Fix Stack Overflow problem by moving large arrays from the stack to the heap #122
Workflow file for this run
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| ### | |
| # Build hdf4, hdf5 dependencies and cache them in a combined directory. | |
| ### | |
| name: Run netCDF-Fortran Linux tests | |
| on: [pull_request, workflow_dispatch] | |
| concurrency: | |
| group: ${{ github.workflow}}-${{ github.head_ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| build-deps: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| hdf5: [ 1.12.2 ] | |
| netcdf: [ v4.7.4, v4.8.1, v4.9.0, main ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install System dependencies | |
| shell: bash -l {0} | |
| run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev gfortran | |
| ### | |
| # Set Environmental Variables | |
| ### | |
| - run: echo "CFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/include" >> $GITHUB_ENV | |
| - run: echo "LDFLAGS=-L${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
| - run: echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
| ### | |
| # Installing libhdf4 and libhdf5 | |
| ### | |
| - name: Cache libhdf5-${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
| id: cache-hdf5 | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
| key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
| - name: Build libhdf5-${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
| if: steps.cache-hdf5.outputs.cache-hit != 'true' | |
| run: | | |
| pushd $HOME | |
| wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$(echo ${{ matrix.hdf5 }} | cut -d. -f 1,2)/hdf5-${{ matrix.hdf5 }}/src/hdf5-${{ matrix.hdf5 }}.tar.bz2 | |
| tar -jxf hdf5-${{ matrix.hdf5 }}.tar.bz2 | |
| pushd hdf5-${{ matrix.hdf5 }} | |
| ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} --enable-hl --with-szlib | |
| make -j | |
| make install -j | |
| popd | |
| if [[ ${{ matrix.netcdf }} != "main" ]]; then | |
| git clone -b ${{ matrix.netcdf}} https://github.com/Unidata/netcdf-c | |
| pushd netcdf-c | |
| autoreconf -if | |
| CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
| make -j install | |
| popd | |
| fi | |
| popd | |
| build-deps-par: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| hdf5: [ 1.12.2 ] | |
| netcdf: [ v4.7.4, v4.8.1, v4.9.0, main ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install System dependencies | |
| shell: bash -l {0} | |
| run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev gfortran mpich libmpich-dev | |
| ### | |
| # Set Environmental Variables | |
| ### | |
| - run: echo "CC=mpicc" >> $GITHUB_ENV | |
| - run: echo "CFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/include" >> $GITHUB_ENV | |
| - run: echo "LDFLAGS=-L${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
| - run: echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
| ### | |
| # Installing libhdf4 and libhdf5 | |
| ### | |
| - name: Cache libhdf5-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-par | |
| id: cache-hdf5-par | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
| key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-par | |
| - name: Build libhdf5-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-par | |
| if: steps.cache-hdf5-par.outputs.cache-hit != 'true' | |
| run: | | |
| pushd $HOME | |
| wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$(echo ${{ matrix.hdf5 }} | cut -d. -f 1,2)/hdf5-${{ matrix.hdf5 }}/src/hdf5-${{ matrix.hdf5 }}.tar.bz2 &> /dev/null | |
| tar -jxf hdf5-${{ matrix.hdf5 }}.tar.bz2 | |
| pushd hdf5-${{ matrix.hdf5 }} | |
| ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} --enable-hl --with-szlib --enable-parallel | |
| make -j | |
| make install -j | |
| popd | |
| if [[ ${{ matrix.netcdf }} != "main" ]]; then | |
| git clone -b ${{ matrix.netcdf}} https://github.com/Unidata/netcdf-c | |
| pushd netcdf-c | |
| autoreconf -if | |
| CC=${CC} CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
| make -j install | |
| popd | |
| fi | |
| popd | |
| nf-autotools: | |
| needs: build-deps | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| hdf5: [ 1.12.2 ] | |
| netcdf: [ v4.7.4, v4.8.1, v4.9.0, main ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install System dependencies | |
| shell: bash -l {0} | |
| run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev libzstd-dev | |
| ### | |
| # Set Environmental Variables | |
| ### | |
| - run: echo "CFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/include" >> $GITHUB_ENV | |
| - run: echo "LDFLAGS=-L${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
| - run: echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
| - run: echo "HDF5_PLUGIN_PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
| - run: echo "HDF5_PLUGIN_DIR=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
| ### | |
| # Fetch Cache | |
| ### | |
| - name: Fetch HDF Cache | |
| id: cache-hdf | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
| key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
| - name: Check Cache | |
| shell: bash -l {0} | |
| run: ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} && ls ${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf}}/lib | |
| ### | |
| # Configure and build | |
| ### | |
| - name: Build netcdf-c if main | |
| run: | | |
| pushd $HOME | |
| git clone -b ${{ matrix.netcdf}} https://github.com/Unidata/netcdf-c | |
| pushd netcdf-c | |
| autoreconf -if | |
| CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} --with-plugin-dir=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib | |
| make -j install | |
| popd | |
| popd | |
| if: ${{ matrix.netcdf }} == "main" | |
| - name: Run autoconf | |
| shell: bash -l {0} | |
| run: autoreconf -if | |
| - name: Configure | |
| shell: bash -l {0} | |
| run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure | |
| - name: Look at config.log if error | |
| shell: bash -l {0} | |
| run: cat config.log | |
| if: ${{ failure() }} | |
| - name: Print Summary | |
| shell: bash -l {0} | |
| run: cat libnetcdff.settings | |
| - name: Build Library and Utilities | |
| shell: bash -l {0} | |
| run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make -j | |
| if: ${{ success() }} | |
| - name: Build Tests | |
| shell: bash -l {0} | |
| run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check TESTS="" -j | |
| if: ${{ success() }} | |
| - name: Run Tests | |
| shell: bash -l {0} | |
| run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check -j | |
| if: ${{ success() }} | |
| #- name: Make Distcheck | |
| # shell: bash -l {0} | |
| # run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make distcheck -j | |
| nf-autotools-par: | |
| needs: build-deps-par | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| hdf5: [ 1.12.2 ] | |
| netcdf: [ v4.7.4, v4.8.1, v4.9.0, main ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install System dependencies | |
| shell: bash -l {0} | |
| run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev mpich libmpich-dev libzstd-dev | |
| ### | |
| # Set Environmental Variables | |
| ### | |
| - run: echo "CC=mpicc" >> $GITHUB_ENV | |
| - run: echo "FC=mpifort" >> $GITHUB_ENV | |
| - run: echo "CFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/include" >> $GITHUB_ENV | |
| - run: echo "LDFLAGS=-L${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
| - run: echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
| - run: echo "HDF5_PLUGIN_PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
| - run: echo "HDF5_PLUGIN_DIR=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
| ### | |
| # Fetch Cache | |
| ### | |
| - name: Fetch HDF Cache | |
| id: cache-hdf-par | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
| key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }}-par | |
| - name: Check Cache | |
| shell: bash -l {0} | |
| run: ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} && ls ${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf}}/lib | |
| ### | |
| # Configure and build | |
| ### | |
| - name: Build netcdf-c if main | |
| run: | | |
| pushd $HOME | |
| git clone -b ${{ matrix.netcdf}} https://github.com/Unidata/netcdf-c | |
| pushd netcdf-c | |
| autoreconf -if | |
| CC=${CC} CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} --with-plugin-dir=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib | |
| make -j install | |
| popd | |
| popd | |
| if: ${{ matrix.netcdf }} == "main" | |
| - name: Run autoconf | |
| shell: bash -l {0} | |
| run: autoreconf -if | |
| - name: Configure | |
| shell: bash -l {0} | |
| run: CC=${CC} CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --enable-parallel-tests | |
| - name: Look at config.log if error | |
| shell: bash -l {0} | |
| run: cat config.log | |
| if: ${{ failure() }} | |
| - name: Print Summary | |
| shell: bash -l {0} | |
| run: cat libnetcdff.settings | |
| - name: Build Library and Utilities | |
| shell: bash -l {0} | |
| run: CC=${CC} CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make -j | |
| if: ${{ success() }} | |
| - name: Build Tests | |
| shell: bash -l {0} | |
| run: CC=${CC} CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check TESTS="" -j | |
| if: ${{ success() }} | |
| - name: Run Tests | |
| shell: bash -l {0} | |
| run: CC=${CC} CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make check -j | |
| if: ${{ success() }} | |
| #- name: Make Distcheck | |
| # shell: bash -l {0} | |
| # run: CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} make distcheck -j | |
| nf-cmake: | |
| needs: build-deps | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| hdf5: [ 1.12.2 ] | |
| netcdf: [ v4.7.4, v4.8.1, v4.9.0, main ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install System dependencies | |
| shell: bash -l {0} | |
| run: sudo apt update && sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev libzstd-dev | |
| ### | |
| # Set Environmental Variables | |
| ### | |
| - run: echo "CFLAGS=-I${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/include" >> $GITHUB_ENV | |
| - run: echo "LDFLAGS=-L${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
| - run: echo "LD_LIBRARY_PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
| - run: echo "CMAKE_PREFIX_PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf}}" >> $GITHUB_ENV | |
| - run: echo "HDF5_PLUGIN_PATH=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
| - run: echo "HDF5_PLUGIN_DIR=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib" >> $GITHUB_ENV | |
| ### | |
| # Fetch Cache | |
| ### | |
| - name: Fetch HDF Cache | |
| id: cache-hdf5 | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
| key: hdf5-${{ runner.os }}-${{ matrix.hdf5 }}-${{ matrix.netcdf }} | |
| - name: Check Cache | |
| shell: bash -l {0} | |
| run: ls ${HOME}/environments && ls ${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} && ls ${HOME}/environments/${{ matrix.hdf5 }}-${{matrix.netcdf}}/lib | |
| ### | |
| # Configure and build | |
| ### | |
| - name: Build netcdf-c if main | |
| run: | | |
| pushd $HOME | |
| git clone -b ${{ matrix.netcdf}} https://github.com/Unidata/netcdf-c | |
| pushd netcdf-c | |
| autoreconf -if | |
| CFLAGS=${CFLAGS} LDFLAGS=${LDFLAGS} LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ./configure --disable-static --enable-shared --prefix=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }} --with-plugin-dir=${HOME}/environments/${{ matrix.hdf5 }}-${{ matrix.netcdf }}/lib | |
| make -j install | |
| popd | |
| popd | |
| if: ${{ matrix.netcdf }} == "main" | |
| - name: Perform out-of-directory build | |
| shell: bash -l {0} | |
| run: LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake -Bbuild -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH} | |
| - name: Print Summary | |
| shell: bash -l {0} | |
| run: cat build/libnetcdff.settings | |
| - name: Build All | |
| shell: bash -l {0} | |
| run: LD_LIBRARY_PATH=${LD_LIBRARY_PATH} cmake --build build --parallel | |
| if: ${{ success() }} | |
| - name: Run Tests | |
| shell: bash -l {0} | |
| run: LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ctest --test-dir build | |
| if: ${{ success() }} | |
| - name: Look at LastTest.log if error | |
| shell: bash -l {0} | |
| run: | | |
| cat build/Testing/Temporary/LastTest.log | |
| LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ctest --test-dir build --rerun-failed --output-on-failure | |
| if: ${{ failure() }} |