506 overhaul cmakelist for constructing shared and static libraries of memilio 2025

.github/actions/linux-build/action.yml

@@ -39,16 +39,15 @@ runs:
       run: |
         sudo apt-get -qq update
         sudo apt-get -qq -y install lcov ccache
+        sudo apt-get -qq -y install gfortran-9
         if [[ "${{ inputs.optional-dependencies }}" == "ON" ]]; then
           sudo apt-get -qq -y install libhdf5-dev 
         fi
         if [[ "${{ inputs.compiler }}" == "gcc" ]]; then
           if [[ "${{ inputs.version }}" == "min" ]]; then
-            sudo apt-get -qq -y install gcc-9
-            sudo apt-get -qq -y install g++-9
+            sudo apt-get -qq -y install gcc-9 g++-9 
           else        
-            sudo apt-get -qq -y install gcc-11
-            sudo apt-get -qq -y install g++-11
+             sudo apt-get -qq -y install gcc-11 g++-11 
           fi
         elif [[ "${{ inputs.compiler }}" == "clang" ]]; then
           if [[ "${{ inputs.version }}" == "min" ]]; then
@@ -76,6 +75,7 @@ runs:
       shell: bash
       run: |
         cd cpp
+        export FC=/usr/bin/gfortran-9
         if [[ "${{ inputs.compiler }}" == "gcc" ]]; then
           if [[ "${{ inputs.version }}" == "min" ]]; then
             export CC=/usr/bin/gcc-9
@@ -97,7 +97,7 @@ runs:
           exit 1
         fi
         mkdir -p build && cd build
-        cmake -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache -DCMAKE_BUILD_TYPE=${{ inputs.config }} -DMEMILIO_ENABLE_IPOPT=ON -DMEMILIO_TEST_COVERAGE=${{ inputs.coverage }} -DMEMILIO_SANITIZE_ADDRESS=${{ inputs.sanitizers }} -DMEMILIO_SANITIZE_UNDEFINED=${{ inputs.sanitizers }} -DMEMILIO_USE_BUNDLED_JSONCPP=${{ inputs.optional-dependencies }} -DMEMILIO_ENABLE_OPENMP=${{ inputs.openmp }} ..
+        cmake -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache -DCMAKE_Fortran_COMPILER=/usr/bin/gfortran-9 -DCMAKE_BUILD_TYPE=${{ inputs.config }} -DMEMILIO_ENABLE_IPOPT=ON -DMEMILIO_TEST_COVERAGE=${{ inputs.coverage }} -DMEMILIO_SANITIZE_ADDRESS=${{ inputs.sanitizers }} -DMEMILIO_SANITIZE_UNDEFINED=${{ inputs.sanitizers }} -DMEMILIO_USE_BUNDLED_JSONCPP=${{ inputs.optional-dependencies }} -DMEMILIO_ENABLE_OPENMP=${{ inputs.openmp }} ..
         make -j4
     - name: create build dir archive
       shell: bash

.github/actions/windows-build/action.yml

@@ -48,7 +48,7 @@ runs:
           call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" amd64
         )
         cmake --version
-        cmake -G "Ninja" -DCMAKE_BUILD_TYPE=${{ inputs.config }} -DMEMILIO_USE_BUNDLED_JSONCPP=${{ inputs.optional-dependencies }} -DHDF5_USE_STATIC_LIBRARIES=ON -DHDF5_DIR="${{github.workspace}}/hdf5/share/cmake/hdf5" ..
+        cmake -G "Ninja" -DCMAKE_BUILD_TYPE=${{ inputs.config }} -DMEMILIO_ENABLE_IPOPT=OFF -DMEMILIO_USE_BUNDLED_JSONCPP=${{ inputs.optional-dependencies }} -DHDF5_USE_STATIC_LIBRARIES=ON -DHDF5_DIR="${{github.workspace}}/hdf5/share/cmake/hdf5" ..
         cmake --build . -- -j 4
     - name: Upload built binary files
       uses: actions/upload-artifact@v4

cpp/CMakePresets.json

@@ -0,0 +1,228 @@
+{
+    "version": 5, 
+    "cmakeMinimumRequired": {
+      "major": 3,
+      "minor": 24,
+      "patch": 0
+    },
+    "configurePresets": [
+      {
+        "name": "base-config",
+        "hidden": true,
+        "description": "Base settings common to all configurations.",
+        "binaryDir": "${sourceDir}/build/${presetName}",
+        "cacheVariables": {
+          "CMAKE_INSTALL_PREFIX": "${sourceDir}/install/${presetName}",
+          "CMAKE_CXX_STANDARD": "17",
+          "CMAKE_CXX_STANDARD_REQUIRED": "ON",
+          "CMAKE_CXX_EXTENSIONS": "OFF",
+          "CMAKE_EXPORT_COMPILE_COMMANDS": "ON",
+          "MEMILIO_BUILD_TESTS": "ON",
+          "MEMILIO_BUILD_EXAMPLES": "ON",
+          "MEMILIO_BUILD_MODELS": "ON",
+          "MEMILIO_BUILD_BENCHMARKS": "ON",
+          "MEMILIO_USE_BUNDLED_EIGEN": "ON",
+          "MEMILIO_USE_BUNDLED_BOOST": "ON",
+          "MEMILIO_USE_BUNDLED_JSONCPP": "ON",
+          "MEMILIO_USE_BUNDLED_SPDLOG": "ON",
+          "MEMILIO_ENABLE_MPI": "OFF",
+          "MEMILIO_ENABLE_OPENMP": "OFF",
+          "MEMILIO_ENABLE_IPOPT": "OFF",
+          "MEMILIO_ENABLE_PROFILING": "OFF",
+          "MEMILIO_SANITIZE_ADDRESS": "OFF",
+          "MEMILIO_SANITIZE_UNDEFINED": "OFF",
+          "MEMILIO_TEST_COVERAGE": "OFF",
+          "MEMILIO_ENABLE_WARNINGS": "ON",
+          "MEMILIO_ENABLE_WARNINGS_AS_ERRORS": "ON",
+          "MEMILIO_BUILD_SHARED_LIBS": "OFF",
+          "MEMILIO_ENABLE_INSTALL": "OFF"
+        }
+      },
+      {
+        "name": "unix-base",
+        "hidden": true,
+        "inherits": "base-config",
+        "description": "Base settings for Unix-like systems (Linux, macOS)",
+        "generator": "Ninja",
+        "condition": {
+          "type": "not",
+          "condition": { "type": "equals", "lhs": "${hostSystemName}", "rhs": "Windows" }
+        }
+      },
+      {
+        "name": "windows-base",
+        "hidden": true,
+        "inherits": "base-config",
+        "description": "Base settings for Windows.",
+        "generator": "Visual Studio 17 2022",
+        "architecture": "x64",
+        "condition": { "type": "equals", "lhs": "${hostSystemName}", "rhs": "Windows" },
+         "cacheVariables": { "MEMILIO_BUILD_SHARED_LIBS": "OFF" }
+      },
+      {
+        "name": "system-libs-mixin",
+        "hidden": true,
+        "description": "Mixin to use system libraries instead of bundled ones.",
+        "cacheVariables": {
+          "MEMILIO_USE_BUNDLED_EIGEN": "OFF",
+          "MEMILIO_USE_BUNDLED_BOOST": "OFF",
+          "MEMILIO_USE_BUNDLED_JSONCPP": "OFF",
+          "MEMILIO_USE_BUNDLED_SPDLOG": "OFF"
+        }
+      },
+      {
+        "name": "unix-debug",
+        "displayName": "Unix Debug (Ninja, Bundled Libs)",
+        "inherits": "unix-base",
+        "cacheVariables": { "CMAKE_BUILD_TYPE": "Debug" }
+      },
+      {
+        "name": "windows-debug",
+        "displayName": "Windows Debug (VS 2022, Bundled Libs)",
+        "inherits": "windows-base",
+        "cacheVariables": { "CMAKE_BUILD_TYPE": "Debug" }
+      },
+      {
+        "name": "unix-debug-system",
+        "displayName": "Unix Debug (Ninja, System Libs)",
+        "inherits": ["unix-debug", "system-libs-mixin"]
+      },
+      {
+        "name": "windows-debug-system",
+        "displayName": "Windows Debug (VS 2022, System Libs)",
+        "inherits": ["windows-debug", "system-libs-mixin"]
+      },
+      {
+        "name": "unix-release",
+        "displayName": "Unix Release (Ninja, Bundled Libs)",
+        "inherits": "unix-base",
+        "cacheVariables": { "CMAKE_BUILD_TYPE": "Release" }
+      },
+      {
+        "name": "windows-release",
+        "displayName": "Windows Release (VS 2022, Bundled Libs)",
+        "inherits": "windows-base",
+        "cacheVariables": { "CMAKE_BUILD_TYPE": "Release" }
+      },
+      {
+        "name": "unix-release-system",
+        "displayName": "Unix Release (Ninja, System Libs)",
+        "inherits": ["unix-release", "system-libs-mixin"]
+      },
+      {
+        "name": "windows-release-system",
+        "displayName": "Windows Release (VS 2022, System Libs)",
+        "inherits": ["windows-release", "system-libs-mixin"]
+      },
+      {
+        "name": "unix-relwithdebinfo",
+        "displayName": "Unix RelWithDebInfo (Ninja, Bundled Libs)",
+        "inherits": "unix-base",
+        "cacheVariables": { "CMAKE_BUILD_TYPE": "RelWithDebInfo" }
+      },
+      {
+        "name": "windows-relwithdebinfo",
+        "displayName": "Windows RelWithDebInfo (VS 2022, Bundled Libs)",
+        "inherits": "windows-base",
+        "cacheVariables": { "CMAKE_BUILD_TYPE": "RelWithDebInfo" }
+      },
+      {
+        "name": "unix-debug-asan",
+        "displayName": "Unix Debug + Address Sanitizer",
+        "inherits": "unix-debug",
+        "cacheVariables": { "MEMILIO_SANITIZE_ADDRESS": "ON" }
+      },
+      {
+        "name": "unix-debug-ubsan",
+        "displayName": "Unix Debug + Undefined Behavior Sanitizer",
+        "inherits": "unix-debug",
+        "cacheVariables": { "MEMILIO_SANITIZE_UNDEFINED": "ON" }
+      },
+      {
+        "name": "unix-debug-asan-ubsan",
+        "displayName": "Unix Debug + ASan + UBSan",
+        "inherits": "unix-debug",
+        "cacheVariables": { "MEMILIO_SANITIZE_ADDRESS": "ON", "MEMILIO_SANITIZE_UNDEFINED": "ON" }
+      },
+       {
+        "name": "unix-debug-coverage",
+        "displayName": "Unix Debug + Code Coverage",
+        "inherits": "unix-debug",
+        "cacheVariables": { "MEMILIO_TEST_COVERAGE": "ON" }
+      },
+      {
+        "name": "unix-release-openmp",
+        "displayName": "Unix Release + OpenMP",
+        "inherits": "unix-release",
+        "cacheVariables": { "MEMILIO_ENABLE_OPENMP": "ON" }
+      },
+      {
+        "name": "unix-release-mpi",
+        "displayName": "Unix Release + MPI",
+        "inherits": "unix-release",
+        "cacheVariables": { "MEMILIO_ENABLE_MPI": "ON" }
+      },
+       {
+        "name": "unix-release-ipopt",
+        "displayName": "Unix Release + Ipopt",
+        "inherits": "unix-release",
+        "cacheVariables": { "MEMILIO_ENABLE_IPOPT": "ON" }
+      },
+       {
+        "name": "unix-release-profiling",
+        "displayName": "Unix Release + Profiling",
+        "inherits": "unix-release",
+        "cacheVariables": { "MEMILIO_ENABLE_PROFILING": "ON" }
+      },
+      {
+        "name": "unix-release-install",
+        "displayName": "Unix Release + Install",
+        "inherits": "unix-release",
+        "cacheVariables": { "MEMILIO_ENABLE_INSTALL": "ON" }
+      },
+      {
+        "name": "windows-release-install",
+        "displayName": "Windows Release + Install",
+        "inherits": "windows-release",
+        "cacheVariables": { "MEMILIO_ENABLE_INSTALL": "ON" }
+      }
+    ],
+    "buildPresets": [
+      { "name": "build-unix-debug", "configurePreset": "unix-debug", "configuration": "Debug" },
+      { "name": "build-unix-debug-system", "configurePreset": "unix-debug-system", "configuration": "Debug" },
+      { "name": "build-unix-release", "configurePreset": "unix-release", "configuration": "Release" },
+      { "name": "build-unix-release-system", "configurePreset": "unix-release-system", "configuration": "Release" },
+      { "name": "build-unix-relwithdebinfo", "configurePreset": "unix-relwithdebinfo", "configuration": "RelWithDebInfo" },
+      { "name": "build-unix-debug-asan", "configurePreset": "unix-debug-asan", "configuration": "Debug" },
+      { "name": "build-unix-debug-ubsan", "configurePreset": "unix-debug-ubsan", "configuration": "Debug" },
+      { "name": "build-unix-debug-asan-ubsan", "configurePreset": "unix-debug-asan-ubsan", "configuration": "Debug" },
+      { "name": "build-unix-debug-coverage", "configurePreset": "unix-debug-coverage", "configuration": "Debug" },
+      { "name": "build-unix-release-openmp", "configurePreset": "unix-release-openmp", "configuration": "Release" },
+      { "name": "build-unix-release-mpi", "configurePreset": "unix-release-mpi", "configuration": "Release" },
+      { "name": "build-unix-release-ipopt", "configurePreset": "unix-release-ipopt", "configuration": "Release" },
+      { "name": "build-unix-release-profiling", "configurePreset": "unix-release-profiling", "configuration": "Release" },
+      { "name": "build-unix-release-install", "configurePreset": "unix-release-install", "configuration": "Release" },
+      { "name": "build-windows-debug", "configurePreset": "windows-debug", "configuration": "Debug" },
+      { "name": "build-windows-debug-system", "configurePreset": "windows-debug-system", "configuration": "Debug" },
+      { "name": "build-windows-release", "configurePreset": "windows-release", "configuration": "Release" },
+      { "name": "build-windows-release-system", "configurePreset": "windows-release-system", "configuration": "Release" },
+      { "name": "build-windows-relwithdebinfo", "configurePreset": "windows-relwithdebinfo", "configuration": "RelWithDebInfo" },
+      { "name": "build-windows-release-install", "configurePreset": "windows-release-install", "configuration": "Release" }
+    ],
+    "testPresets": [
+      { "name": "test-unix-debug", "configurePreset": "unix-debug", "configuration": "Debug", "output": {"outputOnFailure": true} },
+      { "name": "test-unix-debug-system", "configurePreset": "unix-debug-system", "configuration": "Debug", "output": {"outputOnFailure": true} },
+      { "name": "test-unix-release", "configurePreset": "unix-release", "configuration": "Release", "output": {"outputOnFailure": true} },
+      { "name": "test-unix-release-system", "configurePreset": "unix-release-system", "configuration": "Release", "output": {"outputOnFailure": true} },
+      { "name": "test-unix-relwithdebinfo", "configurePreset": "unix-relwithdebinfo", "configuration": "RelWithDebInfo", "output": {"outputOnFailure": true} },
+      { "name": "test-unix-debug-asan", "configurePreset": "unix-debug-asan", "configuration": "Debug", "output": {"outputOnFailure": true} },
+      { "name": "test-unix-debug-ubsan", "configurePreset": "unix-debug-ubsan", "configuration": "Debug", "output": {"outputOnFailure": true} },
+      { "name": "test-unix-debug-asan-ubsan", "configurePreset": "unix-debug-asan-ubsan", "configuration": "Debug", "output": {"outputOnFailure": true} },
+      { "name": "test-unix-debug-coverage", "configurePreset": "unix-debug-coverage", "configuration": "Debug", "output": {"outputOnFailure": true} },
+      { "name": "test-windows-debug", "configurePreset": "windows-debug", "configuration": "Debug", "output": {"outputOnFailure": true} },
+      { "name": "test-windows-debug-system", "configurePreset": "windows-debug-system", "configuration": "Debug", "output": {"outputOnFailure": true} },
+      { "name": "test-windows-release", "configurePreset": "windows-release", "configuration": "Release", "output": {"outputOnFailure": true} },
+      { "name": "test-windows-release-system", "configurePreset": "windows-release-system", "configuration": "Release", "output": {"outputOnFailure": true} },
+      { "name": "test-windows-relwithdebinfo", "configurePreset": "windows-relwithdebinfo", "configuration": "RelWithDebInfo", "output": {"outputOnFailure": true} }
+   ]
+  }

cpp/benchmarks/CMakeLists.txt

@@ -1,38 +1,70 @@
-set(BENCHMARK_ENABLE_TESTING OFF CACHE BOOL "Disable benchmark testing" FORCE)
+# Attempt to find pre-installed Google Benchmark
+set(MEMILIO_BENCHMARK_VERSION "v1.9.2" CACHE STRING "GoogleTest version to use")
 
-# set(BENCHMARK_ENABLE_EXCEPTIONS OFF CACHE BOOL "Disable benchmark exceptions" FORCE)
-set(BENCHMARK_ENABLE_INSTALL OFF CACHE BOOL "Don't install benchmark" FORCE)
-set(BENCHMARK_DOWNLOAD_DEPENDENCIES OFF CACHE BOOL "Don't download dependencies" FORCE)
-set(BENCHMARK_ENABLE_GTEST_TESTS OFF CACHE BOOL "Disable Google Test in benchmark" FORCE)
+# Configure Google Benchmark build options BEFORE MakeAvailable
+set(BENCHMARK_ENABLE_TESTING OFF CACHE BOOL "" FORCE) # Don't build benchmark's tests
+set(BENCHMARK_ENABLE_INSTALL OFF CACHE BOOL "" FORCE) # Don't install benchmark
+set(BENCHMARK_ENABLE_GTEST_TESTS OFF CACHE BOOL "" FORCE) # Don't require gtest
 
-include(FetchContent)
-FetchContent_Declare(benchmark
+FetchContent_Declare(google_benchmark
     GIT_REPOSITORY https://github.com/google/benchmark.git
-    GIT_TAG v1.6.1)
-FetchContent_GetProperties(benchmark)
+    GIT_TAG        ${MEMILIO_BENCHMARK_VERSION}
+    GIT_SHALLOW    TRUE
+)
+FetchContent_MakeAvailable(google_benchmark)
 
-if(NOT benchmark_POPULATED)
-    FetchContent_Populate(benchmark)
-    set(CMAKE_SUPPRESS_DEVELOPER_WARNINGS 1 CACHE BOOL "")
-    add_subdirectory(${benchmark_SOURCE_DIR} ${benchmark_BINARY_DIR} EXCLUDE_FROM_ALL)
-    unset(CMAKE_SUPPRESS_DEVELOPER_WARNINGS)
-endif()
 
-set_target_properties(benchmark PROPERTIES FOLDER "Extern")
+if(TARGET benchmark::benchmark)
+    set(MEMILIO_BENCHMARK_LIBRARY benchmark::benchmark)
+else()
+    message(FATAL_ERROR "FetchContent for Google Benchmark did not provide target 'benchmark::benchmark'.")
+endif() 
 
-add_executable(integrator_step_benchmark integrator_step.cpp)
-target_link_libraries(integrator_step_benchmark PRIVATE memilio ode_secir benchmark::benchmark)
 
-add_executable(flow_simulation_ode_secirvvs_benchmark flow_simulation_ode_secirvvs.cpp)
-target_link_libraries(flow_simulation_ode_secirvvs_benchmark PRIVATE memilio ode_secirvvs benchmark::benchmark)
 
-add_executable(flow_simulation_ode_seir_benchmark flow_simulation_ode_seir.cpp)
-target_link_libraries(flow_simulation_ode_seir_benchmark PRIVATE memilio ode_seir benchmark::benchmark)
+# Helper function to add benchmark executables
+function(add_memilio_benchmark NAME SOURCES)
+    set(MEMILIO_DEPS ${ARGN})
 
-add_executable(simulation_benchmark simulation.cpp)
-target_link_libraries(simulation_benchmark PRIVATE memilio ode_secir benchmark::benchmark)
-add_executable(graph_simulation_benchmark graph_simulation.cpp)
-target_link_libraries(graph_simulation_benchmark PRIVATE memilio ode_secirvvs benchmark::benchmark)
+    add_executable(${NAME} ${SOURCES})
+    target_link_libraries(${NAME} PRIVATE
+        memilio
+        ${MEMILIO_DEPS}
+        ${MEMILIO_BENCHMARK_LIBRARY}
+    )
+endfunction()
 
-add_executable(abm_benchmark abm.cpp)
-target_link_libraries(abm_benchmark PRIVATE abm benchmark::benchmark)
+
+# Define benchmark executables
+add_memilio_benchmark(memilio_abm_benchmark
+    abm.cpp
+    abm
+)
+
+if(MEMILIO_HAS_JSONCPP)
+    add_memilio_benchmark(memilio_graph_simulation_benchmark
+        graph_simulation.cpp
+        ode_secirvvs
+    )
+
+    add_memilio_benchmark(memilio_flow_simulation_ode_seir_benchmark
+        flow_simulation_ode_seir.cpp
+        ode_seir
+    )
+
+
+    add_memilio_benchmark(memilio_flow_simulation_ode_secirvvs_benchmark
+        flow_simulation_ode_secirvvs.cpp
+        ode_secirvvs
+    )
+
+    add_memilio_benchmark(integrator_secir_benchmark
+        integrator_secir_sim.cpp
+        ode_secir
+    )
+
+    add_memilio_benchmark(memilio_integrator_step_benchmark
+        integrator_step.cpp
+        ode_secir
+    )
+endif()