SciCompMod · mknaranja · Apr 24, 2025 · Mar 31, 2025 · Mar 31, 2025 · Mar 31, 2025
diff --git a/.github/actions/build/action.yml b/.github/actions/build/action.yml
@@ -6,15 +6,15 @@ runs:
       shell: bash
       run: |
         sudo apt-get -qq update
-        sudo apt-get -qq install gcc-11
-        sudo apt-get -qq -y install g++-11
-        sudo apt-get -qq -y install lcov        
+        sudo apt-get -qq install gcc-13
+        sudo apt-get -qq -y install g++-13
+        sudo apt-get -qq -y install lcov     
     - name: Build
       shell: 
       # ensure that the installed compiler version is used
       run: |
-        export CC=/usr/bin/gcc-11
-        export CXX=/usr/bin/g++-11
+        export CC=/usr/bin/gcc-13
+        export CXX=/usr/bin/g++-13
         mkdir build && cd build
         cmake -DCMAKE_BUILD_TYPE=Debug -DGMGPOLAR_TEST_COVERAGE=ON ..
         make -j4

diff --git a/.github/actions/test/action.yml b/.github/actions/test/action.yml
@@ -30,25 +30,25 @@ runs:
         cd build/tests
         sudo chmod a+x gmgpolar_tests
         ./gmgpolar_tests  --gtest_output="xml:testreport.xml"
-    - name: Compute code coverage
-      shell: bash
-      # compute code coverage
-      run: |
-        cd build
-        cmake --build . --target coverage/fast
-    - name: Upload test report
-      uses: actions/upload-artifact@v4
-      with:
-        name: test-report
-        path: build/tests/testreport.xml
-        if-no-files-found: error
-        retention-days: 3
-    - name: Upload coverage reports
-      uses: actions/upload-artifact@v4
-      with:
-        name: test-coverage-reports
-        path: |
-          build/coverage.info
-          build/coverage
-        if-no-files-found: error
-        retention-days: 1       
+    # - name: Compute code coverage
+    #   shell: bash
+    #   # compute code coverage
+    #   run: |
+    #     cd build
+    #     cmake --build . --target coverage/fast
+    # - name: Upload test report
+    #   uses: actions/upload-artifact@v4
+    #   with:
+    #     name: test-report
+    #     path: build/tests/testreport.xml
+    #     if-no-files-found: error
+    #     retention-days: 3
+    # - name: Upload coverage reports
+    #   uses: actions/upload-artifact@v4
+    #   with:
+    #     name: test-coverage-reports
+    #     path: |
+    #       build/coverage.info
+    #       build/coverage
+    #     if-no-files-found: error
+    #     retention-days: 1       
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -14,35 +14,35 @@ jobs:
     if: github.event.pull_request.draft == false
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/build
 
   run-unit-test:
     needs: install-and-build
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: ./.github/actions/test
         with:
           build-artifact: build-cpp-linux-gmgpolar
 
-  codecov:
-    if: github.event.pull_request.draft == false
-    needs: [run-unit-test]
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-      - name: Install dependencies
-        run: |
-          sudo apt-get -qq update
-          sudo apt-get -qq -y install git curl
-      - name: Download cpp coverage report
-        uses: actions/download-artifact@v3
-        with:
-          name: test-coverage-reports
-      - name: Deploy to codecov.io
-        uses: codecov/codecov-action@v3
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          files: ./coverage.info
-          verbose: true          
+  # codecov:
+  #   if: github.event.pull_request.draft == false
+  #   needs: [run-unit-test]
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - uses: actions/checkout@v4
+  #     - name: Install dependencies
+  #       run: |
+  #         sudo apt-get -qq update
+  #         sudo apt-get -qq -y install git curl
+  #     - name: Download cpp coverage report
+  #       uses: actions/download-artifact@v4
+  #       with:
+  #         name: test-coverage-reports
+  #     - name: Deploy to codecov.io
+  #       uses: codecov/codecov-action@v3
+  #       with:
+  #         token: ${{ secrets.CODECOV_TOKEN }}
+  #         files: ./coverage.info
+  #         verbose: true          
diff --git a/.gitignore b/.gitignore
@@ -2,8 +2,6 @@
 
 .vscode/
 
-.github/
-
 Output/
 
 *.vtu

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -8,123 +8,50 @@ option(GMGPOLAR_USE_MUMPS "Use MUMPS to solve linear systems." OFF)
 set(CMAKE_CXX_STANDARD 20)
 set(CMAKE_CXX_STANDARD_REQUIRED True)
 
+set(CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
+
 if(NOT CMAKE_BUILD_TYPE)
     set(CMAKE_BUILD_TYPE Release)
 endif()
 
-set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -Wall -Wextra -pedantic -Wno-unused")
-set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O2 -mtune=generic")
-
-# # Mumps: Sparse Matrix Solver
-# set(MUMPS_PREFIX_PATH "~/spack/opt/spack/linux-ubuntu20.04-icelake/gcc-9.4.0/mumps-5.6.2-m4xrhc4mshzrxmgptzbpult3nbf6qrzk")
-# include_directories(${MUMPS_PREFIX_PATH}/include)
-# link_directories(${MUMPS_PREFIX_PATH}/lib)
-
-# # Metis: Matrix reordering for Mumps
-# set(METIS_PREFIX_PATH "~/spack/opt/spack/linux-ubuntu20.04-icelake/gcc-9.4.0/metis-5.1.0-bgoncx22w55soviybggl5ydjakvkm34v")
-# include_directories(${METIS_PREFIX_PATH}/include)
-# link_directories(${METIS_PREFIX_PATH}/lib)
-
-# # Likwid: Performance monitoring
-# set(LIKWID_PREFIX_PATH "~/spack/opt/spack/linux-ubuntu20.04-icelake/gcc-9.4.0/likwid-5.3.0-6mvx2snsqnamuyhaqspd6gxkfuaso36g")
-# include_directories(${LIKWID_PREFIX_PATH}/include)
-# link_directories(${LIKWID_PREFIX_PATH}/lib)
-
-# Include directories for the project
-include_directories(include)
-
-# 1. Create a library target for the PolarGrid module
-file(GLOB_RECURSE POLAR_GRID_SOURCES "src/PolarGrid/*.cpp")
-add_library(PolarGrid STATIC ${POLAR_GRID_SOURCES})
-target_include_directories(PolarGrid PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src/PolarGrid)
-
-# 2. Create a library target for the InputFunctions module
-file(GLOB_RECURSE INPUT_FUNCTIONS_SOURCES
-    "src/InputFunctions/DensityProfileCoefficients/*.cpp"
-    "src/InputFunctions/DomainGeometry/*.cpp"
-    "src/InputFunctions/ExactSolution/*.cpp"
-    "src/InputFunctions/BoundaryConditions/*.cpp"
-    "src/InputFunctions/SourceTerms/*.cpp"
-)
-add_library(InputFunctions STATIC ${INPUT_FUNCTIONS_SOURCES})
-target_include_directories(InputFunctions PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/src/InputFunctions)
-
-# 3. Collect all the common source files for GMGPolar into a library
-file(GLOB_RECURSE GMG_POLAR_SOURCES "src/GMGPolar/*.cpp")
-file(GLOB_RECURSE MULTIGRID_METHODS_SOURCES "src/GMGPolar/MultigridMethods/*.cpp")
-file(GLOB_RECURSE LEVEL_SOURCES "src/Level/*.cpp")
-file(GLOB_RECURSE STENCIL_SOURCES "src/Stencil/*.cpp")
-file(GLOB_RECURSE INTERPOLATION_SOURCES "src/Interpolation/*.cpp")
-file(GLOB_RECURSE DIRECT_SOLVER_SOURCES "src/DirectSolver/*.cpp" "src/DirectSolverGive/*.cpp" "src/DirectSolverTake/*.cpp" "src/DirectSolverGiveCustomLU/*.cpp" "src/DirectSolverTakeCustomLU/*.cpp")
-file(GLOB_RECURSE RESIDUAL_SOURCES "src/Residual/*.cpp" "src/Residual/ResidualGive/*.cpp" "src/Residual/ResidualTake/*.cpp")
-file(GLOB_RECURSE SMOOTHER_SOURCES "src/Smoother/*.cpp" "src/SmootherGive/*.cpp" "src/SmootherTake/*.cpp")
-file(GLOB_RECURSE EXTRAPOLATED_SMOOTHER_SOURCES "src/ExtrapolatedSmoother/*.cpp" "src/ExtrapolatedSmoother/ExtrapolatedSmootherGive/*.cpp" "src/ExtrapolatedSmoother/ExtrapolatedSmootherTake/*.cpp")
-
-# 4. Create the GMGPolarLib library and link PolarGrid and InputFunctions
-add_library(GMGPolarLib STATIC
-    ${GMG_POLAR_SOURCES}
-    ${MULTIGRID_METHODS_SOURCES}
-    ${LEVEL_SOURCES}
-    ${STENCIL_SOURCES}
-    ${INTERPOLATION_SOURCES}
-    ${DIRECT_SOLVER_SOURCES}
-    ${RESIDUAL_SOURCES}
-    ${SMOOTHER_SOURCES}
-    ${EXTRAPOLATED_SMOOTHER_SOURCES}
-)
-# Link PolarGrid and InputFunctions to GMGPolarLib
-target_link_libraries(GMGPolarLib PUBLIC PolarGrid InputFunctions)
-
-# Link Likwid to GMGPolarLib
-if(GMGPOLAR_USE_LIKWID)
-    target_link_libraries(GMGPolarLib PUBLIC likwid)
-    target_compile_definitions(GMGPolarLib PUBLIC "-DLIKWID_PERFMON")
-    add_compile_definitions(GMGPOLAR_USE_LIKWID)
-endif()
-
-# Link Mumps to GMGPolarLib
-if(GMGPOLAR_USE_MUMPS)
-    set(MUMPS_LIBRARIES
-        mumps_common
-        smumps
-        dmumps
-        mpiseq
-        metis
-    )
-    target_link_libraries(GMGPolarLib PUBLIC ${MUMPS_LIBRARIES})
-    add_compile_definitions(GMGPOLAR_USE_MUMPS)
-endif()
-
-# Add OpenMP flags if available and link to GMGPolarLib
-find_package(OpenMP REQUIRED)
-if(OpenMP_CXX_FOUND)
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
-    target_link_libraries(GMGPolarLib PUBLIC OpenMP::OpenMP_CXX)
+set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -Wall -Wextra -pedantic -Wno-unused -Wno-psabi")
+set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O2 -mtune=generic -Wno-psabi")
+
+# code coverage analysis
+# Note: this only works under linux and with make
+# Ninja creates different directory names which do not work together with this scrupt
+# as STREQUAL is case-sensitive https://github.com/TriBITSPub/TriBITS/issues/131, also allow DEBUG as accepted input
+option(GMGPOLAR_TEST_COVERAGE "Enable GCov coverage analysis (adds a 'coverage' target)" OFF)
+
+if(CMAKE_BUILD_TYPE STREQUAL "Debug" OR CMAKE_BUILD_TYPE STREQUAL "DEBUG")
+    if(GMGPOLAR_TEST_COVERAGE)
+        message(STATUS "Coverage enabled")
+        include(CodeCoverage)
+        append_coverage_compiler_flags()
+        setup_target_for_coverage_lcov(
+            NAME coverage
+            EXECUTABLE tests/gmgpolar_tests
+            LCOV_ARGS --ignore-errors gcov,mismatch
+            EXCLUDE "${CMAKE_SOURCE_DIR}/tests*" "${CMAKE_SOURCE_DIR}/src/InputFunctions*" "${CMAKE_BINARY_DIR}/*" "/usr*"
+        )
+    endif()
 endif()
 
-# 5. Add the main executable target (gmgpolar)
-set(MAIN_SOURCE "src/main.cpp")
-add_executable(gmgpolar ${MAIN_SOURCE})
-
-# 6. Add another executable target (convergence_order)
-set(CONVERGENCE_ORDER_SOURCE "src/convergence_order.cpp")
-add_executable(convergence_order ${CONVERGENCE_ORDER_SOURCE})
-
-set(WEAK_SCALING_SOURCE "src/weak_scaling.cpp")
-add_executable(weak_scaling ${WEAK_SCALING_SOURCE})
+include_directories(include)
+add_subdirectory(src)
 
-set(STRONG_SCALING_SOURCE "src/strong_scaling.cpp")
-add_executable(strong_scaling ${STRONG_SCALING_SOURCE})
+add_executable(gmgpolar src/main.cpp)
+add_executable(convergence_order src/convergence_order.cpp)
+add_executable(weak_scaling src/weak_scaling.cpp)
+add_executable(strong_scaling src/strong_scaling.cpp)
 
-# 7. Link GMGPolarLib (which now includes PolarGrid and InputFunctions) to both executables
 target_link_libraries(gmgpolar PRIVATE GMGPolarLib)
 target_link_libraries(convergence_order PRIVATE GMGPolarLib)
 target_link_libraries(weak_scaling PRIVATE GMGPolarLib)
 target_link_libraries(strong_scaling PRIVATE GMGPolarLib)
 
-# 9. Enable testing and include other directories
 if(GMGPOLAR_BUILD_TESTS)
     enable_testing()
     add_subdirectory(third-party)
     add_subdirectory(tests)
-endif()
+endif()
-Original file line number
+Diff line change
@@ Expand Up / @@ -2,8 +2,6 @@ @@
     .vscode/
-    .github/
     Output/
     *.vtu
@@ Expand Down @@