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nemo_v5_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
# NEMOv5 integrations tests that are not run on GHA systems.
name: NEMOv5 Integration Tests
on:
push
jobs:
run_if_on_mirror:
if: ${{ github.repository == 'stfc/PSyclone-mirror' }}
runs-on: self-hosted
env:
NEMODIR_NAME: NEMOv5_Jan25
steps:
- uses: actions/checkout@v3
with:
submodules: recursive
# This is required to get the commit history for merge commits for
# the ci-skip check below.
fetch-depth: '0'
- name: Check for [skip ci] in commit message
uses: mstachniuk/ci-skip@v1
with:
# This setting causes the tests to 'fail' if [skip ci] is specified
fail-fast: true
commit-filter: '[skip ci]'
- name: Install dependencies
run: |
module load python/${PYTHON_VERSION}
python -m venv .runner_venv
source .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 .
# PSyclone passthrough for 5.0-beta of NEMO.
- name: NEMO 5.0 gfortran passthrough
# Only bother doing passthrough if this is a re-run of a previous test.
if: ${{ github.run_attempt != '1' }}
run: |
# Set up environment
source /apps/spack/psyclone-spack/spack-repo/share/spack/setup-env.sh
spack unload && spack load nemo-build-environment%gcc@14
source .runner_venv/bin/activate
export PSYCLONE_NEMO_DIR=${GITHUB_WORKSPACE}/examples/nemo/scripts
export PSYCLONE_HOME=${PWD}/.runner_venv
export NEMO_DIR=${HOME}/${NEMODIR_NAME}
export TEST_DIR=BENCH_PASSTHROUGH_GCC
# Set up FCM: PATHs are loaded from SPACK, we only need to set the FCFLAGS
cd $NEMO_DIR
cp $PSYCLONE_NEMO_DIR/KGOs/arch-linux_spack.fcm arch/arch-linux_spack.fcm
export FCFLAGS="-fdefault-real-8 -O2 -fcray-pointer -ffree-line-length-none -g"
# Clean up and compile
rm -rf tests/${TEST_DIR}
./makenemo -r BENCH -m linux_spack -n ${TEST_DIR} -p ${PSYCLONE_NEMO_DIR}/passthrough.py \
add_key "key_nosignedzero" -j 4 -v 1
# Run test
cd $NEMO_DIR/tests/${TEST_DIR}/EXP00
cp $PSYCLONE_NEMO_DIR/KGOs/namelist_cfg_bench_small namelist_cfg
mpirun -np 4 ./nemo
tail run.stat
# This was produced with gfortran, so we can do an exact diff
diff $PSYCLONE_NEMO_DIR/KGOs/run.stat.bench.gfortran.small.10steps run.stat
- name: NEMO 5.0 nvidia passthrough
# Only bother doing passthrough if this is a re-run of a previous test.
if: ${{ github.run_attempt != '1' }}
run: |
# Set up environment
source /apps/spack/psyclone-spack/spack-repo/share/spack/setup-env.sh
spack unload && spack load nemo-build-environment%nvhpc@24.5
source .runner_venv/bin/activate
export PSYCLONE_NEMO_DIR=${GITHUB_WORKSPACE}/examples/nemo/scripts
export PSYCLONE_HOME=${PWD}/.runner_venv
export NEMO_DIR=${HOME}/${NEMODIR_NAME}
export TEST_DIR=BENCH_PASSTHROUGH_NVHPC
# Set up FCM: PATHs are loaded from SPACK, we only need to set the FCFLAGS
cd $NEMO_DIR
cp $PSYCLONE_NEMO_DIR/KGOs/arch-linux_spack.fcm arch/arch-linux_spack.fcm
export FCFLAGS="-i4 -Mr8 -O2 -nofma -Mnovect -g"
# Clean up and compile
# Without key_mpi_off it fails to compile (even without psyclone)
rm -rf tests/${TEST_DIR}
./makenemo -r BENCH -m linux_spack -n ${TEST_DIR} -p ${PSYCLONE_NEMO_DIR}/passthrough.py \
add_key "key_mpi_off key_nosignedzero" -j 4 -v 1
# Run test
cd $NEMO_DIR/tests/${TEST_DIR}/EXP00
cp $PSYCLONE_NEMO_DIR/KGOs/namelist_cfg_bench_small namelist_cfg
./nemo
tail run.stat
diff $PSYCLONE_NEMO_DIR/KGOs/run.stat.bench.nvhpc.small.10steps run.stat
export VAR_TIME=$(awk '/ step /{print $3}' timing.output | head -n 1 | sed -e 's/s//')
echo "Time-stepping duration = " $VAR_TIME
- name: NEMO 5.0 Intel passthrough
# Only bother doing passthrough if this is a re-run of a previous test.
if: ${{ github.run_attempt != '1' }}
run: |
# Set up environment
source /apps/spack/psyclone-spack/spack-repo/share/spack/setup-env.sh
spack unload && spack load nemo-build-environment%oneapi
source .runner_venv/bin/activate
export PSYCLONE_NEMO_DIR=${GITHUB_WORKSPACE}/examples/nemo/scripts
export PSYCLONE_HOME=${PWD}/.runner_venv
export NEMO_DIR=${HOME}/${NEMODIR_NAME}
export TEST_DIR=BENCH_PASSTHROUGH_ONEAPI
# Set up FCM: PATHs are loaded from SPACK, we only need to set the FCFLAGS
cd $NEMO_DIR
cp $PSYCLONE_NEMO_DIR/KGOs/arch-linux_spack.fcm arch/arch-linux_spack.fcm
export FCFLAGS="-i4 -r8 -O2 -fp-model precise -fno-alias -g"
# Clean up and compile
rm -rf tests/${TEST_DIR}
./makenemo -r BENCH -m linux_spack -n ${TEST_DIR} -p ${PSYCLONE_NEMO_DIR}/passthrough.py \
add_key "key_nosignedzero" -j 4 -v 1
# Run test
cd $NEMO_DIR/tests/${TEST_DIR}/EXP00
cp $PSYCLONE_NEMO_DIR/KGOs/namelist_cfg_bench_small namelist_cfg
mpirun -np 6 ./nemo
tail run.stat
diff $PSYCLONE_NEMO_DIR/KGOs/run.stat.bench.oneapi.small.10steps run.stat
- name: NEMO 5.0 gfortran OpenMP for CPUs
run: |
# Set up environment
source /apps/spack/psyclone-spack/spack-repo/share/spack/setup-env.sh
spack unload && spack load nemo-build-environment%gcc@14
source .runner_venv/bin/activate
export PSYCLONE_NEMO_DIR=${GITHUB_WORKSPACE}/examples/nemo/scripts
export PSYCLONE_HOME=${PWD}/.runner_venv
export NEMO_DIR=${HOME}/${NEMODIR_NAME}
export TEST_DIR=BENCH_OMP_THREADING_GCC
# Set up FCM: PATHs are loaded from SPACK, we only need to set the FCFLAGS
cd $NEMO_DIR
cp $PSYCLONE_NEMO_DIR/KGOs/arch-linux_spack.fcm arch/arch-linux_spack.fcm
export FCFLAGS="-fdefault-real-8 -O2 -fcray-pointer -ffree-line-length-none -g -fopenmp"
# Clean up and compile
rm -rf tests/${TEST_DIR}
./makenemo -r BENCH -m linux_spack -n ${TEST_DIR} -p ${PSYCLONE_NEMO_DIR}/omp_cpu_trans.py \
add_key "key_nosignedzero" -j 4 -v 1
# Run test
cd $NEMO_DIR/tests/${TEST_DIR}/EXP00
cp $PSYCLONE_NEMO_DIR/KGOs/namelist_cfg_bench_small namelist_cfg
OMP_NUM_THREADS=4 mpirun -np 1 ./nemo
tail run.stat
diff $PSYCLONE_NEMO_DIR/KGOs/run.stat.bench.gfortran.small.10steps run.stat
export TIME_sec=$(grep "local proces" timing.output | head -n 1 | awk '{print $4}' | tr -d s)
${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"'"-"'"$GITHUB_RUN_ATTEMPT"'",
ci_test: "NEMOv5 OpenMP for CPU", nemo_version: "NEMOv5", system: "GlaDos",
compiler:"gfortran-14" , date: new Date(), elapsed_time: '"${TIME_sec}"'})'
- name: NEMO 5.0 nvidia OpenMP for GPUs (BENCH - managed memory)
run: |
# Set up environment
source /apps/spack/psyclone-spack/spack-repo/share/spack/setup-env.sh
spack unload && spack load nemo-build-environment%nvhpc@24.5
source .runner_venv/bin/activate
export PSYCLONE_NEMO_DIR=${GITHUB_WORKSPACE}/examples/nemo/scripts
export PSYCLONE_HOME=${PWD}/.runner_venv
export NEMO_DIR=${HOME}/${NEMODIR_NAME}
export TEST_DIR=BENCH_OMP_OFFLOAD_NVHPC
# Set up FCM: PATHs are loaded from SPACK, we only need to set the FCFLAGS
# We compile with "-O2 -Mnofma -Mnovect -gpu=math_uniform" to permit comparison of the results.
cd $NEMO_DIR
cp $PSYCLONE_NEMO_DIR/KGOs/arch-linux_spack.fcm arch/arch-linux_spack.fcm
export FCFLAGS="-i4 -Mr8 -O2 -Mnofma -Mnovect -g -mp=gpu -gpu=mem:managed,math_uniform"
# Clean up and compile
# Without key_mpi_off it fails to compile (even without psyclone)
rm -rf tests/${TEST_DIR}
./makenemo -r BENCH -m linux_spack -n ${TEST_DIR} -p ${PSYCLONE_NEMO_DIR}/omp_gpu_trans.py \
add_key "key_mpi_off key_nosignedzero" -j 4 -v 1
# Run test
cd $NEMO_DIR/tests/${TEST_DIR}/EXP00
cp $PSYCLONE_NEMO_DIR/KGOs/namelist_cfg_bench_small namelist_cfg
./nemo
# tail run.stat
diff $PSYCLONE_NEMO_DIR/KGOs/run.stat.bench.nvhpc.small.10steps run.stat
export TIME_sec=$(grep "local proces" timing.output | head -n 1 | awk '{print $4}' | tr -d s)
${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"'"-"'"$GITHUB_RUN_ATTEMPT"'",
ci_test: "NEMOv5 OpenMP for GPU (BENCH)", nemo_version: "NEMOv5", system: "GlaDos",
compiler:"nvhpc-24.5" , date: new Date(), elapsed_time: '"${TIME_sec}"'})'
- name: NEMO 5.0 nvidia OpenMP for GPUs (UKMO ORCA1 - managed memory)
run: |
# Set up environment
source /apps/spack/psyclone-spack/spack-repo/share/spack/setup-env.sh
spack unload && spack load nemo-build-environment%nvhpc@24.5
source .runner_venv/bin/activate
export PSYCLONE_NEMO_DIR=${GITHUB_WORKSPACE}/examples/nemo/scripts
export PSYCLONE_HOME=${PWD}/.runner_venv
export NEMO_DIR=${HOME}/${NEMODIR_NAME}
export TEST_DIR=ORCA1_OMP_OFFLOAD_NVHPC
# Set up FCM: PATHs are loaded from SPACK, we only need to set the FCFLAGS
# We compile at "-O2 -Mnofma -Mnovect -gpu=math_uniform" to permit comparison of the results.
cd $NEMO_DIR
cp $PSYCLONE_NEMO_DIR/KGOs/arch-linux_spack.fcm arch/arch-linux_spack.fcm
export FCFLAGS="-i4 -Mr8 -O2 -Mnofma -Mnovect -g -mp=gpu -gpu=mem:managed,math_uniform"
# Clean up and compile
# Without key_mpi_off it fails to compile (even without psyclone)
rm -rf cfgs/${TEST_DIR}
./makenemo -r GOSI10p0.0_like_eORCA1 -m linux_spack -n ${TEST_DIR} -p ${PSYCLONE_NEMO_DIR}/omp_gpu_trans.py \
add_key "key_mpi_off key_nosignedzero" -j 4 -v 1
# Run test
cd $NEMO_DIR/cfgs/${TEST_DIR}/EXP00
ln -sf /archive/NEMO_INPUTS/NEMOv5_MO_original_files/ancil/eORCA1/link/* .
./nemo
diff $PSYCLONE_NEMO_DIR/KGOs/run.stat.orca1.nvhpc.10steps run.stat
export TIME_sec=$(grep "local proces" timing.output | head -n 1 | awk '{print $4}' | tr -d s)
${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"'"-"'"$GITHUB_RUN_ATTEMPT"'",
ci_test: "NEMOv5 OpenMP for GPU (ORCA1)", nemo_version: "NEMOv5", system: "GlaDos",
compiler:"nvhpc-24.5" , date: new Date(), elapsed_time: '"${TIME_sec}"'})'
- name: NEMO 5.0 nvidia OpenMP for GPUs (UKMO ORCA2 - managed memory)
run: |
# Set up environment
source /apps/spack/psyclone-spack/spack-repo/share/spack/setup-env.sh
spack unload && spack load nemo-build-environment%nvhpc@24.5
source .runner_venv/bin/activate
export PSYCLONE_NEMO_DIR=${GITHUB_WORKSPACE}/examples/nemo/scripts
export PSYCLONE_HOME=${PWD}/.runner_venv
export NEMO_DIR=${HOME}/${NEMODIR_NAME}
export TEST_DIR=ORCA2_OMP_OFFLOAD_NVHPC
# Set up FCM: PATHs are loaded from SPACK, we only need to set the FCFLAGS
# We compile at "-O2 -Mnofma -Mnovect -gpu=math_uniform" to permit comparison of the results.
cd $NEMO_DIR
cp $PSYCLONE_NEMO_DIR/KGOs/arch-linux_spack.fcm arch/arch-linux_spack.fcm
export FCFLAGS="-i4 -Mr8 -O2 -Mnofma -Mnovect -g -mp=gpu -gpu=mem:managed,math_uniform"
# Clean up and compile
# Without key_mpi_off it fails to compile (even without psyclone)
rm -rf cfgs/${TEST_DIR}
./makenemo -r ORCA2_ICE_PISCES -m linux_spack -n ${TEST_DIR} -p ${PSYCLONE_NEMO_DIR}/omp_gpu_trans.py \
add_key "key_mpi_off key_nosignedzero" -j 4 -v 1
# Run test
cd $NEMO_DIR/cfgs/${TEST_DIR}/EXP00
ln -sf ../../../ORCA2_ICE_v4.2.0/* .
./nemo
diff $PSYCLONE_NEMO_DIR/KGOs/run.stat.orca2.nvhpc.10steps run.stat
export TIME_sec=$(grep "local proces" timing.output | head -n 1 | awk '{print $4}' | tr -d s)
${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"'"-"'"$GITHUB_RUN_ATTEMPT"'",
ci_test: "NEMOv5 OpenMP for GPU (ORCA2)", nemo_version: "NEMOv5", system: "GlaDos",
compiler:"nvhpc-24.5" , date: new Date(), elapsed_time: '"${TIME_sec}"'})'