MUSICA v0.4.0

.dockerignore

@@ -4,15 +4,15 @@
 # add things to copy
 !CMakeLists.txt
 !Dockerfile
-!Dockerfile.ccpp
 !Dockerfile.mpi
 !Dockerfile.mpi_openmp
 !Dockerfile.openmp
-!ccpp
-!cmake
+!musica
+!musica-fortran
 !docs
-!include
+!cmake
 !lib
-!packaging
 !src
-!test
+!test
+!.gitmodules
+!.git

.github/workflows/test.yml

@@ -46,4 +46,18 @@ jobs:
     - name: build Docker image
       run: docker build -t musica-mpi-openmp -f Dockerfile.mpi_openmp .
     - name: run tests in container
-      run: docker run --name test-container -t musica-mpi-openmp bash -c 'make test'
+      run: docker run --name test-container -t musica-mpi-openmp bash -c 'make test'
+  build_test_connections_musica-fortran:
+    runs-on: ubuntu-latest
+    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    steps:
+    - name: delete unnessary tools to free up space
+      run: rm -rf /opt/hostedtoolcache
+
+    - uses: actions/checkout@v2
+      with:
+        submodules: recursive
+    - name: build Docker image
+      run: docker build -t musica-fortran -f Dockerfile.fortran .
+    - name: run tests in container
+      run: docker run --name test-container -t musica-fortran bash -c 'make test'

CMakeLists.txt

@@ -1,53 +1,55 @@
-################################################################################
-# Preamble
-
 cmake_minimum_required(VERSION 3.21)
-set(CMAKE_USER_MAKE_RULES_OVERRIDE "cmake/SetDefaults.cmake")
 
 project(
   musica
-  VERSION 0.3.0
+  VERSION 0.4.0
   LANGUAGES Fortran CXX C
 )
 
+set(CMAKE_MODULE_PATH "${CMAKE_MODULE_PATH};${CMAKE_CURRENT_LIST_DIR}/cmake")
+set(CMAKE_USER_MAKE_RULES_OVERRIDE "${CMAKE_MODULE_PATH}/SetDefaults.cmake")
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR})
-set(CMAKE_MODULE_PATH "${CMAKE_MODULE_PATH};${PROJECT_SOURCE_DIR}/cmake")
 
-if(NOT CMAKE_BUILD_TYPE)
-  set(CMAKE_BUILD_TYPE "Release" CACHE STRING
-      "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel."
-      FORCE)
-endif(NOT CMAKE_BUILD_TYPE)
+################################################################################
+include(CMakeDependentOption)
 
-message ( STATUS "CMake build configuration for musica(${CMAKE_BUILD_TYPE}) ${PROJECT_VERSION}" )
+# Library options to build
+option(USE_MUSICA "Use MUSICA" ON)
+message(STATUS "Building MUSICA sources into a library : ${USE_MUSICA}")
 
-include(musica_util)
-checkout_submodules()
+option(USE_MUSICA_FORTRAN "Use MUSICA Fortran interface" OFF)
+message(STATUS "Building MUSICA-Fortran sources into a library : ${USE_MUSICA_FORTRAN}")
 
 ################################################################################
 # Projet wide setup options
-include(CMakeDependentOption)
+cmake_dependent_option(
+  ENABLE_TESTS "Builds tests that ensures each enabled MUSICA component can be used" ON "USE_MUSICA" OFF)
+message(STATUS "Build tests for MUSICA : ${ENABLE_TESTS}")
 
-option( ENABLE_TESTS "Builds tests that ensures each enabled MUSICA component can be used" OFF )
+cmake_dependent_option(
+  ENABLE_TUVX "Builds TUV-x, a photolysis calculator library" ON "USE_MUSICA" OFF)
+message(STATUS "Build TUV-x : ${ENABLE_TUVX}")
 
-option( ENABLE_TUVX "Builds TUV-x, a photolysis calculator library" ON )
-option( ENABLE_MICM "Adds MICM, a model independent chemical mechanism solver" ON )
+cmake_dependent_option(
+  ENABLE_MICM "Adds MICM, a model independent chemical mechanism solver" ON "USE_MUSICA" OFF)
+message(STATUS "Build MICM : ${ENABLE_MICM}")
 
-option( ENABLE_CCPP "Builds the CCPP library" OFF )
+cmake_dependent_option(
+  ENABLE_MPI "Enable MPI parallel support" OFF "USE_MUSICA" OFF)
+message(STATUS "Enable MPI parallel support : ${ENABLE_MPI}")
 
-option( ENABLE_MPI "Enable MPI parallel support" OFF)
-option( ENABLE_OPENMP "Enable OpemMP support" OFF )
+cmake_dependent_option(
+  ENABLE_OPENMP "Enable OpemMP support" OFF "USE_MUSICA" OFF)
+message(STATUS "Enable OpemMP support : ${ENABLE_OPENMP}")
 
-option( CREATE_ENVIRONMENT_MODULE "Creates an Lmod environment module file that can be installed on the same machine this library is installed to." OFF )
+cmake_dependent_option(
+  CREATE_ENVIRONMENT_MODULE "Creates an Lmod environment module file that can be installed on the same machine this library is installed to." OFF "USE_MUSICA" OFF)
+message(STATUS "Creates an Lmod environment module : ${CREATE_ENVIRONMENT_MODULE}")
 
 if(CREATE_ENVIRONMENT_MODULE)
   set(INSTALL_MODULE_FILE_PATH "" CACHE STRING "This is the path of the modulefiles location that the Lmod files should be installed to.")
 endif()
 
-# Set up include and lib directories
-set( MUSICA_MOD_DIR "${PROJECT_BINARY_DIR}/include" )
-set( MUSICA_LIB_DIR "${PROJECT_BINARY_DIR}/libs" )
-
 include(GNUInstallDirs)
 set(INSTALL_PREFIX "musica-${PROJECT_VERSION}")
 set(INSTALL_MOD_DIR "${INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}")
@@ -78,146 +80,19 @@ elseif(${CMAKE_Fortran_COMPILER_ID} MATCHES "PGI")
 endif()
 
 ################################################################################
-# Dependencies
-
-include(cmake/dependencies.cmake)
-
-##############################################################################
-# MUSICA targets
-
-####################
 # MUSICA
-add_library(musica STATIC)
-add_library(musica::musica ALIAS musica)
-
-set_target_properties(musica PROPERTIES
-  ARCHIVE_OUTPUT_DIRECTORY ${MUSICA_LIB_DIR}
-  Fortran_MODULE_DIRECTORY ${MUSICA_MOD_DIR}
-  VERSION ${PROJECT_VERSION}
-  SOVERSION ${PROJECT_VERSION_MAJOR}
-)
-
-target_link_libraries(musica 
-  PUBLIC
-    PkgConfig::netcdff
-    ${JSON_LIB}
-)
-
-target_include_directories(musica
-  PUBLIC  
-    $<BUILD_INTERFACE:${MUSICA_MOD_DIR}>
-    $<INSTALL_INTERFACE:${INSTALL_MOD_DIR}>
-)
-
-target_include_directories(musica
-  PUBLIC
-    $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>
-    $<INSTALL_INTERFACE:${INSTALL_MOD_DIR}>
-)
-
-add_subdirectory(src)
-
-####################
-# MUSICA-core
-add_library(musicacore_object)
-add_library(musica::musicacore ALIAS musicacore_object)
-add_subdirectory(lib/musica-core/src)
-
-set_target_properties(musicacore_object PROPERTIES
-  ARCHIVE_OUTPUT_DIRECTORY ${MUSICA_LIB_DIR}
-  Fortran_MODULE_DIRECTORY ${MUSICA_MOD_DIR}
-)
-
-target_include_directories(musicacore_object 
-  PUBLIC  
-    $<BUILD_INTERFACE:${MUSICA_MOD_DIR}>
-    $<INSTALL_INTERFACE:${INSTALL_MOD_DIR}>
-)
-
-target_link_libraries(musicacore_object 
-  PUBLIC
-    PkgConfig::netcdff
-)
-
-# add the sources to musica
-target_sources(musica
-  PRIVATE
-    $<TARGET_OBJECTS:musicacore_object>
-)
-
-####################
-# TUV-x
-if (ENABLE_TUVX)
-  add_definitions(-DMUSICA_USE_TUVX)
-
-  set(TUVX_MOD_DIR ${MUSICA_MOD_DIR})
-  set(TUVX_LIB_DIR ${MUSICA_LIB_DIR})
-  add_subdirectory(lib/tuv-x/src)
-
-  set_target_properties(tuvx_object PROPERTIES
-    ARCHIVE_OUTPUT_DIRECTORY ${MUSICA_LIB_DIR}
-    Fortran_MODULE_DIRECTORY ${MUSICA_MOD_DIR}
-  )
-
-  target_include_directories(tuvx_object 
-    PUBLIC  
-      $<BUILD_INTERFACE:${MUSICA_MOD_DIR}>
-      $<INSTALL_INTERFACE:${INSTALL_MOD_DIR}>
-  )
-
-  target_link_libraries(tuvx_object 
-    PUBLIC
-      musicacore_object
-  )
-
-  # add the sources to musica
-  target_sources(musica
-    PRIVATE
-      $<TARGET_OBJECTS:tuvx_object>
-  )
+if(USE_MUSICA)
+  add_subdirectory(musica)
 endif()
 
-####################
-# MICM
-if (ENABLE_MICM)
-  add_definitions(-DMUSICA_USE_MICM)
-  target_compile_features(musica PUBLIC cxx_std_20)
-
-  target_include_directories(musica
-    PUBLIC  
-      $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/lib/micm/include>
-      $<INSTALL_INTERFACE:${INSTALL_MOD_DIR}>
-  )
-
-  install(
-    DIRECTORY 
-      ${PROJECT_SOURCE_DIR}/lib/micm/include/micm
-    DESTINATION 
-      ${INSTALL_MOD_DIR}
-  )
+# MUSICA-Fortran
+if(USE_MUSICA_FORTRAN)
+  add_subdirectory(musica-fortran)
 endif()
 
-####################
-# CCPP
-
-if(ENABLE_CCPP)
-  add_subdirectory(ccpp)
-endif()
-
-
 ################################################################################
 # Tests
-
-# only include packaging if we are the top level project being built
-if(PROJECT_IS_TOP_LEVEL AND ENABLE_TESTS)
+if(ENABLE_TESTS)
   enable_testing()
-  add_subdirectory(test)
+  add_subdirectory(musica/test)
 endif()
-
-################################################################################
-# Packaging
-
-# only include packaging if we are the top level project being built
-if(PROJECT_IS_TOP_LEVEL)
-  add_subdirectory(packaging)
-endif()

Dockerfile

@@ -12,26 +12,28 @@ RUN dnf -y update \
         valgrind \
     && dnf clean all
 
-# install json-fortran
+# Install json-fortran
 RUN curl -LO https://github.com/jacobwilliams/json-fortran/archive/8.2.0.tar.gz \
     && tar -zxvf 8.2.0.tar.gz \
     && cd json-fortran-8.2.0 \
-    && export FC=gfortran \
     && mkdir build \
     && cd build \
     && cmake -D SKIP_DOC_GEN:BOOL=TRUE .. \
     && make install
 
-# copy the musica core code
-COPY . /musica/
+# Set environment variables
+ENV FC=gfortran
+ENV JSON_FORTRAN_HOME="/usr/local/jsonfortran-gnu-8.2.0"
 
-# get a tag and build the model
-RUN mkdir /build \
-    && cd /build \
-    && export JSON_FORTRAN_HOME="/usr/local/jsonfortran-gnu-8.2.0" \
-    && cmake  \
-             -D ENABLE_TESTS=ON \
-          ../musica \
-    && make install -j 8
+# Copy the musica code
+COPY . musica
 
-WORKDIR /build
+# Build
+RUN cd musica \
+    && cmake -S . \
+             -B build \
+             -D ENABLE_TESTS=ON \
+    && cd build \
+    && make install -j 8 
+
+WORKDIR musica/build