Type erasure (#771)

* Implement type-erased MICM solvers with runtime CUDA loading

This refactors the MICM wrapper to use type erasure for solver and state
classes, enabling a uniform ABI regardless of CUDA availability. CUDA
solvers are now loaded at runtime via dlopen/dlsym on Linux.

Key changes:
- Add IMicmSolver and IState interfaces for type erasure
- Create CpuSolver/CpuState implementations using internal std::variant
- Add CudaLoader singleton for runtime CUDA plugin loading
- Create separate libmusica_cuda.so plugin with factory functions
- Remove #ifdef MUSICA_ENABLE_CUDA from public headers
- Simplify Python bindings to single _musica module
- Update tests to use runtime CUDA detection with GTEST_SKIP

Benefits:
- Single libmusica.so works with or without CUDA
- No ABI differences between CUDA and non-CUDA builds
- Single Python wheel can optionally use CUDA at runtime
- Reduced recompilation needed for different build variants

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Refactor CMake to use target_sources and link Python against musica

- Replace source variable collection with direct target_sources() calls
- Python module now links against musica library instead of compiling
  all sources directly
- Remove unused MODE parameter from musica_setup_target function
- Remove MUSICA_ONLY_PYTHON option (musica library always built)

This simplifies the build and ensures Python bindings use the same
compiled library as C/C++ users.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Inline musica_setup_target into src/CMakeLists.txt

Move the musica target configuration directly into src/CMakeLists.txt
and remove the now-unused setup_musica_target.cmake file. This
simplifies the build system by keeping all musica library configuration
in one place.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Remove musica_cuda_abi_version function

The ABI version checking is not necessary for the CUDA plugin.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* removing unused options, simplifying cmake

* Add prebuilt musica support for faster Python wheel builds

On Linux, the musica library is now prebuilt once during cibuildwheel's
before-all hook, then reused for all Python version builds. This avoids
rebuilding the C++/Fortran code 5 times (once per Python version).

Changes:
- Add MUSICA_USE_PREBUILT CMake option to use find_package(musica)
- Update dependencies.cmake to skip fetching deps when using prebuilt
- Update prepare_build_environment_linux.sh to prebuild musica
- Update pyproject.toml with Linux override for prebuilt
- Update repair_wheel_gpu.sh for new CUDA plugin architecture
- Update python/bindings/CMakeLists.txt for prebuilt CUDA plugin

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Add prebuilt musica support for Windows and macOS wheel builds

Extends the prebuilt library optimization (previously Linux-only) to
Windows and macOS. The C++/Fortran code is now compiled once per
platform in the before-all hook, then reused for all Python versions.

- Update prepare_build_environment_macos.sh to prebuild musica
- Add prepare_build_environment_windows.sh for MSYS2 environment
- Configure scikit-build to use prebuilt libraries on all platforms

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Fix prebuilt musica dependencies for CARMA

When using a prebuilt musica library with CARMA enabled, the exported
targets reference BLAS::BLAS and LAPACK::LAPACK. The musicaConfig.cmake
must find these dependencies before loading the exported targets.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Hide yaml-cpp from public API using opaque pointer

Refactor Configuration struct to use void* instead of YAML::Node* to
hide yaml-cpp as an implementation detail. This removes yaml-cpp from
the public header, eliminating the need to expose it as a dependency
when using prebuilt musica libraries.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* using different mech config hash

* applyig MUSICA_USE_PREBUILT only for cibuildwheel

* temporarily disable cli tests

* correcting javascript bindings, enabling carma?

* not building carma on windows arm

* adding build shared libs option

* bundling sources

* correcting wheel repair

* Fix macOS wheel delocate by bundling dylib files

The install_prebuilt_so function only handled .so files (Linux), missing
macOS .dylib files. Added platform-specific handling and a custom repair
script that ensures dylibs are bundled before delocate runs.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* Fix Windows duplicate symbol error by building yaml-cpp as shared lib

When MUSICA_BUILD_SHARED_LIBS=ON, yaml-cpp is now also built as shared
to prevent duplicate symbols. mechanism_configuration links yaml-cpp as
PUBLIC, so when it was a DLL with yaml-cpp statically linked, musica
would see duplicate symbols from both libyaml-cpp.a and the DLL.

Also added Windows DLL support to install_prebuilt_libs and updated
the Windows repair script to include prebuilt and clangarm64 paths.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

* trying to fix yaml links

* attempting to fix wheel and cmake build errors

* installing libraries when not prebuilt

* logging

* removing python build from linux runner

* removing python builds from other tests

* micm conditions correction

* Fix Windows wheel repair by installing DLLs to bin/

Add RUNTIME DESTINATION to CMake install rules so that .dll files
are installed alongside import libraries on Windows. Without this,
only .dll.a files were installed to lib/ and delvewheel could not
find the actual DLLs needed for wheel repair.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* correcing nvidia dockerfile

* Fix CudaLoader thread safety with std::call_once (#777)

* Initial plan

* Implement thread-safe CudaLoader using std::call_once

Co-authored-by: K20shores <13836216+K20shores@users.noreply.github.com>

* Make LoadLibrary() const to eliminate const_cast

Co-authored-by: K20shores <13836216+K20shores@users.noreply.github.com>

* bumping mech config tag

* adding const

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: K20shores <13836216+K20shores@users.noreply.github.com>
Co-authored-by: Kyle Shores <kyle.shores44@gmail.com>

* Fix ODR violation in CUDA plugin by separating header from implementation (#779)

* Initial plan

* Fix ODR violation by separating CUDA solver header from implementation

Co-authored-by: K20shores <13836216+K20shores@users.noreply.github.com>

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: K20shores <13836216+K20shores@users.noreply.github.com>

* pr comments, updating micm api

* micm commit

* correcting map type

* removing log

* bumping micm tag, not saving animation in CI

---------

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>
Co-authored-by: Copilot <198982749+Copilot@users.noreply.github.com>
Co-authored-by: K20shores <13836216+K20shores@users.noreply.github.com>

Author: 3 people

.github/workflows/mac.yml

@@ -38,18 +38,12 @@ jobs:
       - name: Install dependencies
         run: brew install netcdf netcdf-fortran
 
-      - uses: actions/setup-python@v5
-      - run: pip install numpy --user
-
       - name: Run Cmake 
         run: |
-            PYTHON_PATH=$(which python)
             cmake -S . -B build \
                 -D CMAKE_CXX_FLAGS=-Wl,-ld_classic \
                 -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-                -D MUSICA_GIT_TAG=${{ github.sha }} \
-                -D MUSICA_ENABLE_PYTHON_LIBRARY=ON \
-                -D Python3_EXECUTABLE=$PYTHON_PATH 
+                -D MUSICA_GIT_TAG=${{ github.sha }}
 
       - name: Build
         run: cmake --build build --verbose

.github/workflows/ubuntu.yml

@@ -21,9 +21,6 @@ jobs:
           - { cpp: g++-13, c: gcc-13, fc: gfortran-13}
           - { cpp: g++-14, c: gcc-14, fc: gfortran-14}
           - { cpp: clang++, c: clang, fc: gfortran-12}
-        options: 
-          - {micm: ON, tuvx: OFF, carma: OFF, python: ON}
-          - {micm: OFF, tuvx: ON, carma: OFF, python: OFF}
         build_type: [Release]
     env:
       CC: ${{ matrix.compiler.c }}
@@ -37,16 +34,11 @@ jobs:
         run: |
           sudo apt-get update
           sudo apt-get install -y liblapack-dev libblas-dev build-essential libnetcdf-dev libnetcdff-dev
-          sudo apt-get install -y python3-numpy
 
       - name: Run Cmake
         run: |
           cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} \
                               -D MUSICA_GIT_TAG=${{ github.sha }} \
-                              -D MUSICA_ENABLE_MICM=${{ matrix.options.micm }} \
-                              -D MUSICA_ENABLE_TUVX=${{ matrix.options.tuvx }} \
-                              -D MUSICA_ENABLE_CARMA=${{ matrix.options.carma }} \
-                              -D MUSICA_ENABLE_PYTHON_LIBRARY=${{ matrix.options.python }} \
                               -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
       - name: Build

.github/workflows/windows.yml

@@ -23,15 +23,8 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      if: ${{ matrix.architecture == 'Win32' }}
-      with:
-        python-version: '3.x'
-        architecture: x86
-
     - name: Run CMake
-      run: cmake -S . -B build -A ${{ matrix.architecture }} -D MUSICA_GIT_TAG=${{ github.sha }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_CARMA=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
+      run: cmake -S . -B build -A ${{ matrix.architecture }} -D MUSICA_GIT_TAG=${{ github.sha }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_CARMA=OFF -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
     - name: Build
       run: cmake --build build --config ${{ matrix.build_type }} --parallel
@@ -53,7 +46,7 @@ jobs:
         run: curl -fsSL -o LLVM${{ matrix.version }}.exe https://github.com/llvm/llvm-project/releases/download/llvmorg-${{ matrix.version }}/LLVM-${{ matrix.version }}-win64.exe ; 7z x LLVM${{ matrix.version }}.exe -y -o"C:/Program Files/LLVM"
 
       - name: Run CMake
-        run: cmake -S . -B build -DCMAKE_CXX_COMPILER="C:/Program Files/LLVM/bin/clang++.exe" -DCMAKE_C_COMPILER="C:/Program Files/LLVM/bin/clang.exe" -G"MinGW Makefiles" -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_CARMA=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
+        run: cmake -S . -B build -DCMAKE_CXX_COMPILER="C:/Program Files/LLVM/bin/clang++.exe" -DCMAKE_C_COMPILER="C:/Program Files/LLVM/bin/clang.exe" -G"MinGW Makefiles" -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_CARMA=OFF -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
       - name: Build
         run: cmake --build build --parallel
@@ -71,15 +64,8 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python
-        uses: actions/setup-python@v4
-        if: ${{ matrix.architecture == 'Win32' }}
-        with:
-          python-version: '3.x'
-          architecture: x86
-
       - name: Run CMake
-        run: cmake -S . -B build -A ${{ matrix.architecture }} -T ClangCL -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_CARMA=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D CMAKE_POLICY_VERSION_MINIMUM=3.5
+        run: cmake -S . -B build -A ${{ matrix.architecture }} -T ClangCL -D MUSICA_GIT_TAG=${{ github.sha }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_CARMA=OFF -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 
       - name: Build
         run: cmake --build build --config Debug --parallel
@@ -96,10 +82,6 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        # for some reason the debug build fails with an error in the python library
-        # something about the usage of mechanism configuration and variants causes missing type information
-        # This commit for mechanism configuration works: 903150064277e024b0afcfc879df419e1cefc87b
-        # This one doesn't: a3ef728c69f619f80c272d634bc2a17ca5ab4de9
         build_type: [Release]
 
     steps:
@@ -122,7 +104,6 @@ jobs:
                               -D MUSICA_ENABLE_MICM=ON \
                               -D MUSICA_ENABLE_TUVX=OFF \
                               -D MUSICA_ENABLE_CARMA=ON \
-                              -D MUSICA_ENABLE_PYTHON_LIBRARY=ON \
                               -D MUSICA_BUILD_FORTRAN_INTERFACE=ON \
                               -D CMAKE_POLICY_VERSION_MINIMUM=3.5
 

.gitignore

@@ -45,3 +45,5 @@ javascript/wasm/musica.wasm
 # Julia build artifacts
 julia/Manifest.toml
 julia/deps/lib/
+
+.claude

CMakeLists.txt

@@ -30,12 +30,13 @@ option(MUSICA_BUILD_DOCS "Build the documentation" OFF)
 option(MUSICA_ENABLE_MICM "Enable MICM" ON)
 option(MUSICA_ENABLE_TUVX "Enable TUV-x" ON)
 option(MUSICA_ENABLE_CARMA "Enable CARMA" ON)
-option(MUSICA_ENABLE_PIC "Build the library with position independent code" OFF)
 option(MUSICA_ENABLE_COVERAGE "Enable code coverage output" OFF)
 option(MUSICA_BUNDLE_DEPENDENCIES "Bundle dependencies with the library" ON)
 option(MUSICA_ENABLE_JAVASCRIPT "Build the JavaScript addon" OFF)
 option(MUSICA_ENABLE_JULIA "Build the Julia wrapper" OFF)
 option(MUSICA_CREATE_ENVIRONMENT_MODULE "Create an Lmod environment module file" OFF)
+option(MUSICA_USE_PREBUILT "Use a prebuilt musica library instead of building from source" OFF)
+option(MUSICA_BUILD_SHARED_LIBS "Build MUSICA as shared libraries" OFF)
 
 set(MUSICA_GPU_TYPE "None" CACHE STRING "The GPU type being targeted")
 
@@ -44,9 +45,6 @@ set(MUSICA_SET_MICM_DEFAULT_VECTOR_SIZE "4" CACHE STRING "Set MICM vector-ordere
 cmake_dependent_option(
   MUSICA_ENABLE_PYTHON_LIBRARY "Adds pybind11, a lightweight header-only library that exposes C++ types in Python and vice versa" OFF "MUSICA_BUILD_C_CXX_INTERFACE" OFF)
 
-cmake_dependent_option(
-  MUSICA_ONLY_PYTHON "Build only the Python bindings. This option is used when building Python wheels primarily" OFF "MUSICA_ENABLE_PYTHON_LIBRARY" OFF)
-
 ################################################################################
 # Projet wide setup variables 
 set(MUSICA_INSTALL_INCLUDE_DIR ${CMAKE_INSTALL_INCLUDEDIR})
@@ -116,7 +114,13 @@ endif()
 ################################################################################
 # MUSICA
 if(MUSICA_BUILD_C_CXX_INTERFACE)
-  add_subdirectory(src)
+  if(MUSICA_USE_PREBUILT)
+    # Use prebuilt musica library - useful for faster Python wheel builds
+    find_package(musica REQUIRED)
+    message(STATUS "Using prebuilt musica library")
+  else()
+    add_subdirectory(src)
+  endif()
 endif()
 
 if(MUSICA_BUILD_DOCS)

cmake/dependencies.cmake

@@ -22,10 +22,11 @@ endif()
 
 ################################################################################
 # Mechanism Configuration
+# Skip if using prebuilt musica (already includes mechanism_configuration)
 
-if(MUSICA_BUILD_C_CXX_INTERFACE)
+if(MUSICA_BUILD_C_CXX_INTERFACE AND NOT MUSICA_USE_PREBUILT)
   set_git_default(MECH_CONFIG_GIT_REPOSITORY https://github.com/NCAR/MechanismConfiguration.git)
-  set_git_default(MECH_CONFIG_GIT_TAG v1.1.1)
+  set_git_default(MECH_CONFIG_GIT_TAG fcf550e5b3e97cb13d93a382cd4230578eb923f0)
 
   FetchContent_Declare(mechanism_configuration
       GIT_REPOSITORY ${MECH_CONFIG_GIT_REPOSITORY}
@@ -34,12 +35,8 @@ if(MUSICA_BUILD_C_CXX_INTERFACE)
       FIND_PACKAGE_ARGS NAMES mechanism_configuration
   )
 
-  set(MECH_CONFIG_ENABLE_PYTHON_LIBRARY OFF CACHE BOOL "" FORCE)
   set(MECH_CONFIG_ENABLE_TESTS OFF CACHE BOOL "" FORCE)
-
-  if (MUSICA_ENABLE_PYTHON_LIBRARY OR MUSICA_ENABLE_PIC)
-    set(MECH_CONFIG_ENABLE_PIC ON CACHE BOOL "" FORCE)
-  endif()
+  set(MECH_CONFIG_BUILD_SHARED_LIBS ${MUSICA_BUILD_SHARED_LIBS} CACHE BOOL "" FORCE)
 
   FetchContent_MakeAvailable(mechanism_configuration)
 endif()
@@ -72,10 +69,11 @@ endif()
 
 ################################################################################
 # MICM
+# Skip if using prebuilt musica (already includes micm)
 
-if (MUSICA_ENABLE_MICM AND MUSICA_BUILD_C_CXX_INTERFACE)
+if (MUSICA_ENABLE_MICM AND MUSICA_BUILD_C_CXX_INTERFACE AND NOT MUSICA_USE_PREBUILT)
   set_git_default(MICM_GIT_REPOSITORY https://github.com/NCAR/micm.git)
-  set_git_default(MICM_GIT_TAG v3.11.0)
+  set_git_default(MICM_GIT_TAG e854d2cf4d0abc7c6fb243e5406e751c462f3679)
 
   FetchContent_Declare(micm
       GIT_REPOSITORY ${MICM_GIT_REPOSITORY}
@@ -87,6 +85,7 @@ if (MUSICA_ENABLE_MICM AND MUSICA_BUILD_C_CXX_INTERFACE)
   set(MICM_ENABLE_TESTS OFF)
   set(MICM_ENABLE_EXAMPLES OFF)
   set(MICM_DEFAULT_VECTOR_SIZE ${MUSICA_SET_MICM_DEFAULT_VECTOR_SIZE})
+  set(MICM_BUILD_SHARED_LIBS ${MUSICA_BUILD_SHARED_LIBS} CACHE BOOL "" FORCE)
   if(NOT APPLE)
     set(MICM_GPU_TYPE ${MUSICA_GPU_TYPE})
   endif()
@@ -96,8 +95,9 @@ endif()
 
 ################################################################################
 # TUV-x
+# Skip if using prebuilt musica (already includes tuvx)
 
-if (MUSICA_ENABLE_TUVX AND MUSICA_BUILD_C_CXX_INTERFACE)
+if (MUSICA_ENABLE_TUVX AND MUSICA_BUILD_C_CXX_INTERFACE AND NOT MUSICA_USE_PREBUILT)
   set(TUVX_ENABLE_TESTS OFF CACHE BOOL "" FORCE)
   set(TUVX_MOD_DIR ${MUSICA_MOD_DIR} CACHE STRING "" FORCE)
   set(TUVX_INSTALL_MOD_DIR ${MUSICA_INSTALL_MOD_DIR} CACHE STRING "" FORCE)
@@ -123,13 +123,20 @@ endif()
 
 ################################################################################
 # CARMA
-if(MUSICA_ENABLE_CARMA AND MUSICA_BUILD_C_CXX_INTERFACE)
+# Skip if using prebuilt musica (already includes carma)
+
+if(MUSICA_ENABLE_CARMA AND MUSICA_BUILD_C_CXX_INTERFACE AND NOT MUSICA_USE_PREBUILT)
   set_git_default(CARMA_GIT_REPOSITORY https://github.com/NCAR/CARMA-ACOM-dev.git)
   set_git_default(CARMA_GIT_TAG develop-carma-box)
+
   set(CARMA_MOD_DIR ${MUSICA_MOD_DIR} CACHE STRING "" FORCE)
   set(CARMA_INSTALL_MOD_DIR ${MUSICA_INSTALL_MOD_DIR} CACHE STRING "" FORCE)
   set(CARMA_INSTALL_INCLUDE_DIR ${MUSICA_INSTALL_INCLUDE_DIR} CACHE STRING "" FORCE)
 
+  # CARMA needs these
+  find_package(BLAS REQUIRED)
+  find_package(LAPACK REQUIRED)
+
   FetchContent_Declare(carma
       GIT_REPOSITORY ${CARMA_GIT_REPOSITORY}
       GIT_TAG ${CARMA_GIT_TAG}

cmake/musicaConfig.cmake.in

@@ -8,6 +8,11 @@ if("@MUSICA_ENABLE_TUVX@" STREQUAL "ON" OR "@MUSICA_ENABLE_CARMA@" STREQUAL "ON"
   pkg_check_modules(netcdff IMPORTED_TARGET REQUIRED netcdf-fortran)
 endif()
 
+if("@MUSICA_ENABLE_CARMA@" STREQUAL "ON")
+  find_dependency(BLAS)
+  find_dependency(LAPACK)
+endif()
+
 include("${CMAKE_CURRENT_LIST_DIR}/@PROJECT_NAME@_Exports.cmake")
 
 check_required_components("@PROJECT_NAME@")

cmake/setup_musica_target.cmake

@@ -42,6 +42,7 @@ RUN cd musica \
     -D MUSICA_ENABLE_INSTALL=OFF \
     -D MUSICA_ENABLE_TUVX=OFF \
     -D MUSICA_ENABLE_CARMA=OFF \
+    -D MUSICA_BUILD_SHARED_LIBS=ON \
     -D MUSICA_SET_MICM_DEFAULT_VECTOR_SIZE=1 \
     && cd build \
-    && make -j 2
+    && make 

docker/Dockerfile.nvhpc

@@ -117,6 +117,7 @@ end subroutine get_user_defined_rate_parameters_strides_c
     real(c_double) :: temperature
     real(c_double) :: pressure
     real(c_double) :: air_density
+    real(c_double) :: pH
   end type conditions_t
 
   type :: strides_t