Performance Test #1778
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name: Performance Test | |
on: | |
push: | |
branches: | |
- develop | |
- master | |
- fix_perftest | |
pull_request: | |
branches: | |
- master | |
workflow_dispatch: | |
schedule: | |
- cron: '48 4 * * *' | |
jobs: | |
build: | |
name: Performance Test | |
runs-on: ubuntu-22.04 | |
strategy: | |
matrix: | |
python-version: [3.9] | |
steps: | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- uses: actions/checkout@v3 | |
with: | |
fetch-depth: 20 | |
- name: Install apt dependencies | |
uses: ./.github/actions/install-apt-dependencies | |
- run: pip3 install petab shyaml build | |
- run: echo "${HOME}/.local/bin/" >> $GITHUB_PATH | |
- run: echo "${GITHUB_WORKSPACE}/tests/performance/" >> $GITHUB_PATH | |
# install AMICI | |
- name: Create AMICI sdist | |
run: | | |
cd python/sdist \ | |
&& check_time.sh create_sdist python3 -m build --sdist | |
- name: Install AMICI sdist | |
run: | | |
AMICI_PARALLEL_COMPILE=2 check_time.sh \ | |
install_sdist pip3 install -v --user \ | |
$(ls -t python/sdist/dist/amici-*.tar.gz | head -1) | |
# retrieve test model | |
- run: git clone --depth 1 https://github.com/ICB-DCM/CS_Signalling_ERBB_RAS_AKT | |
# import test model | |
- name: Import test model | |
run: | | |
AMICI_IMPORT_NPROCS=2 check_time.sh petab_import python tests/performance/test.py import | |
- name: "Upload artifact: CS_Signalling_ERBB_RAS_AKT_petab" | |
uses: actions/upload-artifact@v3 | |
with: | |
name: model_performance_test | |
path: model_performance_test | |
# install model package | |
- name: Install test model | |
run: > | |
check_time.sh install_model tests/performance/test.py compile; | |
for opt in O0 O1 O2; | |
do | |
check_time.sh install_model_${opt} tests/performance/test.py compile_${opt}; | |
done | |
# run simulations | |
- name: forward_simulation | |
run: > | |
check_time.sh forward_simulation tests/performance/test.py forward_simulation; | |
for opt in O0 O1 O2; | |
do | |
check_time.sh forward_simulation tests/performance/test.py forward_simulation_${opt}; | |
done | |
- name: forward_sensitivities | |
run: > | |
check_time.sh forward_sensitivities tests/performance/test.py forward_sensitivities; | |
for opt in O0 O1 O2; | |
do | |
check_time.sh forward_sensitivities tests/performance/test.py forward_sensitivities_${opt}; | |
done | |
- name: adjoint_sensitivities | |
run: > | |
check_time.sh adjoint_sensitivities tests/performance/test.py adjoint_sensitivities; | |
for opt in O0 O1 O2; | |
do | |
check_time.sh adjoint_sensitivities tests/performance/test.py adjoint_sensitivities_${opt}; | |
done | |
- name: forward_simulation_non_optimal_parameters | |
run: | | |
check_time.sh forward_simulation_non_optimal_parameters tests/performance/test.py forward_simulation_non_optimal_parameters; | |
for opt in O0 O1 O2; | |
do | |
check_time.sh forward_simulation_non_optimal_parameters tests/performance/test.py forward_simulation_non_optimal_parameters_${opt}; | |
done | |
- name: adjoint_sensitivities_non_optimal_parameters | |
run: | | |
check_time.sh adjoint_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_sensitivities_non_optimal_parameters; | |
for opt in O0 O1 O2; | |
do | |
check_time.sh adjoint_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_sensitivities_non_optimal_parameters_${opt}; | |
done | |
- name: forward_steadystate_sensitivities_non_optimal_parameters | |
run: | | |
check_time.sh forward_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py forward_steadystate_sensitivities_non_optimal_parameters; | |
for opt in O0 O1 O2; | |
do | |
check_time.sh forward_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py forward_steadystate_sensitivities_non_optimal_parameters_${opt}; | |
done | |
- name: adjoint_steadystate_sensitivities_non_optimal_parameters | |
run: | | |
check_time.sh adjoint_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_steadystate_sensitivities_non_optimal_parameters; | |
for opt in O0 O1 O2; | |
do | |
check_time.sh adjoint_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_steadystate_sensitivities_non_optimal_parameters_${opt}; | |
done |