Merge pull request #3 from wgyang/main

Fix integration test errors
SimVascular · Apr 16, 2024 · 5673d26 · 5673d26
2 parents 614de21 + 6541336
commit 5673d26
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Showing 24 changed files with 391 additions and 94 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
diff --git a/.github/workflows/test_macos12.yml b/.github/workflows/test_macos12.yml
@@ -0,0 +1,33 @@
+name: macOS 12
+on: [push, pull_request]
+jobs:
+ test:
+ runs-on: macos-12
+ steps:
+ - uses: actions/checkout@v3
+ - name: Install MacOS dependencies
+ run: |
+ brew reinstall -v gcc
+ brew install -v cmake vtk openblas lapack mesa open-mpi qt
+ brew install lcov
+ sudo ln -s /usr/local/opt/qt5/mkspecs /usr/local/mkspecs
+ sudo ln -s /usr/local/opt/qt5/plugins /usr/local/plugins
+ - name: Build svFSIplus
+ run: |
+ mkdir build
+ cd build
+ cmake -DENABLE_COVERAGE=ON -DENABLE_ARRAY_INDEX_CHECKING=ON -DENABLE_UNIT_TEST=ON ..
+ make -j2
+ - name: Install test dependencies
+ run: |
+ conda create -n svfsiplus python=3.9
+ conda run -n svfsiplus pip install pytest pytest-cov pytest-mock numpy meshio pandas
+ - name: Run integration tests
+ run: |
+ git lfs pull
+ cd tests
+ conda run -n svfsiplus pytest -rPv --durations=0
+ - name: Run unit tests
+ run: |
+ cd build/svFSI-build/Source/svFSI
+ ctest --verbose
diff --git a/.github/workflows/test_ubuntu20.yml b/.github/workflows/test_ubuntu20.yml
@@ -0,0 +1,25 @@
+name: Ubuntu 20.04
+on: [push, pull_request]
+jobs:
+ test:
+ runs-on: ubuntu-20.04
+ container: msalvad/ubuntu20_vtk9:v1
+ steps:
+ - uses: actions/checkout@v3
+ - name: Build svFSIplus
+ run: |
+ mkdir build
+ cd build
+ cmake -DENABLE_COVERAGE=ON -DENABLE_ARRAY_INDEX_CHECKING=ON -DENABLE_UNIT_TEST=ON ..
+ make -j2
+ cd ..
+ - name: Run integration tests
+ run: |
+ git config --global --add safe.directory /__w/svFSIplus/svFSIplus
+ git lfs pull
+ cd tests
+ conda run -n svfsiplus pytest -rPv --durations=0
+ - name: Run unit tests
+ run: |
+ cd build/svFSI-build/Source/svFSI
+ ctest --verbose
diff --git a/.github/workflows/test_ubuntu22.yml b/.github/workflows/test_ubuntu22.yml
@@ -0,0 +1,38 @@
+name: Ubuntu 22.04
+on: [push, pull_request]
+jobs:
+ test:
+ runs-on: ubuntu-22.04
+ container: msalvad/ubuntu22_vtk9:v1
+ steps:
+ - uses: actions/checkout@v3
+ - name: Build svFSIplus
+ run: |
+ mkdir build
+ cd build
+ cmake -DENABLE_COVERAGE=ON -DENABLE_ARRAY_INDEX_CHECKING=ON -DENABLE_UNIT_TEST=ON ..
+ make -j2
+ cd ..
+ - name: Run integration tests
+ run: |
+ git config --global --add safe.directory /__w/svFSIplus/svFSIplus
+ git lfs pull
+ cd tests
+ conda run -n svfsiplus pytest -rPv --durations=0
+ - name: Run unit tests
+ run: |
+ cd build/svFSI-build/Source/svFSI
+ ctest --verbose
+ - name: Generate code coverage
+ run: |
+ cd build/svFSI-build
+ make coverage
+ - name: Save coverage report
+ uses: actions/upload-artifact@v3
+ with:
+ name: coverage_report
+ path: build/svFSI-build/coverage
+ - name: Upload coverage reports to Codecov
+ uses: codecov/codecov-action@v3
+ env:
+ CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -88,6 +88,7 @@ set(SV_PETSC_DIR "" CACHE STRING "Path to a local install of the PETSc linear al
 set(ENABLE_COVERAGE OFF CACHE BOOL "Enable code coverage")
 set(ENABLE_ARRAY_INDEX_CHECKING OFF CACHE BOOL "Enable Array index checking")
 set(SV_LOCAL_VTK_PATH "" CACHE STRING "Path to a local build of VTK.")
+set(ENABLE_UNIT_TEST OFF CACHE BOOL "Enable Unit Test by Google Test")
 
 #-----------------------------------------------------------------------------
 # RPATH handling
@@ -147,6 +148,7 @@ ExternalProject_Add(svFSI
  #-DSV_USE_PETSC:BOOL=${SV_USE_PETSC}
  -DSV_PETSC_DIR:STRING=${SV_PETSC_DIR}
  -DENABLE_COVERAGE:BOOL=${ENABLE_COVERAGE}
+ -DENABLE_UNIT_TEST:BOOL=${ENABLE_UNIT_TEST}
  -DENABLE_ARRAY_INDEX_CHECKING:BOOL=${ENABLE_ARRAY_INDEX_CHECKING}
  -DSV_LOCAL_VTK_PATH:STRING=${SV_LOCAL_VTK_PATH}
  ${SV_APPLE_CMAKE_ARGS}

diff --git a/Code/Source/svFSI/CMakeLists.txt b/Code/Source/svFSI/CMakeLists.txt
@@ -260,4 +260,56 @@ if(ENABLE_COVERAGE)
  WORKING_DIRECTORY ${CMAKE_BINARY_DIR})
 endif()
 
+# unit tests and Google Test
+if(ENABLE_UNIT_TEST)
+
+ # link pthread on ubuntu20
+ find_package(Threads REQUIRED)
+
+ # install Google Test
+ include(FetchContent)
+ FetchContent_Declare(
+ googletest
+ URL https://github.com/google/googletest/archive/03597a01ee50ed33e9dfd640b249b4be3799d395.zip
+ )
+ FetchContent_MakeAvailable(googletest)
+ enable_testing()
+ include(GoogleTest)
+
+ # add test.cpp for unit test
+
+ # remove the main.cpp and add test.cpp
+ list(APPEND CSRCS "../../../tests/unitTests/test.cpp")
+ list(REMOVE_ITEM CSRCS "main.cpp")
+
+ # include source files (same as what svFSI does except for main.cpp)
+ add_executable(run_all_unit_tests ${CSRCS})
+
+ # libraries
+ target_link_libraries(run_all_unit_tests
+ ${GLOBAL_LIBRARIES}
+ ${INTELRUNTIME_LIBRARIES}
+ ${ZLIB_LIBRARY}
+ ${BLAS_LIBRARIES}
+ ${LAPACK_LIBRARIES}
+ ${METIS_SVFSI_LIBRARY_NAME}
+ ${PARMETIS_SVFSI_LIBRARY_NAME}
+ ${TETGEN_LIBRARY_NAME}
+ ${TINYXML_LIBRARY_NAME}
+ ${SV_LIB_SVFSILS_NAME}${SV_MPI_NAME_EXT}
+ ${VTK_LIBRARIES}
+ )
+
+ # link Google Test
+ target_link_libraries(
+ run_all_unit_tests
+ gtest
+ GTest::gtest_main 
+ pthread # link pthread on ubuntu20
+ )
+
+ # gtest_discover_tests(runUnitTest)
+ add_test(NAME all_unit_tests COMMAND run_all_unit_tests)
+
+endif()
 
diff --git a/tests/cases/cep/cable_TTP_1d/result_001.vtu b/tests/cases/cep/cable_TTP_1d/result_001.vtu
diff --git a/tests/cases/cep/cable_TTP_1d/svFSI.xml b/tests/cases/cep/cable_TTP_1d/svFSI.xml
@@ -31,8 +31,8 @@
 <Add_equation type="CEP" > 
  <Coupled> true </Coupled>
  <Min_iterations> 1 </Min_iterations> 
- <Max_iterations> 5 </Max_iterations> 
- <Tolerance> 1e-6 </Tolerance> 
+ <Max_iterations> 2 </Max_iterations> 
+ <Tolerance> 1e-12 </Tolerance> 
 
  <Domain id="1" >
  <Electrophysiology_model> TTP </Electrophysiology_model> 
@@ -58,7 +58,7 @@
 
  <LS type="GMRES" >
  <Max_iterations> 100 </Max_iterations> 
- <Tolerance> 1e-6 </Tolerance>
+ <Tolerance> 1e-12 </Tolerance>
  <Krylov_space_dimension> 50 </Krylov_space_dimension>
  </LS>
 

diff --git a/tests/cases/cep/niederer_benchmark_ECGs_quadrature/result_BICG_CN_epicardium_BO_001.vtu b/tests/cases/cep/niederer_benchmark_ECGs_quadrature/result_BICG_CN_epicardium_BO_001.vtu
diff --git a/tests/cases/cep/niederer_benchmark_ECGs_quadrature/result_CG_RK4_myocardium_BO_001.vtu b/tests/cases/cep/niederer_benchmark_ECGs_quadrature/result_CG_RK4_myocardium_BO_001.vtu
diff --git a/tests/cases/cep/niederer_benchmark_ECGs_quadrature/result_GMRES_FE_epicardium_TTP_001.vtu b/tests/cases/cep/niederer_benchmark_ECGs_quadrature/result_GMRES_FE_epicardium_TTP_001.vtu
diff --git a/tests/cases/cep/niederer_benchmark_ECGs_quadrature/result_GMRES_FE_pfib_AP_001.vtu b/tests/cases/cep/niederer_benchmark_ECGs_quadrature/result_GMRES_FE_pfib_AP_001.vtu
diff --git a/tests/cases/cep/niederer_benchmark_ECGs_quadrature/svFSI_BICG_CN_epicardium_BO.xml b/tests/cases/cep/niederer_benchmark_ECGs_quadrature/svFSI_BICG_CN_epicardium_BO.xml
@@ -68,7 +68,7 @@
  <Coupled> true </Coupled>
  <Min_iterations> 1 </Min_iterations> 
  <Max_iterations> 1 </Max_iterations> 
- <Tolerance> 1e-6 </Tolerance> 
+ <Tolerance> 1e-12 </Tolerance> 
 
  <Domain id="1" >
  <Electrophysiology_model> BO </Electrophysiology_model>
@@ -105,7 +105,7 @@
 
  <LS type="BICG" >
  <Max_iterations> 100 </Max_iterations>
- <Tolerance> 1e-6 </Tolerance>
+ <Tolerance> 1e-12 </Tolerance>
  </LS>
 
  <ECGLeads>

diff --git a/tests/cases/cep/niederer_benchmark_ECGs_quadrature/svFSI_CG_RK4_myocardium_BO.xml b/tests/cases/cep/niederer_benchmark_ECGs_quadrature/svFSI_CG_RK4_myocardium_BO.xml
@@ -68,7 +68,7 @@
  <Coupled> true </Coupled>
  <Min_iterations> 1 </Min_iterations> 
  <Max_iterations> 1 </Max_iterations> 
- <Tolerance> 1e-6 </Tolerance> 
+ <Tolerance> 1e-12 </Tolerance> 
 
  <Domain id="1" >
  <Electrophysiology_model> BO </Electrophysiology_model>
@@ -105,7 +105,7 @@
 
  <LS type="CG" >
  <Preconditioner> svfsi </Preconditioner> 
- <Tolerance> 1e-6 </Tolerance>
+ <Tolerance> 1e-12 </Tolerance>
  </LS>
 
  <ECGLeads>

diff --git a/tests/cases/cep/niederer_benchmark_ECGs_quadrature/svFSI_GMRES_FE_epicardium_TTP.xml b/tests/cases/cep/niederer_benchmark_ECGs_quadrature/svFSI_GMRES_FE_epicardium_TTP.xml
@@ -68,7 +68,7 @@
  <Coupled> true </Coupled>
  <Min_iterations> 1 </Min_iterations> 
  <Max_iterations> 1 </Max_iterations> 
- <Tolerance> 1e-6 </Tolerance> 
+ <Tolerance> 1e-12 </Tolerance> 
 
  <Domain id="1" >
  <Electrophysiology_model> TTP </Electrophysiology_model>
@@ -117,7 +117,7 @@
 
  <LS type="GMRES" >
  <Max_iterations> 100 </Max_iterations>
- <Tolerance> 1e-6 </Tolerance>
+ <Tolerance> 1e-12 </Tolerance>
  <Krylov_space_dimension> 50 </Krylov_space_dimension>
  </LS>
 

diff --git a/tests/cases/cep/niederer_benchmark_ECGs_quadrature/svFSI_GMRES_FE_pfib_AP.xml b/tests/cases/cep/niederer_benchmark_ECGs_quadrature/svFSI_GMRES_FE_pfib_AP.xml
@@ -68,7 +68,7 @@
  <Coupled> true </Coupled>
  <Min_iterations> 1 </Min_iterations> 
  <Max_iterations> 1 </Max_iterations> 
- <Tolerance> 1e-6 </Tolerance> 
+ <Tolerance> 1e-12 </Tolerance> 
 
  <Domain id="1" >
  <Electrophysiology_model> AP </Electrophysiology_model>
@@ -105,7 +105,7 @@
 
  <LS type="GMRES" >
  <Max_iterations> 100 </Max_iterations>
- <Tolerance> 1e-6 </Tolerance>
+ <Tolerance> 1e-12 </Tolerance>
  <Krylov_space_dimension> 50 </Krylov_space_dimension>
  </LS>
 

diff --git a/tests/cases/cep/purkinje/result_001.vtu b/tests/cases/cep/purkinje/result_001.vtu
diff --git a/tests/cases/cep/purkinje/svFSI.xml b/tests/cases/cep/purkinje/svFSI.xml
@@ -39,8 +39,8 @@
 <Add_equation type="CEP" > 
  <Coupled> true </Coupled>
  <Min_iterations> 1 </Min_iterations> 
- <Max_iterations> 3 </Max_iterations> 
- <Tolerance> 1e-6 </Tolerance> 
+ <Max_iterations> 2 </Max_iterations> 
+ <Tolerance> 1e-12 </Tolerance> 
 
  <Domain id="1" >
  <Electrophysiology_model> TTP </Electrophysiology_model>
@@ -68,7 +68,7 @@
 
  <LS type="GMRES" >
  <Max_iterations> 100 </Max_iterations>
- <Tolerance> 1e-6 </Tolerance>
+ <Tolerance> 1e-12 </Tolerance>
  <Krylov_space_dimension> 50 </Krylov_space_dimension>
  </LS>
 

diff --git a/tests/cases/cep/spiral_BO_2d/result_001.vtu b/tests/cases/cep/spiral_BO_2d/result_001.vtu