Update MUSICA library (#393)

mattldawson · web-flow · commit 883b99c861f3 · 2025-06-24T11:45:27.000-07:00
Tag name (required for release branches): Originator(s): Matt Dawson Description (include the issue title, and the keyword ['closes', 'fixes', 'resolves'] followed by the issue number): Updates to use latest MUSICA library and run Terminator and Chapman configurations. closes #321 Describe any changes made to build system: updated commits for cloning musica library and CMake flags Describe any changes made to the namelist: none List any changes to the defaults for the input datasets (e.g. boundary datasets): none List all files eliminated and why: none List all files added and what they do: none List all existing files that have been modified, and describe the changes: (Helpful git command: `git diff --name-status development...<your_branch_name>`) | File | Description | | --------------------------------------------------- | ------------------------------------------------------------------------- | | src/physics/utils/musica_sima_namelist.F90 | Updated log message text for MUSICA configuration. | | src/physics/utils/musica_ccpp_dependencies.F90 | Renamed some variables and added a function to set initial conditions. | | src/physics/ncar_ccpp | Updated submodule commit pointer. | | src/control/cam_initfiles.F90 | Added check to enforce presence of the initial dataset. | | src/control/cam_comp.F90 | Moved initialization of MUSICA species concentrations to timestep_init to avoid having them be overwritten with zeros. | | cime_config/buildlib | Updated MUSICA linker flags and added a new CMake build flag. | | cime_config/atm_musica_config.py | Updated MUSICA_TAG to the new commit version. | | .gitmodules | Revised ncar-physics submodule URL and commit tag. | If there are new failures (compared to the `test/existing-test-failures.txt` file), have them OK'd by the gatekeeper, note them here, and add them to the file. If there are baseline differences, include the test and the reason for the diff. What is the nature of the change? Roundoff? derecho/intel/aux_sima: all tests pass derecho/gnu/aux_sima: all tests pass If this changes climate describe any run(s) done to evaluate the new climate in enough detail that it(they) could be reproduced: N/A CAM-SIMA date used for the baseline comparison tests if different than latest: N/A
diff --git a/.gitmodules b/.gitmodules
@@ -20,7 +20,7 @@
 [submodule "ncar-physics"]
         path          = src/physics/ncar_ccpp
 	url           = https://github.com/ESCOMP/atmospheric_physics
-	fxtag         = 4a31043bb8bd6179db3b59db4895b0563b78af88
+	fxtag         = 2b66267fe263d9268effeaa1d47e3c03e6121d74
         fxrequired    = AlwaysRequired
         fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 [submodule "rrtmgp-data"]
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 = "cc39bb00d2220fc81c85b22d3ceea4a39bd2bacf"
+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 -lyaml-cpp"
+            musica_libs = _get_musica_libs(caseroot)
             if not musica_libs in cam_linked_libs:
                 _set_musica_lib_path(musica_install_path, caseroot)
 
@@ -249,6 +250,60 @@ 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.
+
+    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 += f"-DCASEROOT={caseroot} "
+        args += f"-DCOMPILER={build.get_value('COMPILER')} "
+        args += f"-DOS={build.get_value('OS')} "
+        args += f"-DMACH={case.get_value('MACH')} "
+        args += "-DCMAKE_C_COMPILER_WORKS=1 "
+        args += "-DCMAKE_Fortran_COMPILER_WORKS=1 "
+        args += "-DCMAKE_CXX_COMPILER_WORKS=1 "
+        args += f"-DDEBUG={build.get_value('DEBUG')} "
+        cmd = f"cmake {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()
+
+    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
+    """
+    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++"
+
+    return musica_libs
+
 ###############################################################################
 def _build_musica(clone_dest: str) -> str:
 ###############################################################################
@@ -266,19 +321,29 @@ 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 MUSICA_SET_MICM_DEFAULT_VECTOR_SIZE=128",
         ".."
     ]
     try:
@@ -365,14 +430,14 @@ 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 -lyaml-cpp"
+        f"CAM_LINKED_LIBS=-L{os.path.join(musica_install_path, 'lib64')} {musica_libs}"
     ]
     try:
         subprocess.run(command, cwd=caseroot, stdout=subprocess.PIPE,
@@ -385,8 +450,6 @@ 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
@@ -86,7 +86,7 @@ subroutine cam_init(caseid, ctitle, model_doi_url,                         &
 
       use cam_initfiles,             only: cam_initfiles_open
       use dyn_grid,                  only: model_grid_init
-      use phys_comp,                 only: phys_init
+      use phys_comp,                 only: phys_init, phys_suite_name
       use phys_comp,                 only: phys_register
       use dyn_comp,                  only: dyn_init
 !      use cam_restart,               only: cam_read_restart
@@ -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)
+           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/control/cam_initfiles.F90 b/src/control/cam_initfiles.F90
@@ -224,6 +224,10 @@ subroutine cam_initfiles_open()
       ! Open initial dataset
 
       if (initial_run) then
+         if (trim(ncdata) == 'ncdata' .or. trim(ncdata) == trim(unset_path_str)) then
+            call endrun(subname//': ERROR: Missing initial dataset. '// &
+                                 'Please set "ncdata" in the CAM namelist')
+         end if
          call cam_get_file(ncdata, ncdata_loc)
          allocate(fh_ini, stat=iret)
          if (iret /= 0) then
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 4a31043bb8bd6179db3b59db4895b0563b78af88
+Subproject commit 2b66267fe263d9268effeaa1d47e3c03e6121d74
diff --git a/src/physics/utils/musica_ccpp_dependencies.F90 b/src/physics/utils/musica_ccpp_dependencies.F90
diff --git a/src/physics/utils/musica_sima_namelist.F90 b/src/physics/utils/musica_sima_namelist.F90
