[WIP] run_neon fixes and improvements

python/ctsm/site_and_regional/neon_site.py

@@ -50,7 +50,8 @@ def build_base_case(
                     self.cesmroot, "cime_config", "usermods_dirs", "clm", "NEON", self.name
                 )
             ]
-        case_path = super().build_base_case(cesmroot, output_root, res, compset, user_mods_dirs)
+        case_path = super().build_base_case(cesmroot, output_root, res, compset, user_mods_dirs,
+                                            overwrite=overwrite, setup_only=setup_only)
 
         return case_path
 
@@ -68,6 +69,8 @@ def run_case(
         no_batch=False,
         rerun=False,
         experiment=False,
+        no_input_data_check=False,
+        xmlchange=None,
     ):
         """
         Run case.
@@ -92,6 +95,8 @@ def run_case(
             default False
         experiment: str, opt
             name of experiment, default False
+        no_input_data_check: bool, opt
+            default False
         """
         user_mods_dirs = [
             os.path.join(self.cesmroot, "cime_config", "usermods_dirs", "clm", "NEON", self.name)
@@ -110,6 +115,8 @@ def run_case(
             no_batch,
             rerun,
             experiment,
+            no_input_data_check,
+            xmlchange,
         )
 
     def modify_user_nl(self, case_root, run_type, rundir, site_lines=None):

python/ctsm/site_and_regional/run_tower.py

@@ -233,7 +233,9 @@ def main(description):
         setup_only,
         no_batch,
         rerun,
+        no_input_data_check,
         user_version,
+        xmlchange,
     ) = get_parser(sys.argv, description, valid_neon_sites, valid_plumber_sites)
 
     if output_root:
@@ -278,6 +280,8 @@ def main(description):
                     no_batch=no_batch,
                     rerun=rerun,
                     experiment=experiment,
+                    no_input_data_check=no_input_data_check,
+                    xmlchange=xmlchange,
                 )
 
     # -- check for available plumber data:
@@ -306,4 +310,6 @@ def main(description):
                     no_batch=no_batch,
                     rerun=rerun,
                     experiment=experiment,
+                    no_input_data_check=no_input_data_check,
+                    xmlchange=xmlchange,
                 )

python/ctsm/site_and_regional/tower_arg_parse.py

@@ -58,7 +58,7 @@ def get_parser(args, description, valid_neon_sites, valid_plumber_sites):
         "--base-case",
         help="""
                 Root Directory of base case build
-                [default: %(default)s]
+                [default: CESMROOT/NEONSITE]
                 """,
         action="store",
         dest="base_case_root",
@@ -104,6 +104,18 @@ def get_parser(args, description, valid_neon_sites, valid_plumber_sites):
         default=False,
     )
 
+    parser.add_argument(
+        "--no-input-data-check", "--no-check-input-data",
+        help="""
+                Don't check for input data. Implies --setup-only.
+                [default: %(default)s]
+                """,
+        action="store_true",
+        dest="no_input_data_check",
+        required=False,
+        default=False,
+    )
+
     parser.add_argument(
         "--rerun",
         help="""
@@ -185,6 +197,17 @@ def get_parser(args, description, valid_neon_sites, valid_plumber_sites):
         choices=["v1", "v2", "v3"],
     )
 
+    parser.add_argument(
+        "--xmlchange",
+        help="""
+                Any xmlchanges (e.g., CLM_CO2_TYPE=constant,CCSM_CO2_PPMV=500)
+                [default: %(default)s]
+                """,
+        required=False,
+        type=str,
+        default=None,
+    )
+
     args = parse_args_and_handle_standard_logging_options(args, parser)
 
     if args.neon_sites:
@@ -230,6 +253,10 @@ def get_parser(args, description, valid_neon_sites, valid_plumber_sites):
         root_logger = logging.getLogger()
         root_logger.setLevel(logging.WARN)
 
+    # --no-input-data-check implies --setup-only
+    if args.no_input_data_check and not args.setup_only:
+        args.setup_only = True
+
     return (
         neon_sites,
         plumber_sites,
@@ -243,5 +270,7 @@ def get_parser(args, description, valid_neon_sites, valid_plumber_sites):
         args.setup_only,
         args.no_batch,
         args.rerun,
+        args.no_input_data_check,
         args.user_version,
+        args.xmlchange,
     )

python/ctsm/site_and_regional/tower_site.py

@@ -128,6 +128,7 @@ def build_base_case(
             abort("Input output_root directory does NOT exist: " + str(output_root))
 
         case_path = os.path.join(output_root, self.name)
+        print(case_path)
 
         logger.info("base_case_name : %s", self.name)
         logger.info("user_mods_dir  : %s", user_mods_dirs[0])
@@ -296,6 +297,8 @@ def run_case(
         no_batch,
         rerun,
         experiment,
+        no_input_data_check,
+        xmlchange,
     ):
         """
         Run case.
@@ -445,11 +448,19 @@ def run_case(
             if not rundir:
                 rundir = case.get_value("RUNDIR")
 
+            if xmlchange:
+                xmlchange_list = xmlchange.split(",")
+                for setting in xmlchange_list:
+                    setting_split = setting.split("=")
+                    case.set_value(*setting_split)
+
             self.modify_user_nl(case_root, run_type, rundir)
 
             case.create_namelists()
+
             # explicitly run check_input_data
-            case.check_all_input_data()
+            if not no_input_data_check:
+                case.check_all_input_data()
             if not setup_only:
                 case.submit(no_batch=no_batch)
                 print("-----------------------------------")