Merge branch 'development' into hplin/hk_conv_rebase

Author: jimmielin

cime_config/buildlib

@@ -147,28 +147,40 @@ def _build_cam():
         # build the library
         #-------------------------------------------------------
 
-        # If dynamical core is MPAS, setup its build infrastructure so it can be built along with CAM below.
-        if dycore == "mpas":
-            _setup_mpas(case)
-
         complib = os.path.join(libroot, "libatm.a")
         makefile = os.path.join(casetools, "Makefile")
 
         cmd = f"{gmake} complib -j {gmake_j} MODEL=cam COMPLIB={complib}"
-        cmd += f" -f {makefile} {get_standard_makefile_args(case)} "
+        cmd += f" -f {makefile} {get_standard_makefile_args(case)}"
 
         # Add C Pre-Processor (CPP) definitions, if present:
         if config.cpp_defs:
             ccpp_defs_str = ' '.join(config.cpp_defs)
             cmd += f" USER_CPPDEFS='{ccpp_defs_str}'"
 
+        # If dynamical core is MPAS, prepare its build infrastructure so it can be built along with CAM-SIMA below.
+        if dycore == "mpas":
+            _prepare_mpas(case)
+
+            optional_mpas_features = []
+
+            if case.get_value("USE_ESMF_LIB"):
+                optional_mpas_features.append("+ESMF_LIBRARY")
+                optional_mpas_features.append("+PERF_MOD_LIBRARY")
+
+            if config.get_value("dyn_kind") == "REAL32":
+                optional_mpas_features.append("+SINGLE_PRECISION")
+
+            if len(optional_mpas_features) > 0:
+                cmd += " OPTIONAL_MPAS_FEATURES=\"" + " ".join(optional_mpas_features) + "\""
+
         retcode, out, err = run_cmd(cmd)
-        _LOGGER.info("%s: \n\n output:\n %s \n\n err:\n\n%s\n", cmd, out, err)
+        _LOGGER.info("Command %s:\n\nstdout:\n%s\n\nstderr:\n%s\n", cmd, out, err)
         expect(retcode == 0, f"Command {cmd} failed with rc={retcode}")
 
-def _setup_mpas(case: Case) -> None:
+def _prepare_mpas(case: Case) -> None:
     """
-    Setup MPAS build infrastructure.
+    Prepare MPAS build infrastructure.
     """
 
     atm_src_root = os.path.normpath(case.get_value("COMP_ROOT_DIR_ATM"))
@@ -177,7 +189,7 @@ def _setup_mpas(case: Case) -> None:
     mpas_dycore_src_root = os.path.join(atm_src_root, "src", "dynamics", "mpas", "dycore", "src")
     mpas_dycore_bld_root = os.path.join(atm_bld_root, "mpas")
 
-    # Make sure `mpas_dycore_src_root` exists. If not, it is likely that `./manage_externals/checkout_externals` did not succeed.
+    # Make sure `mpas_dycore_src_root` exists. If not, it is likely that `./bin/git-fleximod update` did not succeed.
     if os.path.isfile(mpas_dycore_src_root):
         raise FileExistsError(1, "Unexpected file", mpas_dycore_src_root)
 

cime_config/cam_autogen.py

@@ -392,7 +392,7 @@ def generate_registry(data_search, build_cache, atm_root, bldroot,
                                    gen_fort_indent, source_mods_dir, atm_root,
                                    logger=_LOGGER, schema_paths=data_search,
                                    error_on_no_validate=True)
-            retcode, reg_file_list, ic_names, registry_constituents = retvals
+            retcode, reg_file_list, ic_names, registry_constituents, vars_init_value = retvals
             # Raise error if gen_registry failed:
             if retcode != 0:
                 emsg = "ERROR:Unable to generate CAM data structures from {}, err = {}"
@@ -406,15 +406,16 @@ def generate_registry(data_search, build_cache, atm_root, bldroot,
         # Save build details in the build cache
         reg_file_paths = [x.file_path for x in reg_file_list if x.file_path]
         build_cache.update_registry(gen_reg_file, registry_files, dycore,
-                                    reg_file_paths, ic_names, registry_constituents)
+                                    reg_file_paths, ic_names, registry_constituents, vars_init_value)
     else:
         # If we did not run the registry generator, retrieve info from cache
         reg_file_paths = build_cache.reg_file_list()
         ic_names = build_cache.ic_names()
         registry_constituents = build_cache.constituents()
+        vars_init_value = build_cache.vars_init_value()
     # End if
 
-    return genreg_dir, do_gen_registry, reg_file_paths, ic_names, registry_constituents
+    return genreg_dir, do_gen_registry, reg_file_paths, ic_names, registry_constituents, vars_init_value
 
 ###############################################################################
 def generate_physics_suites(build_cache, preproc_defs, host_name,
@@ -659,7 +660,8 @@ def generate_physics_suites(build_cache, preproc_defs, host_name,
 ###############################################################################
 def generate_init_routines(build_cache, bldroot, force_ccpp, force_init,
                            source_mods_dir, gen_fort_indent,
-                           cap_database, ic_names, registry_constituents):
+                           cap_database, ic_names, registry_constituents,
+                           vars_init_value):
 ###############################################################################
     """
     Generate the host model initialization source code files
@@ -697,7 +699,7 @@ def generate_init_routines(build_cache, bldroot, force_ccpp, force_init,
         #   within write_init_files (so that write_init_files can be the place
         #   where the source include files are stored).
         source_paths = [source_mods_dir, _REG_GEN_DIR]
-        retmsg = write_init_files(cap_database, ic_names, registry_constituents,
+        retmsg = write_init_files(cap_database, ic_names, registry_constituents, vars_init_value,
                                   init_dir, _find_file, source_paths,
                                   gen_fort_indent, _LOGGER)
 

cime_config/cam_build_cache.py

@@ -227,6 +227,7 @@ def __init__(self, build_cache):
         self.__reg_gen_files = []
         self.__ic_names = {}
         self.__constituents = []
+        self.__vars_init_value = []
         if os.path.exists(build_cache):
             # Initialize build cache state
             _, cache = read_xml_file(build_cache)
@@ -257,6 +258,9 @@ def __init__(self, build_cache):
                             stdname = item.get('standard_name')
                             itext = clean_xml_text(item)
                             self.__constituents.append(itext)
+                        elif item.tag == 'vars_init_value_entry':
+                            itext = clean_xml_text(item)
+                            self.__vars_init_value.append(itext)
                         else:
                             emsg = "ERROR: Unknown registry tag, '{}'"
                             raise ValueError(emsg.format(item.tag))
@@ -318,7 +322,7 @@ def __init__(self, build_cache):
         # end if
 
     def update_registry(self, gen_reg_file, registry_source_files,
-                        dycore, reg_file_list, ic_names, constituents):
+                        dycore, reg_file_list, ic_names, constituents, vars_init_value):
         """Replace the registry cache data with input data
         """
         self.__dycore = dycore
@@ -334,6 +338,7 @@ def update_registry(self, gen_reg_file, registry_source_files,
         # and should already be of type dict:
         self.__ic_names = ic_names
         self.__constituents = constituents
+        self.__vars_init_value = vars_init_value
 
     def update_ccpp(self, suite_definition_files, scheme_files, host_files,
                     xml_files, namelist_meta_files, namelist_groups,
@@ -410,6 +415,9 @@ def write(self):
             const_entry = ET.SubElement(registry, 'constituent_entry')
             const_entry.text = stdname
         # end for
+        for stdname in self.__vars_init_value:
+            var_entry = ET.SubElement(registry, 'vars_init_value_entry')
+            var_entry.text = stdname
         # CCPP
         ccpp = ET.SubElement(new_cache, 'CCPP')
         for sfile in self.__sdfs.values():
@@ -617,5 +625,9 @@ def constituents(self):
         """Return a copy of the registry constituents list"""
         return list(self.__constituents)
 
+    def vars_init_value(self):
+        """Return a copy of the list of variables with initial_value"""
+        return list(self.__vars_init_value)
+
 #############
 # End of file

cime_config/cam_config.py

@@ -854,7 +854,7 @@ def generate_cam_src(self, gen_fort_indent):
         retvals = generate_registry(data_search, build_cache, self.__atm_root,
                                     self.__bldroot, source_mods_dir,
                                     dyn, gen_fort_indent)
-        reg_dir, force_ccpp, reg_files, ic_names, registry_constituents = retvals
+        reg_dir, force_ccpp, reg_files, ic_names, registry_constituents, vars_init_value = retvals
 
         #Add registry path to config object:
         reg_dir_desc = "Location of auto-generated registry code."
@@ -887,7 +887,8 @@ def generate_cam_src(self, gen_fort_indent):
         init_dir = generate_init_routines(build_cache, self.__bldroot,
                                           force_ccpp, force_init,
                                           source_mods_dir, gen_fort_indent,
-                                          capgen_db, ic_names, registry_constituents)
+                                          capgen_db, ic_names, registry_constituents,
+                                          vars_init_value)
 
         #Add registry path to config object:
         init_dir_desc = "Location of auto-generated physics initialization code."

src/data/generate_registry_data.py

@@ -1758,6 +1758,30 @@ def _create_constituent_list(registry):
     # end for
     return constituent_list
 
+###############################################################################
+def _create_variables_with_initial_value_list(registry):
+###############################################################################
+    """
+    Create a list of all variables with initial_value defined in the registry.
+    To be used by write_init_files.py to allow these variables to
+    not error when not found in the initial conditions file.
+    """
+    vars_init_value_list = []
+    for section in registry:
+        if section.tag == 'file':
+            for obj in section:
+                if obj.tag == 'variable':
+                    for subobj in obj:
+                        if subobj.tag == 'initial_value':
+                            stdname = obj.get('standard_name')
+                            vars_init_value_list.append(stdname)
+                        # end if (only if initial_value node is found)
+                    # end for
+                # end if (ignore other node types)
+            # end for
+        # end if (ignore other node types)
+    # end for
+    return vars_init_value_list
 
 ###############################################################################
 def gen_registry(registry_file, dycore, outdir, indent,
@@ -1767,7 +1791,7 @@ def gen_registry(registry_file, dycore, outdir, indent,
     """Parse a registry XML file and generate source code and metadata.
     <dycore> is the name of the dycore for DP coupling specialization.
     <config> is a dictionary containing other configuration items for
-       souce code customization.
+       source code customization.
     Source code and metadata is output to <outdir>.
     <src_mod> is the location of the builds SourceMods/src.cam directory
     <src_root> is the top of the component tree
@@ -1819,7 +1843,8 @@ def gen_registry(registry_file, dycore, outdir, indent,
         retcode = 1
         files = None
         ic_names = None
-        constituents = None
+        registry_constituents = None
+        vars_init_value = None
     else:
         library_name = registry.get('name')
         emsg = f"Parsing registry, {library_name}"
@@ -1830,9 +1855,10 @@ def gen_registry(registry_file, dycore, outdir, indent,
         # See comment in _create_ic_name_dict
         ic_names = _create_ic_name_dict(registry)
         registry_constituents = _create_constituent_list(registry)
+        vars_init_value = _create_variables_with_initial_value_list(registry)
         retcode = 0 # Throw exception on error
     # end if
-    return retcode, files, ic_names, registry_constituents
+    return retcode, files, ic_names, registry_constituents, vars_init_value
 
 def main():
     """Function to execute when module called as a script"""

src/data/write_init_files.py

@@ -47,8 +47,8 @@
 #Main function
 ##############
 
-def write_init_files(cap_database, ic_names, registry_constituents, outdir,
-                     file_find_func, source_paths, indent, logger,
+def write_init_files(cap_database, ic_names, registry_constituents, vars_init_value,
+                     outdir, file_find_func, source_paths, indent, logger,
                      phys_check_filename=None, phys_input_filename=None):
 
     """
@@ -239,7 +239,8 @@ def write_init_files(cap_database, ic_names, registry_constituents, outdir,
 
         # Write physics_read_data subroutine:
         write_phys_read_subroutine(outfile, host_dict, host_vars, host_imports,
-                                   phys_check_fname_str, constituent_set)
+                                   phys_check_fname_str, constituent_set,
+                                   vars_init_value)
 
         outfile.blank_line()
 
@@ -810,7 +811,8 @@ def get_dimension_info(hvar):
     return vdim_name, legal_dims, fail_reason
 
 def write_phys_read_subroutine(outfile, host_dict, host_vars, host_imports,
-                               phys_check_fname_str, constituent_set):
+                               phys_check_fname_str, constituent_set,
+                               vars_init_value):
 
     """
     Write the "physics_read_data" subroutine, which
@@ -866,10 +868,20 @@ def write_phys_read_subroutine(outfile, host_dict, host_vars, host_imports,
             if levnm is not None:
                 call_str += f"'{levnm}', "
             # end if
-            call_str += f"timestep, {var_locname})"
+            err_on_not_found_string = ""
+            if var_stdname in vars_init_value:
+                # if initial value is available, do not throw error when not found in initial condition file.
+                err_on_not_found_string = ", error_on_not_found=.false."
+            # end if
+            call_str += f"timestep, {var_locname}{err_on_not_found_string})"
         else:
-            call_str = f"call endrun('Cannot read {var_locname} from file'" + \
+            # if initial value is assigned, then it can be ignored
+            if var_stdname in vars_init_value:
+                call_str = f"if(masterproc) write(iulog,*) '{var_locname} already has an initial_value, using it now. It also cannot be read from file: {reason}'"
+            else:
+                call_str = f"call endrun('Cannot read {var_locname} from file'" + \
                 f"//', {reason}')"
+            # end if
         # end if
 
         # Add string to dictionary: