From 37224423f62d9a71922cb6fe9beca1516d9403a4 Mon Sep 17 00:00:00 2001
From: Jiwon Gim <55209567+boulderdaze@users.noreply.github.com>
Date: Tue, 25 Feb 2025 17:46:31 -0700
Subject: [PATCH] Update MUSICA index mapping API and CMake script (#208)

Originator(s): @boulderdaze

Summary (include the keyword ['closes', 'fixes', 'resolves'] and issue
number):

- Reworked the CMake script for the case where the MUSICA library is
linked from the installed version.
- Updated MUSICA index mapping API.
- Updated Dockerfile for MUSICA.

Describe any changes made to the namelist: N/A

List all files eliminated and why: Please refer to the `Files changed`
tab

List all files added and what they do: Please refer to the `Files
changed` tab

List all existing files that have been modified, and describe the
changes: Please refer to the `Files changed` tab

List any test failures: N/A

Is this a science-changing update? New physics package, algorithm
change, tuning changes, etc? No
---
 schemes/musica/tuvx/musica_ccpp_tuvx.F90 |   6 +-
 test/CMakeLists.txt                      |   5 +-
 test/docker/Dockerfile.musica            |  28 ++++--
 test/docker/Dockerfile.musica.no_install |  10 +-
 test/musica/CMakeLists.txt               | 122 +++++++++++------------
 test/musica/micm/CMakeLists.txt          |   7 +-
 test/musica/tuvx/CMakeLists.txt          |  63 ++----------
 7 files changed, 100 insertions(+), 141 deletions(-)

diff --git a/schemes/musica/tuvx/musica_ccpp_tuvx.F90 b/schemes/musica/tuvx/musica_ccpp_tuvx.F90
index 293a2905..eaac00dc 100644
--- a/schemes/musica/tuvx/musica_ccpp_tuvx.F90
+++ b/schemes/musica/tuvx/musica_ccpp_tuvx.F90
@@ -133,7 +133,7 @@ subroutine tuvx_init(vertical_layer_dimension, vertical_interface_dimension, &
                        errmsg, errcode)
     use ccpp_constituent_prop_mod, only: ccpp_constituent_prop_ptr_t
     use musica_tuvx, only: grid_map_t, profile_map_t, radiator_map_t
-    use musica_util, only: error_t, configuration_t
+    use musica_util, only: error_t, configuration_t, MUSICA_INDEX_MAPPINGS_MAP_ANY
     use musica_ccpp_namelist, only: filename_of_tuvx_micm_mapping_configuration
     use musica_ccpp_util, only: PI
     use musica_ccpp_tuvx_height_grid, &
@@ -486,8 +486,8 @@ subroutine tuvx_init(vertical_layer_dimension, vertical_interface_dimension, &
     end if
 
     photolysis_rate_constants_mapping => &
-        index_mappings_t( config, photolysis_rate_constants_ordering, &
-                          micm_rate_parameter_ordering, error )
+        index_mappings_t( config, MUSICA_INDEX_MAPPINGS_MAP_ANY, &
+        photolysis_rate_constants_ordering, micm_rate_parameter_ordering, error )
     if (has_error_occurred( error, errmsg, errcode )) then
       deallocate( tuvx )
       tuvx => null()
diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt
index 9ac2d8c0..3ab88891 100644
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.21)
 
 project(
   atmosphericphysics
-  VERSION 0.0.0
+  VERSION 0.1.0
   LANGUAGES Fortran C CXX
 )
 
@@ -10,6 +10,9 @@ 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_CXX_STANDARD 20)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
 # ---------------------------------------------------------------------------------------------
 # NOTE: If 'CCPP_ENABLE_MUSICA_TESTS' is enabled, this is no longer a stand-alone CMake project.
 #       The MUSICA CCPP wrapper requires both the MUSICA library and ccpp-framework/src.
diff --git a/test/docker/Dockerfile.musica b/test/docker/Dockerfile.musica
index dbab331b..8c1dfdcc 100644
--- a/test/docker/Dockerfile.musica
+++ b/test/docker/Dockerfile.musica
@@ -5,8 +5,9 @@
 
 FROM ubuntu:22.04
 
-ARG MUSICA_GIT_TAG=326b5119768d5be9654baf96ae3bd6a1b757fdc8
+ARG MUSICA_GIT_TAG=cc39bb00d2220fc81c85b22d3ceea4a39bd2bacf
 ARG CAM_SIMA_CHEMISTRY_DATA_TAG=ea3539f1d7b71162e8a78d900ecbe265ba870e3d
+ARG USE_INSTALLED_MUSICA_LIB=ON
 ARG BUILD_TYPE=Debug
 
 RUN apt update \
@@ -47,30 +48,34 @@ RUN sudo apt update \
 ENV FC=mpif90
 ENV FFLAGS="-I/usr/include/"
 
-# Install MUSICA (MUSICA-C)
+# Install MUSICA
 RUN git clone https://github.com/NCAR/musica.git \
     && cd musica \
     && git checkout ${MUSICA_GIT_TAG} \
     && cmake -S . -B build \
-             -D CMAKE_BUILD_TYPE=${BUILD_TYPE} \
+             -D CMAKE_BUILD_TYPE=Release \
              -D MUSICA_ENABLE_TESTS=OFF \
-             -D MUSICA_BUILD_FORTRAN_INTERFACE=OFF \
-             -D MUSICA_ENABLE_MICM=ON \
-             -D MUSICA_ENABLE_TUVX=ON \
+             -D MUSICA_ENABLE_INSTALL=ON \
+             -D MUSICA_BUILD_FORTRAN_INTERFACE=ON \
              -D CMAKE_Fortran_COMPILER=mpif90 \
-             -D CMAKE_C_COMPILER=mpicc \
              -D CMAKE_CXX_COMPILER=mpicxx \
     && cd build \
     && sudo make install
 
+ENV FFLAGS="${FFLAGS} \
+            -I/usr/local/include/micm \
+            -I/usr/local/include/musica \
+            -I/usr/local/include/musica/micm \
+            -I/usr/local/include/musica/tuvx \
+            -I/usr/local/include/musica/fortran"
+
 COPY . atmospheric_physics
 RUN sudo chown -R test_user:test_user atmospheric_physics
 
 # Clone the MUSICA chemistry data set repository
 RUN git clone https://github.com/NCAR/cam-sima-chemistry-data.git \
     && cd cam-sima-chemistry-data \
-    && git checkout ${CAM_SIMA_CHEMISTRY_DATA_TAG} \
-    && mv mechanisms /home/test_user/atmospheric_physics/schemes/musica/configurations
+    && git checkout ${CAM_SIMA_CHEMISTRY_DATA_TAG}
 
 # Make CCPP-framework available before building test
 RUN cd atmospheric_physics/test \
@@ -90,6 +95,11 @@ RUN cd atmospheric_physics/test \
              -D CMAKE_BUILD_TYPE=${BUILD_TYPE} \
              -D CCPP_ENABLE_MUSICA_TESTS=ON \
              -D CCPP_ENABLE_MEMCHECK=ON \
+             -D CMAKE_Fortran_COMPILER=mpif90 \
+             -D CMAKE_CXX_COMPILER=mpicxx \
     && cmake --build ./build
 
+# Move the MUSICA configuration to the build root to make the data available for testing
+RUN mv /home/test_user/cam-sima-chemistry-data/mechanisms /home/test_user/atmospheric_physics/test/build/musica_configurations
+
 WORKDIR /home/test_user/atmospheric_physics/test/build
diff --git a/test/docker/Dockerfile.musica.no_install b/test/docker/Dockerfile.musica.no_install
index 1a4acd79..6abec992 100644
--- a/test/docker/Dockerfile.musica.no_install
+++ b/test/docker/Dockerfile.musica.no_install
@@ -8,8 +8,9 @@
 
 FROM ubuntu:22.04
 
-ARG MUSICA_GIT_TAG=326b5119768d5be9654baf96ae3bd6a1b757fdc8
+ARG MUSICA_GIT_TAG=cc39bb00d2220fc81c85b22d3ceea4a39bd2bacf
 ARG CAM_SIMA_CHEMISTRY_DATA_TAG=ea3539f1d7b71162e8a78d900ecbe265ba870e3d
+ARG USE_INSTALLED_MUSICA_LIB=OFF
 ARG BUILD_TYPE=Debug
 
 RUN apt update \
@@ -49,7 +50,6 @@ RUN sudo apt update \
 
 ENV FC=mpif90
 ENV FFLAGS="-I/usr/include/"
-ENV MUSICA_GIT_TAG=${MUSICA_GIT_TAG}
 
 COPY . atmospheric_physics
 RUN sudo chown -R test_user:test_user atmospheric_physics
@@ -57,8 +57,7 @@ RUN sudo chown -R test_user:test_user atmospheric_physics
 # Clone the MUSICA chemistry data set repository
 RUN git clone https://github.com/NCAR/cam-sima-chemistry-data.git \
     && cd cam-sima-chemistry-data \
-    && git checkout ${CAM_SIMA_CHEMISTRY_DATA_TAG} \
-    && mv mechanisms /home/test_user/atmospheric_physics/schemes/musica/configurations
+    && git checkout ${CAM_SIMA_CHEMISTRY_DATA_TAG}
 
 # Make ccpp-framework available before building test
 RUN cd atmospheric_physics/test \
@@ -80,4 +79,7 @@ RUN cd atmospheric_physics/test \
              -D CCPP_ENABLE_MEMCHECK=ON \
     && cmake --build ./build
 
+# Move the MUSICA configuration to the build root to make the data available for testing
+RUN mv /home/test_user/cam-sima-chemistry-data/mechanisms /home/test_user/atmospheric_physics/test/build/musica_configurations
+
 WORKDIR /home/test_user/atmospheric_physics/test/build
diff --git a/test/musica/CMakeLists.txt b/test/musica/CMakeLists.txt
index f060ac59..1b3e24ad 100644
--- a/test/musica/CMakeLists.txt
+++ b/test/musica/CMakeLists.txt
@@ -1,17 +1,52 @@
-include(FetchContent)
+# If the MUSICA library is not installed, it will fetch
+# the MUSICA repository to build the library
+if(NOT $ENV{USE_INSTALLED_MUSICA_LIB})  # Set by docker
+  include(FetchContent)
 
-FetchContent_Declare(musica
-  GIT_REPOSITORY https://github.com/NCAR/musica.git
-  GIT_TAG        $ENV{MUSICA_GIT_TAG}  # Set by docker
+  FetchContent_Declare(musica
+    GIT_REPOSITORY https://github.com/NCAR/musica.git
+    GIT_TAG        $ENV{MUSICA_GIT_TAG}  # Set by docker
+  )
+
+  set(MUSICA_BUILD_C_CXX_INTERFACE ON)
+  set(MUSICA_BUILD_FORTRAN_INTERFACE ON)
+  set(MUSICA_ENABLE_TESTS OFF)
+  set(MUSICA_ENABLE_INSTALL OFF)
+
+  FetchContent_MakeAvailable(musica)
+
+else()
+  if (CMAKE_Fortran_COMPILER_ID MATCHES "GNU")
+    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -ffree-line-length-none")
+  endif()
+
+  link_directories("/usr/local/lib")
+endif()
+
+find_package(Python REQUIRED)
+
+# Test metadata against the source code
+file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/metadata_test)
+add_custom_target(
+  copy_metadata_test_files ALL ${CMAKE_COMMAND} -E copy
+  ${CMAKE_CURRENT_SOURCE_DIR}/../../schemes/musica/musica_ccpp.meta
+  ${CMAKE_CURRENT_SOURCE_DIR}/../../schemes/musica/musica_ccpp.F90
+  ${CMAKE_BINARY_DIR}/metadata_test
 )
-message(STATUS "Using MUSICA commit: $ENV{MUSICA_GIT_TAG}")
 
-set(MUSICA_BUILD_C_CXX_INTERFACE ON)
-set(MUSICA_BUILD_FORTRAN_INTERFACE ON)
-set(MUSICA_ENABLE_TESTS OFF)
-set(MUSICA_ENABLE_INSTALL OFF)
+add_test(
+  NAME test_metadata_against_source_code
+  COMMAND ${Python_EXECUTABLE} ${CMAKE_BINARY_DIR}/../$ENV{CCPP_FORTRAN_TOOLS_PATH}/offline_check_fortran_vs_metadata.py
+  --directory ${CMAKE_BINARY_DIR}/metadata_test
+)
 
-FetchContent_MakeAvailable(musica)
+# Test musica scheme metadata against the CCPP standard names
+add_test(
+  NAME test_musica_metadata_against_ccpp_standard_names
+  COMMAND ${Python_EXECUTABLE} ${CMAKE_BINARY_DIR}/../$ENV{CCPP_STD_NAMES_PATH}/tools/meta_stdname_check.py
+  --metafile-loc ${CMAKE_BINARY_DIR}/metadata_test/musica_ccpp.meta
+  --stdname-dict ${CMAKE_BINARY_DIR}/../$ENV{CCPP_STD_NAMES_PATH}/standard_names.xml
+)
 
 # MUSICA CCPP API test
 add_executable(test_musica_api test_musica_api.F90 musica_ccpp_namelist.F90)
@@ -36,12 +71,7 @@ target_sources(test_musica_api
 
 target_link_libraries(test_musica_api
   PRIVATE
-    musica::musica-fortran
-)
-
-set_target_properties(test_musica_api
-  PROPERTIES
-  LINKER_LANGUAGE Fortran
+    musica-fortran musica yaml-cpp stdc++ netcdff
 )
 
 add_test(
@@ -52,62 +82,23 @@ add_test(
 
 add_memory_check_test(test_musica_api $<TARGET_FILE:test_musica_api> "" ${CMAKE_RUNTIME_OUTPUT_DIRECTORY})
 
-# copy MUSICA configuration data into the build folder
-add_custom_target(
-  copy_micm_configs ALL ${CMAKE_COMMAND} -E copy_directory
-  ${CMAKE_CURRENT_SOURCE_DIR}/../../schemes/musica/configurations ${CMAKE_BINARY_DIR}/musica_configurations
-)
-
-add_subdirectory(micm)
-add_subdirectory(tuvx)
-
-# Test metadata against the source code
-find_package(Python REQUIRED)
-
-file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/metadata_test)
-add_custom_target(
-  copy_metadata_test_files ALL ${CMAKE_COMMAND} -E copy
-  ${CMAKE_CURRENT_SOURCE_DIR}/../../schemes/musica/musica_ccpp.meta
-  ${CMAKE_CURRENT_SOURCE_DIR}/../../schemes/musica/musica_ccpp.F90
-  ${CMAKE_BINARY_DIR}/metadata_test
-)
-
-add_test(
-  NAME test_metadata_against_source_code
-  COMMAND ${Python_EXECUTABLE} ${CMAKE_BINARY_DIR}/../$ENV{CCPP_FORTRAN_TOOLS_PATH}/offline_check_fortran_vs_metadata.py
-  --directory ${CMAKE_BINARY_DIR}/metadata_test
-)
-
-# Test musica scheme metadata against the CCPP standard names
-add_test(
-  NAME test_musica_metadata_against_ccpp_standard_names
-  COMMAND ${Python_EXECUTABLE} ${CMAKE_BINARY_DIR}/../$ENV{CCPP_STD_NAMES_PATH}/tools/meta_stdname_check.py
-  --metafile-loc ${CMAKE_BINARY_DIR}/metadata_test/musica_ccpp.meta
-  --stdname-dict ${CMAKE_BINARY_DIR}/../$ENV{CCPP_STD_NAMES_PATH}/standard_names.xml
-)
-
 # MUSICA species test
 add_executable(test_musica_species test_musica_species.F90 musica_ccpp_namelist.F90)
 
 target_sources(test_musica_species
   PUBLIC
-  ${MUSICA_CCPP_SOURCES}
-  ${TO_BE_CCPPIZED_SRC_PATH}/ccpp_const_utils.F90
-  ${TO_BE_CCPPIZED_SRC_PATH}/ccpp_tuvx_utils.F90
-  ${CCPP_SRC_PATH}/ccpp_constituent_prop_mod.F90
-  ${CCPP_SRC_PATH}/ccpp_hash_table.F90
-  ${CCPP_SRC_PATH}/ccpp_hashable.F90
-  ${CCPP_TEST_SRC_PATH}/ccpp_kinds.F90
+    ${MUSICA_CCPP_SOURCES}
+    ${TO_BE_CCPPIZED_SRC_PATH}/ccpp_const_utils.F90
+    ${TO_BE_CCPPIZED_SRC_PATH}/ccpp_tuvx_utils.F90
+    ${CCPP_SRC_PATH}/ccpp_constituent_prop_mod.F90
+    ${CCPP_SRC_PATH}/ccpp_hash_table.F90
+    ${CCPP_SRC_PATH}/ccpp_hashable.F90
+    ${CCPP_TEST_SRC_PATH}/ccpp_kinds.F90
 )
 
 target_link_libraries(test_musica_species
   PRIVATE
-    musica::musica-fortran
-)
-
-set_target_properties(test_musica_species
-  PROPERTIES
-  LINKER_LANGUAGE Fortran
+    musica-fortran musica yaml-cpp stdc++ netcdff
 )
 
 add_test(
@@ -116,4 +107,7 @@ add_test(
   WORKING_DIRECTORY ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}
 )
 
-add_memory_check_test(test_musica_species $<TARGET_FILE:test_musica_species> "" ${CMAKE_RUNTIME_OUTPUT_DIRECTORY})
\ No newline at end of file
+add_memory_check_test(test_musica_species $<TARGET_FILE:test_musica_species> "" ${CMAKE_RUNTIME_OUTPUT_DIRECTORY})
+
+add_subdirectory(micm)
+add_subdirectory(tuvx)
diff --git a/test/musica/micm/CMakeLists.txt b/test/musica/micm/CMakeLists.txt
index 0c1c7853..6a8735be 100644
--- a/test/musica/micm/CMakeLists.txt
+++ b/test/musica/micm/CMakeLists.txt
@@ -8,12 +8,7 @@ target_sources(test_micm_util
 
 target_link_libraries(test_micm_util
   PRIVATE
-    musica::musica-fortran
-)
-
-set_target_properties(test_micm_util
-  PROPERTIES
-  LINKER_LANGUAGE Fortran
+    musica-fortran musica yaml-cpp stdc++ netcdff
 )
 
 add_test(
diff --git a/test/musica/tuvx/CMakeLists.txt b/test/musica/tuvx/CMakeLists.txt
index c12d0d57..c8571a9c 100644
--- a/test/musica/tuvx/CMakeLists.txt
+++ b/test/musica/tuvx/CMakeLists.txt
@@ -10,12 +10,7 @@ target_sources(test_tuvx_height_grid
 
 target_link_libraries(test_tuvx_height_grid
   PRIVATE
-    musica::musica-fortran
-)
-
-set_target_properties(test_tuvx_height_grid
-  PROPERTIES
-  LINKER_LANGUAGE Fortran
+    musica-fortran musica yaml-cpp stdc++ netcdff
 )
 
 add_test(
@@ -38,12 +33,7 @@ target_sources(test_tuvx_wavelength_grid
 
 target_link_libraries(test_tuvx_wavelength_grid
   PRIVATE
-    musica::musica-fortran
-)
-
-set_target_properties(test_tuvx_wavelength_grid
-  PROPERTIES
-  LINKER_LANGUAGE Fortran
+    musica-fortran musica yaml-cpp stdc++ netcdff
 )
 
 add_test(
@@ -67,12 +57,7 @@ target_sources(test_tuvx_temperature
 
 target_link_libraries(test_tuvx_temperature
   PRIVATE
-    musica::musica-fortran
-)
-
-set_target_properties(test_tuvx_temperature
-  PROPERTIES
-  LINKER_LANGUAGE Fortran
+    musica-fortran musica yaml-cpp stdc++ netcdff
 )
 
 add_test(
@@ -96,12 +81,7 @@ target_sources(test_tuvx_surface_albedo
 
 target_link_libraries(test_tuvx_surface_albedo
   PRIVATE
-    musica::musica-fortran
-)
-
-set_target_properties(test_tuvx_surface_albedo
-  PROPERTIES
-  LINKER_LANGUAGE Fortran
+    musica-fortran musica yaml-cpp stdc++ netcdff
 )
 
 add_test(
@@ -126,12 +106,7 @@ target_sources(test_tuvx_extraterrestrial_flux
 
 target_link_libraries(test_tuvx_extraterrestrial_flux
   PRIVATE
-    musica-fortran
-)
-
-set_target_properties(test_tuvx_extraterrestrial_flux
-  PROPERTIES
-  LINKER_LANGUAGE Fortran
+    musica-fortran musica yaml-cpp stdc++ netcdff
 )
 
 add_test(
@@ -157,12 +132,7 @@ target_sources(test_tuvx_cloud_optics
 
 target_link_libraries(test_tuvx_cloud_optics
   PRIVATE
-    musica::musica-fortran
-)
-
-set_target_properties(test_tuvx_cloud_optics
-  PROPERTIES
-  LINKER_LANGUAGE Fortran
+    musica-fortran musica yaml-cpp stdc++ netcdff
 )
 
 add_test(
@@ -187,12 +157,7 @@ target_sources(test_tuvx_aerosol_optics
 
 target_link_libraries(test_tuvx_aerosol_optics
   PRIVATE
-    musica::musica-fortran
-)
-
-set_target_properties(test_tuvx_aerosol_optics
-  PROPERTIES
-  LINKER_LANGUAGE Fortran
+    musica-fortran musica yaml-cpp stdc++ netcdff
 )
 
 add_test(
@@ -220,12 +185,7 @@ target_sources(test_tuvx_gas_species
 
 target_link_libraries(test_tuvx_gas_species
   PRIVATE
-    musica::musica-fortran
-)
-
-set_target_properties(test_tuvx_gas_species
-  PROPERTIES
-  LINKER_LANGUAGE Fortran
+    musica-fortran musica yaml-cpp stdc++ netcdff
 )
 
 add_test(
@@ -254,12 +214,7 @@ target_sources(test_tuvx_load_species
 
 target_link_libraries(test_tuvx_load_species
   PRIVATE
-    musica::musica-fortran
-)
-
-set_target_properties(test_tuvx_load_species
-  PROPERTIES
-  LINKER_LANGUAGE Fortran
+    musica-fortran musica yaml-cpp stdc++ netcdff
 )
 
 add_test(