Update build scripts (#106)

* update build scripts

* update packaging

* add fortran to project by default

* add fortran compiler to python image

* move fortran mod files to include dir

* separate shared fortran utility module

* fix fortran wrapper build for optional MICM and TUVX inclusion

* update integration builds

* make MICM and TUV-x not dependent on CXX interface

* add more output to fortran packaging script

* only build micm with c++ interface

* update buidl scripts

* specify TUV-x install include paths

* disable TUV-x for some tests

* include fortran compiler in docs build

* update tag for TUV-x

* don't build with TUV-x for doc gen

.github/workflows/fetch_content_integration.yml

@@ -2,8 +2,6 @@ name: FetchContentIntegration
 
 on: 
   push:
-    branches:
-      - main
   pull_request:
   workflow_dispatch:
 

.github/workflows/gh_pages.yml

@@ -10,6 +10,11 @@ jobs:
   build-and-deploy:
     name: Build and deploy to gh-pages
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        gcc-version: [13]
+    env:
+      FC: gfortran-${{ matrix.gcc-version }}
     steps:
       - uses: actions/checkout@v3
         with:

.github/workflows/mac.yml

@@ -35,7 +35,7 @@ jobs:
       - 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_ENABLE_PYTHON_LIBRARY=ON -D Python3_EXECUTABLE=$PYTHON_PATH
+          cmake -S . -B build -D CMAKE_CXX_FLAGS=-Wl,-ld_classic -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON -D Python3_EXECUTABLE=$PYTHON_PATH
 
       - name: Build
         run: cmake --build build --verbose --parallel 10
@@ -60,7 +60,7 @@ jobs:
         run: brew install netcdf netcdf-fortran
 
       - name: Run Cmake 
-        run: cmake -S . -B build -D CMAKE_CXX_FLAGS=-Wl,-ld_classic -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_BUILD_FORTRAN_INTERFACE=ON
+        run: cmake -S . -B build -D CMAKE_CXX_FLAGS=-Wl,-ld_classic -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_BUILD_FORTRAN_INTERFACE=ON
 
       - name: Build
         run: cmake --build build --verbose --parallel 10

.github/workflows/ubuntu.yml

@@ -38,7 +38,7 @@ jobs:
       - run: pip install -r python/requirements.txt
 
       - name: Run Cmake 
-        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }}  -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
+        run: cmake -S . -B build -D CMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
 
       - name: Build
         run: cmake --build build --verbose --parallel 10

.github/workflows/windows.yml

@@ -30,7 +30,7 @@ jobs:
       - run: pip install -r python/requirements.txt
 
       - name: Run Cmake 
-        run: cmake -S . -B build -G "MinGW Makefiles"  -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
+        run: cmake -S . -B build -G "MinGW Makefiles" -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
 
       - name: Build
         run: cmake --build build --parallel
@@ -59,7 +59,7 @@ jobs:
     - run: pip install -r python/requirements.txt
 
     - name: Run CMake
-      run: cmake -S . -B build -G "Visual Studio 16 2019" -A ${{ matrix.architecture }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }}  -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
+      run: cmake -S . -B build -G "Visual Studio 16 2019" -A ${{ matrix.architecture }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
 
     - name: Build
       run: cmake --build build --config ${{ matrix.build_type }} --parallel
@@ -87,7 +87,7 @@ jobs:
     - run: pip install -r python/requirements.txt
 
     - name: Run CMake
-      run: cmake -S . -B build -G "Visual Studio 17 2022" -A ${{ matrix.architecture }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }}  -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
+      run: cmake -S . -B build -G "Visual Studio 17 2022" -A ${{ matrix.architecture }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
 
     - name: Build
       run: cmake --build build --config ${{ matrix.build_type }} --parallel
@@ -111,7 +111,7 @@ jobs:
       - run: pip install -r python/requirements.txt
 
       - 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_ENABLE_PYTHON_LIBRARY=ON
+        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_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
 
       - name: Build
         run: cmake --build build --parallel
@@ -139,7 +139,7 @@ jobs:
       - run: pip install -r python/requirements.txt
 
       - name: Run CMake
-        run: cmake -S . -B build -G "Visual Studio 16 2019" -A ${{ matrix.architecture }} -T ClangCL -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
+        run: cmake -S . -B build -G "Visual Studio 16 2019" -A ${{ matrix.architecture }} -T ClangCL -D MUSICA_ENABLE_TUVX=OFF -D MUSICA_ENABLE_PYTHON_LIBRARY=ON
 
       - name: Build
         run: cmake --build build --config Debug --parallel

CMakeLists.txt

@@ -29,12 +29,8 @@ option(MUSICA_ENABLE_MPI "Enable MPI parallel support" OFF)
 option(MUSICA_ENABLE_OPENMP "Enable OpemMP support" OFF)
 option(MUSICA_ENABLE_MEMCHECK "Enable memory checking" OFF)
 option(MUSICA_BUILD_DOCS "Build the documentation" OFF)
-
-cmake_dependent_option(
-  MUSICA_ENABLE_TUVX "Builds TUV-x, a photolysis calculator library" ON "MUSICA_BUILD_FORTRAN_INTERFACE" OFF)
-
-cmake_dependent_option(
-  MUSICA_ENABLE_MICM "Adds MICM, a model independent chemical mechanism solver" ON "MUSICA_BUILD_C_CXX_INTERFACE" OFF)
+option(MUSICA_ENABLE_MICM "Enable MICM" ON)
+option(MUSICA_ENABLE_TUVX "Enable TUV-x" ON)
 
 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/dependencies.cmake

@@ -30,7 +30,7 @@ endif()
 ################################################################################
 # MICM
 
-if (MUSICA_ENABLE_MICM)
+if (MUSICA_ENABLE_MICM AND MUSICA_BUILD_C_CXX_INTERFACE)
   FetchContent_Declare(micm
       GIT_REPOSITORY https://github.com/NCAR/micm.git
       GIT_TAG 2a5cd4e11a6973974f3c584dfa9841d70e0a42d5
@@ -41,13 +41,15 @@ endif()
 ################################################################################
 # TUV-x
 
-if (MUSICA_ENABLE_TUVX)
+if (MUSICA_ENABLE_TUVX AND MUSICA_BUILD_C_CXX_INTERFACE)
   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_INCLUDE_DIR} CACHE STRING "" FORCE)
+  set(TUVX_INSTALL_INCLUDE_DIR ${MUSICA_INSTALL_INCLUDE_DIR} CACHE STRING "" FORCE)
 
   FetchContent_Declare(tuvx
     GIT_REPOSITORY https://github.com/NCAR/tuv-x.git
-    GIT_TAG main
+    GIT_TAG 6ff27992da1485392329208b736d2ec1522dafa3
   )
 
   FetchContent_MakeAvailable(tuvx)

docker/Dockerfile

@@ -4,8 +4,10 @@ RUN dnf -y update \
     && dnf -y install \
         cmake \
         gcc-c++ \
+        gfortran \
         gdb \
         git \
+        lapack-devel \
         lcov \
         make \
         netcdf-fortran-devel \

docker/Dockerfile.docs

@@ -27,6 +27,7 @@ RUN echo "The suffix is '$SWITCHER_SUFFIX'"
 RUN mkdir /build \
       && cd /build \
       && cmake -D MUSICA_BUILD_DOCS=ON \
+               -D MUSICA_ENABLE_TUVX=OFF \
                /musica \
       && make docs
 

docker/Dockerfile.fortran-gcc.integration

@@ -40,6 +40,7 @@ RUN cd musica \
              -D CMAKE_BUILD_TYPE=Release \
              -D MUSICA_ENABLE_TESTS=ON \
              -D MUSICA_ENABLE_MICM=ON \
+             -D MUSICA_ENABLE_TUVX=OFF \
     && cd build \
     && make install
 
@@ -49,6 +50,8 @@ RUN cd musica/fortran/test/fetch_content_integration \
     && cmake .. \
         -D CMAKE_BUILD_TYPE=Release \
         -D MUSICA_GIT_TAG=${MUSICA_GIT_TAG} \
+        -D MUSICA_ENABLE_MICM=ON \
+        -D MUSICA_ENABLE_TUVX=OFF \
     && make
 
 WORKDIR musica/fortran/test/fetch_content_integration/build

docker/Dockerfile.fortran-intel

@@ -22,11 +22,13 @@ RUN apt update \
     zlib1g-dev \
     && apt clean 
 
-# Build netcdf-fortran
-ENV CXX=icpx
-ENV CC=icx
-ENV FC=ifx
+# Set environment variables to install MUSICA using gcc
+ENV CXX=g++
+ENV CC=gcc
+ENV FC=gfortran
+ENV FFLAGS="-I/usr/include/"
 
+# Build netcdf-fortran
 RUN git clone https://github.com/Unidata/netcdf-fortran.git \
     && cd netcdf-fortran \
     && git checkout v4.6.0 \
@@ -35,10 +37,6 @@ RUN git clone https://github.com/Unidata/netcdf-fortran.git \
     && make -j 8 \
     && make install
 
-# Set environment variables to install MUSICA using gcc
-ENV FC=gfortran
-ENV FFLAGS="-I/usr/include/"
-
 # Copy the musica code
 COPY . musica
 
@@ -47,7 +45,6 @@ RUN cd musica \
     && cmake -S . \
              -B build \
              -D MUSICA_ENABLE_TESTS=ON \
-             -D MUSICA_ENABLE_TUVX=OFF \
              -D CMAKE_BUILD_TYPE=Release \
     && cd build \
     && make install
@@ -61,6 +58,7 @@ RUN cd musica/fortran/test/fetch_content_integration \
     && mkdir build && cd build \
     && cmake .. \
         -D CMAKE_BUILD_TYPE=Release \
+        -D CMAKE_EXE_LINKER_FLAGS="-Wl,--copy-dt-needed-entries" \
         -D MUSICA_GIT_TAG=${MUSICA_GIT_TAG} \
     && make
 

docker/Dockerfile.fortran-nvhpc

@@ -15,6 +15,7 @@ RUN apt update \
     gcc \
     gfortran \
     git \
+    liblapack-dev \
     lcov \
     libcurl4-openssl-dev \
     libhdf5-dev \
@@ -27,11 +28,13 @@ RUN apt update \
     zlib1g-dev \
     && apt clean 
 
-# Build netcdf-fortran
-ENV CXX=nvc++
-ENV CC=nvc
-ENV FC=nvfortran
+# Set environment variables to install MUSICA using gcc
+ENV CXX=g++
+ENV CC=gcc
+ENV FC=gfortran
+ENV FFLAGS="-I/usr/include/"
 
+# Build netcdf-fortran
 RUN git clone https://github.com/Unidata/netcdf-fortran.git \
     && cd netcdf-fortran \
     && git checkout v4.6.0 \
@@ -40,10 +43,6 @@ RUN git clone https://github.com/Unidata/netcdf-fortran.git \
     && make -j 8 \
     && make install
 
-# Set environment variables to install MUSICA using gcc
-ENV FC=gfortran
-ENV FFLAGS="-I/usr/include/"
-
 # Copy the musica code
 COPY . musica
 
@@ -52,7 +51,6 @@ RUN cd musica \
     && cmake -S . \
              -B build \
              -D MUSICA_ENABLE_TESTS=ON \
-             -D MUSICA_ENABLE_TUVX=OFF \
              -D CMAKE_BUILD_TYPE=Release \
     && cd build \
     && make install
@@ -66,6 +64,7 @@ RUN cd musica/fortran/test/fetch_content_integration \
     && mkdir build && cd build \
     && cmake .. \
         -D CMAKE_BUILD_TYPE=Release \
+        -D CMAKE_EXE_LINKER_FLAGS="-Wl,--copy-dt-needed-entries" \
         -D MUSICA_GIT_TAG=${MUSICA_GIT_TAG} \
     && make
 

docker/Dockerfile.memcheck

@@ -4,8 +4,10 @@ RUN dnf -y update \
     && dnf -y install \
         cmake \
         gcc-c++ \
+        gfortran \
         gdb \
         git \
+        lapack-devel \
         lcov \
         make \
         netcdf-fortran-devel \

docker/Dockerfile.mpi

@@ -12,7 +12,9 @@ WORKDIR /home/test_user
 RUN sudo dnf -y install \
         cmake \
         gcc-c++ \
+        gfortran \
         git \
+        lapack-devel \
         lcov \
         make \
         netcdf-fortran-devel \

docker/Dockerfile.mpi_openmp

@@ -12,7 +12,9 @@ WORKDIR /home/test_user
 RUN sudo dnf -y install \
         cmake \
         gcc-c++ \
+        gfortran \
         git \
+        lapack-devel \
         lcov \
         make \
         netcdf-fortran-devel \

docker/Dockerfile.openmp

@@ -12,7 +12,9 @@ WORKDIR /home/test_user
 RUN sudo dnf -y install \
         cmake \
         gcc-c++ \
+        gfortran \
         git \
+        lapack-devel \
         lcov \
         make \
         netcdf-fortran-devel \

docker/Dockerfile.python

@@ -4,8 +4,11 @@ RUN dnf -y update \
     && dnf -y install \
         cmake \
         gcc-c++ \
+        gcc-fortran \
         git \
+        lapack-devel \
         make \
+        netcdf-fortran-devel \
         python-devel \
         pip \
     && dnf clean all
@@ -22,6 +25,7 @@ RUN cd musica \
              -B build \
              -D CMAKE_BUILD_TYPE=Release \
              -D MUSICA_ENABLE_PYTHON_LIBRARY=ON \
+             -D MUSICA_ENABLE_TUVX=OFF \
     && cd build \
     && make install -j 8
 

fortran/CMakeLists.txt

@@ -7,6 +7,11 @@ project(
 )
 
 message (STATUS "CMake build configuration for ${PROJECT_NAME} (${CMAKE_BUILD_TYPE}) ${PROJECT_VERSION}")
+message (STATUS "  MICM: ${MUSICA_ENABLE_MICM}")
+message (STATUS "  TUV-x: ${MUSICA_ENABLE_TUVX}")
+message (STATUS "  Tests: ${MUSICA_ENABLE_TESTS}")
+message (STATUS "  Install: ${MUSICA_ENABLE_INSTALL}")
+message (STATUS "  C/C++ Interface: ${MUSICA_BUILD_C_CXX_INTERFACE}")
 
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
 
@@ -41,9 +46,20 @@ target_link_libraries(musica-fortran
 
 target_sources(musica-fortran
   PRIVATE
-    micm.F90
-    tuvx.F90
+    util.F90
 )
+if (MUSICA_ENABLE_MICM)
+  target_sources(musica-fortran
+    PRIVATE
+      micm.F90
+  )
+endif()
+if (MUSICA_ENABLE_TUVX)
+  target_sources(musica-fortran
+    PRIVATE
+      tuvx.F90
+  )
+endif()
 
 # Add flags for gfortran
 if(${CMAKE_Fortran_COMPILER_ID} MATCHES "GNU")