Collect performance metrics by using one MPI_Gather instead of multip… #266
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| name: OpenMPI | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - github_action | |
| paths-ignore: | |
| - '**/*.md' | |
| - '**/*.txt' | |
| - '**/*.jpg' | |
| - '**/*.png' | |
| - 'tests/*' | |
| - 'datasets/*' | |
| pull_request: | |
| branches: master | |
| paths-ignore: | |
| - '**/*.md' | |
| - '**/*.txt' | |
| - '**/*.jpg' | |
| - '**/*.png' | |
| - 'tests/*' | |
| - 'datasets/*' | |
| env: | |
| PNETCDF_VERSION: 1.12.3 | |
| HDF5_VERSION: 1.14.2 | |
| NETCDF4_VERSION: 4.9.2 | |
| ADIOS_VERSION: 2.8.3 | |
| LOG_VOL_VERSION: 1.4.0 | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 60 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up dependencies | |
| run: | | |
| set -x | |
| sudo apt-get update | |
| sudo apt-get install automake autoconf libtool libtool-bin m4 | |
| # zlib | |
| sudo apt-get install zlib1g-dev | |
| # OpenMPI | |
| sudo apt-get install openmpi-bin openmpi-common libopenmpi-dev libgtk2.0-dev | |
| echo "---- location of OpenMPI C compiler ----" | |
| which mpicc | |
| - name: Install PnetCDF | |
| run: | | |
| set -x | |
| cd ${GITHUB_WORKSPACE} | |
| echo "Install PnetCDF on ${GITHUB_WORKSPACE}/PnetCDF" | |
| rm -rf PnetCDF ; mkdir PnetCDF ; cd PnetCDF | |
| curl -LO https://parallel-netcdf.github.io/Release/pnetcdf-${PNETCDF_VERSION}.tar.gz | |
| tar -zxf pnetcdf-${PNETCDF_VERSION}.tar.gz | |
| cd pnetcdf-${PNETCDF_VERSION} | |
| ./configure --prefix=${GITHUB_WORKSPACE}/PnetCDF \ | |
| --silent \ | |
| --disable-fortran \ | |
| --disable-cxx | |
| make -s LIBTOOLFLAGS=--silent V=1 -j 8 install > qout 2>&1 | |
| make -s distclean >> qout 2>&1 | |
| - name: Dump PnetCDF log file | |
| if: ${{ failure() }} | |
| run: | | |
| set -x | |
| cat ${GITHUB_WORKSPACE}/PnetCDF/pnetcdf-${PNETCDF_VERSION}/qout | |
| cat ${GITHUB_WORKSPACE}/PnetCDF/pnetcdf-${PNETCDF_VERSION}/config.log | |
| - name: Install HDF5 | |
| if: ${{ success() }} | |
| run: | | |
| set -x | |
| cd ${GITHUB_WORKSPACE} | |
| echo "Install HDF5 on ${GITHUB_WORKSPACE}/HDF5" | |
| rm -rf HDF5 ; mkdir HDF5 ; cd HDF5 | |
| VER_MAJOR=${HDF5_VERSION%.*} | |
| VER_NOPATCH=${HDF5_VERSION%-*} # remove patch version | |
| curl -LO https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${VER_MAJOR}/hdf5-${VER_NOPATCH}/src/hdf5-${HDF5_VERSION}.tar.gz | |
| tar -zxf hdf5-${HDF5_VERSION}.tar.gz | |
| cd hdf5-${HDF5_VERSION} | |
| ./configure --prefix=${GITHUB_WORKSPACE}/HDF5 \ | |
| --silent \ | |
| --enable-hl \ | |
| --enable-parallel \ | |
| --enable-build-mode=production \ | |
| --disable-doxygen-doc \ | |
| --disable-doxygen-man \ | |
| --disable-doxygen-html \ | |
| --disable-tools \ | |
| --disable-tests \ | |
| --disable-fortran \ | |
| --disable-cxx \ | |
| CC=mpicc | |
| make -s LIBTOOLFLAGS=--silent V=1 -j 8 install > qout 2>&1 | |
| make -s distclean >> qout 2>&1 | |
| - name: Dump HDF5 log file | |
| if: ${{ failure() }} | |
| run: | | |
| set -x | |
| cat ${GITHUB_WORKSPACE}/HDF5/hdf5-${HDF5_VERSION}/qout | |
| cat ${GITHUB_WORKSPACE}/HDF5/hdf5-${HDF5_VERSION}/config.log | |
| - name: Install NetCDF-C | |
| if: ${{ success() }} | |
| run: | | |
| set -x | |
| cd ${GITHUB_WORKSPACE} | |
| echo "Install NetCDF-C on ${GITHUB_WORKSPACE}/NetCDF" | |
| rm -rf NetCDF ; mkdir NetCDF ; cd NetCDF | |
| curl -LO https://github.com/Unidata/netcdf-c/archive/refs/tags/v${NETCDF4_VERSION}.tar.gz | |
| tar -zxf v${NETCDF4_VERSION}.tar.gz | |
| cd netcdf-c-${NETCDF4_VERSION} | |
| # TODO: Always use an official release. E3SM-IO requires NetCDF-C 4.9.0 or later. | |
| # rm -rf netcdf-c | |
| # git clone -q https://github.com/Unidata/netcdf-c.git | |
| # cd netcdf-c | |
| # autoreconf -i | |
| ./configure --prefix=${GITHUB_WORKSPACE}/NetCDF \ | |
| --silent \ | |
| --disable-dap \ | |
| --disable-nczarr \ | |
| --disable-nczarr-filters \ | |
| --disable-filter-testing \ | |
| --disable-byterange \ | |
| CC=mpicc \ | |
| CPPFLAGS="-I${GITHUB_WORKSPACE}/HDF5/include" \ | |
| LDFLAGS="-L${GITHUB_WORKSPACE}/HDF5/lib" \ | |
| LIBS="-lhdf5" | |
| make -s LIBTOOLFLAGS=--silent V=1 -j 8 install > qout 2>&1 | |
| make -s distclean >> qout 2>&1 | |
| - name: Dump NetCDF-C log file | |
| if: ${{ failure() }} | |
| run: | | |
| set -x | |
| cat ${GITHUB_WORKSPACE}/NetCDF/netcdf-c-${NETCDF4_VERSION}/qout | |
| cat ${GITHUB_WORKSPACE}/NetCDF/netcdf-c-${NETCDF4_VERSION}/config.log | |
| - name: Install ADIOS2 | |
| if: ${{ success() }} | |
| run: | | |
| set -x | |
| cd ${GITHUB_WORKSPACE} | |
| echo "Install ADIOS2 on ${GITHUB_WORKSPACE}/ADIOS" | |
| rm -rf ADIOS ; mkdir ADIOS ; cd ADIOS | |
| curl -LO https://github.com/ornladios/ADIOS2/archive/refs/tags/v${ADIOS_VERSION}.tar.gz | |
| tar -zxf v${ADIOS_VERSION}.tar.gz | |
| mkdir adios2_build | |
| cd adios2_build | |
| cmake -DCMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/ADIOS \ | |
| -DADIOS2_USE_MPI=ON \ | |
| -DADIOS2_USE_Fortran=OFF \ | |
| -DADIOS2_USE_Python=OFF \ | |
| -DADIOS2_USE_ZeroMQ=OFF \ | |
| -DADIOS2_USE_HDF5=OFF \ | |
| -DADIOS2_USE_IME=OFF \ | |
| -DADIOS2_USE_BZip2=OFF \ | |
| -DADIOS2_USE_ZFP=OFF \ | |
| -DADIOS2_USE_SZ=OFF \ | |
| -DADIOS2_USE_MGARD=OFF \ | |
| -DADIOS2_USE_PNG=OFF \ | |
| -DADIOS2_USE_Blosc=OFF \ | |
| -DADIOS2_BUILD_EXAMPLES=OFF \ | |
| -DBUILD_TESTING=OFF \ | |
| -DBUILD_SHARED_LIBS=OFF \ | |
| -DADIOS2_USE_SST=ON \ | |
| -DADIOS2_USE_BP5=ON \ | |
| ../ADIOS2-${ADIOS_VERSION} | |
| make -j 8 install > qout 2>&1 | |
| make clean >> qout 2>&1 | |
| - name: Dump ADIOS log file | |
| if: ${{ failure() }} | |
| run: | | |
| set -x | |
| cat ${GITHUB_WORKSPACE}/ADIOS/adios2_build/qout | |
| - name: Install Log VOL | |
| if: ${{ success() }} | |
| run: | | |
| set -x | |
| cd ${GITHUB_WORKSPACE} | |
| echo "Install Log VOL connector on ${GITHUB_WORKSPACE}/LOGVOL" | |
| rm -rf LOGVOL ; mkdir LOGVOL ; cd LOGVOL | |
| curl -LO https://github.com/DataLib-ECP/vol-log-based/archive/refs/tags/logvol.${LOG_VOL_VERSION}.tar.gz | |
| tar -zxf logvol.${LOG_VOL_VERSION}.tar.gz | |
| cd vol-log-based-logvol.${LOG_VOL_VERSION} | |
| autoreconf -i | |
| ./configure --prefix=${GITHUB_WORKSPACE}/LOGVOL \ | |
| --silent \ | |
| --with-hdf5=${GITHUB_WORKSPACE}/HDF5 | |
| make -s LIBTOOLFLAGS=--silent V=1 -j 8 install > qout 2>&1 | |
| make -s distclean >> qout 2>&1 | |
| - name: Dump log file | |
| if: ${{ failure() }} | |
| run: | | |
| set -x | |
| cat ${GITHUB_WORKSPACE}/LOGVOL/vol-log-based-logvol.${LOG_VOL_VERSION}/qout | |
| cat ${GITHUB_WORKSPACE}/LOGVOL/vol-log-based-logvol.${LOG_VOL_VERSION}/config.log | |
| - name: Build and check E3SM_IO with PnetCDF only | |
| if: ${{ success() }} | |
| run: | | |
| set -x | |
| cd ${GITHUB_WORKSPACE} | |
| rm -rf ./test_output | |
| autoreconf -i | |
| ./configure --with-pnetcdf=${GITHUB_WORKSPACE}/PnetCDF \ | |
| CC=mpicc CXX=mpicxx \ | |
| CFLAGS=-fno-var-tracking-assignments \ | |
| CXXFLAGS=-fno-var-tracking-assignments | |
| make -j 8 | |
| make check | |
| - name: Dump log files if E3SM_IO with PnetCDF-only test failed | |
| if: ${{ failure() }} | |
| run: | | |
| set -x | |
| cd ${GITHUB_WORKSPACE} | |
| cat test.sh.log utils/*.log | |
| - name: Build and check E3SM_IO with HDF5 only | |
| if: ${{ success() }} | |
| run: | | |
| set -x | |
| make -s distclean | |
| ./configure --with-hdf5=${GITHUB_WORKSPACE}/HDF5 \ | |
| CC=mpicc CXX=mpicxx \ | |
| CFLAGS=-fno-var-tracking-assignments \ | |
| CXXFLAGS=-fno-var-tracking-assignments | |
| make -j 8 | |
| make check | |
| - name: Dump log files if E3SM_IO with HDF5-only test failed | |
| if: ${{ failure() }} | |
| run: | | |
| set -x | |
| cd ${GITHUB_WORKSPACE} | |
| cat test.sh.log utils/*.log | |
| - name: Build and check E3SM_IO with HDF5 Log VOL connector only | |
| if: ${{ success() }} | |
| run: | | |
| set -x | |
| make -s distclean | |
| ./configure --with-hdf5=${GITHUB_WORKSPACE}/HDF5 \ | |
| --with-logvol=${GITHUB_WORKSPACE}/LOGVOL \ | |
| CC=mpicc CXX=mpicxx \ | |
| CFLAGS=-fno-var-tracking-assignments \ | |
| CXXFLAGS=-fno-var-tracking-assignments | |
| make -j 8 | |
| make check | |
| - name: Dump log files if E3SM_IO with HDF5 Log VOL connector test failed | |
| if: ${{ failure() }} | |
| run: | | |
| set -x | |
| cd ${GITHUB_WORKSPACE} | |
| cat test.sh.log utils/*.log | |
| - name: Build and check E3SM_IO with NetCDF4 only | |
| if: ${{ success() }} | |
| run: | | |
| set -x | |
| make -s distclean | |
| ./configure --with-netcdf4=${GITHUB_WORKSPACE}/NetCDF \ | |
| CC=mpicc CXX=mpicxx \ | |
| CFLAGS=-fno-var-tracking-assignments \ | |
| CXXFLAGS=-fno-var-tracking-assignments | |
| make -j 8 | |
| make check | |
| - name: Dump log files if E3SM_IO with NetCDF4-only test failed | |
| if: ${{ failure() }} | |
| run: | | |
| set -x | |
| cd ${GITHUB_WORKSPACE} | |
| cat test.sh.log utils/*.log | |
| - name: Build and check E3SM_IO with ADIOS only | |
| if: ${{ success() }} | |
| run: | | |
| set -x | |
| make -s distclean | |
| ./configure --with-adios2=${GITHUB_WORKSPACE}/ADIOS \ | |
| CC=mpicc CXX=mpicxx \ | |
| CFLAGS=-fno-var-tracking-assignments \ | |
| CXXFLAGS=-fno-var-tracking-assignments | |
| make -j 8 | |
| make check | |
| - name: Dump log files if E3SM_IO with ADIOS-only test failed | |
| if: ${{ failure() }} | |
| run: | | |
| set -x | |
| cd ${GITHUB_WORKSPACE} | |
| cat test.sh.log utils/*.log | |
| - name: Build and check E3SM_IO with all APIs | |
| if: ${{ success() }} | |
| run: | | |
| set -x | |
| make -s distclean | |
| ./configure --with-pnetcdf=${GITHUB_WORKSPACE}/PnetCDF \ | |
| --with-hdf5=${GITHUB_WORKSPACE}/HDF5 \ | |
| --with-netcdf4=${GITHUB_WORKSPACE}/NetCDF \ | |
| --with-logvol=${GITHUB_WORKSPACE}/LOGVOL \ | |
| --with-adios2=${GITHUB_WORKSPACE}/ADIOS \ | |
| CC=mpicc CXX=mpicxx \ | |
| CFLAGS=-fno-var-tracking-assignments \ | |
| CXXFLAGS=-fno-var-tracking-assignments \ | |
| TESTMPIRUN="mpiexec --oversubscribe" | |
| make -j 8 | |
| make check | |
| - name: Dump log files if E3SM_IO test failed | |
| if: ${{ failure() }} | |
| run: | | |
| set -x | |
| cd ${GITHUB_WORKSPACE} | |
| cat test.sh.log utils/*.log | |
| cat config.log | |
| ls -r ./test_output | |
| - name: Test E3SM_IO all APIs -- parallel runs | |
| if: ${{ success() }} | |
| run: | | |
| set -x | |
| make ptest | |
| - name: Test make distcheck | |
| if: ${{ success() }} | |
| run: | | |
| set -x | |
| make distcheck DISTCHECK_CONFIGURE_FLAGS="--with-pnetcdf=${GITHUB_WORKSPACE}/PnetCDF --with-hdf5=${GITHUB_WORKSPACE}/HDF5 --with-netcdf4=${GITHUB_WORKSPACE}/NetCDF --with-logvol=${GITHUB_WORKSPACE}/LOGVOL --with-adios2=${GITHUB_WORKSPACE}/ADIOS CC=mpicc CXX=mpicxx CFLAGS=-fno-var-tracking-assignments CXXFLAGS=-fno-var-tracking-assignments" | |
| make distclean | |