Merge branch 'feature/wjiang/command_line' of github.com:GEOS-ESM/GEO…

…S_Util into feature/wjiang/command_line

pre/remap_restart/remap_catchANDcn.py

@@ -47,25 +47,25 @@ def remap(self):
 
      print("\nRemapping " + model + ".....\n")
 
-     cwdir        = os.getcwd()
-     bindir       = os.path.dirname(os.path.realpath(__file__))
-     in_bc_base    = config['input']['shared']['bc_base']
-     in_bc_version = config['input']['shared']['bc_version']
-     out_bc_base   = config['output']['shared']['bc_base']
-     out_bc_version= config['output']['shared']['bc_version']
-     out_dir      = config['output']['shared']['out_dir']
-     expid        = config['output']['shared']['expid']
-     in_wemin     = config['input']['surface']['wemin']
-     out_wemin    = config['output']['surface']['wemin']
-     surflay      = config['output']['surface']['surflay']
-     in_tilefile  = config['input']['surface']['catch_tilefile']
+     cwdir          = os.getcwd()
+     bindir         = os.path.dirname(os.path.realpath(__file__))
+     in_bc_base     = config['input']['shared']['bc_base']
+     in_bc_version  = config['input']['shared']['bc_version']
+     out_bc_base    = config['output']['shared']['bc_base']
+     out_bc_version = config['output']['shared']['bc_version']
+     out_dir        = config['output']['shared']['out_dir']
+     expid          = config['output']['shared']['expid']
+     in_wemin       = config['input']['surface']['wemin']
+     out_wemin      = config['output']['surface']['wemin']
+     surflay        = config['output']['surface']['surflay']
+     in_tilefile    = config['input']['surface']['catch_tilefile']
 
      if not in_tilefile :
         agrid        = config['input']['shared']['agrid']
         ogrid        = config['input']['shared']['ogrid']
         omodel       = config['input']['shared']['omodel']
         stretch      = config['input']['shared']['stretch']
-        bc_geomdir  = get_geomdir(in_bc_base, in_bc_version, agrid, ogrid, omodel, stretch)
+        bc_geomdir   = get_geomdir(in_bc_base, in_bc_version, agrid, ogrid, omodel, stretch)
         in_tilefile  = glob.glob(bc_geomdir + '/*.til')[0]
 
      agrid        = config['output']['shared']['agrid']

pre/remap_restart/remap_command_line.py

@@ -68,8 +68,8 @@ def parse_args(program_description):
     p_command.add_argument('-np',    action='store_true',     help="No prompt. Overwrite config files without prompting questions")
     p_command.add_argument('-lbl',   action='store_true',     help="Label output restarts with bc_versions and resolutions")
     p_command.add_argument('-noagcm_import_rst', action='store_true',     help="Do not remap agcm_import_rst file")
-    p_command.add_argument('-in_bc_base', default="",        help="Boundary conditions base directory (without bc_version and resolution infomation) for input restart")
-    p_command.add_argument('-out_bc_base',  default="",      help="Boundary conditions base directory (without bc_version and resolution infomation) for new restarts")
+    p_command.add_argument('-in_bc_base', default="",         help="Boundary conditions base dir (w/o bc_version and resolution info) for input restarts")
+    p_command.add_argument('-out_bc_base',default="",         help="Boundary conditions base dir (w/o bc_version and resolution info) for new restarts")
     p_command.add_argument('-zoom',                           help= "Zoom parameter (search radius) for input surface restarts")
 
     p_command.add_argument('-qos',        default="debug",    help="SLURM quality-of-service", choices=['debug', 'allnccs'])

pre/remap_restart/remap_params.tpl

@@ -14,8 +14,8 @@ input:
     # (coupled) ocean model: data, MOM5, MOM6
     omodel: data
     agrid:
-    bc_version: none
     bc_base:
+    bc_version: none
     expid:
     ogrid:
     rst_dir:
@@ -35,8 +35,8 @@ output:
     # (coupled) ocean model: data, MOM5, MOM6
     omodel: data
     agrid:
-    bc_version: none
     bc_base:
+    bc_version: none
     expid:
     ogrid:
     out_dir:

pre/remap_restart/remap_questions.py

@@ -80,7 +80,7 @@ def ask_questions():
         {
             "type": "confirm",
             "name": "input:shared:MERRA-2",
-            "message": "Remap archived MERRA-2 restarts?\n",
+            "message": "Remap archived MERRA-2 restarts? (NCCS/Discover only; elsewhere, select 'N' and complete full config; requires nc4 restarts.)\n",
             "default": False,
         },
         {
@@ -304,14 +304,14 @@ def ask_questions():
             "type": "path",
             "name": "input:shared:bc_base",
             "message": "\nEnter BCs base directory for input restarts: \n",
-            "when": lambda x: 'Customize ' in x.get('input:shared:bc_base'),
+            "when": lambda x: 'Custom ' in x.get('input:shared:bc_base'),
         },
         # dummy (invisible) question to retrieve input:shared:bc_base
         {
             "type": "text",
             "name": "input:shared:bc_base",
             "message": "retrieve and echo bcs",
-            # always return false, so questions never shows but changes ogrid
+            # always return false, so questions never shows
             "when": lambda x: echo_bcs(x, 'input')
         },
 
@@ -327,14 +327,14 @@ def ask_questions():
             "type": "path",
             "name": "output:shared:bc_base",
             "message": "\nEnter BCs base directory for new restarts: \n",
-            "when": lambda x: 'Customize ' in x.get('output:shared:bc_base'),
+            "when": lambda x: 'Custom ' in x.get('output:shared:bc_base'),
         },
         # dummy (invisible) question to retrieve output:shared:bc_base
         {
             "type": "text",
             "name": "output:shared:bc_base",
             "message": "retrieve and echo bcs",
-            # always return false, so questions never shows but changes ogrid
+            # always return false, so questions never shows
             "when": lambda x: echo_bcs(x, 'output')
         },
 

pre/remap_restart/remap_utils.py

@@ -17,9 +17,9 @@
 
 # top-level directory for BCs (machine-dependent)
 
-choices_bc_base  =[ "DISCOVER  : /discover/nobackup/projects/gmao/bcs_shared/fvInput/ExtData/esm/tiles",
-                    "NAS       : /nobackup/gmao_SIteam/ModelData/bcs_shared/fvInput/ExtData/esm/tiles", 
-                    "Customize : " ]
+choices_bc_base  =[ "NCCS/Discover : /discover/nobackup/projects/gmao/bcs_shared/fvInput/ExtData/esm/tiles",
+                    "NAS           : /nobackup/gmao_SIteam/ModelData/bcs_shared/fvInput/ExtData/esm/tiles", 
+                    "Custom "                                                                                 ]
 
 # define "choices", "message" strings, and "validate" lists that are used multiple times
 #   (and related definitions, even if they are used just once).
@@ -497,9 +497,9 @@ def get_topodir(bc_base, bc_version, agrid, ogrid, model, stretch):
   agrid_name = gridStr.split('_')[0]
   bc_topo = ''
   if 'GM4' == bc_version:
-     bc_topo = bc_base+ '/'+ bc_version + '/TOPO/TOPO_'+agrid_name
+     bc_topo = bc_base + '/' + bc_version + '/TOPO/TOPO_' + agrid_name
   else:
-     bc_topo = bc_base+ '/'+ bc_version + '/TOPO/TOPO_'+agrid_name + '/smoothed'
+     bc_topo = bc_base + '/' + bc_version + '/TOPO/TOPO_' + agrid_name + '/smoothed'
 
   return bc_topo
 

pre/remap_restart/tests/amip_c180Toc90.yaml

@@ -13,8 +13,8 @@ input:
     agrid: C180
     # (coupled) ocean model: data, MOM5, MOM6
     omodel: data
-    bc_version: NL3
     bc_base: /discover/nobackup/projects/gmao/bcs_shared/fvInput/ExtData/esm/tiles
+    bc_version: NL3
     expid: JM_v10.22.2_L072_C180_AMIP
     ogrid: 1440X720
     rst_dir: /discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/amip_c180Toc90/inputs/
@@ -31,8 +31,8 @@ output:
     stretch: false
     # (coupled) ocean model: data, MOM5, MOM6
     omodel: data
-    bc_version: NL3
     bc_base: /discover/nobackup/projects/gmao/bcs_shared/fvInput/ExtData/esm/tiles
+    bc_version: NL3
     expid: C90CS_JM_v10.22.2_L072_C180_AMIP
     ogrid: C90
     out_dir: $NOBACKUP/REMAP_TESTS/amip_c180Toc90/

pre/remap_restart/tests/c180Toc360.yaml

@@ -13,8 +13,8 @@ input:
     # (coupled) ocean model: data, MOM5, MOM6
     omodel: data
     agrid: C180
-    bc_version: NL3
     bc_base: /discover/nobackup/projects/gmao/bcs_shared/fvInput/ExtData/esm/tiles
+    bc_version: NL3
     expid: Jason-3_4_NL_REAMIP_MERRA2_C180
     ogrid: 1440X720
     rst_dir: /discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/c180Toc360/inputs/
@@ -31,8 +31,8 @@ output:
     stretch: false
     # (coupled) ocean model: data, MOM5, MOM6
     omodel: data
-    bc_version: NL3
     bc_base: /discover/nobackup/projects/gmao/bcs_shared/fvInput/ExtData/esm/tiles
+    bc_version: NL3
     expid: C360CS_Jason-3_4_NL_REAMIP_MERRA2_C180
     ogrid: C360
     out_dir: $NOBACKUP/REMAP_TESTS/c360Toc24/

pre/remap_restart/tests/c24Toc12.yaml

@@ -13,8 +13,8 @@ input:
     # (coupled) ocean model: data, MOM5, MOM6
     omodel: data
     agrid: C24
-    bc_version: NL3
     bc_base: /discover/nobackup/projects/gmao/bcs_shared/fvInput/ExtData/esm/tiles
+    bc_version: NL3
     expid: ''
     ogrid: 360X180
     rst_dir: /discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/c24Toc12/inputs
@@ -31,8 +31,8 @@ output:
     stretch: false
     # (coupled) ocean model: data, MOM5, MOM6
     omodel: data
-    bc_version: NL3
     bc_base: /discover/nobackup/projects/gmao/bcs_shared/fvInput/ExtData/esm/tiles
+    bc_version: NL3
     expid: hello
     ogrid: 360X180
     out_dir: $NOBACKUP/REMAP_TESTS/c24Toc12/

pre/remap_restart/tests/c360Toc24.yaml

@@ -13,8 +13,8 @@ input:
     stretch: false
     # (coupled) ocean model: data, MOM5, MOM6
     omodel: data
-    bc_version: NL3
     bc_base: /discover/nobackup/projects/gmao/bcs_shared/fvInput/ExtData/esm/tiles
+    bc_version: NL3
     expid: x0046a
     ogrid: C360
     rst_dir: /discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/c360Toc24/inputs
@@ -31,8 +31,8 @@ output:
     stretch: false
     # (coupled) ocean model: data, MOM5, MOM6
     omodel: data
-    bc_version: NL3
     bc_base: /discover/nobackup/projects/gmao/bcs_shared/fvInput/ExtData/esm/tiles
+    bc_version: NL3
     expid: C24c_x0046a
     ogrid: 360X180
     out_dir: $NOBACKUP/REMAP_TESTS/c360Toc24/

pre/remap_restart/tests/f522Toc360.yaml

@@ -13,8 +13,8 @@ input:
     # (coupled) ocean model: data, MOM5, MOM6
     omodel: data
     agrid: C720
-    bc_version: ICA
     bc_base: /discover/nobackup/projects/gmao/bcs_shared/fvInput/ExtData/esm/tiles
+    bc_version: ICA
     expid: f522_fp
     ogrid: C720
     rst_dir: /discover/nobackup/projects/gmao/SIteam/Remapping_Test_Cases/f522Toc360/inputs/
@@ -30,8 +30,8 @@ output:
     stretch: false
     # (coupled) ocean model: data, MOM5, MOM6
     omodel: data
-    bc_version: NL3
     bc_base: /discover/nobackup/projects/gmao/bcs_shared/fvInput/ExtData/esm/tiles
+    bc_version: NL3
     expid: remap
     ogrid: 360X180
     out_dir: $NOBACKUP/REMAP_TESTS/f522Toc360/