Merge branch 'development' into hplin/rk_stratiform

Author: jimmielin

.gitmodules

@@ -20,9 +20,15 @@
 [submodule "ncar-physics"]
         path          = src/physics/ncar_ccpp
 	url           = https://github.com/ESCOMP/atmospheric_physics
-	fxtag         = atmos_phys0_10_001
+	fxtag         = 0af2e2b80bc2f8597b685bf08b0917233ce84afa
         fxrequired    = AlwaysRequired
         fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
+[submodule "rrtmgp-data"]
+	path = src/physics/utils/rrtmgp-data
+	url = https://github.com/earth-system-radiation/rrtmgp-data.git
+        fxrequired    = AlwaysRequired
+        fxtag         = v1.8
+        fxDONOTUSEurl = https://github.com/earth-system-radiation/rrtmgp-data.git
 [submodule "ccs_config"]
         path          = ccs_config
         url           = https://github.com/ESMCI/ccs_config_cesm.git

cime_config/atm_musica_config.py

@@ -4,7 +4,8 @@
 """
 
 MUSICA_CCPP_SCHEME_NAME = "musica_ccpp"
+MUSICA_CONFIG_DIR_NAME = "musica_configurations"
 MUSICA_REPO_URL = "https://github.com/NCAR/musica.git"
 MUSICA_TAG = "cc39bb00d2220fc81c85b22d3ceea4a39bd2bacf"
 CHEMISTRY_DATA_REPO_URL = "https://github.com/NCAR/cam-sima-chemistry-data.git"
-CHEMISTRY_DATA_TAG = "2b58f2410ec7a565bcf80dee16ec20f6bc35d78b"
+CHEMISTRY_DATA_TAG = "71ed143c54b0d5d6e3e70f3d05d413fddcf8d59e"

cime_config/buildlib

@@ -12,7 +12,7 @@ import subprocess
 import logging
 
 from cam_config import ConfigCAM # CAM's configure structure
-from atm_musica_config import MUSICA_CCPP_SCHEME_NAME
+from atm_musica_config import MUSICA_CCPP_SCHEME_NAME, MUSICA_CONFIG_DIR_NAME
 from atm_musica_config import MUSICA_REPO_URL, MUSICA_TAG
 from atm_musica_config import CHEMISTRY_DATA_REPO_URL, CHEMISTRY_DATA_TAG
 
@@ -176,21 +176,22 @@ def _build_cam():
         # If MUSICA-CCPP scheme is used in a suite, download
         # the MUSICA configuration and build the MUSICA library
         if MUSICA_CCPP_SCHEME_NAME in scheme_names:
-            _download_musica_configuration(caseroot)
+            _ = _download_musica_configuration(caseroot)
             musica_install_path = _build_musica(caseroot)
 
             cam_linked_libs = case.get_value("CAM_LINKED_LIBS")
             musica_libs = "-lmusica-fortran -lmusica -lyaml-cpp"
             if not musica_libs in cam_linked_libs:
                 _set_musica_lib_path(musica_install_path, caseroot)
 
-            cmd += ' USER_INCLDIR="'\
-                    f'-I{os.path.join(musica_install_path, "include", "micm")} '\
-                    f'-I{os.path.join(musica_install_path, "include", "musica")} '\
-                    f'-I{os.path.join(musica_install_path, "include", "musica", "micm")} '\
-                    f'-I{os.path.join(musica_install_path, "include", "musica", "tuvx")} '\
-                    f'-I{os.path.join(musica_install_path, "include", "musica", "fortran")} '\
+            cmd += (' USER_INCLDIR="'
+                    f'-I{os.path.join(musica_install_path, "include", "micm")} '
+                    f'-I{os.path.join(musica_install_path, "include", "musica")} '
+                    f'-I{os.path.join(musica_install_path, "include", "musica", "micm")} '
+                    f'-I{os.path.join(musica_install_path, "include", "musica", "tuvx")} '
+                    f'-I{os.path.join(musica_install_path, "include", "musica", "fortran")} '
                     '"'
+                    )
 
         retcode, out, err = run_cmd(cmd)
         _LOGGER.info("Command %s:\n\nstdout:\n%s\n\nstderr:\n%s\n", cmd, out, err)
@@ -284,8 +285,8 @@ def _build_musica(clone_dest: str) -> str:
         subprocess.run(command, cwd=bld_path, stdout=subprocess.PIPE,
                        stderr=subprocess.PIPE, text=True, check=False)
     except subprocess.CalledProcessError as e:
-        raise subprocess.CalledProcessError(e.returncode, e.cmd, "The subprocess \
-            for cmake to configure the MUSICA CMake project failed.") from e
+        raise subprocess.CalledProcessError(e.returncode, e.cmd,
+            "The subprocess for cmake to configure the MUSICA CMake project failed.") from e
     except FileNotFoundError as e:
         raise FileNotFoundError("The 'cmake' command was not found.") from e
     except OSError as e:
@@ -294,10 +295,10 @@ def _build_musica(clone_dest: str) -> str:
     command = ["cmake", "--build", ".", "--target", "install"]
     try:
         subprocess.run(command, cwd=bld_path, stdout=subprocess.PIPE,
-                       stderr=subprocess.PIPE, text=True, check=False)
+                       text=True, check=False)
     except subprocess.CalledProcessError as e:
-        raise subprocess.CalledProcessError(e.returncode, e.cmd, "The subprocess \
-            for cmake to build the MUSICA library failed.") from e
+        raise subprocess.CalledProcessError(e.returncode, e.cmd,
+            "The subprocess for cmake to build the MUSICA library failed.") from e
     except FileNotFoundError as e:
         raise FileNotFoundError("The 'cmake' command was not found.") from e
     except OSError as e:
@@ -308,7 +309,7 @@ def _build_musica(clone_dest: str) -> str:
     return musica_install_path
 
 ###############################################################################
-def _download_musica_configuration(download_dest: str) -> None:
+def _download_musica_configuration(download_dest: str) -> str:
 ###############################################################################
     """
     Downloads the MUSICA configuration and renames the configuration
@@ -321,13 +322,14 @@ def _download_musica_configuration(download_dest: str) -> None:
         Exception: If the directory to be renamed is not found or
             any other exceptions occur during the renaming process,
             an exception is raised with the error message.
+    Returns:
+        musica_config_path: path to the MUSICA configuration directory
     """
-    musica_config_dir_name = "musica_configurations"
 
     _clone_and_checkout(CHEMISTRY_DATA_REPO_URL, CHEMISTRY_DATA_TAG, download_dest)
 
     original_dir = os.path.join(download_dest, "cam-sima-chemistry-data", "mechanisms")
-    renamed_dir = os.path.join(download_dest, "cam-sima-chemistry-data", musica_config_dir_name)
+    renamed_dir = os.path.join(download_dest, "cam-sima-chemistry-data", MUSICA_CONFIG_DIR_NAME)
     try:
         os.rename(original_dir, renamed_dir)
     except FileNotFoundError as e:
@@ -339,12 +341,14 @@ def _download_musica_configuration(download_dest: str) -> None:
     except OSError as e:
         raise OSError("An error occurred while renaming.") from e
 
-    musica_config_path = os.path.join(download_dest, musica_config_dir_name)
+    musica_config_path = os.path.join(download_dest, MUSICA_CONFIG_DIR_NAME)
     if os.path.exists(musica_config_path):
         shutil.rmtree(musica_config_path)
 
     shutil.move(renamed_dir, download_dest)
 
+    return musica_config_path
+
 ###############################################################################
 def _set_musica_lib_path(musica_install_path: str, caseroot: str) -> None:
 ###############################################################################
@@ -374,8 +378,8 @@ def _set_musica_lib_path(musica_install_path: str, caseroot: str) -> None:
         subprocess.run(command, cwd=caseroot, stdout=subprocess.PIPE,
                        stderr=subprocess.PIPE, text=True, check=False)
     except subprocess.CalledProcessError as e:
-        raise subprocess.CalledProcessError(e.returncode, e.cmd, "The subprocess \
-            for xmlchange to set the MUSICA library path failed.") from e
+        raise subprocess.CalledProcessError(e.returncode, e.cmd,
+            "The subprocess for xmlchange to set the MUSICA library path failed.") from e
     except FileNotFoundError as e:
         raise FileNotFoundError("The 'xmlchange' command was not found.") from e
     except OSError as e:
@@ -408,8 +412,8 @@ def _clone_and_checkout(repo_url: str, tag_name: str, clone_dest: str) -> None:
         subprocess.run(["git", "clone", repo_url, repo_path],
            stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True, check=False)
     except subprocess.CalledProcessError as e:
-        raise subprocess.CalledProcessError(e.returncode, e.cmd, f"The subprocess \
-            for git to clone the repository {repo_url} failed.") from e
+        raise subprocess.CalledProcessError(e.returncode, e.cmd,
+            f"The subprocess for git to clone the repository {repo_url} failed.") from e
     except FileNotFoundError as e:
         raise FileNotFoundError("The 'git' command was not found.") from e
     except OSError as e:
@@ -419,8 +423,8 @@ def _clone_and_checkout(repo_url: str, tag_name: str, clone_dest: str) -> None:
         subprocess.run(["git", "-C", repo_path, "checkout", tag_name],
            stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True, check=False)
     except subprocess.CalledProcessError as e:
-        raise subprocess.CalledProcessError(e.returncode, e.cmd, f"The subprocess \
-            for git to checkout the branch {tag_name} failed.") from e
+        raise subprocess.CalledProcessError(e.returncode, e.cmd,
+            f"The subprocess for git to checkout the branch {tag_name} failed.") from e
     except FileNotFoundError as e:
         raise FileNotFoundError("The 'git' command was not found.") from e
     except OSError as e:

cime_config/buildnml

@@ -22,7 +22,7 @@ from CIME.Tools.standard_script_setup import *
 from CIME.XML.standard_module_setup   import *
 from CIME.buildnml                    import create_namelist_infile, parse_input
 from CIME.case                        import Case
-from CIME.utils                       import expect
+from CIME.utils                       import expect, symlink_force
 
 # Save local (cime_config) directory path:
 _CIME_CONFIG_PATH = os.path.dirname(os.path.abspath(__file__))
@@ -35,8 +35,10 @@ from cam_config import ConfigCAM
 # HistoryConfig allows translation from user_nl_cam into Fortran namelists
 from hist_config import HistoryConfig
 
-#Import CAM's ParamGen class:
+# Import CAM's ParamGen class:
 from atm_in_paramgen import AtmInParamGen
+# Import specific names associated with the MUSICA scheme
+from atm_musica_config import MUSICA_CCPP_SCHEME_NAME, MUSICA_CONFIG_DIR_NAME
 
 # Open CIME case log:
 _LOGGER = logging.getLogger(__name__)
@@ -166,7 +168,7 @@ def buildnml(case, caseroot, compname):
     gen_indent = 3
 
     #Generate model code and meta-data:
-    _ = config.generate_cam_src(gen_indent)
+    scheme_names = config.generate_cam_src(gen_indent)
 
     #----------------------------------------------------------------
     # Create namelist attribute dictionary (to set namelist defaults):
@@ -376,6 +378,21 @@ def buildnml(case, caseroot, compname):
             # end for
         # end with
 
+        # If MUSICA-CCPP scheme is used in a suite, create symlinks in the run
+        # directory pointing to the MUSICA configuration data located in the caseroot
+        if MUSICA_CCPP_SCHEME_NAME in scheme_names:
+            musica_config_src_dir = os.path.join(caseroot, MUSICA_CONFIG_DIR_NAME)
+            musica_config_dest_dir = os.path.join(rundir, MUSICA_CONFIG_DIR_NAME)
+
+            if os.path.exists(musica_config_src_dir):
+                os.makedirs(musica_config_dest_dir, exist_ok=True)
+                for root, _, files in os.walk(musica_config_src_dir):
+                    rel_path = os.path.relpath(root, musica_config_src_dir)
+                    dest_dir = os.path.join(musica_config_dest_dir, rel_path)
+
+                    os.makedirs(dest_dir, exist_ok=True)
+                    for file in files:
+                        symlink_force(os.path.join(root, file), os.path.join(dest_dir, file))
 
 ###############################################################################
 def _main_func():

cime_config/cam_autogen.py

@@ -601,20 +601,20 @@ def generate_physics_suites(build_cache, preproc_defs, host_name,
     # So go-ahead and copy all of the source code from
     # there to the bld directory:
     if do_gen_ccpp:
-        # Set CCPP physics "utilities" path
-        atm_phys_util_dir = os.path.join(atm_schemes_path, "utilities")
+        # Set CCPP physics 'utilities' path
+        atm_phys_utilities_dir  = os.path.join(atm_schemes_path, "utilities")
 
-        # Check that directory exists
-        if not os.path.isdir(atm_phys_util_dir):
+        # Check that the directory exists
+        if not os.path.isdir(atm_phys_utilities_dir):
             # CAM-SIMA will likely not run without this, so raise an error
-            emsg = "ERROR: Unable to find CCPP physics utilities directory:\n"
-            emsg += f" {atm_phys_util_dir}\n Have you run 'git-fleximod'?"
+            emsg = "ERROR: Unable to find CCPP physics 'utilities' directory:\n"
+            emsg += f" {atm_phys_utilities_dir}\n Have you run 'git-fleximod'?"
             raise CamAutoGenError(emsg)
         # end if
 
-        # Copy all utility source files to the build directory
-        atm_phys_util_files = glob.glob(os.path.join(atm_phys_util_dir, "*.F90"))
-        for util_file in atm_phys_util_files:
+        # Copy all 'utilities' source files to the build directory
+        atm_phys_utilities_files = glob.glob(os.path.join(atm_phys_utilities_dir, "*.F90"))
+        for util_file in atm_phys_utilities_files:
             shutil.copy(util_file, physics_blddir)
         # end for
 
@@ -632,11 +632,32 @@ def generate_physics_suites(build_cache, preproc_defs, host_name,
             raise CamAutoGenError(emsg)
         # end if
 
+        # Copy all 'to_be_ccppized' source files to the build directory
         atm_phys_to_be_ccppized_files = glob.glob(os.path.join(atm_phys_to_be_ccppized_dir, "*.F90"))
         for to_be_ccppized_file in atm_phys_to_be_ccppized_files:
            shutil.copy(to_be_ccppized_file, physics_blddir)
         # end for
-    # end if
+
+        # Copy 'phys_utils' modules to the build directory,
+        # as SIMA's pio_reader module depends on them.
+        # Note: This requirement will likely disappear once
+        # the abstract File I/O interface has been moved to the
+        # CCPP-framework itself.
+        atm_phys_phys_utils_dir = os.path.join(atm_phys_top_dir, "phys_utils")
+
+        # Check that the directory exists
+        if not os.path.isdir(atm_phys_phys_utils_dir):
+            # CAM-SIMA will likely not run without this, so raise an error
+            emsg = "ERROR: Unable to find CCPP physics 'phys_utils' directory:\n"
+            emsg += f" {atm_phys_phys_utils_dir}\n Have you run 'git-fleximod'?"
+            raise CamAutoGenError(emsg)
+
+        # Copy all 'phys_utils' source files to the build directory
+        atm_phys_phys_utils_files = glob.glob(os.path.join(atm_phys_phys_utils_dir, "*.F90"))
+        for util_file in atm_phys_phys_utils_files:
+            shutil.copy(util_file, physics_blddir)
+
+    # end if (do_gen_ccpp)
 
     if do_gen_ccpp or do_gen_nl:
         # save build details in the build cache

cime_config/namelist_definition_cam.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 
-<entry_id_pg version="0.1">
+<entry_id_pg version="2.0">
 
 <!-- Initial Conditions -->
 
@@ -364,6 +364,23 @@
     </values>
   </entry>
 
+<!-- Host model chemistry settings -->
+
+  <entry id="musica_config">
+    <type>char*256</type>
+    <category>chemistry</category>
+    <group>chemistry_nl</group>
+    <desc>
+      Configuration option for the
+      MUSICA chemistry package.
+
+      Default: none
+    </desc>
+    <values>
+      <value>none</value>
+    </values>
+  </entry>
+
 <!-- Tropopause -->
   <entry id="tropopause_climo_file">
     <type>char*256</type>

cime_config/testdefs/testlist_cam.xml

@@ -61,6 +61,15 @@
       <option name="comment">Test for Hack shallow convection scheme</option>
     </options>
   </test>
+  <test compset="FPHYStest" grid="ne3pg3_ne3pg3_mg37" name="SMS_Ln2" testmods="cam/outfrq_dme_adjust_derecho">
+    <machines>
+      <machine name="derecho" compiler="gnu" category="aux_sima"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:10:00</option>
+      <option name="comment">Test for dme_adjust scheme</option>
+    </options>
+  </test>
   <test compset="FPHYStest" grid="ne3pg3_ne3pg3_mg37" name="SMS_Ln2" testmods="cam/outfrq_rk_stratiform_derecho">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_sima"/>

cime_config/testdefs/testmods_dirs/cam/outfrq_dme_adjust_derecho/shell_commands

@@ -0,0 +1 @@
+ ./xmlchange CAM_CONFIG_OPTS="--dyn none --physics-suites dme_adjust"

cime_config/testdefs/testmods_dirs/cam/outfrq_dme_adjust_derecho/user_nl_cam

@@ -0,0 +1,7 @@
+ncdata='/glade/campaign/cesm/community/amwg/sima_baselines/cam_sima_test_snapshots/cam_ne3pg3_dme_adjust_snapshot_derecho_gnu_before_c20250416.nc'
+ncdata_check='/glade/campaign/cesm/community/amwg/sima_baselines/cam_sima_test_snapshots/cam_ne3pg3_dme_adjust_snapshot_derecho_gnu_after_c20250416.nc'
+debug_output=0
+pver=32
+hist_add_inst_fields;h2: Q,PS
+hist_output_frequency;h2: nsteps
+hist_write_nstep0;h2: .true.

docker/Dockerfile.musica

@@ -77,11 +77,29 @@ RUN /home/cam_sima_user/CAM-SIMA/cime/scripts/create_newcase --case $CASE_NAME \
 
 WORKDIR $CASE_NAME
 
-RUN ./case.setup
-
+RUN ./xmlchange COMPILER=gnu
+RUN ./xmlchange DEBUG=true
 RUN ./xmlchange CAM_CONFIG_OPTS="--dyn none --physics-suites musica"
-RUN ./xmlchange ROF_NCPL=48
 RUN ./xmlchange STOP_OPTION=nsteps
 RUN ./xmlchange STOP_N=5
 
+# Match the GLC timestep to atmosphere timestep
+RUN ./xmlchange ATM_NCPL=48
+RUN ./xmlchange GLC_NCPL=48
+
+# Avoid writing restart files
+RUN ./xmlchange REST_N=100
+
+RUN ./case.setup
+
+# Specify the path to the MUSICA configuraiton files by adding the following lines to the `user_nl_cam` file.
+# For example, to configure the Chapman mechanisms, include these lines. 
+# filename_of_micm_configuration=/home/cam_sima_user/case_name/test-case/musica_configurations/chapman/micm/config.json
+# filename_of_tuvx_configuration=/home/cam_sima_user/case_name/test-case/musica_configurations/chapman/tuvx/config.json
+# filename_of_tuvx_micm_mapping_configuration=/home/cam_sima_user/case_name/test-case/musica_configurations/chapman/tuvx_micm_mapping.json
+
+# You can run the model with the snapshot file by adding this line to the end of 'user_nl_cam' file on Derecho.
+# Note that this snapshot contains only ten time slices.
+# ncdata=/glade/campaign/cesm/community/amwg/sima_baselines/cam_sima_test_snapshots/cam_ne3pg3_kessler_snapshot_derecho_gnu_before_c20240412.nc
+
 RUN ./case.build