merge dev

Author: boulderdaze

cime_config/atm_musica_config.py

@@ -1,9 +1,10 @@
 """
 The URLs and tags provided in this script are read by buildlib to build
-and install the MUSICA library, as well as to download the MUSICA configuration."
+and install the MUSICA library, as well as to download the MUSICA configuration.
 """
 
+MUSICA_CCPP_SCHEME_NAME = "musica_ccpp"
 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 = "b81cbc2e61c41ecd2d09167d6736daf1bf1be149"
+CHEMISTRY_DATA_TAG = "2b58f2410ec7a565bcf80dee16ec20f6bc35d78b"

cime_config/buildlib

@@ -12,6 +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_REPO_URL, MUSICA_TAG
 from atm_musica_config import CHEMISTRY_DATA_REPO_URL, CHEMISTRY_DATA_TAG
 
@@ -25,11 +26,12 @@ sys.path.append(os.path.join(__CIMEROOT, "CIME", "Tools"))
 #pylint: disable=wrong-import-position
 # CIME imports
 from CIME.case import Case
-from CIME.utils import run_cmd, expect, symlink_force
+from CIME.utils import run_cmd, expect
 from CIME.utils import stop_buffering_output
 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
 #pylint: enable=wrong-import-position
 
 check_minimum_python_version(3, 7) #CAM requires version 3.7 or greater
@@ -76,10 +78,9 @@ def _build_cam():
         # Re-run source generator in case registry, CCPP suites, or
         # generator scripts have been modified, and
         # to extract required source code paths:
-        config.generate_cam_src(gen_indent)
+        scheme_names = config.generate_cam_src(gen_indent)
 
         dycore = config.get_value('dyn')
-        phys_suites = config.get_value('physics_suites')
         reg_dir = config.get_value('reg_dir')
         init_dir = config.get_value('init_dir')
         phys_dirs_str = config.get_value('phys_dirs')
@@ -172,17 +173,23 @@ def _build_cam():
             if len(optional_mpas_features) > 0:
                 cmd += " OPTIONAL_MPAS_FEATURES=\"" + " ".join(optional_mpas_features) + "\""
 
-        # If the physics suite is MUSICA, build the MUSICA library and get configuration
-        if phys_suites == "musica":
-            _build_musica_library(case)
+        # 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)
+            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(bldroot, "musica", "include", "micm")} '\
-                    f'-I{os.path.join(bldroot, "musica", "include", "musica")} '\
-                    f'-I{os.path.join(bldroot, "musica", "include", "musica", "micm")} '\
-                    f'-I{os.path.join(bldroot, "musica", "include", "musica", "tuvx")} '\
-                    f'-I{os.path.join(bldroot, "musica", "include", "musica", "fortran")} '\
+                    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)
@@ -242,74 +249,68 @@ def _copy2_as_needed(src: str, dst: str) -> None:
                 shutil.copy2(src, dst)
 
 ###############################################################################
-def _build_musica_library(case: Case) -> None:
+def _build_musica(clone_dest: str) -> str:
 ###############################################################################
     """
     Builds and installs the MUSICA library.
 
     Args:
-        case (Case)
+        clone_dest: destination where the repository will be cloned
 
     Raises:
         Exception: If configuring the CMake MUSICA project fails or
             the MUSICA library build fails, an exception is raised.
 
+    Returns:
+        musica_install_path: path to the MUSICA installation directory
     """
-    install_dir_name = "install"
-    build_type = "Release"
-    caseroot = os.path.normpath(case.get_value("CASEROOT"))
-    _clone_and_checkout(MUSICA_REPO_URL, MUSICA_TAG, caseroot)
+    _clone_and_checkout(MUSICA_REPO_URL, MUSICA_TAG, clone_dest)
 
-    bld_path = os.path.join(caseroot, "musica", "build")
+    bld_path = os.path.join(clone_dest, "musica", "build")
     if os.path.exists(bld_path):
         shutil.rmtree(bld_path)
     os.makedirs(bld_path)
 
-    # To install the target, the working directory must be the build directory.
+    # To install the target, the working directory must be the build (CMake binary) directory.
     current_dir = os.getcwd()
     os.chdir(bld_path)
 
+    install_dir = "install"
     command = [
         "cmake",
-        f"-DCMAKE_INSTALL_PREFIX={install_dir_name}",
-        f"-DCMAKE_BUILD_TYPE={build_type}",
-        "-DMUSICA_ENABLE_TESTS=OFF",
-        "-DMUSICA_BUILD_FORTRAN_INTERFACE=ON",
+        f"-D CMAKE_INSTALL_PREFIX={install_dir}",
+        "-D CMAKE_BUILD_TYPE=Release",
+        "-D MUSICA_ENABLE_TESTS=OFF",
+        "-D MUSICA_BUILD_FORTRAN_INTERFACE=ON",
         ".."
     ]
-    result = subprocess.run(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True, check=False)
-    if result.returncode != 0:
-        raise Exception(f"Unable to configure the MUSICA CMake project. Error: {result.stderr}")
+    try:
+        subprocess.run(command, 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
+    except FileNotFoundError as e:
+        raise FileNotFoundError("The 'cmake' command was not found.") from e
+    except OSError as e:
+        raise OSError("An error occurred while executing the 'cmake' command.") from e
 
     command = ["cmake", "--build", ".", "--target", "install"]
-    result = subprocess.run(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True, check=False)
-    if result.returncode != 0:
-        raise Exception(f"Unable to build the MUSICA library. Error: {result.stderr}")
-
-    # Create symlinks pointing to the MUSICA libraries in the ATM build directory
-    atm_bld_root = os.path.join(case.get_value("EXEROOT"), "atm", "obj")
-    musica_lib_root = os.path.join(atm_bld_root, "musica", "lib")
-    os.makedirs(musica_lib_root, exist_ok=True)
-
-    installed_lib_path = os.path.join(bld_path, install_dir_name, "lib64")
-    root, _, files = next(os.walk(installed_lib_path, topdown=True))
-    for file in files:
-        symlink_force(os.path.join(root, file), os.path.join(musica_lib_root, file))
-
-    # Create symlinks pointing to the MUSICA include files in the ATM build directory
-    musica_include_root = os.path.join(atm_bld_root, "musica", "include")
-    os.makedirs(musica_include_root, exist_ok=True)
-
-    installed_include_path = os.path.join(bld_path, install_dir_name, "include")
-    for root, _, files in os.walk(installed_include_path):
-        rel_path = os.path.relpath(root, installed_include_path)
-        dest_dir = os.path.join(musica_include_root, 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))
+    try:
+        subprocess.run(command, 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 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:
+        raise OSError("An error occurred while executing the 'cmake' command.") from e
 
     os.chdir(current_dir)
+    musica_install_path = os.path.join(bld_path, install_dir)
+
+    return musica_install_path
 
 ###############################################################################
 def _download_musica_configuration(download_dest: str) -> None:
@@ -319,7 +320,7 @@ def _download_musica_configuration(download_dest: str) -> None:
     directory to match the name in the MUSICA-CCPP configuration.
 
     Args:
-        download_dest: destination where configuration will be downloaded.
+        download_dest: destination where configuration will be downloaded
 
     Raises:
         Exception: If the directory to be renamed is not found or
@@ -334,14 +335,14 @@ def _download_musica_configuration(download_dest: str) -> None:
     renamed_dir = os.path.join(download_dest, "cam-sima-chemistry-data", musica_config_dir_name)
     try:
         os.rename(original_dir, renamed_dir)
-    except FileNotFoundError:
-        raise FileNotFoundError(f"The directory '{original_dir}' was not found.")
-    except FileExistsError:
-        raise FileExistsError(f"The destination directory '{renamed_dir}' already exists.")
-    except PermissionError:
-        raise PermissionError(f"Permission denied to rename '{original_dir}'.")
+    except FileNotFoundError as e:
+        raise FileNotFoundError(f"The directory '{original_dir}' was not found.") from e
+    except FileExistsError as e:
+        raise FileExistsError(f"The destination directory '{renamed_dir}' already exists.") from e
+    except PermissionError as e:
+        raise PermissionError(f"Permission denied to rename '{original_dir}'.") from e
     except OSError as e:
-        raise OSError(f"An error occurred while renaming: {e}")
+        raise OSError("An error occurred while renaming.") from e
 
     musica_config_path = os.path.join(download_dest, musica_config_dir_name)
     if os.path.exists(musica_config_path):
@@ -350,15 +351,58 @@ def _download_musica_configuration(download_dest: str) -> None:
     shutil.move(renamed_dir, download_dest)
 
 ###############################################################################
-def _clone_and_checkout(repo_url: str, tag_name: str, clone_dest: str):
+def _set_musica_lib_path(musica_install_path: str, caseroot: str) -> None:
+###############################################################################
+    """
+    Sets the MUSICA libraries path to CAM_LINKED_LIBS, allowing the libraries
+    to be linked during the CESM build process.
+
+    Args:
+        musica_install_path: path to the MUSICA installation directory
+        caseroot: CASEROOT where the xmlchange command is located
+
+    Raises:
+        Exception: If the subprocess for the xmlchange command fails,
+            an exception is raised with the error message.
+    """
+
+    current_dir = os.getcwd()
+    os.chdir(caseroot)
+
+    unlock_file("env_build.xml", 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"
+    ]
+    try:
+        subprocess.run(command, 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
+    except FileNotFoundError as e:
+        raise FileNotFoundError("The 'xmlchange' command was not found.") from e
+    except OSError as e:
+        raise OSError("An error occurred while executing the 'xmlchange' command.") from e
+
+    os.chdir(current_dir)
+
+    lock_file("env_build.xml", caseroot)
+
+###############################################################################
+def _clone_and_checkout(repo_url: str, tag_name: str, clone_dest: str) -> None:
 ###############################################################################
     """
     Clones a Git repository from the URL and checks out a specific branch.
 
     Args:
-        repo_url: The URL of the Git repository to clone
-        tag_name: The tag name to check out
-        clone_dest: destination where the repository will be cloned.
+        repo_url: URL of the Git repository to clone
+        tag_name: tag name to check out
+        clone_dest: destination where the repository will be cloned
 
     Raises:
         Exception: If the `git clone` or `git checkout` commands fail,
@@ -370,17 +414,27 @@ def _clone_and_checkout(repo_url: str, tag_name: str, clone_dest: str):
     if os.path.exists(repo_path):
         shutil.rmtree(repo_path)
 
-    result = subprocess.run(["git", "clone", repo_url, repo_path],
-                            stderr=subprocess.PIPE, text=True, check=False)
-    if result.returncode != 0:
-        raise Exception(f"Unable to clone the repository: {repo_url}. \
-                        Error: {result.stderr}")
-
-    result = subprocess.run(["git", "-C", repo_path, "checkout", tag_name],
-                            stderr=subprocess.PIPE, text=True, check=False)
-    if result.returncode != 0:
-        raise Exception(f"Unable to checkout the branch: {tag_name}. \
-                        Error: {result.stderr}")
+    try:
+        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
+    except FileNotFoundError as e:
+        raise FileNotFoundError("The 'git' command was not found.") from e
+    except OSError as e:
+        raise OSError("An error occurred while executing the 'git' command.") from e
+
+    try:
+        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
+    except FileNotFoundError as e:
+        raise FileNotFoundError("The 'git' command was not found.") from e
+    except OSError as e:
+        raise OSError("An error occurred while executing the 'git' command.") from e
 
 ###############################################################################
 

cime_config/buildnml

@@ -166,7 +166,7 @@ def buildnml(case, caseroot, compname):
     gen_indent = 3
 
     #Generate model code and meta-data:
-    config.generate_cam_src(gen_indent)
+    _ = config.generate_cam_src(gen_indent)
 
     #----------------------------------------------------------------
     # Create namelist attribute dictionary (to set namelist defaults):

cime_config/cam_autogen.py

@@ -452,6 +452,7 @@ def generate_physics_suites(build_cache, preproc_defs, host_name,
     # Find the SDFs specified for this model build
     sdfs = []
     scheme_files = []
+    scheme_names = set()
     xml_files = {} # key is scheme, value is xml file path
     for sdf in phys_suites_str.split(';'):
         sdf_path = _find_file(f"suite_{sdf}.xml", suite_search)
@@ -467,6 +468,8 @@ def generate_physics_suites(build_cache, preproc_defs, host_name,
         # Given an SDF, find all the schemes it calls
         _, suite = read_xml_file(sdf_path)
         sdf_schemes = _find_schemes_in_sdf(suite)
+        #Add schemes to set of all scheme names:
+        scheme_names.update(sdf_schemes)
         # For each scheme, find its metadata file
         for scheme in sdf_schemes:
             if scheme in all_scheme_files:
@@ -655,7 +658,7 @@ def generate_physics_suites(build_cache, preproc_defs, host_name,
     # End if
 
     return [physics_blddir, genccpp_dir], do_gen_ccpp, cap_output_file,       \
-        xml_files.values(), capgen_db
+        xml_files.values(), capgen_db, scheme_names
 
 ###############################################################################
 def generate_init_routines(build_cache, bldroot, force_ccpp, force_init,

cime_config/cam_config.py

@@ -868,7 +868,7 @@ def generate_cam_src(self, gen_fort_indent):
                                           self.__atm_root, self.__bldroot,
                                           reg_dir, reg_files, source_mods_dir,
                                           force_ccpp)
-        phys_dirs, force_init, _, nml_fils, capgen_db = retvals
+        phys_dirs, force_init, _, nml_fils, capgen_db, scheme_names = retvals
 
         # Add namelist definition files to dictionary:
         for nml_fil in nml_fils:
@@ -899,6 +899,9 @@ def generate_cam_src(self, gen_fort_indent):
         #--------------------------------------------------------------
         build_cache.write()
 
+        #Return the set of all scheme names present in the SDFs:
+        return scheme_names
+
     #++++++++++++++++++++++++
 
     def ccpp_phys_set(self, cam_nml_attr_dict, phys_nl_pg_dict):

docker/Dockerfile.musica

@@ -75,19 +75,18 @@ ENV ESMFMKFILE=/usr/local/lib/esmf.mk
 RUN /home/cam_sima_user/CAM-SIMA/cime/scripts/create_newcase --case $CASE_NAME \
     --compset FPHYStest --res ne5_ne5_mg37 --run-unsupported
 
-WORKDIR $CASE_NAME 
+WORKDIR $CASE_NAME
 
 RUN ./case.setup
 
 # Set the GLC timestep to match the atmosphere timestep
 RUN ./xmlchange GLC_NCP=48
 RUN ./xmlchange ATM_NCPL=48
+RUN ./xmlchange CAM_CONFIG_OPTS="--dyn none --physics-suites musica"
 RUN ./xmlchange STOP_OPTION=nsteps
 RUN ./xmlchange STOP_N=5
-RUN ./xmlchange CAM_CONFIG_OPTS="--dyn none --physics-suites musica"
-RUN ./xmlchange CAM_LINKED_LIBS="-L/home/cam_sima_user/scratch/test-case/bld/atm/obj/musica/lib -lmusica-fortran -lmusica -lyaml-cpp"
 
 # Avoid writing restart files
 RUN ./xmlchange REST_N=100
 
-RUN ./case.build
+RUN ./case.build