Fix memory leaks, add parallel examples for testing and support valgrind githib actions #1230
Workflow file for this run
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| # | |
| # basic.yml | |
| # | |
| # The MIT License | |
| # | |
| # Copyright (c) 2020-2023 Omics Data Automation, Inc. | |
| # | |
| # Permission is hereby granted, free of charge, to any person obtaining a copy | |
| # of this software and associated documentation files (the "Software"), to deal | |
| # in the Software without restriction, including without limitation the rights | |
| # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | |
| # copies of the Software, and to permit persons to whom the Software is | |
| # furnished to do so, subject to the following conditions: | |
| # | |
| # The above copyright notice and this permission notice shall be included in | |
| # all copies or substantial portions of the Software. | |
| # | |
| # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | |
| # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | |
| # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | |
| # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | |
| # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | |
| # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | |
| # THE SOFTWARE. | |
| # | |
| name: build | |
| on: | |
| push: | |
| paths-ignore: | |
| - '**/*.md' | |
| pull_request: | |
| paths-ignore: | |
| - '**/*.md' | |
| env: | |
| CMAKE_BUILD_TYPE: Coverage | |
| CMAKE_BUILD_DIR: ${{github.workspace}}/build | |
| HADOOP_VER: 3.2.4 | |
| AWSSDK_VER: 1.8.x | |
| GCSSDK_VER: v1.24.0 | |
| # Only used to install Catch2 on Ubuntu from source | |
| # MacOS uses brew that installs v3.1.0 | |
| # Ubuntu distributions are currently on v2.13.9 | |
| CATCH2_VER: v2.13.9 | |
| jobs: | |
| build: | |
| strategy: | |
| matrix: | |
| os: [ubuntu-20.04] | |
| # All supported types | |
| # type: [basic, basic-no-hdfs, basic-codec, hdfs, gcs, azure, azurite, aws] | |
| type: [basic, basic-no-hdfs, basic-codec, hdfs, gcs, azure, aws] | |
| include: | |
| - os: macos-13 | |
| type: basic | |
| openssl-version: 1.1 | |
| - os: macos-13 | |
| type: basic | |
| openssl-version: 3 | |
| - os: ubuntu-22.04 | |
| type: basic | |
| #- os: ubuntu-22.04 | |
| #type: azurite | |
| - os: ubuntu-22.04 | |
| type: aws | |
| - os: ubuntu-22.04 | |
| type: gcs | |
| - os: ubuntu-22.04 | |
| type: azure | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Create Build Environment | |
| shell: bash | |
| run: | | |
| mkdir -p $CMAKE_BUILD_DIR | |
| # For extracting cached Catch2 | |
| sudo chmod a+rwx /usr/local/include /usr/local/lib /usr/local/share /usr/local/share/doc | |
| mkdir -p /usr/local/share/vcpkg/ports | |
| - name: Cache AWS SDK | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/awssdk-install | |
| key: awssdk-${{env.AWSSDK_VER}}-${{matrix.os}}-openssl-${{matrix.openssl-version}}-v1 | |
| - name: Cache GCS SDK | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/gcssdk-install | |
| key: gcssdk-${{env.GCSSDK_VER}}-${{matrix.os}}-openssl-${{matrix.openssl-version}}-v1 | |
| - name: Cache Catch2 artifacts | |
| if: startsWith(matrix.os,'ubuntu') | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/catch2-install | |
| key: catch2-${{env.CATCH2_VER}}-v0-${{matrix.os}} | |
| - name: Cache Distributed FileSystems | |
| if: matrix.type == 'hdfs' || matrix.type == 'gcs' | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{runner.workspace}}/hadoop-${{env.HADOOP_VER}} | |
| key: dfs-${{env.HADOOP_VER}}-v1-${{matrix.os}}-openssl-v1 | |
| - name: Install Prereqs and Configure CMake - Ubuntu | |
| if: startsWith(matrix.os,'ubuntu') | |
| shell: bash | |
| working-directory: ${{env.CMAKE_BUILD_DIR}} | |
| run: | | |
| sudo apt-get update -q | |
| sudo apt-get -y install cmake lcov | |
| sudo apt-get -y install zlib1g-dev libssl-dev uuid-dev libcurl4-openssl-dev | |
| # sudo apt-get -y install catch2 | |
| INSTALL_DIR=~/catch2-install CATCH2_VER=$CATCH2_VER $GITHUB_WORKSPACE/.github/scripts/install_catch2.sh | |
| export ENABLE_ZSTD=0 | |
| export ENABLE_BLOSC=0 | |
| if [[ ${{matrix.type}} == "basic-no-hdfs" ]]; then | |
| export USE_HDFS="-DUSE_HDFS=0" | |
| fi | |
| if [[ ${{matrix.type}} == "basic-codec" ]]; then | |
| source $GITHUB_WORKSPACE/.github/scripts/install_supported_codec.sh | |
| fi | |
| echo "CMAKE VERSION=$(cmake --version)" | |
| cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=$CMAKE_BUILD_TYPE \ | |
| -DCMAKE_PREFIX_PATH=~/catch2-install \ | |
| -DENABLE_ZSTD=$ENABLE_ZSTD -DENABLE_BLOSC=$ENABLE_BLOSC \ | |
| -DAWSSDK_VERSION=$AWSSDK_VER -DGCSSDK_VERSION=$GCSSDK_VER $USE_HDFS | |
| - name: Install Prereqs and Configure CMake - MacOS | |
| if: startsWith(matrix.os, 'macOS') | |
| shell: bash | |
| working-directory: ${{env.CMAKE_BUILD_DIR}} | |
| run: | | |
| brew list cmake &>/dev/null || brew install cmake | |
| brew list lcov &>/dev/null || brew install lcov | |
| brew list openssl@${{matrix.openssl-version}} &>/dev/null || brew install openssl@${{matrix.openssl-version}} | |
| brew list ossp-uuid &>/dev/null || brew install ossp-uuid | |
| brew list catch2 &>/dev/null || brew install catch2 | |
| cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=$CMAKE_BUILD_TYPE -DAWSSDK_VERSION=$AWSSDK_VER \ | |
| -DGCSSDK_VERSION=$GCSSDK_VER | |
| # GCS SDK needs OPENSSL_ROOT_DIR set for MAC, so build here | |
| make -j4 | |
| env: | |
| OPENSSL_ROOT_DIR: /usr/local/opt/openssl@${{matrix.openssl-version}} | |
| - name: Build and Test | |
| if: startsWith(matrix.type, 'basic') | |
| shell: bash | |
| working-directory: ${{env.CMAKE_BUILD_DIR}} | |
| run: | | |
| make -j4 | |
| make tests -j 4 | |
| export TILEDB_BENCHMARK=1 | |
| time TILEDB_BOOKKEEPING_STATS=1 TILEDB_CACHE=1 test/test_sparse_array_benchmark | |
| export TILEDB_DISABLE_FILE_LOCKING=1 | |
| time test/test_sparse_array_benchmark | |
| export TILEDB_KEEP_FILE_HANDLES_OPEN=1 | |
| time test/test_sparse_array_benchmark | |
| test/test_print_array_schema $GITHUB_WORKSPACE/test/inputs/examples_ws/sparse_arrays/my_array_B | |
| test/test_print_book_keeping $GITHUB_WORKSPACE/test/inputs/examples_ws/sparse_arrays/my_array_B/__4FECD19A-4F7D-4D21-B170-A2D111C8FCC44550772224_1652300381620 | |
| - name: Build and Test - Distributed FileSystems | |
| if: startsWith(matrix.type, 'basic') != true | |
| shell: bash | |
| working-directory: ${{env.CMAKE_BUILD_DIR}} | |
| run: | | |
| if [[ ${{matrix.type}} == "azurite" ]]; then | |
| source $GITHUB_WORKSPACE/.github/scripts/mkcert.sh | |
| source $GITHUB_WORKSPACE/.github/scripts/install_azurite.sh | |
| elif [[ ${{matrix.type}} == "minio" ]]; then | |
| source $GITHUB_WORKSPACE/.github/scripts/mkcert.sh | |
| source $GITHUB_WORKSPACE/.github/scripts/install_minio.sh | |
| elif [[ ${{matrix.type}} == "aws" ]]; then | |
| source $GITHUB_WORKSPACE/.github/scripts/install_aws.sh | |
| else | |
| source $GITHUB_WORKSPACE/.github/scripts/install_hadoop.sh | |
| fi | |
| source $GITHUB_WORKSPACE/.github/scripts/run_dfs_tests.sh | |
| env: | |
| INSTALL_DIR: ${{runner.workspace}} | |
| INSTALL_TYPE: ${{matrix.type}} | |
| R_TAR: ${{secrets.R_NEW_TAR}} | |
| AZ_TAR: ${{secrets.AZ_TAR}} | |
| AZURITE_TAR: ${{secrets.AZURITE_TAR}} | |
| AWS_TAR: ${{secrets.AWS_TAR}} | |
| - name: Upload Report to CodeCov | |
| uses: codecov/codecov-action@v4 | |
| env: | |
| CODECOV_TOKEN: ${{secrets.CODECOV_TOKEN}} |