \ | |
| [email protected]~pybind ^mercury+mpi+ofi+sm+ucx ^[email protected] ^[email protected] fabrics=sockets,tcp,udp,shm ^boost+iostreams+serialization | |
| - name: Compile A4MD | |
| run: | | |
| echo "Activating Spack" | |
| . ${SPACK_DIR}/share/spack/setup-env.sh | |
| echo "Build and Install A4MD" | |
| cd ${GITHUB_WORKSPACE} | |
| ls && pwd | |
| mkdir build | |
| cd build | |
| export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:${A4MD_INSTALL_PREFIX}/lib/pkgconfig | |
| cmake --version | |
| cmake \ | |
| -DCMAKE_INSTALL_PREFIX=${A4MD_INSTALL_PREFIX} \ | |
| -DCMAKE_PREFIX_PATH=${A4MD_INSTALL_PREFIX} \ | |
| -DCMAKE_BUILD_TYPE=Debug \ | |
| -DPython3_ROOT_DIR=${PYTHON_PREFIX_PATH}/bin \ | |
| -Ddtl_dspaces=ON \ | |
| -Ddtl_dimes=OFF \ | |
| -Ddtl_decaf=OFF \ | |
| -Dbuild_examples=ON \ | |
| -Dbuild_tests=OFF \ | |
| -Dbuild_wrap=OFF \ | |
| .. | |
| make VERBOSE=1 install -j | |
| - name: Build A4MD Test | |
| run: | | |
| . ${SPACK_DIR}/share/spack/setup-env.sh | |
| cd ${GITHUB_WORKSPACE}/.github/basic_test | |
| mkdir -p build | |
| mkdir -p test_install | |
| cd build | |
| cmake \ | |
| -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/.github/basic_test/test_install \ | |
| -DCMAKE_PREFIX_PATH=${A4MD_INSTALL_PREFIX} \ | |
| -DA4MD_PREFIX=${A4MD_INSTALL_PREFIX} \ | |
| -DCMAKE_BUILD_TYPE=Debug \ | |
| -DPython3_ROOT_DIR=${PYTHON_PREFIX_PATH}/bin \ | |
| .. | |
| make VERBOSE=1 install -j | |
| - name: Test A4MD | |
| run: | | |
| . ${SPACK_DIR}/share/spack/setup-env.sh | |
| export PATH=${PATH}:${A4MD_INSTALL_PREFIX}/bin:${A4MD_INSTALL_PREFIX}/sbin | |
| export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${A4MD_INSTALL_PREFIX}/lib:${A4MD_INSTALL_PREFIX}/lib64 | |
| echo "Launching basic prod-cons test" | |
| cd ${GITHUB_WORKSPACE}/.github/basic_test/test_install/bin | |
| flux start --test-size=1 /bin/bash ./flux_prod_cons.sh "${A4MD_INSTALL_PREFIX}" "${A4MD_INSTALL_PREFIX}" "${MERCURY_CONNECTION_STRING}" | |
| # cd ${GITHUB_WORKSPACE}/.github/basic_test | |
| # flux start --test-size=1 /bin/bash ./flux_prod_cons.sh "${A4MD_INSTALL_PREFIX}" "${A4MD_INSTALL_PREFIX}" "${MERCURY_CONNECTION_STRING}" | |
| - name: Upload log files as artifact for inspection | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ matrix.os }}_${{ matrix.compiler }}_${{ matrix.gcc_version }}_${{ matrix.flux }}_outputs | |
| compression-level: 9 | |
| if-no-files-found: error | |
| path: | | |
| ${GITHUB_WORKSPACE}/.github/basic_test/*.err | |
| ${GITHUB_WORKSPACE}/.github/basic_test/*.out | |
| ${GITHUB_WORKSPACE}/.github/basic_test/dataspaces.conf | |
| ${GITHUB_WORKSPACE}/.github/basic_test/conf.ds |