gcm_setup python conversion support

.circleci/config.yml

@@ -1,11 +1,11 @@
 version: 2.1
 
 # Anchors in case we need to override the defaults from the orb
-#baselibs_version: &baselibs_version v7.29.0
-#bcs_version: &bcs_version v11.6.0
+#baselibs_version: &baselibs_version v8.5.0
+#bcs_version: &bcs_version v12.0.0
 
 orbs:
-  ci: geos-esm/circleci-tools@4
+  ci: geos-esm/circleci-tools@5
 
 workflows:
   build-test:
@@ -21,7 +21,10 @@ workflows:
           #baselibs_version: *baselibs_version
           repo: GEOSgcm
           checkout_fixture: true
-          mepodevelop: true
+          # V12 code uses a special branch for now.
+          fixture_branch: feature/sdrabenh/gcm_v12
+          # We comment out this as it will "undo" the fixture_branch
+          #mepodevelop: true
           persist_workspace: true # Needs to be true to run fv3/gcm experiment, costs extra
 
       # Run AMIP GCM (1 hour, no ExtData)
@@ -45,7 +48,7 @@ workflows:
             - docker-hub-creds
           matrix:
             parameters:
-              compiler: [gfortran, ifort]
+              compiler: [ifort]
           requires:
             - build-GEOSgcm-on-<< matrix.compiler >>
           repo: GEOSgcm

CHANGELOG.md

@@ -9,12 +9,24 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- Added choice 'blank' for qos in remap_restart python pacakage
+- Added hydrostatic question in remap_restart python pacakage
+- Added function to remap from stretched restarts to stretched restarts
+- Added remapping for GEOS-IT restarts
+- Added new res C1120
+- NOTE: If running on SLES15 remap tests will not be zero diff for GOCART RST but are zero diff for all other
+- Add support for v13 BCs
+
 ### Changed
 
 ### Fixed
 
+- Fixed issue with SLES15 in remapping
+
 ### Removed
 
+- Removed detection of OS at NCCS as it is all SLES15 now
+
 ### Deprecated
 
 ## [2.1.7] - 2025-04-23

coupled_diagnostics/g5lib/confocn.py

@@ -1,17 +1,17 @@
 '''
-@EXPDSC
+{{ EXPDSC }}
 
 ### Put detailed experiment description here ###
 '''
 import os
 from datetime import date
 
-expid='@EXPID'
-cmpexp='@EXPID'
-data_path='@EXPDIR'
+expid='{{ EXPID }}'
+cmpexp='{{ EXPID }}'
+data_path='{{ EXPDIR }}'
 plot_path=data_path+'/plots_ocn'
-basin_mask='@COUPLEDIR/basin_mask/@OGCM_IMx@OGCM_JM/basin_mask.nc'
-grid_spec='@COUPLEDIR/a@AGCM_IMx@AGCM_JM_o@OGCM_IMx@OGCM_JM/INPUT/grid_spec.nc'
+basin_mask='{{ COUPLEDIR }}/basin_mask/{{ OGCM_IM }}x{{ OGCM_JM }}/basin_mask.nc'
+grid_spec='{{ COUPLEDIR }}/a{{ AGCM_IM }}x{{ AGCM_JM }}_o{{ OGCM_IM }}x{{ OGCM_JM }}/INPUT/grid_spec.nc'
 
 start_year=1980
 end_year=1981

coupled_diagnostics/g5lib/plotocn.j

@@ -1,13 +1,13 @@
 #!/bin/csh 
-#SBATCH --job-name=@PLOT_T
+#SBATCH --job-name={{ PLOT_T }}
 #SBATCH --ntasks=20
 #SBATCH --time=12:00:00 
 #SBATCH -o plotocn.out
 
 source /usr/share/modules/init/csh
 module purge
 module load python/GEOSpyD/Ana2019.10_py2.7
-set SCRDIR=@GEOSDIR/coupled_diagnostics
+set SCRDIR={{ GEOSDIR }}/coupled_diagnostics
 set G5LIBDIR=$SCRDIR
 set ANADIR=$SCRDIR/analysis
 set VERIFICATION=$SCRDIR/verification
@@ -18,9 +18,9 @@ else if ( ($HOSTNAME =~ "pfe"*) || ($HOSTNAME =~ r[0-9]*i[0-9]*n[0-9]*) || ($HOS
     setenv OCEANVAL /nobackup/gmao_SIteam/ModelData/oceanval/verification
 endif 
 
-set EXPID=@EXPID
-set HOMDIR=@HOMDIR
-set EXPDIR=@EXPDIR
+set EXPID={{ EXPID }}
+set HOMDIR={{ HOMDIR }}
+set EXPDIR={{ EXPDIR }}
 set WORKDIR=$EXPDIR/plot
 
 setenv PYTHONPATH ${G5LIBDIR}:${VERIFICATION}:${HOMDIR}/..

post/stats.F90

@@ -1053,8 +1053,16 @@ end subroutine init_levs
                     zlev(lev).eq.750 .or. zlev(lev).eq.600 .or. &
                     zlev(lev).eq.500 .or. zlev(lev).eq.400 .or. &
                     zlev(lev).eq.300 .or. zlev(lev).eq.200 .or. &
-                    zlev(lev).eq.100 .or. zlev(lev).eq.70  .or. &
-                    zlev(lev).eq.30  .or. zlev(lev).eq.10  ) then
+                    zlev(lev).eq.100 .or. zlev(lev).eq.90  .or. &
+                    zlev(lev).eq.80  .or. zlev(lev).eq.70  .or. &
+                    zlev(lev).eq.60  .or. zlev(lev).eq.50  .or. &
+                    zlev(lev).eq.40  .or. zlev(lev).eq.30  .or. &
+                    zlev(lev).eq.20  .or. zlev(lev).eq.10  .or. &
+                    zlev(lev).eq.9   .or. zlev(lev).eq.8   .or. &
+                    zlev(lev).eq.7   .or. zlev(lev).eq.6   .or. &
+                    zlev(lev).eq.5   .or. zlev(lev).eq.4   .or. &
+                    zlev(lev).eq.3   .or. zlev(lev).eq.2   .or. &
+                    zlev(lev).eq.1 ) then
                     write(6,1005) int(zlev(lev)),trim(regions(iregion)),&
                                   trim(fields_3d(n)%name),nymd,nhms,hour,&
                                   rms(iregion,lev,nfield,nt,1),&

pre/NSIDC-OSTIA_SST-ICE_blend/regrid_forcing_esmf.F90

@@ -31,6 +31,10 @@ module GenESMFGridCompMod
      integer                   :: PJM
      integer                   :: GPIM
      integer                   :: GPJM
+     integer                   :: OIM
+     integer                   :: OJM
+     integer                   :: GOIM
+     integer                   :: GOJM
      type(ESMF_Time)           :: start_time
      type(ESMF_Time)           :: end_time
      logical                   :: select_time
@@ -277,6 +281,15 @@ subroutine Initialize ( GC, IMPORT, EXPORT, CLOCK, RC )
     PrivateState%ogrid=ogrid
     PrivateState%pgrid=pgrid
 
+! Query Ogrid to save IM and JM
+    call MAPL_GridGet(ogrid, localCellCountPerDim=COUNTS, &
+         globalCellCountPerDim=dims, RC=STATUS)
+    VERIFY_(STATUS)            
+    PrivateState%oim=counts(1) 
+    PrivateState%ojm=counts(2) 
+    PrivateState%goim=dims(1)  
+    PrivateState%gojm=dims(2)  
+
 ! Query Pgrid to save IM and JM
     call MAPL_GridGet(pgrid, localCellCountPerDim=COUNTS, &
          globalCellCountPerDim=dims, RC=STATUS)
@@ -346,6 +359,8 @@ subroutine RUN ( GC, IMPORT, EXPORT, CLOCK, RC )
 
   integer :: IM, JM
   integer :: IM_WORLD, JM_WORLD
+  integer :: OIM, OJM
+  integer :: OIM_WORLD, OJM_WORLD
   type(ESMF_Grid) :: ogrid, pgrid
   type(ESMF_VM) :: vm
   type(ESMF_Time) :: currentTime, dateN
@@ -360,6 +375,7 @@ subroutine RUN ( GC, IMPORT, EXPORT, CLOCK, RC )
   type (MAPL_MetaComp), pointer          :: MAPL 
   logical :: amIRoot,dowrite
   type(ESMF_Time) :: start_interval, end_interval
+  real    :: gmax, gmin
 
 !=============================================================================
 
@@ -405,6 +421,11 @@ subroutine RUN ( GC, IMPORT, EXPORT, CLOCK, RC )
 
    UNIT_W = getfile(filename)
 
+   OIM = PrivateState%oim
+   OJM = PrivateState%ojm
+   OIM_WORLD = PrivateState%goim
+   OJM_WORLD = PrivateState%gojm
+
    IM = PrivateState%pim
    JM = PrivateState%pjm
    IM_WORLD = PrivateState%gpim
@@ -484,13 +505,17 @@ subroutine RUN ( GC, IMPORT, EXPORT, CLOCK, RC )
    !   read(unit_r) odata
       call MAPL_VarRead(unit_r, grid=ogrid, a=odata, rc=status)
       VERIFY_(STATUS)
-      ! transform data from ocean (tripolar or Reynolds) to mit-cubed
+      ! Check global max/min
+      call MAPL_MaxMin('In data: ', odata)
+      ! transform data from ocean (tripolar or Reynolds) to cubed
       call privateState%regridder%regrid(odata,pdata,rc=status)
       VERIFY_(status) 
       if (privateState%fix_fraction) then
          where(pdata > 1.0) pdata = 1.0
          where(pdata < 0.0) pdata = 0.0
       end if
+      ! Check global max/min
+      call MAPL_MaxMin('Out data: ', pdata)
    !   write(unit_w) pdata
       if (doWrite) then
          call MAPL_VarWrite(unit_w, grid=pgrid, a=pdata, rc=status)

pre/remap_restart/remap_catchANDcn.py

@@ -124,25 +124,32 @@ def remap(self):
         NPE = 160
 
      PARTITION =''
-     QOS  = config['slurm_pbs']['qos']
+     QOS       =''
+
+     qos  = config['slurm_pbs']['qos']
      TIME  = "1:00:00"
-     if QOS != "debug": TIME="12:00:00"
+     if qos != "debug": TIME="3:00:00"
 
      NNODE = ''
      job = ''
      if GEOS_SITE == 'NAS':
        job = "PBS"
        CONSTRAINT = 'cas_ait'
        NNODE = (NPE-1)//40 + 1
+       if (qos != ''):
+         QOS = "#PBS  -q "+qos
      else:
        job = "SLURM"
        partition = config['slurm_pbs']['partition']
        if (partition != ''):
          PARTITION = "#SBATCH --partition=" + partition
 
        CONSTRAINT = '"[cas|mil]"'
+       if (qos != ''):
+         QOS = "#SBATCH  --qos="+qos
 
      account    = config['slurm_pbs']['account']
+
      # even if the (MERRA-2) input restarts are binary, the output restarts will always be nc4 (remap_bin2nc.py)
      suffix = '_rst.' + suffix
      out_rstfile = expid + os.path.basename(in_rstfile).split('_rst')[0].split('.')[-1]+suffix
@@ -364,7 +371,7 @@ def has_catch_rst(text):
             "type": "text",
             "name": "slurm_pbs:qos",
             "message": message_qos,
-            "default": "debug",
+            "default": "",
         },
 
         {

pre/remap_restart/remap_command_line.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 #
 # remap_restarts package:
-#   remap_command_line.py parses and converts the command-line arguments and converts the information 
+#   remap_command_line.py parses and converts the command-line arguments and converts the information
 #   into matching "Answers" for the questionary (remap_questions.py)
 #
 import os
@@ -64,10 +64,11 @@ def parse_args(program_description):
     p_command.add_argument('-ocnmdlout',   default='data',    help='Ocean model for new restarts',          choices=choices_omodel)
     p_command.add_argument('-in_stretch',  default=False,     help='Stretched CS params of input restarts', choices=choices_stretch)
     p_command.add_argument('-out_stretch', default=False,     help='Stretched CS params for new restarts',  choices=choices_stretch)
-    
+
     # Unlike remap_questions.py, command-line feature does not deduce Catch vs. CatchCN[40,45] for simplicity, thus requires input argument
     p_command.add_argument('-catch_model',default='catch',    help='Catchment[CN] model', choices=choices_catchmodel)
 
+    p_command.add_argument('-nonhydrostatic', action='store_true',     help=" non hydrostatic upper air")
     p_command.add_argument('-nobkg', action='store_true',     help="Do not remap bkg files")
     p_command.add_argument('-nolcv', action='store_true',     help="Do not write lcv file")
     p_command.add_argument('-np',    action='store_true',     help="No prompt. Overwrite config files without prompting questions")
@@ -77,10 +78,11 @@ def parse_args(program_description):
     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_pbs quality-of-service", choices=['debug', 'allnccs', 'normal'])
+    p_command.add_argument('-qos',        default="",    help="slurm_pbs quality-of-service", choices=['', 'debug', 'allnccs', 'normal'])
     account = get_account()
     p_command.add_argument('-account',    default=account,    help="slurm_pbs account")
-    p_command.add_argument('-partition',  default='',         help="slurm_pbs partition")
+    p_command.add_argument('-partition',  default='',       help="slurm_pbs partition")
+
     p_command.add_argument('-rs',         default='3',        help="Flag indicating which restarts to regrid: 1 (upper air); 2 (surface); 3 (both)", choices=['1','2','3'])
 
     # Parse using parse_known_args so we can pass the rest to the remap scripts
@@ -128,6 +130,7 @@ def get_answers_from_command_line(cml):
    answers["output:shared:stretch"]    = cml.out_stretch
    answers["output:analysis:bkg"]      = not cml.nobkg
    answers["output:analysis:lcv"]      = not cml.nolcv
+   answers["input:air:hydrostatic"]    = not cml.nonhydrostatic
    if cml.rs == '1':
      answers["output:air:remap"]            = True
      answers["output:surface:remap_water"]  = False
@@ -143,7 +146,7 @@ def get_answers_from_command_line(cml):
 
    answers["output:air:agcm_import_rst"] = not cml.noagcm_import_rst
 
-   if cml.zoom: 
+   if cml.zoom:
       answers["input:surface:zoom"]    = cml.zoom
    else:
       # zoom_default fills 'input:shared:agrid'
@@ -162,7 +165,7 @@ def get_answers_from_command_line(cml):
    answers["slurm_pbs:account"]    = cml.account
    answers["slurm_pbs:qos"]        = cml.qos
    answers["slurm_pbs:partition"]  = cml.partition
-  
+
    return answers
 
 if __name__ == "__main__":
@@ -175,7 +178,7 @@ def get_answers_from_command_line(cml):
    with open("raw_command.yaml", "w") as f:
      yaml.dump(config, f)
 
-   config = get_config_from_answers(answers, config_tpl= True) 
+   config = get_config_from_answers(answers, config_tpl= True)
    with open("params_from_command.yaml", "w") as f:
      yaml.dump(config, f)
 

pre/remap_restart/remap_lake_landice_saltwater.py

@@ -139,10 +139,12 @@ def remap(self):
        cmd = exe + out_til + ' ' + in_til + ' InData/'+ saltwater_internal + ' 0 ' + str(zoom)
        self.run_and_log(cmd, log_name)
 
-       # split Saltwater
-       if  config['output']['surface']['split_saltwater']:
-         print("\nSplitting Saltwater...\n")
-         cmd = bindir+'/SaltIntSplitter.x ' + out_til + ' ' + 'OutData/' + saltwater
+       # split Saltwater Internal
+       # NOTE: split_saltwater==True means that the input restarts are already split.
+       #       So we do not split them again.
+       if not config['output']['surface']['split_saltwater']:
+         print("\nSplitting Saltwater Internal...\n")
+         cmd = bindir+'/SaltIntSplitter.x ' + out_til + ' ' + 'OutData/' + saltwater_internal
 #         subprocess.call(shlex.split(cmd))
          openwater = ''
          seaice  = ''
@@ -152,6 +154,17 @@ def remap(self):
        cmd = exe + out_til + ' ' + in_til + ' InData/'+ saltwater_import + ' 0 ' + str(zoom)
        self.run_and_log(cmd, log_name)
 
+       # split Saltwater Import
+       # NOTE: split_saltwater==True means that the input restarts are already split.
+       #       So we do not split them again.
+       if not config['output']['surface']['split_saltwater']:
+         print("\nSplitting Saltwater Import...\n")
+         cmd = bindir+'/SaltIntSplitter.x ' + out_til + ' ' + 'OutData/' + saltwater_import
+#         subprocess.call(shlex.split(cmd))
+         openwater = ''
+         seaice  = ''
+         self.run_and_log(cmd, log_name)
+
      if (openwater):
        cmd = exe + out_til + ' ' + in_til + ' InData/' + openwater + ' 0 ' + str(zoom)
        self.run_and_log(cmd, log_name)

pre/remap_restart/remap_params.tpl

@@ -7,7 +7,7 @@
 input:
   air:
     drymass: 1
-    hydrostatic: 0
+    hydrostatic: true
   shared:
     MERRA-2: false
     GEOS-IT: false
@@ -64,5 +64,5 @@ output:
     lcv: false
 slurm_pbs:
   account:
-  qos:
+  qos: ''
   partition: ''