Updates to introduce new version of Catchment-CN: Catchment-CN5.1

CHANGELOG.md

@@ -11,7 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
-- Added ntasks-per-node
+- Support for CatchmentCNCLM51.
+- Added ntasks-per-node 
 
 ### Changed
 
@@ -21,6 +22,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- Fixed zoom value when there is landice. It will be determined by input tilefile
 - Fixed Restart=1 when the domain is not global.
 
 ### Removed

GEOSldas_App/GEOSldas_HIST.rc

@@ -202,10 +202,12 @@ EASEv2_M36.LM:           1
 >>>HIST_CATCHCN<<<        'CNTOTC'   , 'GridComp'  ,
 >>>HIST_CATCHCN<<<        'CNVEGC'   , 'GridComp'  ,
 >>>HIST_CATCHCN<<<        'CNROOT'   , 'GridComp'  ,
->>>HIST_CATCHCNCLM45<<<   'CNFROOTC' , 'GridComp'  ,
+>>>HIST_CATCHCNCLM51<<<   'CNFROOTC' , 'GridComp'  ,
 >>>HIST_CATCHCN<<<        'CNNPP'    , 'GridComp'  ,
 >>>HIST_CATCHCN<<<        'CNGPP'    , 'GridComp'  ,
 >>>HIST_CATCHCN<<<        'CNSR'     , 'GridComp'  ,
+>>>HIST_CATCHCNCLM51<<<   'CNAR'     , 'GridComp'  ,
+>>>HIST_CATCHCNCLM51<<<   'CNHR'     , 'GridComp'  ,
 >>>HIST_CATCHCN<<<        'CNNEE'    , 'GridComp'  ,
 >>>HIST_CATCHCN<<<        'CNXSMR'   , 'GridComp'  ,
 >>>HIST_CATCHCN<<<        'CNADD'    , 'GridComp'  ,
@@ -308,10 +310,12 @@ EASEv2_M36.LM:           1
 >>>HIST_CATCHCN<<<        'CNTOTC'   , 'GridComp'  ,
 >>>HIST_CATCHCN<<<        'CNVEGC'   , 'GridComp'  ,
 >>>HIST_CATCHCN<<<        'CNROOT'   , 'GridComp'  ,
->>>HIST_CATCHCNCLM45<<<   'CNFROOTC' , 'GridComp'  ,
+>>>HIST_CATCHCNCLM51<<<   'CNFROOTC' , 'GridComp'  ,
 >>>HIST_CATCHCN<<<        'CNNPP'    , 'GridComp'  ,
 >>>HIST_CATCHCN<<<        'CNGPP'    , 'GridComp'  ,
 >>>HIST_CATCHCN<<<        'CNSR'     , 'GridComp'  ,
+>>>HIST_CATCHCNCLM51<<<   'CNAR'     , 'GridComp'  ,
+>>>HIST_CATCHCNCLM51<<<   'CNHR'     , 'GridComp'  ,
 >>>HIST_CATCHCN<<<        'CNNEE'    , 'GridComp'  ,
 >>>HIST_CATCHCN<<<        'CNXSMR'   , 'GridComp'  ,
 >>>HIST_CATCHCN<<<        'CNADD'    , 'GridComp'  ,

GEOSldas_App/GEOSldas_LDAS.rc

@@ -31,8 +31,9 @@ CATCHMENT_SPINUP: 0
 
 # ---- Choice of land surface model (for LAND tiles)
 #
-#    1 : Catchment model   (default)
+#    1 : Catchment model     (default)
 #    2 : CatchmentCN-CLM4.0
+#    4 : CatchmentCN-CLM5.1  (edit "ntasks-per-node" in batinp file to increase memory unless on EASEv2_M36)
 #
 LSM_CHOICE: 1
 

GEOSldas_App/ldas.py

@@ -3,7 +3,6 @@
 import os
 import sys
 import glob
-import linecache
 import shutil
 import fileinput
 import time
@@ -222,8 +221,6 @@ def __init__(self, cmdLineArgs):
             self.catch = 'catch'
         elif _lsm_choice_int == 2 :
             self.catch = 'catchcnclm40'
-        elif _lsm_choice_int == 3 :
-            self.catch = 'catchcnclm45'
         elif _lsm_choice_int == 4 :
             self.catch = 'catchcnclm51'
         _lsm_choice_int = None
@@ -312,18 +309,7 @@ def __init__(self, cmdLineArgs):
         inpgeom_= None
         # assigning Gridname
         if 'GRIDNAME' not in self.ExeInputs :
-            tmptile = os.path.realpath(self.ExeInputs['TILING_FILE'])
-            extension = os.path.splitext(tmptile)[1]
-            if extension == '.domain':
-              extension = os.path.splitext(tmptile)[0]
-            gridname_ =''
-            if extension == '.til':
-               gridname_ = linecache.getline(tmptile, 3).strip()
-            else:
-               nc_file = netCDF4.Dataset(tmptile,'r')
-               gridname_ = nc_file.getncattr('Grid_Name')
-            # in case it is an old name: SMAP-EASEvx-Mxx
-            gridname_ = gridname_.replace('SMAP-','').replace('-M','_M')
+            gridname_ = get_gridname(self.ExeInputs['TILING_FILE'])
             self.ExeInputs['GRIDNAME']  = gridname_
 
         if 'POSTPROC_HIST' not in self.ExeInputs:
@@ -374,7 +360,8 @@ def __init__(self, cmdLineArgs):
            self.in_tilefile =os.path.realpath(in_tilefiles_[0])
 
         if self.with_land:
-           assert int(self.ExeInputs['LSM_CHOICE']) <= 2, "\nLSM_CHOICE=3 (Catchment-CN4.5) is no longer supported. Please set LSM_CHOICE to 1 (Catchment) or 2 (Catchment-CN4.0)"
+           assert int(self.ExeInputs['LSM_CHOICE']) <= 2 or int(self.ExeInputs['LSM_CHOICE']) == 4,   \
+                "\nLSM_CHOICE=3 (Catchment-CN4.5) is no longer supported. Please set LSM_CHOICE to 1 (Catchment), 2 (Catchment-CN4.0), or 4 (Catchment-CN5.1)."
            if RESTART_str in ['1', '2']:
               y4m2='Y%4d/M%02d' % (self.begDates[0].year, self.begDates[0].month)
               y4m2d2_h2m2='%4d%02d%02d_%02d%02d' % (self.begDates[0].year, self.begDates[0].month,
@@ -412,12 +399,10 @@ def __init__(self, cmdLineArgs):
                 self.in_rstfile  = '/discover/nobackup/projects/gmao/ssd/land/l_data/LandRestarts_for_Regridding' \
                                    '/CatchCN/M36/20150301_0000/catchcnclm40_internal_dummy'
                 self.in_tilefile = '/discover/nobackup/projects/gmao/bcs_shared/legacy_bcs/Heracles-NL/SMAP_EASEv2_M36/SMAP_EASEv2_M36_964x406.til'
-              elif (self.catch == 'catchcnclm45'):
-                self.in_rstfile  = '/discover/nobackup/projects/gmao/ssd/land/l_data/LandRestarts_for_Regridding' \
-                                   '/CatchCN/M36/19800101_0000/catchcnclm45_internal_dummy'
-                self.in_tilefile = '/discover/nobackup/projects/gmao/bcs_shared/legacy_bcs/Icarus-NLv3/Icarus-NLv3_EASE/SMAP_EASEv2_M36/SMAP_EASEv2_M36_964x406.til'
+              elif (self.catch == 'catchcnclm51'):
+                sys.exit('Error. RESTART=0 not (yet) available for Catchment-CN5.1.\n')
               else:
-                sys.exit('need to provide at least dummy files')
+                sys.exit('Error. Unknown model version.')
 
         # DEAL WITH mwRTM input from exec
         self.assim = True if self.ExeInputs.get('LAND_ASSIM', 'NO').upper() == 'YES' and self.with_land else False
@@ -797,6 +782,9 @@ def createLnRstBc(self) :
            if ("catchcn" in self.catch):
               os.symlink(self.bcs_dir_landshared + 'CO2_MonthlyMean_DiurnalCycle.nc4', \
                           self.inpdir+'/CO2_MonthlyMean_DiurnalCycle.nc4')
+           if (self.catch=="catchcnclm51"):
+              os.symlink(self.bcs_dir_landshared + 'ctsm51_params.c210923_forCNCLM.nc', \
+                          self.inpdir+'/ctsm51_params.c210923_forCNCLM.nc')
 
         # create and link restart
         print ("Creating and linking restart...")
@@ -867,6 +855,7 @@ def createLnRstBc(self) :
            config['output']['surface']['wemin']          = wemin_out
 
            if RESTART_str == "M" : # restart from merra2
+             config['input']['surface']['zoom'] = '2'
              yyyymm = int(YYYYMMDDHH[0:6])
              merra2_expid = "d5124_m2_jan10"
              if yyyymm < 197901 :
@@ -898,7 +887,6 @@ def createLnRstBc(self) :
              catch_obj.remap()
            if self.with_landice:
              config['output']['surface']['remap_water'] = True
-             config['input']['surface']['zoom'] = '2'
              landice_obj = lake_landice_saltwater(config_obj = config)
              landice_obj.remap()
 
@@ -1104,6 +1092,13 @@ def createRCFiles(self):
         if self.ladas_cpl > 0:
             # edit resolution info in ensupd nml file
             sp.run(['sed', '-i', 's/<CFnnnn>/'+self.agcm_res+'/g', self.rundir+'/LDASsa_SPECIAL_inputs_ensupd.nml'])
+
+        #CN_CLM51 nml
+        if (self.catch=="catchcnclm51"):
+            cnclm51_nml = glob.glob(etcdir+'/CN_CLM51.nml')
+            for nmlfile in cnclm51_nml:
+                shortfile=self.rundir+'/'+nmlfile.split('/')[-1]
+                shutil.copy2(nmlfile, shortfile)
 
         # get optimzed NX and IMS
         optimized_distribution_file = tempfile.NamedTemporaryFile(delete=False)
@@ -1230,6 +1225,8 @@ def createRCFiles(self):
                       ldasrcInp[keyn]= valn
                    if('catchcn' in self.catch):
                       ldasrcInp['CO2_MonthlyMean_DiurnalCycle_FILE']= '../input/CO2_MonthlyMean_DiurnalCycle.nc4'
+                      if (self.catch=="catchcnclm51"):
+                          ldasrcInp['CNCLM51_PARAM_FILE']= '../input/ctsm51_params.c210923_forCNCLM.nc'
                    else:
                       # remove catchcn-specific entries that do not apply to catch model
                       ldasrcInp.pop('DTCN',None)

GEOSldas_App/process_hist.csh

@@ -40,19 +40,19 @@ sed -i -e  s/\'GRIDNAME\'/$GRIDNAME/g $HISTRC
 if($LSM_CHOICE == 1) then
    set GridComp = CATCH
    sed -i '/^>>>HIST_CATCHCN<<</d'         $HISTRC
-   sed -i '/^>>>HIST_CATCHCNCLM45<<</d'    $HISTRC
+   sed -i '/^>>>HIST_CATCHCNCLM51<<</d'    $HISTRC
 endif
 
 if($LSM_CHOICE == 2) then
    set GridComp = CATCHCN
-   sed -i '/^>>>HIST_CATCHCNCLM45<<</d'    $HISTRC
+   sed -i '/^>>>HIST_CATCHCNCLM51<<</d'    $HISTRC
    sed -i 's/>>>HIST_CATCHCN<<</''/g'      $HISTRC
 endif
 
-if($LSM_CHOICE == 3) then
+if($LSM_CHOICE == 4) then
    set GridComp = CATCHCN
    sed -i 's/>>>HIST_CATCHCN<<</''/g'      $HISTRC
-   sed -i 's/>>>HIST_CATCHCNCLM45<<</''/g' $HISTRC
+   sed -i 's/>>>HIST_CATCHCNCLM51<<</''/g' $HISTRC
 endif
 
 if($AEROSOL_DEPOSITION == 0) then

GEOSldas_App/setup_utils.py

@@ -5,11 +5,13 @@
 
 from collections import OrderedDict
 from datetime    import timedelta
-
+import netCDF4
+import linecache
 
 def generate_echo(inpfile, ladas_cpl = 0):
    """
-    Echo generator of inpfile, ignore line starts with "## "
+    Echo generator of inpfile
+    Pick default values from GEOS_SurfaceGridComp.rc via special string "GEOS[xxxx]=>".
    """
    if ladas_cpl == 0 :
       use_rc_defaults = 'GEOSldas=>'    # use defaults for LDAS
@@ -267,7 +269,9 @@ def printResourceInputSampleFile():
    print ('#                        IMPORTANT REQUIREMENT: total #writers = writers-per-node * oserver_nodes >= 2;')
    print ('#                        jobs will hang when oserver_nodes = writers-per-node = 1.')
    print ('# - ntasks-per-node  = requesting fewer ntasks-per-node than total number of cores per node increases allocated memory;')
-   print ('#                        ntasks_model should be a multiple of ntasks-per-node') 
+   print ('#                        defaults to number of cores per node;')
+   print ('#                        ntasks_model should be a multiple of ntasks-per-node;')
+   print ('#                        edit ntasks-per-node when running CatchCNCLM51 on resolution other than EASEv2_M36') 
    print ('# - constraint       = name of chip set(s) (NCCS default is "[mil|cas]", NAS default is "cas_ait")')
    print ('#')
    for key in optionalKeys:
@@ -310,3 +314,23 @@ def hours_to_hhmmss(hours):
 
     # Format as HHMMSS
     return f"{hours:02d}{minutes:02d}{seconds:02d}"
+
+def get_gridname(tilefile):
+    """
+    get name of atmospheric grid from header/attributes of tile file (*.til) 
+    """
+
+    gridname_ =''
+    tmptile   = os.path.realpath(tilefile)
+    extension = os.path.splitext(tmptile)[1]
+    if extension == '.domain':
+        extension = os.path.splitext(tmptile)[0]
+    if extension == '.til':
+        gridname_ = linecache.getline(tmptile, 3).strip()
+    else:
+       nc_file = netCDF4.Dataset(tmptile,'r')
+       gridname_ = nc_file.getncattr('Grid_Name')
+    # in case it is an old name: SMAP-EASEvx-Mxx: change to EASEvx_Mxx
+    gridname_ = gridname_.replace('SMAP-','').replace('-M','_M')
+    return gridname_
+

GEOSldas_App/tile_bin2nc4.F90

@@ -365,6 +365,8 @@ FUNCTION getAttribute (SHORT_NAME, LNAME, UNT) result (str_atr)
     case ('CNNPP');                            LONG_NAME = 'CN_net_primary_production';                                        UNITS = 'kg m-2 s-1'
     case ('CNGPP');                            LONG_NAME = 'CN_gross_primary_production';                                      UNITS = 'kg m-2 s-1'
     case ('CNSR');                             LONG_NAME = 'CN_total_soil_respiration';                                        UNITS = 'kg m-2 s-1'
+    case ('CNAR');                             LONG_NAME = 'CN_total_autotrophic_respiration';                                 UNITS = 'kg m-2 s-1'
+    case ('CNHR');                             LONG_NAME = 'CN_total_heterotrophic_respiration';                               UNITS = 'kg m-2 s-1'
     case ('CNNEE');                            LONG_NAME = 'CN_net_ecosystem_exchange';                                        UNITS = 'kg m-2 s-1'
     case ('CNXSMR');                           LONG_NAME = 'abstract_C_pool_to_meet_excess_MR_demand';                         UNITS = 'kg m-2'
     case ('CNADD');                            LONG_NAME = 'CN_added_to_maintain_positive_C';                                  UNITS = 'kg m-2 s-1'