Port SE dycore to CAMDEN

cime_config/buildlib

@@ -94,7 +94,6 @@ def _build_cam():
                  os.path.join(atm_root, "src", "control"),
                  os.path.join(atm_root, "src", "cpl",
                               case.get_value("COMP_INTERFACE")),
-                 os.path.join(atm_root, "src", "dynamics", dycore),
                  os.path.join(atm_root, "src", "dynamics", "utils"),
                  os.path.join(atm_root, "src", "physics", "utils"),
                  os.path.join(atm_root, "src", "utils")]
@@ -103,12 +102,28 @@ def _build_cam():
                 paths.append(path)
             # End if
         # End for
-        #If using the CMEPS/NUOPC coupler, then add additional path:
+
+        # Add dynamics source code directories:
+        for direc in config.get_value("dyn_src_dirs"):
+            dyn_dir = os.path.join(atm_root, "src", "dynamics", direc)
+            if dyn_dir not in paths:
+                #Add to list of filepaths if not already present:
+                paths.append(dyn_dir)
+
+        # Add analytical IC source code directories:
+        paths.append(os.path.join(atm_root, "src", "dynamics", "tests")) #Required due to namelist call.
+        if dycore != "none":
+            paths.append(os.path.join(atm_root, "src", "dynamics", "tests",
+                                      "initial_conditions"))
+
+        # If using the CMEPS/NUOPC coupler, then add additional path:
         if case.get_value("COMP_INTERFACE") == "nuopc":
             paths.append(os.path.join(__CIMEROOT, "src", "drivers",
                                       "nuopc", "nuopc_cap_share"))
         # End if
-        with open(filepath_src, "w") as filepath:
+
+        # Write Filepath text file
+        with open(filepath_src, "w", encoding='utf-8') as filepath:
             filepath.write("\n".join(paths))
             filepath.write("\n")
         # End with
@@ -132,6 +147,10 @@ def _build_cam():
             .format(gmake, gmake_j, complib, makefile,
                     get_standard_makefile_args(case))
 
+        # Add C Pre-Processor (CPP) definitions, if present:
+        if config.cpp_defs:
+            cmd += " USER_CPPDEFS='{}'".format(' '.join(config.cpp_defs))
+
         retcode, out, err = run_cmd(cmd)
         _LOGGER.info("%s: \n\n output:\n %s \n\n err:\n\n%s\n", cmd, out, err)
         expect(retcode == 0, "Command {} failed with rc={}".format(cmd, retcode))

cime_config/buildnml

@@ -39,6 +39,12 @@ _LOGGER = logging.getLogger(__name__)
 #HELPER FUNCTIONS
 #################
 
+class CamBuildnmlError(ValueError):
+    """Class used to handle CAM buildnml errors
+    (e.g., log user errors without backtrace)"""
+
+##################
+
 # This simplifies the filename mangling for different cases.
 def _create_ic_filename(inst_string, i_or_r,
                         run_refcase, run_refdate, run_reftod):
@@ -50,13 +56,13 @@ def _create_ic_filename(inst_string, i_or_r,
 def nml_attr_set(config):
 
     """
-    creates a dictionary of namelist attributes
+    Creates a dictionary of namelist attributes
     from the CAM config object, in order to properly
     set namelist defaults.
     """
 
-    #Create new namelist attribute dictionary:
-    cam_nml_attr_dict = dict()
+    #Create new (empty) namelist attribute dictionary:
+    cam_nml_attr_dict = {}
 
     if config:
         #Loop over all CAM configuration settings in config dictionary:
@@ -68,7 +74,7 @@ def nml_attr_set(config):
             #is also a namelist attribute:
             if conf.is_nml_attr:
                 #If so, then add to attribute dictionary:
-                cam_nml_attr_dict[conf_name] = conf.value
+                cam_nml_attr_dict[conf_name] = str(conf.value)
             # End if
         # End for
     # End if
@@ -92,8 +98,6 @@ def buildnml(case, caseroot, compname):
     # End if
     srcroot             = case.get_value("SRCROOT")
     rundir              = case.get_value("RUNDIR")
-    din_loc_root        = case.get_value("DIN_LOC_ROOT")
-    atm_ncpl            = case.get_value("ATM_NCPL")
     cam_namelist_opts   = case.get_value("CAM_NAMELIST_OPTS")
     cam_nml_use_case    = case.get_value("CAM_NML_USE_CASE")
     debug               = case.get_value("DEBUG")
@@ -110,7 +114,7 @@ def buildnml(case, caseroot, compname):
 
     #--------------------------------------------------------------------------
     # Call config_CAM to set the configuration options needed to
-    #   generate CAM's namelist
+    # generate CAM's namelist
     #--------------------------------------------------------------------------
 
     # Create CAM  configure object:
@@ -249,21 +253,52 @@ def buildnml(case, caseroot, compname):
         # Determine location and name of "user_nl_cam" files:
         user_nl_file = os.path.join(caseroot, "user_nl_cam" + inst_string)
 
+        # Check that file actually exists.  If not then throw an error:
+        if not os.path.exists(user_nl_file):
+            emsg = "The file 'user_nl_cam' is missing.  Please run 'case.setup' first."
+            raise CamBuildnmlError(emsg)
+
         # Determine location and name of namelist input file:
         namelist_infile = os.path.join(confdir, "namelist_infile")
 
+        #-----------------------------------------------------------
+        # Determine CCPP physics suite chosen by user, and set suite
+        # name to be a namelist attribute:
+        #-----------------------------------------------------------
+
+        # Find user-chosen CCPP physics suite, and set as an attribute:
+        config.ccpp_phys_set(cam_nml_dict, user_nl_file)
+
+        #--------------------------------
         # Create CIME namelist input file:
+        #--------------------------------
         create_namelist_infile(case, user_nl_file, namelist_infile,
                                "\n".join(infile_lines))
 
         # Convert namelist input file to list:
         namelist_infile_list = [namelist_infile]
 
-        #-----------------------------
-        # Initialize namelist defaults:
-        #-----------------------------
+        #-------------------------------------------------
+        # Initialize only "vert_coord_nl" namelist entries
+        #-------------------------------------------------
+
+        # Initalize vert_coord_nl defaults:
+        nmlgen.init_defaults(namelist_infile_list, cam_nml_dict,
+                             skip_default_for_groups=\
+                             filter(lambda group: group !='vert_coord_nl',
+                                    config.nml_groups))
+
+        #--------------------------------------------
+        # Set "nlev" namelist attribute to equal pver
+        #--------------------------------------------
+
+        cam_nml_dict["nlev"] = nmlgen.get_value("pver")
+
+        #---------------------------------
+        # Initialize all namelist defaults:
+        #---------------------------------
 
-        # Initalize namelist defaults in used namelis groups:
+        # Initalize namelist defaults in used namelist groups:
         nmlgen.init_defaults(namelist_infile_list, cam_nml_dict)
 
         #--------------------------

cime_config/cam_autogen.py

@@ -467,9 +467,15 @@ def generate_physics_suites(ccpp_scripts_path, build_cache, preproc_defs, host_n
             #the host model files list for use by CCPP's capgen:
             host_files.append(reg_file.file_path)
 
+    # Convert preproc defs to string:
+    if preproc_defs:
+        preproc_cache_str = ', '.join(preproc_defs)
+    else:
+        preproc_cache_str = 'UNSET'
+
     if os.path.exists(genccpp_dir):
         do_gen_ccpp = force or build_cache.ccpp_mismatch(sdfs, scheme_files,
-                                                         preproc_defs,
+                                                         preproc_cache_str,
                                                          kind_phys)
     else:
         os.makedirs(genccpp_dir)
@@ -484,18 +490,18 @@ def generate_physics_suites(ccpp_scripts_path, build_cache, preproc_defs, host_n
         _LOGGER.debug("   host files: %s", ", ".join(host_files))
         _LOGGER.debug("   scheme files: %s", ', '.join(scheme_files))
         _LOGGER.debug("   suite definition files: %s", ', '.join(sdfs))
-        _LOGGER.debug("   preproc defs: %s", ', '.join(preproc_defs))
+        _LOGGER.debug("   preproc defs: %s", preproc_cache_str)
         _LOGGER.debug("   output directory: '%s'", genccpp_dir)
         _LOGGER.debug("   kind_phys: '%s'", kind_phys)
 
         # generate CCPP caps
         force_overwrite = False
         capgen(host_files, scheme_files, sdfs, cap_output_file,
-               preproc_defs, gen_hostcap, gen_docfiles, genccpp_dir,
+               preproc_cache_str, gen_hostcap, gen_docfiles, genccpp_dir,
                host_name, kind_phys, force_overwrite, _LOGGER)
 
         # save build details in the build cache
-        build_cache.update_ccpp(sdfs, scheme_files, preproc_defs, kind_phys)
+        build_cache.update_ccpp(sdfs, scheme_files, preproc_cache_str, kind_phys)
         ##XXgoldyXX: v Temporary fix: Copy CCPP Framework source code into
         ##XXgoldyXX: v   generated code directory
         request = DatatableReport("utility_files")