Merge branch 'main' into release

.github/workflows/test.yml

@@ -14,6 +14,17 @@ jobs:
       run: docker build -t musica .
     - name: run tests in container
       run: docker run --name test-container -t musica bash -c 'make test'
+  build_test_connections_without_micm:
+    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:
+    - uses: actions/checkout@v2
+      with:
+        submodules: recursive
+    - name: build Docker image
+      run: docker build -t musica -f Dockerfile.no_micm .
+    - name: run tests in container
+      run: docker run --name test-container -t musica bash -c 'make test'
   build_test_connections_with_openmp:
     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
@@ -47,7 +58,21 @@ jobs:
       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'
-  build_test_connections_musica-fortran:
+  # 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'
+  build_test_connections_musica-fortran-same-compiler:
     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:
@@ -58,6 +83,6 @@ jobs:
       with:
         submodules: recursive
     - name: build Docker image
-      run: docker build -t musica-fortran -f Dockerfile.fortran .
+      run: docker build -t musica-fortran-ubuntu -f Dockerfile.fortran-ubuntu .
     - name: run tests in container
-      run: docker run --name test-container -t musica-fortran bash -c 'make test'
+      run: docker run --name test-container -t musica-fortran-ubuntu bash -c 'make test'

CMakeLists.txt

@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.21)
 
 project(
   musica
-  VERSION 0.4.0
+  VERSION 0.5.0
   LANGUAGES Fortran CXX C
 )
 
@@ -54,6 +54,14 @@ include(GNUInstallDirs)
 set(INSTALL_PREFIX "musica-${PROJECT_VERSION}")
 set(INSTALL_MOD_DIR "${INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}")
 
+# MUSICA library components
+if(ENABLE_TUVX)
+  add_definitions(-DMUSICA_USE_TUVX)
+endif()
+if(ENABLE_MICM)
+  add_definitions(-DMUSICA_USE_MICM)
+endif()
+
 # MPI
 if(ENABLE_MPI)
   add_definitions(-DMUSICA_USE_MPI)

Dockerfile

@@ -9,6 +9,7 @@ RUN dnf -y update \
         lcov \
         make \
         netcdf-fortran-devel \
+        json-devel \
         valgrind \
     && dnf clean all
 
@@ -35,5 +36,5 @@ RUN cd musica \
              -D ENABLE_TESTS=ON \
     && cd build \
     && make install -j 8 
-    
+
 WORKDIR musica/build

Dockerfile.fortran

@@ -9,6 +9,7 @@ RUN apt update \
     libcurl4-openssl-dev \
     libhdf5-dev \
     m4 \
+    nlohmann-json3-dev \
     vim \
     zlib1g-dev \
     git \
@@ -44,6 +45,7 @@ RUN cd musica \
     && cmake -S . \
              -B build \
              -D ENABLE_TESTS=ON \
+             -D ENABLE_TUVX=OFF \
     && cd build \
     && make install -j 8 
 
@@ -67,4 +69,7 @@ RUN cd musica/musica-fortran/test \
     && cmake .. \
     && make
 
+RUN cd musica/musica-fortran/test \
+    && cp -r configs/chapman ./build/chapman
+
 WORKDIR musica/musica-fortran/test/build

Dockerfile.fortran-ubuntu

@@ -0,0 +1,60 @@
+FROM ubuntu:22.04
+
+RUN apt update \
+    && apt -y install \
+    cmake \
+    cmake-curses-gui \
+    curl \
+    libcurl4-openssl-dev \
+    libhdf5-dev \
+    m4 \
+    nlohmann-json3-dev \
+    vim \
+    zlib1g-dev \
+    git \
+    lcov \
+    make \
+    libnetcdff-dev \
+    valgrind \ 
+    gcc \
+    gfortran \
+    g++ \
+    && apt clean 
+
+# Set environment variables to install MUSICA using gcc
+ENV FC=gfortran
+ENV FFLAGS="-I/usr/include/"
+
+# Install json-fortran for gnu version
+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 \
+    && mkdir build \
+    && cd build \
+    && cmake -D SKIP_DOC_GEN:BOOL=TRUE .. \
+    && make install
+
+# Copy the musica code
+COPY . musica
+
+# Set json-fortran variable to install MUSICA using gcc
+ENV JSON_FORTRAN_HOME="/usr/local/jsonfortran-gnu-8.2.0"
+
+# Build and install MUSICA
+RUN cd musica \
+    && cmake -S . \
+             -B build \
+             -D ENABLE_TESTS=ON \
+             -D ENABLE_TUVX=OFF \
+    && cd build \
+    && make install -j 8 
+
+RUN cd musica/musica-fortran/test \
+    && mkdir build && cd build \
+    && cmake .. \
+    && make
+
+RUN cd musica/musica-fortran/test \
+    && cp -r configs/chapman ./build/chapman
+
+WORKDIR musica/musica-fortran/test/build

Dockerfile.mpi

@@ -18,6 +18,7 @@ RUN sudo dnf -y install \
         make \
         netcdf-fortran-devel \
         openmpi-devel \
+        json-devel \
         valgrind-openmpi \
     && dnf clean all
 

Dockerfile.mpi_openmp

@@ -17,6 +17,7 @@ RUN sudo dnf -y install \
         lcov \
         make \
         netcdf-fortran-devel \
+        json-devel \
         openmpi-devel \
         valgrind-openmpi \
     && dnf clean all

Dockerfile.no_micm

@@ -0,0 +1,41 @@
+FROM fedora:35
+
+RUN dnf -y update \
+    && dnf -y install \
+        cmake \
+        gcc-c++ \
+        gcc-gfortran \
+        git \
+        lcov \
+        make \
+        netcdf-fortran-devel \
+        valgrind \
+    && dnf clean all
+
+# 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 \
+    && mkdir build \
+    && cd build \
+    && cmake -D SKIP_DOC_GEN:BOOL=TRUE .. \
+    && make install
+
+# Set environment variables
+ENV FC=gfortran
+ENV JSON_FORTRAN_HOME="/usr/local/jsonfortran-gnu-8.2.0"
+
+# Copy the musica code
+COPY . musica
+
+# Build
+RUN cd musica \
+    && cmake -S . \
+             -B build \
+             -D ENABLE_TESTS=ON \
+             -D ENABLE_TUVX=ON \
+             -D ENABLE_MICM=OFF \
+    && cd build \
+    && make install -j 8 
+
+WORKDIR musica/build

Dockerfile.openmp

@@ -17,6 +17,7 @@ RUN sudo dnf -y install \
         lcov \
         make \
         netcdf-fortran-devel \
+        json-devel \
         openmpi-devel \
         valgrind-openmpi \
     && dnf clean all

README.md

@@ -1,4 +1,5 @@
 # MUSICA
+[![GitHub Releases](https://img.shields.io/github/release/NCAR/musica.svg)](https://github.com/NCAR/musica/releases)
 [![License](https://img.shields.io/github/license/NCAR/musica.svg)](https://github.com/NCAR/musica/blob/main/LICENSE)
 [![CI Status](https://github.com/NCAR/musica/actions/workflows/test.yml/badge.svg)](https://github.com/NCAR/musica/actions/workflows/test.yml)
 <!-- [![DOI](https://zenodo.org/badge/.svg)](https://zenodo.org/badge/latestdoi/) -->
@@ -60,4 +61,4 @@ MUSICAv0 description and evaluation:
     eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2021MS002889},
     year = {2022}
 }
-```
+```

musica-fortran/CMakeLists.txt

@@ -28,7 +28,7 @@ find_package(PkgConfig REQUIRED)
 pkg_check_modules(netcdff IMPORTED_TARGET REQUIRED netcdf-fortran)
 
 # Find MUSICA package
-find_package(musica 0.3.0 REQUIRED)
+find_package(musica 0.5.0 REQUIRED)
 
 target_link_libraries(musica-fortran
  PUBLIC 

musica-fortran/src/micm/CMakeLists.txt

@@ -1,4 +1,4 @@
 target_sources(musica-fortran
   PUBLIC
-  interface.F90
+    micm_mod.F90
 )

musica-fortran/src/micm/micm_c_def.F90

@@ -0,0 +1,32 @@
+interface   
+    function create_micm_c(config_path) bind(C, name="create_micm")
+        use iso_c_binding
+        implicit none
+        type(c_ptr) :: create_micm_c
+        character(len=1, kind=C_CHAR), intent(in) :: config_path(*)
+    end function
+
+    subroutine delete_micm_c(micm_t) bind(C, name="delete_micm")
+        use iso_c_binding
+        implicit none
+        type(c_ptr), value :: micm_t
+    end subroutine
+
+    function micm_create_solver_c(micm_t) bind(C, name="micm_create_solver")
+        use iso_c_binding
+        implicit none
+        integer(c_int) :: micm_create_solver_c  ! TODO(jiwon) return value?
+        type(c_ptr), intent(in), value :: micm_t
+    end function
+
+    subroutine micm_solve_c(micm_t, temperature, pressure, time_step, concentrations, num_concentrations) bind(C, name="micm_solve")
+        use iso_c_binding
+        implicit none
+        type(c_ptr), intent(in), value :: micm_t
+        real(c_double), value :: temperature   
+        real(c_double), value :: pressure
+        real(c_double), value :: time_step
+        real(c_double), dimension(*), intent(inout) :: concentrations
+        integer(c_size_t), value, intent(in) :: num_concentrations
+    end subroutine
+end interface

musica-fortran/src/micm/micm_mod.F90

@@ -0,0 +1,60 @@
+module micm_mod
+    use iso_c_binding
+    implicit none
+
+    private
+    public :: micm_t
+
+    include "micm_c_def.F90"
+
+    type micm_t
+        private
+        type(c_ptr) :: ptr
+    contains
+        procedure :: create_solver => micm_create_solver
+        procedure :: solve => micm_solve
+        final :: delete_micm
+    end type
+
+    interface micm_t
+        procedure create_micm
+    end interface
+
+contains
+    function create_micm(config_path)
+        type(micm_t) :: create_micm
+        character(len=*), intent(in) :: config_path
+        character(len=1, kind=C_CHAR) :: c_config_path(len_trim(config_path) + 1)
+        integer :: N, i
+
+        ! Converting Fortran string to C string
+        N = len_trim(config_path)
+        do i = 1, N
+            c_config_path(i) = config_path(i:i)
+        end do
+        c_config_path(N + 1) = C_NULL_CHAR
+
+        create_micm%ptr = create_micm_c(c_config_path)
+    end function
+
+    subroutine delete_micm(this)
+        type(micm_t) :: this
+        call delete_micm_c(this%ptr)
+    end subroutine
+
+    integer function micm_create_solver(this)
+        class(micm_t), intent(in) :: this
+        micm_create_solver = micm_create_solver_c(this%ptr)
+    end function
+
+    subroutine micm_solve(this, temperature, pressure, time_step, concentrations, num_concentrations)
+        class(micm_t), intent(in) :: this
+        real(c_double), intent(in) :: temperature
+        real(c_double), intent(in) :: pressure
+        real(c_double), intent(in) :: time_step
+        real(c_double), dimension(*), intent(inout) :: concentrations
+        integer(c_size_t), intent(in) :: num_concentrations
+        call micm_solve_c(this%ptr, temperature, pressure, time_step, concentrations, num_concentrations)
+    end subroutine
+
+end module