update musica build and dependencies

mattldawson · mattldawson · commit 265276731532 · 2025-06-13T16:53:36.000-06:00
diff --git a/cime_config/atm_musica_config.py b/cime_config/atm_musica_config.py
@@ -6,6 +6,6 @@
 MUSICA_CCPP_SCHEME_NAME = "musica_ccpp"
 MUSICA_CONFIG_DIR_NAME = "musica_configurations"
 MUSICA_REPO_URL = "https://github.com/NCAR/musica.git"
-MUSICA_TAG = "72c3b398fa4713effc5648b29b8070cb432eebf2"
+MUSICA_TAG = "25fff7ae42d146bf3f83ad5ac18b3caac8701ddd"
 CHEMISTRY_DATA_REPO_URL = "https://github.com/NCAR/cam-sima-chemistry-data.git"
 CHEMISTRY_DATA_TAG = "71ed143c54b0d5d6e3e70f3d05d413fddcf8d59e"
diff --git a/cime_config/buildlib b/cime_config/buildlib
@@ -32,6 +32,7 @@ from CIME.buildlib import parse_input
 from CIME.build import get_standard_makefile_args
 from CIME.Tools.standard_script_setup import check_minimum_python_version
 from CIME.locked_files import lock_file, unlock_file
+from CIME.XML.env_build import EnvBuild
 #pylint: enable=wrong-import-position
 
 check_minimum_python_version(3, 7) #CAM requires version 3.7 or greater
@@ -180,7 +181,7 @@ def _build_cam():
             musica_install_path = _build_musica(caseroot)
 
             cam_linked_libs = case.get_value("CAM_LINKED_LIBS")
-            musica_libs = "-lmusica-fortran -lmusica -lmechanism_configuration -lyaml-cpp -lstdc++"
+            musica_libs = _get_musica_libs(caseroot)
             if not musica_libs in cam_linked_libs:
                 _set_musica_lib_path(musica_install_path, caseroot)
 
@@ -249,6 +250,64 @@ def _copy2_as_needed(src: str, dst: str) -> None:
                 # Example scenario: User added some new source code files.
                 shutil.copy2(src, dst)
 
+###############################################################################
+def _cmake_default_args(caseroot):
+###############################################################################
+# Returns a dictionary of CMake variables based on the Macros.cmake file for
+# the build.
+
+    unlock_file("env_build.xml", caseroot)
+    build = EnvBuild(case_root=caseroot)
+    with Case(caseroot) as case:
+        macro_path = os.path.abspath(os.path.join(caseroot, "cmake_macros", ""))
+        args = "-DCONVERT_TO_MAKE=ON "
+        args += "-DCASEROOT={} ".format(caseroot)
+        args += "-DCOMPILER={} ".format(build.get_value("COMPILER"))
+        args += "-DOS={} ".format(build.get_value("OS"))
+        args += "-DMACH={} ".format(case.get_value("MACH"))
+        args += "-DCMAKE_C_COMPILER_WORKS=1 "
+        args += "-DCMAKE_Fortran_COMPILER_WORKS=1 "
+        args += "-DCMAKE_CXX_COMPILER_WORKS=1 "
+        args += "-DDEBUG={} ".format(build.get_value("DEBUG"))
+        cmd = "cmake {} .".format(args)
+        rc, out, err = run_cmd(cmd, combine_output=True, from_dir=macro_path)
+        expect(rc == 0, "Command {} failed with rc={} out={} err={}".format(cmd, rc, out, err))
+
+        arg_dict = {}
+        for line in out.splitlines():
+            if ":=" in line:
+                key, val = line.split(":=")
+                arg_dict[key.replace('CIME_SET_MAKEFILE_VAR','').strip()] = val.strip()
+
+    unlock_file("env_build.xml", caseroot)
+    return arg_dict
+
+###############################################################################
+def _get_musica_libs(caseroot: str) -> str:
+###############################################################################
+    """
+    Returns the MUSICA libraries to be linked to CAM.
+
+    Args:
+        caseroot: CASEROOT where the xmlchange command is located
+
+    Raises:
+        Exception: If the subprocess for the xmlquery command fails,
+            an exception is raised with the error message.
+
+    Returns:
+        musica_libs: MUSICA libraries to be linked to CAM
+    """
+    unlock_file("env_build.xml", caseroot)
+    build = EnvBuild(case_root=caseroot)
+    if build.get_value("DEBUG"):
+        musica_libs = "-lmusica-fortran -lmusica -lmechanism_configuration -lyaml-cppd -lstdc++"
+    else:
+        musica_libs = "-lmusica-fortran -lmusica -lmechanism_configuration -lyaml-cpp -lstdc++"
+    lock_file("env_build.xml", caseroot)
+
+    return musica_libs
+
 ###############################################################################
 def _build_musica(clone_dest: str) -> str:
 ###############################################################################
@@ -266,20 +325,29 @@ def _build_musica(clone_dest: str) -> str:
         musica_install_path: path to the MUSICA installation directory
     """
     _clone_and_checkout(MUSICA_REPO_URL, MUSICA_TAG, clone_dest)
+    build = EnvBuild(case_root=clone_dest)
+    arg_dict = _cmake_default_args(clone_dest)
 
     bld_path = os.path.join(clone_dest, "musica", "build")
     if os.path.exists(bld_path):
         shutil.rmtree(bld_path)
     os.makedirs(bld_path)
-
     install_dir = "install"
+
+    with Case(clone_dest) as case:
+        if build.get_value("DEBUG"):
+            cmake_build_type = "Debug"
+        else:
+            cmake_build_type = "Release"
+    
     command = [
         "cmake",
         f"-D CMAKE_INSTALL_PREFIX={install_dir}",
-        "-D CMAKE_BUILD_TYPE=Release",
+        f"-D CMAKE_BUILD_TYPE={cmake_build_type}",
+        f"-D CMAKE_Fotran_FLAGS={arg_dict['FFLAGS']}",
         "-D MUSICA_ENABLE_TESTS=OFF",
         "-D MUSICA_BUILD_FORTRAN_INTERFACE=ON",
-        "-D MICM_DEFAULT_VECTOR_SIZE=128",
+        "-D MUSICA_SET_MICM_DEFAULT_VECTOR_SIZE=128",
         ".."
     ]
     try:
@@ -366,14 +434,14 @@ def _set_musica_lib_path(musica_install_path: str, caseroot: str) -> None:
             an exception is raised with the error message.
     """
 
-    unlock_file("env_build.xml", caseroot)
+    musica_libs = _get_musica_libs(caseroot)
 
     command = [
         "./xmlchange",
         "--append",
         # The libraries must be on the same line because CIME flags an
         # error for multi-character arguments preceded by a single dash
-        f"CAM_LINKED_LIBS=-L{os.path.join(musica_install_path, 'lib64')} -lmusica-fortran -lmusica -lmechanism_configuration -lyaml-cpp -lstdc++"
+        f"CAM_LINKED_LIBS=-L{os.path.join(musica_install_path, 'lib64')} {musica_libs}"
     ]
     try:
         subprocess.run(command, cwd=caseroot, stdout=subprocess.PIPE,
@@ -386,8 +454,6 @@ def _set_musica_lib_path(musica_install_path: str, caseroot: str) -> None:
     except OSError as e:
         raise OSError("An error occurred while executing the 'xmlchange' command.") from e
 
-    lock_file("env_build.xml", caseroot)
-
 ###############################################################################
 def _clone_and_checkout(repo_url: str, tag_name: str, clone_dest: str) -> None:
 ###############################################################################
diff --git a/src/control/cam_comp.F90 b/src/control/cam_comp.F90
@@ -100,7 +100,6 @@ subroutine cam_init(caseid, ctitle, model_doi_url,                         &
       use air_composition,           only: air_composition_init
       use cam_ccpp_cap,              only: cam_ccpp_initialize_constituents
       use cam_ccpp_cap,              only: cam_model_const_properties
-      use cam_ccpp_cap,              only: cam_constituents_array
       use physics_grid,              only: columns_on_task
       use vert_coord,                only: pver
       use phys_vars_init_check,      only: mark_as_initialized
@@ -156,7 +155,6 @@ subroutine cam_init(caseid, ctitle, model_doi_url,                         &
       character(len=cx)        :: errmsg
 
       type(ccpp_constituent_prop_ptr_t), pointer :: constituent_properties(:)
-      real(kind_phys),                   pointer :: constituents_array(:,:,:)
       !-----------------------------------------------------------------------
 
       call init_pio_subsystem()
@@ -255,17 +253,14 @@ subroutine cam_init(caseid, ctitle, model_doi_url,                         &
       ! Read tropopause climatology
       call tropopause_climo_read_file()
 
-      ! Temporary:  Prescribe realistic but inaccurate physical quantities
+      ! TEMPORARY:  Prescribe realistic but inaccurate physical quantities
       ! necessary for MUSICA that are currently unavailable in CAM-SIMA.
-      ! It also initializes the MUSICA constituent values until the file
-      ! I/O object is implemented.
       !
       ! Remove this when MUSICA input data are available from CAM-SIMA or
       ! other physics schemes.
       constituent_properties => cam_model_const_properties()
-      constituents_array => cam_constituents_array()
       call musica_ccpp_dependencies_init(columns_on_task, pver, &
-           constituent_properties, constituents_array, phys_suite_name)
+           constituent_properties, phys_suite_name)
 
       ! Initialize orbital data
       call orbital_data_init(columns_on_task)
@@ -295,10 +290,15 @@ subroutine cam_timestep_init()
       !
       !-----------------------------------------------------------------------
 
-      use phys_comp,    only: phys_timestep_init
-      use physics_grid, only: lat_rad, lon_rad
-      use orbital_data, only: orbital_data_advance
-      use stepon,       only: stepon_timestep_init
+      use phys_comp,                only: phys_timestep_init
+      use physics_grid,             only: lat_rad, lon_rad
+      use orbital_data,             only: orbital_data_advance
+      use stepon,                   only: stepon_timestep_init
+      use cam_ccpp_cap,             only: cam_constituents_array
+      use ccpp_kinds,               only: kind_phys
+      use musica_ccpp_dependencies, only: set_initial_musica_concentrations
+
+      real(kind_phys), pointer :: constituents_array(:,:,:)
 
       ! Update current fractional calendar day. Needs to be updated at every timestep.
       calday = get_curr_calday()
@@ -319,6 +319,21 @@ subroutine cam_timestep_init()
       call stepon_timestep_init(dtime_phys, cam_runtime_opts, phys_state, phys_tend,   &
            dyn_in, dyn_out)
       call t_stopf('stepon_timestep_init')
+
+      !----------------------------------------------------------
+      ! TEMPORARY:  Set initial MUSICA constituent values
+      !
+      !            This is a temporary workaround to initialize
+      !            MUSICA constituent values until the file I/O
+      !            capability is implemented.
+      !            Remove this when MUSICA species are initialized
+      !            by CAM-SIMA.
+      !----------------------------------------------------------
+      if (is_first_timestep) then
+         constituents_array => cam_constituents_array()
+         call set_initial_musica_concentrations(constituents_array)
+      end if
+
       !
       !----------------------------------------------------------
       ! PHYS_TIMESTEP_INIT Call the Physics package
diff --git a/src/data/air_composition.F90 b/src/data/air_composition.F90
@@ -179,8 +179,6 @@ subroutine air_composition_init()
 
       liq_num = 0
       ice_num = 0
-      has_liq = .false.
-      has_ice = .false.
       ix = -1
       ! standard dry air (constant composition)
       o2_mwi = 1._kind_phys / 32._kind_phys
@@ -239,9 +237,10 @@ subroutine air_composition_init()
       icnst = 1
       water_species_num = 0
       dry_species_num = 0
-      has_ice = .false.
       do idx = 1, num_advected
          cnst_stdname = const_name(idx)
+         has_liq = .false.
+         has_ice = .false.
          select case (TRIM((cnst_stdname)))
             !
             ! O
@@ -437,6 +436,8 @@ subroutine air_composition_init()
             !
             ! If support for more major species is to be included add code here
             !
+         case default
+            cycle ! skip thermodynamically inactive species
          end select
 
          if (masterproc) then
@@ -460,8 +461,6 @@ subroutine air_composition_init()
             end if
             write(iulog, *) "  "
          end if
-         has_liq = .false.
-         has_ice = .false.
       end do
 
       !Set dry air thermodynamic properities if no dry air species provided:
@@ -565,12 +564,14 @@ subroutine water_composition_update(mmr, ncol, energy_formula, cp_or_cv_dycore,
          ! SE
          ! Note: species index subset to 1: because SIMA currently uses index 0. See GitHub issue #334 in ESCOMP/CAM-SIMA.
          call get_cp(mmr(:ncol,:,:), .false., cp_or_cv_dycore(:ncol,:), &
-                     factor=to_dry_factor, active_species_idx_dycore=thermodynamic_active_species_idx(1:), &
+                     factor=to_dry_factor, &
+                     active_species_idx_dycore=thermodynamic_active_species_idx(1:thermodynamic_active_species_num), &
                      cpdry=cpairv(:ncol,:))
       else if (energy_formula == ENERGY_FORMULA_DYCORE_MPAS) then
          ! MPAS
          ! Note: species index subset to 1: because SIMA currently uses index 0. See GitHub issue #334 in ESCOMP/CAM-SIMA.
-         call get_R(mmr(:ncol,:,:), thermodynamic_active_species_idx(1:), &
+         call get_R(mmr(:ncol,:,:), &
+                    thermodynamic_active_species_idx(1:thermodynamic_active_species_num), &
                     cp_or_cv_dycore(:ncol,:), fact=to_dry_factor, Rdry=rairv(:ncol,:))
 
          ! internal energy coefficient for MPAS
diff --git a/src/physics/ncar_ccpp b/src/physics/ncar_ccpp
@@ -1 +1 @@
-Subproject commit b0284d4675c34f792e21ab316eb1db1ee96b07c4
+Subproject commit 667127a22557aef4a00a6fa40b5bbf272fdb2450
diff --git a/src/physics/utils/musica_ccpp_dependencies.F90 b/src/physics/utils/musica_ccpp_dependencies.F90
