remap upper stretched cube in

CHANGELOG.md

@@ -9,6 +9,10 @@ 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
+
 ### Changed
 
 - Move to use `time_ave_util.x` from MAPL instead of `time_ave.x`

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/remap_restart/remap_catchANDcn.py

@@ -121,16 +121,20 @@ 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']
@@ -140,8 +144,11 @@ def remap(self):
        CONSTRAINT = '"[cas|sky]"'
        if BUILT_ON_SLES15:
          CONSTRAINT = '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
@@ -362,7 +369,7 @@ def has_catch_rst(text):
             "type": "text",
             "name": "slurm_pbs:qos",
             "message": message_qos,
-            "default": "debug",
+            "default": "",
         },
 
         {

pre/remap_restart/remap_command_line.py

@@ -67,6 +67,7 @@ def parse_args(program_description):
     # 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")
@@ -76,10 +77,13 @@ 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")
+    if (BUILT_ON_SLES15):
+      p_command.add_argument('-partition',  default='scutest',help="slurm_pbs partition")
+    else:
+      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
@@ -124,6 +128,7 @@ def get_answers_from_command_line(cml):
    answers["input:shared:stretch"]     = cml.in_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

pre/remap_restart/remap_params.tpl

@@ -7,7 +7,7 @@
 input:
   air:
     drymass: 1
-    hydrostatic: 0
+    hydrostatic: true
   shared:
     MERRA-2: false
     stretch: false
@@ -62,5 +62,5 @@ output:
     lcv: false
 slurm_pbs:
   account:
-  qos:
+  qos: ''
   partition: ''

pre/remap_restart/remap_questions.py

@@ -37,7 +37,10 @@ def echo_bcs(x,opt):
 
 def default_partition(x):
    if x['slurm_pbs:qos'] == 'debug':
-      x['slurm_pbs:partition'] = 'compute'
+      if (BUILT_ON_SLES15):
+         x['slurm_pbs:partition'] = 'scutest'
+      else:
+         x['slurm_pbs:partition'] = 'compute'
       return False
    return True
 
@@ -89,6 +92,13 @@ def ask_questions():
             "validate": lambda text: validate_merra2_time(text) ,
             "when": lambda x: x['input:shared:MERRA-2'],
         },
+        {
+            "type": "confirm",
+            "name": "input:air:hydrostatic",
+            "message": "Is the upper air input hydrostatic? (If you are not sure, don't change the default 'True')\n",
+            "default": True,
+            "when": lambda x: not x['input:shared:MERRA-2'],
+        },
         {
             "type": "path",
             "name": "output:shared:out_dir",
@@ -412,6 +422,7 @@ def ask_questions():
             "name": "slurm_pbs:partition",
             "message": message_partition,
             "default": '',
+            "when": lambda x : default_partition(x),
         },
    ]
    answers = questionary.prompt(questions)
@@ -424,6 +435,7 @@ def ask_questions():
    answers["output:surface:remap_water"] = answers["output:surface:remap"]
    answers["output:surface:remap_catch"] = answers["output:surface:remap"]
    del answers["output:surface:remap"]
+   if answers["input:shared:MERRA-2"] : answers["input:air:hydrostatic"] = True
 
    return answers
 

pre/remap_restart/remap_upper.py

@@ -153,22 +153,27 @@ def remap(self):
        NPE = 5400; nwrit = 6
 
      PARTITION =''
-     QOS  = config['slurm_pbs']['qos']
+     QOS       =''
+     qos       = config['slurm_pbs']['qos']
      TIME = "1:00:00"
      if NPE > 532: 
         assert config['slurm_pbs']['qos'] != 'debug', "qos should be 'allnccs' for NCCS or 'normal' for NAS"
-        TIME = "12:00:00"
+        TIME = "3:00:00"
      NNODE = ''
      job=''
      if GEOS_SITE == "NAS":
        CONSTRAINT = 'cas_ait'
        NNODE = (NPE-1)//40 + 1
        job='PBS'
+       if (qos != ''):
+         QOS = "#PBS  -q "+qos
      else:
        job='SLURM'
        partition = config['slurm_pbs']['partition']
        if (partition != ''):
          PARTITION = "#SBATCH --partition=" + partition
+       if (qos != ''):
+         QOS = "#SBATCH  --qos="+qos
 
        CONSTRAINT = '"[cas|sky]"'
        if BUILT_ON_SLES15:
@@ -179,7 +184,7 @@ def remap(self):
      # to interp_restarts.x. Per the code we use:
      #  -stretched_grid target_lon target_lat stretch_fac
      # If we are not running stretched grid, we should pass in a blank string
-     stretch = config['output']['shared']['stretch']
+     stretch = config['input']['shared']['stretch']
      stretch_str = ""
      if stretch:
         if stretch == 'SG001':
@@ -195,7 +200,24 @@ def remap(self):
 
         # note "reversed" order of args (relative to order in definition of STRETCH_GRID)  
 
-        stretch_str = "-stretched_grid " + str(target_lon) + " " + str(target_lat) + " " + str(stretch_fac)
+        stretch_str = "-stretched_grid_in " + str(target_lon) + " " + str(target_lat) + " " + str(stretch_fac)
+
+     stretch = config['output']['shared']['stretch']
+     if stretch:
+        if stretch == 'SG001':
+          stretch_fac = STRETCH_GRID['SG001'][0]
+          target_lat  = STRETCH_GRID['SG001'][1]
+          target_lon  = STRETCH_GRID['SG001'][2]
+        elif stretch == 'SG002':
+          stretch_fac = STRETCH_GRID['SG002'][0]
+          target_lat  = STRETCH_GRID['SG002'][1]
+          target_lon  = STRETCH_GRID['SG002'][2]
+        else:
+          exit("This stretched grid option is not supported " + str(stretch))
+
+        # note "reversed" order of args (relative to order in definition of STRETCH_GRID)  
+
+        stretch_str = stretch_str+" -stretched_grid_out " + str(target_lon) + " " + str(target_lat) + " " + str(stretch_fac)
 
      # Now, let's create the input.nml file
      # We need to create a namelist for the upper air remapping
@@ -218,9 +240,6 @@ def remap(self):
 cd {out_dir}/upper_data
 /bin/touch input.nml
 
-# The MERRA fvcore_internal_restarts don't include W or DZ, but we can add them by setting
-# HYDROSTATIC = 0 which means HYDROSTATIC = FALSE
-
 if ($?I_MPI_ROOT) then
   # intel scaling suggestions
   #--------------------------
@@ -255,28 +274,35 @@ def remap(self):
     set ioflag = ""
 endif
 
-set drymassFLG = {drymassFLG}
+set hydrostaticIN = {hydrostatic}
+if ( $hydrostaticIN == 'True' ) then
+    set hydrostaticflag = "-in_hydrostatic T"
+else
+    set hydrostaticflag = "-in_hydrostatic F"
+endif
+
+set drymassFLG = {drymass}
 if ($drymassFLG) then
     set dmflag = ""
 else
     set dmflag = "-scalers F"
 endif
 
 {Bin}/esma_mpirun -np {NPE} $interp_restartsX -im {imout} -lm {nlevel} \\
-   -do_hydro {hydrostatic} $ioflag $dmflag -nwriter {nwrit} {stretch_str}
+   $hydrostaticflag {stretch_str} $dmflag -nwriter {nwrit} $ioflag 
 
 """
      account = config['slurm_pbs']['account']
-     drymassFLG  = config['input']['air']['drymass']
+     drymass     = config['input']['air']['drymass']
      hydrostatic = config['input']['air']['hydrostatic']
      nlevel = config['output']['air']['nlevel']
      log_name = out_dir+'/remap_upper_log'
      job_name = 'remap_upper'
      remap_upper_script = remap_template.format(Bin=bindir, account = account, \
-             out_dir = out_dir, log_name = log_name, job_name= job_name, drymassFLG = drymassFLG, \
+             out_dir = out_dir, log_name = log_name, job_name= job_name, drymass = drymass, \
              imout = imout, nwrit = nwrit, NPE = NPE, NNODE = NNODE, \
-             QOS = QOS, TIME = TIME, CONSTRAINT = CONSTRAINT, PARTITION = PARTITION, nlevel = nlevel, hydrostatic = hydrostatic,
-             stretch_str = stretch_str)
+             QOS = QOS, TIME = TIME, CONSTRAINT = CONSTRAINT, PARTITION = PARTITION, nlevel = nlevel, \
+             hydrostatic = hydrostatic, stretch_str = stretch_str)
 
      script_name = './remap_upper.j'
 

pre/remap_restart/remap_utils.py

@@ -116,7 +116,10 @@
 
 message_ogrid_in   = "Select data ocean grid/resolution of input restarts:\n"
 
-message_qos        = "SLURM or PBS quality-of-service (qos)?  (If resolution is c1440 or higher, enter 'allnccs' for NCCS or 'normal' for NAS.)\n"
+message_qos        = """SLURM or PBS quality-of-service (qos)?
+    (Use default 'debug' to get resource faster; or
+     Enter 'allnccs' for NCCS or 'normal' for NAS if resolution is c1440 or higher;
+     or leave it blank)\n"""
 
 message_account    = "Select/enter SLURM or PBS account:\n"
 
@@ -128,20 +131,20 @@
 #SBATCH --ntasks={NPE}
 #SBATCH --job-name={job_name}
 #SBATCH --output={log_name}
-#SBATCH --qos={QOS}
 #SBATCH --time={TIME}
 #SBATCH --constraint={CONSTRAINT}
 {PARTITION}
+{QOS}
 """,
 "PBS": """#!/bin/csh -f
 #PBS -l walltime={TIME}
 #PBS -l select={NNODE}:ncpus=40:mpiprocs=40:model={CONSTRAINT}
 #PBS -N {job_name}
-#PBS -q {QOS}
 #PBS -W group_list={account}
 #PBS -o {log_name}
 #PBS -j oe
 {PARTITION}
+{QOS}
 """
 }
 
@@ -416,7 +419,7 @@ def get_command_line_from_answers(answers):
 
    nobkg  = '' if answers["output:analysis:bkg"] else " -nobkg "
    nolcv  = '' if answers["output:analysis:lcv"] else " -nolcv "
-
+   nonhydrostatic = '' if answers["input:air:hydrostatic"] else " -nonhydrostatic " 
    label  = ' -lbl ' if answers["output:shared:label"] else ""
 
    in_bc_base  = ' -in_bc_base '  + answers.get("input:shared:bc_base")
@@ -447,7 +450,9 @@ def get_command_line_from_answers(answers):
    noagcm_import_rst  = '' if answers["output:air:agcm_import_rst"] else " -noagcm_import_rst "
 
    account = " -account " + answers["slurm_pbs:account"]
-   qos     = " -qos  " + answers["slurm_pbs:qos"]
+   qos = ''
+   if answers["slurm_pbs:qos"] != '':
+     qos     = " -qos  " + answers["slurm_pbs:qos"]
    partition = ''
    if answers["slurm_pbs:partition"] != '':
       partition  = " -partition  " + answers["slurm_pbs:partition"]
@@ -475,6 +480,7 @@ def get_command_line_from_answers(answers):
                                           wemout + \
                                           label + \
                                           nobkg + \
+                                          nonhydrostatic + \
                                           noagcm_import_rst + \
                                           nolcv + \
                                           out_rs + \
@@ -616,5 +622,5 @@ def remove_ogrid_comment(x, opt):
   return False
 
 if __name__ == '__main__' :
-   config = yaml_to_config('c24Toc12.yaml')
+   config = yaml_to_config('remap_params.tpl')
    print_config(config)