new MODIS joint histograms #248
Workflow file for this run
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| # (c) British Crown Copyright 2020, the Met Office. | |
| # All rights reserved. | |
| # | |
| # Redistribution and use in source and binary forms, with or without | |
| # modification, are permitted provided that the following conditions are met: | |
| # | |
| # * Redistributions of source code must retain the above copyright notice, | |
| # this list of conditions and the following disclaimer. | |
| # * Redistributions in binary form must reproduce the above copyright notice, | |
| # this list of conditions and the following disclaimer in the documentation | |
| # and/or other materials provided with the distribution. | |
| # * Neither the name of the Met Office nor the names of its contributors may | |
| # be used to endorse or promote products derived from this softwarewithout | |
| # specific prior written permission. | |
| # | |
| # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" | |
| # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE | |
| # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE | |
| # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE | |
| # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR | |
| # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF | |
| # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS | |
| # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN | |
| # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) | |
| # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF | |
| # THE POSSIBILITY OF SUCH DAMAGE. | |
| # Workflow for continuous integration tests | |
| name: CI | |
| on: [push, pull_request] | |
| jobs: | |
| # This workflow contains a single job called "test" | |
| test: | |
| # The type of runner that the job will run on | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| matrix: | |
| fortran-compiler: [gfortran, gfortran-8, gfortran-7, ifort] | |
| env: | |
| F90: ${{ matrix.fortran-compiler }} | |
| FC: ${{ matrix.fortran-compiler }} | |
| F90FLAGS: "-O3 -ffree-line-length-none -fcheck=bounds -finit-real=nan" | |
| ATOL: 0.0 | |
| RTOL: 0.0 | |
| KGO_VERSION: v002 | |
| NFHOME: /home/runner/netcdf-fortran | |
| LD_LIBRARY_PATH: /home/runner/netcdf-fortran/lib | |
| # Sequence of tasks that will be executed as part of the job | |
| steps: | |
| # Checks-out repository under $GITHUB_WORKSPACE | |
| - uses: actions/checkout@v2 | |
| ############################################################################### | |
| # Initial steps | |
| ############################################################################### | |
| # Set up Python and install dependencies | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.7 | |
| - name: Setup conda | |
| uses: s-weigand/setup-conda@v1 | |
| with: | |
| python-version: 3.7 | |
| - name: Install python packages | |
| run: conda install --yes cartopy matplotlib netcdf4 | |
| # Update system packages | |
| - name: Update system packages | |
| run: sudo apt-get update | |
| # Non compiler-specific environment | |
| - name: Non compiler-specific environment | |
| run: export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${NFHOME}/lib | |
| ############################################################################### | |
| # FORTRAN compilers | |
| ############################################################################### | |
| # | |
| # Install gfortran compiler | |
| # | |
| - name: Install gfortran compiler | |
| if: contains(matrix.fortran-compiler, 'gfortran') | |
| run: sudo apt-get install ${{ matrix.fortran-compiler }} | |
| # | |
| # Intel compilers | |
| # | |
| - name: cache-intel-compilers | |
| id: cache-intel-compilers | |
| if: contains(matrix.fortran-compiler, 'ifort') | |
| uses: actions/cache@v2 | |
| with: | |
| path: /opt/intel | |
| key: intel-${{ runner.os }}-compilers-b | |
| # https://software.intel.com/content/www/us/en/develop/articles/installing-intel-oneapi-toolkits-via-apt.html | |
| # List of packages from Docler file at | |
| # https://github.com/intel/oneapi-containers/blob/master/images/docker/hpckit-devel-ubuntu18.04/Dockerfile | |
| - name: Install Intel compilers and libraries | |
| if: contains(matrix.fortran-compiler, 'ifort') && steps.cache-intel-compilers.outputs.cache-hit != 'true' | |
| run: | | |
| wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB | |
| sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB | |
| sudo add-apt-repository "deb https://apt.repos.intel.com/oneapi all main" | |
| sudo apt-get update | |
| sudo apt-get install intel-hpckit-getting-started intel-oneapi-clck intel-oneapi-common-licensing intel-oneapi-common-vars | |
| sudo apt-get install intel-oneapi-dev-utilities intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic intel-oneapi-compiler-fortran intel-oneapi-itac | |
| # | |
| # Nvidia compilers | |
| # | |
| - name: cache-nvidia-compilers | |
| id: cache-nvidia-compilers | |
| if: contains(matrix.fortran-compiler, 'nvfortran') | |
| uses: actions/cache@v2 | |
| with: | |
| path: /opt/nvidia/hpc_sdk/ | |
| key: nvhpc-${{ runner.os }}-2020-20.7 | |
| - name: Nvidia setup compilers | |
| if: contains(matrix.fortran-compiler, 'nvfortran') && steps.cache-nvidia-compilers.outputs.cache-hit != 'true' | |
| env: | |
| NVCOMPILERS: /opt/nvidia/hpc_sdk | |
| run: | | |
| wget -q https://developer.download.nvidia.com/hpc-sdk/nvhpc-20-7_20.7_amd64.deb https://developer.download.nvidia.com/hpc-sdk/nvhpc-2020_20.7_amd64.deb | |
| sudo apt-get install ./nvhpc-20-7_20.7_amd64.deb ./nvhpc-2020_20.7_amd64.deb | |
| ############################################################################### | |
| # Compiler-specific environment | |
| ############################################################################### | |
| # Environments for ifort and nvidia compilers | |
| - name: Environment for ifort compiler | |
| if: contains(matrix.fortran-compiler, 'ifort') | |
| run: | | |
| echo "CC=icx" > $GITHUB_ENV | |
| echo "FC=ifort" > $GITHUB_ENV | |
| echo "F90FLAGS=-O3 -heap-arrays" > $GITHUB_ENV | |
| - name: Environment for nvfortran compiler | |
| env: | |
| NVCOMPILERS: /opt/nvidia/hpc_sdk | |
| if: contains(matrix.fortran-compiler, 'nvfortran') | |
| run: | | |
| echo "CC=nvc" > $GITHUB_ENV | |
| echo "FC=nvfortran" > $GITHUB_ENV | |
| echo "F90FLAGS=-Mallocatable=03 -Mstandard -Mbounds -Mchkptr -Kieee -Mchkstk" > $GITHUB_ENV | |
| echo "${NVCOMPILERS}/Linux_x86_64/20.7/compilers/bin" >> $GITHUB_PATH | |
| ############################################################################### | |
| # NetCDF C and FORTRAN libraries | |
| ############################################################################### | |
| # NetCDF C library | |
| - name: Install NetCDF library | |
| run: sudo apt-get install libnetcdf-dev | |
| # Cache netcdf FORTRAN library | |
| - name: cache-netcdf-fortran | |
| id: cache-netcdf-fortran | |
| uses: actions/cache@v2 | |
| with: | |
| path: /home/runner/netcdf-fortran | |
| key: netcdf-fortran-4.4.4a-${{ runner.os }}-${{ matrix.fortran-compiler }}-v02 | |
| # Build NetCDF FORTRAN library for current compiler | |
| - name: Build NetCDF FORTRAN library | |
| env: | |
| FCFLAGS: -fPIC | |
| if: steps.cache-netcdf-fortran.outputs.cache-hit != 'true' | |
| run: | | |
| source /opt/intel/oneapi/setvars.sh || true | |
| ${F90} --version | |
| git clone https://github.com/Unidata/netcdf-fortran.git --branch v4.4.4 | |
| cd netcdf-fortran | |
| ./configure --prefix=${NFHOME} | |
| make -j | |
| sudo make install | |
| ############################################################################### | |
| # Build COSP and retrieve input and test files | |
| ############################################################################### | |
| # Build COSP2 driver. Intel Fortran stores automatic arrays in the stack | |
| # by default, whereas GNU Fortran stores them in the heap. This can cause | |
| # segmentation faults with ifort, especially in memory-intensive applications | |
| # like COSP. We tell ifort to use heap arrays. | |
| - name: Build driver | |
| run: | | |
| source /opt/intel/oneapi/setvars.sh || true | |
| ${F90} --version | |
| cd build | |
| make -j driver | |
| # Retrieve and expand large data files | |
| - name: Retrieve data files | |
| run: | | |
| GDFILE='https://docs.google.com/uc?export=download&id=17eK4_DVEvFOE9Uf6siXJDpWZJKT1aqkU' | |
| OUTPATH=driver/data/inputs/UKMO/cosp_input.um_global.nc.gz | |
| wget --no-check-certificate $GDFILE -O $OUTPATH | |
| gunzip ${OUTPATH} | |
| cd driver/data/inputs/UKMO | |
| md5sum -c cosp_input.um_global.nc.md5 | |
| cd ${GITHUB_WORKSPACE} | |
| GDFILE='https://docs.google.com/uc?export=download&id=1s5Ha6Hqnv_hWbRUs8KQpJ4Lxy8uvJDar' | |
| OUTPATH=driver/data/outputs/UKMO/cosp2_output.um_global.gfortran.kgo.$KGO_VERSION.nc.gz | |
| wget --no-check-certificate $GDFILE -O $OUTPATH | |
| gunzip ${OUTPATH} | |
| cd driver/data/outputs/UKMO | |
| md5sum -c cosp2_output.um_global.gfortran.kgo.$KGO_VERSION.nc.md5 | |
| cd ${GITHUB_WORKSPACE} | |
| GDFILE='https://docs.google.com/uc?export=download&id=11dKcIL3EQr7s6jbo4f9GsoW0SufesGbq' | |
| OUTPATH=driver/data/outputs/UKMO/cosp2_output_um.gfortran.kgo.$KGO_VERSION.nc.gz | |
| wget --no-check-certificate $GDFILE -O $OUTPATH | |
| gunzip ${OUTPATH} | |
| cd driver/data/outputs/UKMO | |
| md5sum -c cosp2_output_um.gfortran.kgo.$KGO_VERSION.nc.md5 | |
| cd ${GITHUB_WORKSPACE} | |
| GDFILE='https://docs.google.com/uc?export=download&id=1kY1lRgzd0UhDiQef2u-VgTQql_iut3U2' | |
| OUTPATH=driver/data/outputs/UKMO/cosp2_output.um_global_model_levels.gfortran.kgo.$KGO_VERSION.nc.gz | |
| wget --no-check-certificate $GDFILE -O $OUTPATH | |
| gunzip ${OUTPATH} | |
| cd driver/data/outputs/UKMO | |
| md5sum -c cosp2_output.um_global_model_levels.gfortran.kgo.$KGO_VERSION.nc.md5 | |
| ############################################################################### | |
| # Run COSP2 tests. We could run both tests in one step, but | |
| # doing it this way the output is easier to interpret. | |
| ############################################################################### | |
| # 1. Basic test | |
| - name: Basic test | |
| run: | | |
| source /opt/intel/oneapi/setvars.sh || true | |
| cd driver/run | |
| ./cosp2_test cosp2_input_nl.txt | |
| # 2. UM global snapshot | |
| - name: UM global snapshot | |
| run: | | |
| source /opt/intel/oneapi/setvars.sh || true | |
| cd driver/run | |
| ./cosp2_test cosp2_input_nl.um_global.txt | |
| # 3. UM global snapshot. Diagnostics on model levels. | |
| - name: UM global snapshot. Diagnostics on model levels. | |
| run: | | |
| if [[ "${F90}" = 'gfortran' ]]; then | |
| cd driver/run | |
| ./cosp2_test cosp2_input_nl.um_global_model_levels.txt cosp2_output_nl.um_global_model_levels.txt | |
| else | |
| echo "Test is only run for gfortran compiler." | |
| fi | |
| ############################################################################### | |
| # Compare results against known good outputs. As above, | |
| # we split it in as many steps as tests. | |
| ############################################################################### | |
| # 1. Basic test | |
| - name: Basic against known good output (KGO) | |
| run: | | |
| if [[ "${F90}" != 'gfortran' ]]; then | |
| ATOL=1.0e-20 | |
| RTOL=0.0006 | |
| fi | |
| cd driver | |
| KGO=data/outputs/UKMO/cosp2_output_um.gfortran.kgo.$KGO_VERSION.nc | |
| TST=data/outputs/UKMO/cosp2_output_um.nc | |
| python compare_to_kgo.py ${KGO} ${TST} --atol=${ATOL} --rtol=${RTOL} | |
| # 2. UM global snapshot. The approach used for the basic test would needed | |
| # large tolerances for the ifort compiler. We keep tolerances small for ifort, | |
| # and then we test against the output table. | |
| - name: UM global against known good output (KGO) | |
| run: | | |
| cd driver | |
| KGO=data/outputs/UKMO/cosp2_output.um_global.gfortran.kgo.$KGO_VERSION.nc | |
| TST=data/outputs/UKMO/cosp2_output.um_global.nc | |
| if [[ "${F90}" = 'gfortran' ]]; then | |
| python compare_to_kgo.py ${KGO} ${TST} --atol=${ATOL} --rtol=${RTOL} | |
| else | |
| ATOL=1.0e-20 | |
| RTOL=0.0006 | |
| OUTTST=data/outputs/UKMO/cosp2_output.um_global.out | |
| OUTKGO=data/outputs/UKMO/cosp2_output.um_global.${F90}.kgo.${KGO_VERSION}.out | |
| python compare_to_kgo.py ${KGO} ${TST} --atol=${ATOL} --rtol=${RTOL} \ | |
| --noerror=True --stats_file=${OUTTST} | |
| diff ${OUTKGO} ${OUTTST} | |
| fi | |
| # 3. UM global snapshot. Diagnostics on model levels. Only gfortran. | |
| - name: UM global on model levels against known good output (KGO) | |
| run: | | |
| cd driver | |
| KGO=data/outputs/UKMO/cosp2_output.um_global_model_levels.gfortran.kgo.$KGO_VERSION.nc | |
| TST=data/outputs/UKMO/cosp2_output.um_global_model_levels.nc | |
| if [[ "${F90}" = 'gfortran' ]]; then | |
| python compare_to_kgo.py ${KGO} ${TST} --atol=${ATOL} --rtol=${RTOL} | |
| else | |
| echo "Test only run for gfortran compiler." | |
| fi | |
| ############################################################################### | |
| # Produce plots when it fails during global snapshot tests, | |
| # and create a tarball with outputs. | |
| ############################################################################### | |
| - name: Produce plots and create tarball | |
| if: failure() | |
| run: | | |
| TST_MLEV=data/outputs/UKMO/cosp2_output.um_global_model_levels.nc | |
| cd driver | |
| if [[ -e data/outputs/UKMO/cosp2_output.um_global.nc ]]; then | |
| python plot_test_outputs.py | |
| fi | |
| if [[ -e data/outputs/UKMO/cosp2_output.um_global_model_levels.nc ]]; then | |
| python plot_test_outputs.py --tst_file=$TST_MLEV | |
| fi | |
| cd data/outputs/UKMO | |
| tar --ignore-failed-read -czf outputs.UKMO.tgz cosp2_output.um_global.nc \ | |
| cosp2_output_um.nc cosp2_output.um_global_model_levels.nc *.png \ | |
| cosp2_output.um_global.out | |
| ls -lh | |
| ############################################################################### | |
| # Make output files available if any test fails | |
| ############################################################################### | |
| - name: Upload output file if test fails | |
| if: failure() | |
| uses: actions/[email protected] | |
| with: | |
| name: outputs.UKMO.tgz | |
| path: driver/data/outputs/UKMO/outputs.UKMO.tgz |