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nemo_tests.yml
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# -----------------------------------------------------------------------------
# BSD 3-Clause License
#
# Copyright (c) 2024-2025, 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
make run-passthrough |& 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)
# 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 INPUT_DIR=/archive/NEMO_INPUTS/NEMOv4/ECMWF/eORCA1_GO8/
export MPI_INC_DIR=${I_MPI_ROOT}/include
cd $PSYCLONE_NEMO_DIR
make -j 4 openmp_cpu
make -j 4 compile-openmp_cpu
export OMP_NUM_THREADS=4
make run-openmp_cpu |& tee output.txt
# Check the output is as expected (TODO #2787: improve numerical reproducibility)
tail -n 1 output.txt | grep -q " it : 10" || (echo "Error: 'it : 10' not found!" & false)
tail -n 1 output.txt | grep -q "|ssh|_max: 0.199" || (echo "Error: '|ssh|_max: 0.199' not found!" & false)
tail -n 1 output.txt | grep -q "|U|_max: 0.148" || (echo "Error: '|U|_max: 0.148' not found!" & false)
tail -n 1 output.txt | grep -q "S_min: 0.10" || (echo "Error: 'S_min: 0.10' not found!" & false)
tail -n 1 output.txt | grep -q "S_max: 0.404" || (echo "Error: 'S_max: 0.404' not found!" & false)
export VAR_TIME=$(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"'})'