Address CodeQL issues #7
Workflow file for this run
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| # For most projects, this workflow file will not need changing; you simply need | |
| # to commit it to your repository. | |
| # | |
| # You may wish to alter this file to override the set of languages analyzed, | |
| # or to provide custom queries or build logic. | |
| # | |
| # ******** NOTE ******** | |
| # We have attempted to detect the languages in your repository. Please check | |
| # the `language` matrix defined below to confirm you have the correct set of | |
| # supported CodeQL languages. | |
| # | |
| name: "CodeQL Advanced" | |
| on: | |
| push: | |
| branches: [ "develop" ] | |
| pull_request: | |
| branches: [ "develop" ] | |
| schedule: | |
| - cron: '43 6 * * 3' | |
| jobs: | |
| analyze: | |
| name: Analyze c-cpp | |
| # Runner size impacts CodeQL analysis time. To learn more, please see: | |
| # - https://gh.io/recommended-hardware-resources-for-running-codeql | |
| # - https://gh.io/supported-runners-and-hardware-resources | |
| # - https://gh.io/using-larger-runners (GitHub.com only) | |
| # Consider using larger runners or machines with greater resources for possible analysis time improvements. | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 20 | |
| permissions: | |
| # required for all workflows | |
| security-events: write | |
| # required to fetch internal or private CodeQL packs | |
| packages: read | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - language: c-cpp | |
| build-mode: manual | |
| # CodeQL supports the following values keywords for 'language': 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift' | |
| # Use `c-cpp` to analyze code written in C, C++ or both | |
| # Use 'java-kotlin' to analyze code written in Java, Kotlin or both | |
| # Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both | |
| # To learn more about changing the languages that are analyzed or customizing the build mode for your analysis, | |
| # see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning. | |
| # If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how | |
| # your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4.1.1 | |
| - name: Dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install libtool | |
| git config pull.rebase false | |
| # hdf5 | |
| git clone https://github.com/HDFGroup/hdf5.git | |
| # async vol | |
| git clone https://github.com/hpc-io/vol-async.git | |
| # Argobots | |
| git clone https://github.com/pmodels/argobots.git | |
| # h5bench | |
| git clone https://github.com/zhenghh04/h5bench.git | |
| # mpi | |
| sudo apt-get install libopenmpi-dev | |
| # zlib | |
| sudo apt-get install zlib1g-dev | |
| # python3 | |
| sudo apt-get install python3 | |
| - name: Installation (dependences) | |
| run: | | |
| export mydir="$PWD" | |
| export EXAHDF5_ROOT=$mydir | |
| echo "EXAHDF5_ROOT=$mydir" >> $GITHUB_ENV | |
| export SDK_DIR=$EXAHDF5_ROOT/soft | |
| echo "SDK_DIR=$EXAHDF5_ROOT/soft" >> $GITHUB_ENV | |
| mkdir -p $SDK_DIR | |
| export HDF5_ROOT=$SDK_DIR/hdf5 | |
| echo "HDF5_ROOT=$SDK_DIR/hdf5" >> $GITHUB_ENV | |
| mkdir -p $HDF5_ROOT | |
| export HDF5_HOME=$HDF5_ROOT | |
| export HDF5_DIR=$HDF5_ROOT | |
| echo "HDF5_DIR=$HDF5_ROOT" >> $GITHUB_ENV | |
| export HDF5_VOL_DIR=$SDK_DIR/hdf5/vol | |
| echo "HDF5_VOL_DIR=$SDK_DIR/hdf5/vol" >> $GITHUB_ENV | |
| mkdir -p $HDF5_VOL_DIR | |
| mkdir -p $HDF5_VOL_DIR/lib/ | |
| mkdir -p $HDF5_VOL_DIR/include/ | |
| export ABT_DIR=$SDK_DIR/argobots/ | |
| echo "ABT_DIR=$SDK_DIR/argobots/" >> $GITHUB_ENV | |
| mkdir -p $ABT_DIR | |
| # Compile HDF5 | |
| mkdir -p hdf5/build | |
| cd hdf5/build | |
| cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$HDF5_DIR -DHDF5_ENABLE_PARALLEL:BOOL=ON -DHDF5_ENABLE_THREADSAFE:BOOL=ON -DHDF5_ALLOW_UNSUPPORTED:BOOL=ON .. | |
| make -j2 install | |
| cd - | |
| cd argobots | |
| ./autogen.sh | |
| ./configure --prefix=$ABT_DIR | |
| make && make install -j2 | |
| cd - | |
| # Compile Asynchronous VOL connector | |
| mkdir -p vol-async/build | |
| cd vol-async/build | |
| cmake .. -DCMAKE_INSTALL_PREFIX=$HDF5_VOL_DIR -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx | |
| make all install -j2 | |
| # Initializes the CodeQL tools for scanning. | |
| - name: Initialize CodeQL | |
| uses: github/codeql-action/init@v3 | |
| with: | |
| languages: c-cpp | |
| build-mode: manual | |
| config-file: ./.github/codeql-config.yml | |
| # If you wish to specify custom queries, you can do so here or in a config file. | |
| # By default, queries listed here will override any specified in a config file. | |
| # Prefix the list here with "+" to use these queries and those in the config file. | |
| # For more details on CodeQL's query packs, refer to: | |
| #https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs | |
| queries: +security-extended,security-and-quality | |
| - name: Installation (Cache VOL connector) | |
| run: | | |
| # Compile Cache VOL connector | |
| mkdir -p build | |
| cd build | |
| cmake .. -DCMAKE_INSTALL_PREFIX=$HDF5_VOL_DIR -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx | |
| make all install -j2 | |
| cd .. | |
| # Compile h5bench | |
| mkdir -p h5bench/build | |
| cd h5bench/build | |
| cmake .. -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_INSTALL_PREFIX=$SDK_DIR/h5bench -DWITH_CACHE_VOL:BOOL=ON -DWITH_ASYNC_VOL:BOOL=ON -DCMAKE_C_FLAGS="-I$HDF5_VOL_DIR/include -I$HDF5_DIR/include -L$HDF5_VOL_DIR/lib -L$HDF5_DIR/lib -g" | |
| make all install VERBOSE=1 -j2 | |
| - name: Test Vol-Cache-Node-Local | |
| run: | | |
| ulimit -d unlimited | |
| ulimit -s unlimited | |
| mkdir -p SSD | |
| export PATH=$EXAHDF5_ROOT/soft/h5bench/bin:$HDF5_VOL_DIR/bin:$PATH | |
| export HDF5_PLUGIN_PATH=$HDF5_VOL_DIR/lib | |
| export LD_LIBRARY_PATH=$HDF5_PLUGIN_PATH:$ABT_DIR/lib:$HDF5_ROOT/lib:$HDF5_VOL_DIR/lib:$LD_LIBRARY_PATH | |
| export HDF5_CACHE_DEBUG=100 | |
| printf "HDF5_CACHE_STORAGE_TYPE: SSD\nHDF5_CACHE_STORAGE_PATH: SSD\nHDF5_CACHE_STORAGE_SCOPE: LOCAL\nHDF5_CACHE_STORAGE_SIZE: 128755813888\nHDF5_CACHE_WRITE_BUFFER_SIZE: 17179869184" > cache_1.cfg | |
| export LD_PRELOAD=$ABT_DIR/lib/libabt.so | |
| cat cache_1.cfg | |
| HDF5_VOL_CONNECTOR='' prepare_dataset.exe | |
| export HDF5_VOL_CONNECTOR="cache_ext config=cache_1.cfg;under_vol=512;under_info={under_vol=0;under_info={}}" | |
| for opt in 'yes' 'no' | |
| do | |
| echo "Testing" | |
| HDF5_CACHE_WR=$opt mpirun -np 2 write_cache.exe | |
| HDF5_CACHE_RD=$opt mpirun -np 2 read_cache.exe | |
| HDF5_CACHE_WR=$opt mpirun -np 2 test_dataset.exe | |
| HDF5_CACHE_WR=$opt mpirun -np 2 test_dataset_async_api.exe | |
| HDF5_CACHE_WR=$opt mpirun -np 2 test_group.exe | |
| HDF5_CACHE_WR=$opt mpirun -np 2 test_file.exe | |
| HDF5_CACHE_WR=$opt mpirun -np 2 h5bench_write ./tests/test_h5bench.cfg test.h5 | |
| done | |
| - name: Test Vol-Cache-MEMORY | |
| run: | | |
| ulimit -d unlimited | |
| ulimit -s unlimited | |
| mkdir -p SSD | |
| export PATH=$EXAHDF5_ROOT/soft/h5bench/bin:$HDF5_VOL_DIR/bin:$PATH | |
| export HDF5_PLUGIN_PATH=$HDF5_VOL_DIR/lib | |
| export LD_LIBRARY_PATH=$HDF5_PLUGIN_PATH:$ABT_DIR/lib:$HDF5_ROOT/lib:$HDF5_VOL_DIR/lib:$LD_LIBRARY_PATH | |
| export HDF5_CACHE_DEBUG=100 | |
| printf "HDF5_CACHE_STORAGE_TYPE: MEMORY\nHDF5_CACHE_STORAGE_PATH: SSD\nHDF5_CACHE_STORAGE_SCOPE: LOCAL\nHDF5_CACHE_STORAGE_SIZE: 128755813888\nHDF5_CACHE_WRITE_BUFFER_SIZE: 2147483648" > cache_1.cfg | |
| export LD_PRELOAD=$ABT_DIR/lib/libabt.so | |
| cat cache_1.cfg | |
| HDF5_VOL_CONNECTOR='' prepare_dataset.exe | |
| export HDF5_VOL_CONNECTOR="cache_ext config=cache_1.cfg;under_vol=512;under_info={under_vol=0;under_info={}}" | |
| for opt in 'yes' 'no' | |
| do | |
| echo "Testing" | |
| HDF5_CACHE_LOG_LEVEL=debug HDF5_CACHE_WR=$opt mpirun -np 1 test_dataset.exe | |
| HDF5_CACHE_LOG_LEVEL=debug HDF5_CACHE_WR=$opt mpirun -np 1 write_cache.exe | |
| HDF5_CACHE_RD=$opt mpirun -np 2 read_cache.exe | |
| HDF5_CACHE_WR=$opt mpirun -np 2 test_dataset_async_api.exe | |
| HDF5_CACHE_WR=$opt mpirun -np 2 test_group.exe | |
| HDF5_CACHE_WR=$opt mpirun -np 2 test_file.exe | |
| HDF5_CACHE_WR=$opt mpirun -np 2 h5bench_write ./tests/test_h5bench.cfg test.h5 | |
| done | |
| - name: Perform CodeQL Analysis | |
| uses: github/codeql-action/analyze@v3 | |
| with: | |
| category: "/language:c-cpp" | |
| output: sarif-results | |
| - name: filter-sarif | |
| uses: advanced-security/filter-sarif@main | |
| with: | |
| patterns: | | |
| -**/* | |
| +src/**/* | |
| input: sarif-results | |
| output: sarif-results/c-cpp.sarif | |
| - name: Upload SARIF | |
| uses: github/codeql-action/upload-sarif@v3 | |
| with: | |
| sarif_file: sarif-results/c-cpp.sarif | |
| - name: Upload loc as a Build Artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: sarif-results | |
| path: sarif-results | |
| retention-days: 1 |