#2661 Update changelog, UG, and a docstring #3450
Workflow file for this run
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| # ----------------------------------------------------------------------------- | |
| # BSD 3-Clause License | |
| # | |
| # Copyright (c) 2024, Science and Technology Facilities Council. | |
| # 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 copyright holder nor the names of its | |
| # contributors may be used to endorse or promote products derived from | |
| # this software without 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 HOLDER 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. | |
| # ----------------------------------------------------------------------------- | |
| # Author S. Siso, STFC Daresbury Lab | |
| # This workflow will use a self-hosted runner to perform the more expensive | |
| # integrations tests that are not run on GHA systems. | |
| name: NEMOv4 Integration Tests | |
| on: | |
| push | |
| jobs: | |
| run_if_on_mirror: | |
| if: ${{ github.repository == 'stfc/PSyclone-mirror' }} | |
| runs-on: self-hosted | |
| env: | |
| HDF5_VERSION: 1.14.5 | |
| NETCDF_C_VERSION: 4.9.2 | |
| NETCDF_FORTRAN_VERSION: 4.6.1 | |
| NVFORTRAN_VERSION: 23.7 | |
| ONEAPI_VERSION: 2024.2.1 | |
| PERL_VERSION: 5.40.0 | |
| PYTHON_VERSION: 3.13.0 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| submodules: recursive | |
| # This is required to get the commit history for merge commits for | |
| # the ci-skip check below. | |
| fetch-depth: '0' | |
| - name: Check for [skip ci] in commit message | |
| uses: mstachniuk/ci-skip@v1 | |
| with: | |
| # This setting causes the tests to 'fail' if [skip ci] is specified | |
| fail-fast: true | |
| commit-filter: '[skip ci]' | |
| - name: Install dependencies | |
| run: | | |
| module load python/${PYTHON_VERSION} | |
| python -m venv .runner_venv | |
| . .runner_venv/bin/activate | |
| python -m pip install --upgrade pip | |
| # Uncomment the below to use the submodule version of fparser rather | |
| # than the latest release from pypi. | |
| # pip install external/fparser | |
| pip install .[test] | |
| # Compile nvidia profiling tools | |
| module load nvidia-hpcsdk/${NVFORTRAN_VERSION} | |
| cd lib/profiling/nvidia/ | |
| F90=nvfortran make | |
| # PSyclone passthrough for MetOffice NEMO | |
| - name: NEMO MetOffice Passthrough | |
| run: | | |
| . .runner_venv/bin/activate | |
| export PSYCLONE_NEMO_DIR=${GITHUB_WORKSPACE}/examples/nemo/scripts | |
| export NEMO_DIR=${HOME}/NEMO | |
| cd $PSYCLONE_NEMO_DIR | |
| module load nvidia-hpcsdk/${NVFORTRAN_VERSION} | |
| module load hdf5/${HDF5_VERSION} netcdf_c/${NETCDF_C_VERSION} netcdf_fortran/${NETCDF_FORTRAN_VERSION} | |
| module load perl/${PERL_VERSION} | |
| make -j 4 passthrough | |
| make -j 4 compile-passthrough | |
| # PSyclone, compile and run MetOffice NEMO with OpenMP for GPUs | |
| - name: NEMO MetOffice OpenMP for GPU | |
| run: | | |
| . .runner_venv/bin/activate | |
| export PSYCLONE_NEMO_DIR=${GITHUB_WORKSPACE}/examples/nemo/scripts | |
| export NEMO_DIR=${HOME}/NEMO | |
| cd $PSYCLONE_NEMO_DIR | |
| module load nvidia-hpcsdk/${NVFORTRAN_VERSION} | |
| module load hdf5/${HDF5_VERSION} netcdf_c/${NETCDF_C_VERSION} netcdf_fortran/${NETCDF_FORTRAN_VERSION} | |
| module load perl/${PERL_VERSION} | |
| make -j 4 openmp_gpu | |
| make -j 4 compile-openmp_gpu | |
| export NV_ACC_POOL_THRESHOLD=75 | |
| make run-openmp_gpu |& tee output.txt | |
| # Check the output is as expected for the first 6 digits (if not exit with error message) | |
| tail -n 1 output.txt | grep -q " it : 10" || (echo "Error: 'it : 10' not found!" & false) | |
| tail -n 1 output.txt | grep -q "|ssh|_max: 0.259483" || (echo "Error: '|ssh|_max: 0.259483' not found!" & false) | |
| tail -n 1 output.txt | grep -q "|U|_max: 0.458515" || (echo "Error: '|U|_max: 0.458515' not found!" & false) | |
| tail -n 1 output.txt | grep -q "S_min: 0.482686" || (echo "Error: 'S_min: 0.482686' not found!" & false) | |
| tail -n 1 output.txt | grep -q "S_max: 0.407622" || (echo "Error: 'S_max: 0.407622' not found!" & false) | |
| export VAR_TIME=$(grep -A 1 "Elapsed Time" output.txt | head -n 2 | tail -n 1 | awk '{print $1}') | |
| echo $GITHUB_REF_NAME $GITHUB_SHA $VAR_TIME >> ${HOME}/store_results/performance_history_openmp_gpu | |
| ${HOME}/mongosh-2.1.1-linux-x64/bin/mongosh \ | |
| "mongodb+srv://cluster0.x8ncpxi.mongodb.net/PerformanceMonitoring" \ | |
| --quiet --apiVersion 1 --username ${{ secrets.MONGODB_USERNAME }} \ | |
| --password ${{ secrets.MONGODB_PASSWORD }} \ | |
| --eval 'db.GitHub_CI.insertOne({branch_name: "'"$GITHUB_REF_NAME"'", commit: "'"$GITHUB_SHA"'", | |
| github_job: "'"$GITHUB_RUN_ID"'"-"'"$GITHUB_RUN_ATTEMPT"'", | |
| ci_test: "NEMO OpenMP for GPU", nemo_version: "NEMO MO 4.0.2", system: "GlaDos", | |
| compiler:"nvhpc-'"$NVFORTRAN_VERSION"'", date: new Date(), elapsed_time: '"$VAR_TIME"'})' | |
| # PSyclone, compile and run MetOffice NEMO with OpenACC kernels for GPUs | |
| - name: NEMO MetOffice OpenACC kernels for GPU | |
| run: | | |
| . .runner_venv/bin/activate | |
| export PSYCLONE_NEMO_DIR=${GITHUB_WORKSPACE}/examples/nemo/scripts | |
| export NEMO_DIR=${HOME}/NEMO | |
| cd $PSYCLONE_NEMO_DIR | |
| module load nvidia-hpcsdk/${NVFORTRAN_VERSION} | |
| module load hdf5/${HDF5_VERSION} netcdf_c/${NETCDF_C_VERSION} netcdf_fortran/${NETCDF_FORTRAN_VERSION} | |
| module load perl/${PERL_VERSION} | |
| make -j 4 openacc_kernels | |
| COMPILER_ARCH=linux_nvidia_acc_gpu make -j 4 compile-openacc_kernels | |
| export NV_ACC_POOL_THRESHOLD=75 | |
| make run-openacc_kernels |& tee output.txt | |
| # Check the output is as expected for the first 6 digits (if not exit with error message) | |
| tail -n 1 output.txt | grep -q " it : 10" || (echo "Error: 'it : 10' not found!" & false) | |
| tail -n 1 output.txt | grep -q "|ssh|_max: 0.259483" || (echo "Error: '|ssh|_max: 0.259483' not found!" & false) | |
| tail -n 1 output.txt | grep -q "|U|_max: 0.458515" || (echo "Error: '|U|_max: 0.458515' not found!" & false) | |
| tail -n 1 output.txt | grep -q "S_min: 0.482686" || (echo "Error: 'S_min: 0.482686' not found!" & false) | |
| tail -n 1 output.txt | grep -q "S_max: 0.407622" || (echo "Error: 'S_max: 0.407622' not found!" & false) | |
| export VAR_TIME=$(grep -A 1 "Elapsed Time" output.txt | head -n 2 | tail -n 1 | awk '{print $1}') | |
| echo $GITHUB_REF_NAME $GITHUB_SHA $VAR_TIME >> ${HOME}/store_results/performance_history_openacc_kernels_gpu | |
| ${HOME}/mongosh-2.1.1-linux-x64/bin/mongosh \ | |
| "mongodb+srv://cluster0.x8ncpxi.mongodb.net/PerformanceMonitoring" \ | |
| --quiet --apiVersion 1 --username ${{ secrets.MONGODB_USERNAME }} \ | |
| --password ${{ secrets.MONGODB_PASSWORD }} \ | |
| --eval 'db.GitHub_CI.insertOne({branch_name: "'"$GITHUB_REF_NAME"'", commit: "'"$GITHUB_SHA"'", | |
| github_job: "'"$GITHUB_RUN_ID"'"-"'"$GITHUB_RUN_ATTEMPT"'", | |
| ci_test: "NEMO OpenACC kernels for GPU", nemo_version: "MEMO MO 4.0.2", system: "GlaDos", | |
| compiler:"nvhpc-'"$NVFORTRAN_VERSION"'", date: new Date(), elapsed_time: '"$VAR_TIME"'})' | |
| # PSyclone, compile and run MetOffice NEMO with OpenACC loops for GPUs | |
| - name: NEMO MetOffice OpenACC loops for GPU | |
| run: | | |
| . .runner_venv/bin/activate | |
| export PSYCLONE_NEMO_DIR=${GITHUB_WORKSPACE}/examples/nemo/scripts | |
| export NEMO_DIR=${HOME}/NEMO | |
| cd $PSYCLONE_NEMO_DIR | |
| module load nvidia-hpcsdk/${NVFORTRAN_VERSION} | |
| module load hdf5/${HDF5_VERSION} netcdf_c/${NETCDF_C_VERSION} netcdf_fortran/${NETCDF_FORTRAN_VERSION} | |
| module load perl/${PERL_VERSION} | |
| make -j 4 openacc_loops | |
| COMPILER_ARCH=linux_nvidia_acc_gpu make -j 4 compile-openacc_loops | |
| export NV_ACC_POOL_THRESHOLD=75 | |
| make run-openacc_loops |& tee output.txt | |
| # Check the output is as expected for the first 6 digits (if not exit with error message) | |
| tail -n 1 output.txt | grep -q " it : 10" || (echo "Error: 'it : 10' not found!" & false) | |
| tail -n 1 output.txt | grep -q "|ssh|_max: 0.259483" || (echo "Error: '|ssh|_max: 0.259483' not found!" & false) | |
| tail -n 1 output.txt | grep -q "|U|_max: 0.458515" || (echo "Error: '|U|_max: 0.458515' not found!" & false) | |
| tail -n 1 output.txt | grep -q "S_min: 0.482686" || (echo "Error: 'S_min: 0.482686' not found!" & false) | |
| tail -n 1 output.txt | grep -q "S_max: 0.407622" || (echo "Error: 'S_max: 0.407622' not found!" & false) | |
| export VAR_TIME=$(grep -A 1 "Elapsed Time" output.txt | head -n 2 | tail -n 1 | awk '{print $1}') | |
| echo $GITHUB_REF_NAME $GITHUB_SHA $VAR_TIME >> ${HOME}/store_results/performance_history_openacc_loops_gpu | |
| ${HOME}/mongosh-2.1.1-linux-x64/bin/mongosh \ | |
| "mongodb+srv://cluster0.x8ncpxi.mongodb.net/PerformanceMonitoring" \ | |
| --quiet --apiVersion 1 --username ${{ secrets.MONGODB_USERNAME }} \ | |
| --password ${{ secrets.MONGODB_PASSWORD }} \ | |
| --eval 'db.GitHub_CI.insertOne({branch_name: "'"$GITHUB_REF_NAME"'", commit: "'"$GITHUB_SHA"'", | |
| github_job: "'"$GITHUB_RUN_ID"'"-"'"$GITHUB_RUN_ATTEMPT"'", | |
| ci_test: "NEMO OpenACC loops for GPU", nemo_version: "MEMO MO 4.0.2", system: "GlaDos", | |
| compiler:"nvhpc-'"$NVFORTRAN_VERSION"'", date: new Date(), elapsed_time: '"$VAR_TIME"'})' | |
| # PSyclone, compile and run ECMWF NEMO with OpenMP for CPUs. This uses | |
| # the Intel compiler and does not disable MPI. Therefore we have to ensure | |
| # that we provide the path to the header files for Intel MPI. | |
| - name: NEMO ECMWF OpenMP for CPU | |
| run: | | |
| . .runner_venv/bin/activate | |
| module load oneapi/${ONEAPI_VERSION} | |
| module load hdf5/${HDF5_VERSION} netcdf_c/${NETCDF_C_VERSION} netcdf_fortran/${NETCDF_FORTRAN_VERSION} | |
| module load perl/${PERL_VERSION} | |
| export PSYCLONE_NEMO_DIR=${GITHUB_WORKSPACE}/examples/nemo/scripts | |
| export NEMO_DIR=${HOME}/NEMOGCM_V40 | |
| export COMPILER_ARCH=linux_intel | |
| export ADD_KEYS="IEEE_IS_NAN=ieee_is_nan key_nosignedzero" | |
| export DEL_KEYS="key_iomput" | |
| export MODEL_DIR=/archive/ssiso/ecmwf_eORCA1_GO8/ | |
| export NAMELISTS_DIR=${NEMO_DIR}/testscripts_V40/output/openmp_outer_V40_eORCA1_GO8_Z75_20170906_cray_dp_1x1/ | |
| export MPI_INC_DIR=${I_MPI_ROOT}/include | |
| cd $PSYCLONE_NEMO_DIR | |
| make -j 4 openmp_cpu | |
| make -j 4 compile-openmp_cpu | |
| export OMP_NUM_THREADS=4 | |
| make run-openmp_cpu |& tee output.txt | |
| # Check the output is as expected for the first 6 digits | |
| tail -n 1 output.txt | grep -q " it : 10" || (echo "Error: 'it : 10' not found!" & false) | |
| tail -n 1 output.txt | grep -q "|ssh|_max: 0.199714" || (echo "Error: '|ssh|_max: 0.199714' not found!" & false) | |
| tail -n 1 output.txt | grep -q "|U|_max: 0.148409" || (echo "Error: '|U|_max: 0.148409' not found!" & false) | |
| tail -n 1 output.txt | grep -q "S_min: 0.108530" || (echo "Error: 'S_min: 0.108530' not found!" & false) | |
| tail -n 1 output.txt | grep -q "S_max: 0.404045" || (echo "Error: 'S_max: 0.404045' not found!" & false) | |
| export VAR_TIME=$(grep -A 1 "Elapsed Time" output.txt | head -n 2 | tail -n 1 | awk '{print $1}') | |
| echo $GITHUB_REF_NAME $GITHUB_SHA $VAR_TIME >> ${HOME}/store_results/performance_history_openmp_cpu | |
| ${HOME}/mongosh-2.1.1-linux-x64/bin/mongosh \ | |
| "mongodb+srv://cluster0.x8ncpxi.mongodb.net/PerformanceMonitoring" \ | |
| --quiet --apiVersion 1 --username ${{ secrets.MONGODB_USERNAME }} \ | |
| --password ${{ secrets.MONGODB_PASSWORD }} \ | |
| --eval 'db.GitHub_CI.insertOne({branch_name: "'"$GITHUB_REF_NAME"'", commit: "'"$GITHUB_SHA"'", | |
| github_job: "'"$GITHUB_RUN_ID"'"-"'"$GITHUB_RUN_ATTEMPT"'", | |
| ci_test: "NEMO OpenMP for CPU", nemo_version: "NEMO ECMWF 4.0 V40 with mpp", system: "GlaDos", | |
| compiler:"intel-'"$ONEAPI_VERSION"'" , date: new Date(), | |
| num_omp_threads: '"$OMP_NUM_THREADS"', elapsed_time: '"$VAR_TIME"'})' |