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Performance Test

Performance Test #313

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Performance Test

Performance Test #313

Workflow file for this run

.github/workflows/test_performance.yml at b0d79ff
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: ["3.11"]
steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- uses: actions/checkout@v4
with:
fetch-depth: 20
- name: Install apt dependencies
uses: ./.github/actions/install-apt-dependencies
- run: pip3 install petab shyaml build
- run: echo "${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="" check_time.sh \
install_sdist pip3 install -v --user \
$(ls -t python/sdist/dist/amici-*.tar.gz | head -1)
# retrieve test model
- run: git clone --depth 1 https://github.com/ICB-DCM/CS_Signalling_ERBB_RAS_AKT
# import test model
- name: Import test model
run: |
AMICI_IMPORT_NPROCS=2 check_time.sh petab_import python tests/performance/test.py import
- name: "Upload artifact: CS_Signalling_ERBB_RAS_AKT_petab"
uses: actions/upload-artifact@v4
with:
name: model_performance_test
path: model_performance_test
# install model package
- name: Install test model
run: >
check_time.sh install_model tests/performance/test.py compile;
for opt in O0 O1 O2;
do
check_time.sh install_model_${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