Refactor Stage IC: Move COM and Cycle Variables and Logic from YAML Master Templates to Python Scripts

dev/ci/cases/pr/C48_S2SWA_gefs_RT.yaml

@@ -9,20 +9,20 @@ experiment:
   nens: 30
   interval: 24
   start: cold
-  gefstype: near-real-time
+  gefstype: gefs-real-time
   comroot: {{ 'RUNTESTS' | getenv }}/COMROOT
   expdir: {{ 'RUNTESTS' | getenv }}/EXPDIR
   idate: 2024112500
   edate: 2024112500
   yaml: {{ HOMEgfs }}/dev/ci/cases/yamls/gefs_defaults_ci.yaml
+  icsdir: /lfs/h2/emc/ens/noscrub/eric.sinsky/RETRO_ICS
 
 # TODO run on supported platforms once the gefs forecast and subsequent tasks can succeed with RETRO ICs
 # Add this to run the stage ic job 'icsdir: /lfs/h2/emc/ens/noscrub/eric.sinsky/RETRO_ICS'
 skip_ci_on_hosts:
   - gaeac6
   - gaeac5
   - hercules
-  - wcoss2
   - hera
   - ursa
   - orion

dev/parm/config/gefs/config.base.j2

@@ -64,7 +64,7 @@ export DO_AWIPS="{{ DO_AWIPS }}"         # AWIPS products
 # Experiment mode (cycled or forecast-only)
 export MODE="{{ MODE }}" # cycled/forecast-only
 export DO_TEST_MODE="{{ DO_TEST_MODE }}" # option to change configuration for automated testing
-export GEFSTYPE="{{ GEFSTYPE }}" # near-real-time/gefs-offline
+export GEFSTYPE="{{ GEFSTYPE }}" # gefs-real-time/gefs-offline
 ####################################################
 # DO NOT ADD MACHINE DEPENDENT STUFF BELOW THIS LINE
 # IF YOU HAVE TO MAKE MACHINE SPECIFIC CHANGES BELOW

dev/parm/config/gefs/config.stage_ic.j2

@@ -11,7 +11,7 @@ export ICSDIR="{{ ICSDIR }}" # User provided ICSDIR; blank if not provided
 export BASE_IC="{{ BASE_IC }}" # Platform home for staged ICs
 
 if [[ ${RUN} == "gefs" ]] ; then
-  if [[ ${GEFSTYPE} = "near-real-time" ]] ; then
+  if [[ ${GEFSTYPE} = "gefs-real-time" ]] ; then
     export STAGE_IC_YAML_TMPL="${PARMgfs}/stage/master_gefs_RT.yaml.j2"
   elif [[ ${GEFSTYPE} = "gefs-offline" ]] ; then
     export STAGE_IC_YAML_TMPL="${PARMgfs}/stage/master_gefs.yaml.j2"

dev/workflow/applications/applications.py

@@ -198,7 +198,7 @@ def _get_run_options(self, conf: Configuration) -> Dict[str, Any]:
             run_options[run]['use_aero_anl'] = run_base.get('USE_AERO_ANL', False)
             run_options[run]['do_aero_fcst'] = run_base.get('DO_AERO_FCST', False)
 
-            if run_base.get('GEFSTYPE', "") == "near-real-time":
+            if run_base.get('GEFSTYPE', "") == "gefs-real-time":
                 run_options[run]['do_gefs_real_time'] = True
             elif run_base.get('GEFSTYPE', "") == "gefs-offline":
                 run_options[run]['do_gefs_real_time'] = False

dev/workflow/rocoto/gefs_tasks.py

@@ -85,7 +85,7 @@ def fcst(self):
         if self.app_config.gefstype in ['gefs-offline']:
             dep_dict = {'type': 'task', 'name': f'{self.run}_stage_ic'}
             dependencies.append(rocoto.add_dependency(dep_dict))
-        elif self.app_config.gefstype in ['near-real-time']:
+        elif self.app_config.gefstype in ['gefs-real-time']:
             dep_dict = {'type': 'task', 'name': f'{self.run}_gen_control_ic'}
             dependencies.append(rocoto.add_dependency(dep_dict))
 

dev/workflow/setup_expt.py

@@ -244,7 +244,7 @@ def _common_args(parser):
         parser.add_argument('--interval', help='frequency of forecast (in hours); must be a multiple of 6 or 0 for no forecasts',
                             type=_validate_interval, required=False, default=6)
         parser.add_argument('--icsdir', help='full path to user initial condition directory', type=str, required=False, default='')
-        parser.add_argument('--gefstype', help='type of the gefs experiment: near-real-time or gefs-offline', type=str, required=False, default='')
+        parser.add_argument('--gefstype', help='type of the gefs experiment: gefs-real-time or gefs-offline', type=str, required=False, default='')
         parser.add_argument('--overwrite', help='overwrite previously created experiment (if it exists)',
                             action='store_true', required=False)
         return parser

parm/stage/aero.yaml.j2

@@ -1,17 +1,9 @@
 aero:
     mkdir:
-        {% for mem in range(first_mem, last_mem + 1) %}
-        {% set imem = mem - first_mem %}
-        {% set COMOUT_CHEM_ANALYSIS_MEM = COMOUT_CHEM_ANALYSIS_MEM_list[imem] %}
         - "{{ COMOUT_CHEM_ANALYSIS_MEM }}"
-        {% endfor %}
+
     link_req:
-        {% for mem in range(first_mem, last_mem + 1) %}
-        {% set imem = mem - first_mem %}
-        {% set COMOUT_CHEM_ANALYSIS_MEM = COMOUT_CHEM_ANALYSIS_MEM_list[imem] %}
-        {% for ftype in ["aero_varbc_params.tar"] %}
         {% if path_exists(ICSDIR ~ "/" ~ COMOUT_CHEM_ANALYSIS_MEM | relpath(ROTDIR) ~ "/" ~ RUN ~ ".t" ~ current_cycle_HH ~ "z." ~ ftype) %}
-        - ["{{ ICSDIR }}/{{ COMOUT_CHEM_ANALYSIS_MEM | relpath(ROTDIR) }}/{{ RUN }}.t{{ current_cycle_HH }}z.{{ ftype }}", "{{ COMOUT_CHEM_ANALYSIS_MEM }}"]
+        - ["{{ ICSDIR }}/{{ COMOUT_CHEM_ANALYSIS_MEM | relpath(ROTDIR) }}/{{ RUN }}.t{{ current_cycle_HH }}z.aero_varbc_params.tar",
+           "{{ COMOUT_CHEM_ANALYSIS_MEM }}"]
         {% endif %}
-        {% endfor %}
-        {% endfor %} # mem loop

parm/stage/analysis.yaml.j2

@@ -1,16 +1,8 @@
-{% if path_exists(ICSDIR ~ "/" ~ COMOUT_ATMOS_ANALYSIS_MEM_list[0] | relpath(ROTDIR)) %}
+{% if path_exists(ICSDIR ~ "/" ~ COMOUT_ATMOS_ANALYSIS_MEM | relpath(ROTDIR)) %}
 analysis:
     mkdir:
-        {% for mem in range(first_mem, last_mem + 1) %}
-        {% set imem = mem - first_mem %}
-        {% set COMOUT_ATMOS_ANALYSIS_MEM = COMOUT_ATMOS_ANALYSIS_MEM_list[imem] %}
         - "{{ COMOUT_ATMOS_ANALYSIS_MEM }}"
-        {% endfor %}
     link_req:
-        {% for mem in range(first_mem, last_mem + 1) %}
-        {% set imem = mem - first_mem %}
-        {% set COMOUT_ATMOS_ANALYSIS_MEM = COMOUT_ATMOS_ANALYSIS_MEM_list[imem] %}
-
         {% if DO_JEDIATMVAR %}
 
         {% for itile in range(6) %}
@@ -81,7 +73,6 @@ analysis:
            "{{ COMOUT_ATMOS_ANALYSIS_MEM }}{{ RUN }}.t{{ current_cycle_HH }}z.{{ dest_ftype }}"]
         {% endif %}
         {% endfor %}
-
         {% if DO_LAND_IAU %}
         {% for itile in range(1,7) %}
         - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_ANALYSIS_MEM | relpath(ROTDIR) }}/sfc_inc.tile{{ itile }}.nc",
@@ -90,5 +81,4 @@ analysis:
         {% endif %}
         {% endif %}
 
-        {% endfor %} # mem loop
 {% endif %}

parm/stage/atmosphere_cold.yaml.j2

@@ -1,18 +1,10 @@
 atmosphere_cold:
     mkdir:
-        {% for mem in range(first_mem, last_mem + 1) %}
-        {% set imem = mem - first_mem %}
-        {% set COMOUT_ATMOS_INPUT_MEM = COMOUT_ATMOS_INPUT_MEM_list[imem] %}
         - "{{ COMOUT_ATMOS_INPUT_MEM }}"
-        {% endfor %} # mem loop
     link_req:
-        {% for mem in range(first_mem, last_mem + 1) %}
-        {% set imem = mem - first_mem %}
-        {% set COMOUT_ATMOS_INPUT_MEM = COMOUT_ATMOS_INPUT_MEM_list[imem] %}
-        - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_INPUT_MEM | relpath(ROTDIR) }}/gfs_ctrl.nc", "{{ COMOUT_ATMOS_INPUT_MEM }}"]
+        - ["{{ ICSDIR }}/{{ COMIN_ATMOS_INPUT_MEM | relpath(ROTDIR) }}/gfs_ctrl.nc", "{{ COMOUT_ATMOS_INPUT_MEM }}"]
         {% for ftype in ["gfs_data", "sfc_data"] %}
         {% for ntile in range(1, ntiles + 1) %}
-        - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_INPUT_MEM | relpath(ROTDIR) }}/{{ ftype }}.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_INPUT_MEM }}"]
+        - ["{{ ICSDIR }}/{{ COMIN_ATMOS_INPUT_MEM | relpath(ROTDIR) }}/{{ ftype }}.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_INPUT_MEM }}"]
         {% endfor %} # ntile
         {% endfor %} # ftype
-        {% endfor %} # mem loop

parm/stage/atmosphere_ens_perturbations.yaml.j2

@@ -1,13 +1,5 @@
 atmosphere_ens_perturbation:
     mkdir:
-        {% for mem in range(first_mem + 1, last_mem + 1) %}
-        {% set imem = mem - first_mem %}
-        {% set COMOUT_ATMOS_ANALYSIS_MEM = COMOUT_ATMOS_ANALYSIS_MEM_list[imem] %}
         - "{{ COMOUT_ATMOS_ANALYSIS_MEM }}"
-        {% endfor %} # mem loop
     link_req:
-        {% for mem in range(first_mem + 1, last_mem + 1) %}
-        {% set imem = mem - first_mem %}
-        {% set COMOUT_ATMOS_ANALYSIS_MEM = COMOUT_ATMOS_ANALYSIS_MEM_list[imem] %}
         - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_ANALYSIS_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.fv3_perturbation.nc", "{{ COMOUT_ATMOS_ANALYSIS_MEM }}/{{ RUN }}.t{{ current_cycle_HH }}z.increment.atm.i006.nc"]
-        {% endfor %} # mem loop

parm/stage/atmosphere_nest.yaml.j2

@@ -2,35 +2,19 @@ atmosphere_nest:
     {% set ntile = 7 %}
     {% if EXP_WARM_START == True %}
     mkdir:
-        {% for mem in range(first_mem, last_mem + 1) %}
-        {% set imem = mem - first_mem %}
-        {% set COMOUT_ATMOS_RESTART_PREV_MEM = COMOUT_ATMOS_RESTART_PREV_MEM_list[imem] %}
         - "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}"
-        {% endfor %} # mem loop
     link_req:
-        {% for mem in range(first_mem, last_mem + 1) %}
-        {% set imem = mem - first_mem %}
-        {% set COMOUT_ATMOS_RESTART_PREV_MEM = COMOUT_ATMOS_RESTART_PREV_MEM_list[imem] %}
         {% for ftype in ["fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
         - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.{{ ftype }}.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}/{{ m_prefix }}.{{ ftype }}.nest0{{ ntile-5 }}.tile{{ ntile }}.nc"]
         {% if DO_CA %}
         - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.ca_data.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}/{{ m_prefix }}.ca_data.nest0{{ ntile-5 }}.tile{{ ntile }}.nc"]
         {% endif %}
         {% endfor %}
-        {% endfor %} # mem loop
     {% else %} # cold start
     mkdir:
-        {% for mem in range(first_mem, last_mem + 1) %}
-        {% set imem = mem - first_mem %}
-        {% set COMOUT_ATMOS_INPUT_MEM = COMOUT_ATMOS_INPUT_MEM_list[imem] %}
         - "{{ COMOUT_ATMOS_INPUT_MEM }}"
-        {% endfor %} # mem loop
     link_req:
-        {% for mem in range(first_mem, last_mem + 1) %}
-        {% set imem = mem - first_mem %}
-        {% set COMOUT_ATMOS_INPUT_MEM = COMOUT_ATMOS_INPUT_MEM_list[imem] %}
         {% for ftype in ["gfs_data", "sfc_data"] %}
         - ["{{ COMOUT_ATMOS_INPUT_MEM }}/{{ ftype }}.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_INPUT_MEM }}/{{ ftype }}.nest0{{ ntile-5 }}.tile{{ ntile }}.nc"]
         {% endfor %}
-        {% endfor %} # mem loop
     {% endif %}

parm/stage/atmosphere_warm.yaml.j2

@@ -1,17 +1,8 @@
 atmosphere_warm:
     mkdir:
-        {% for mem in range(first_mem, last_mem + 1) %}
-        {% set imem = mem - first_mem %}
-        {% set COMOUT_ATMOS_RESTART_PREV_MEM = COMOUT_ATMOS_RESTART_PREV_MEM_list[imem] %}
         - "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}"
-        {% set COMOUT_ATMOS_RESTART_MEM = COMOUT_ATMOS_RESTART_MEM_list[imem] %}
         - "{{ COMOUT_ATMOS_RESTART_MEM }}"
-        {% endfor %} # mem loop
     link_req:
-        {% for mem in range(first_mem, last_mem + 1) %}
-        {% set imem = mem - first_mem %}
-        {% set COMOUT_ATMOS_RESTART_PREV_MEM = COMOUT_ATMOS_RESTART_PREV_MEM_list[imem] %}
-        {% set COMOUT_ATMOS_RESTART_MEM = COMOUT_ATMOS_RESTART_MEM_list[imem] %}
         {% if path_exists(ICSDIR ~ "/" ~ COMOUT_ATMOS_RESTART_PREV_MEM | relpath(ROTDIR) ~ "/" ~ m_prefix ~ ".atm_stoch.res.nc") %}
         - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.atm_stoch.res.nc", "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}"]
         {% endif %} # path_exists
@@ -31,4 +22,3 @@ atmosphere_warm:
         - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.sfcanl_data.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_RESTART_MEM }}"]
         {% endif %} # path_exists
         {% endfor %} # ntile
-        {% endfor %} # mem loop

parm/stage/atmosphere_warm_RT.yaml.j2

@@ -7,8 +7,6 @@ atmosphere_warm_RT:
         {% set mid_cyc = ("%02d" | format(previous_cycle_HH | int + half_window)) ~ "0000" %}
         {% set restart_mem_path = ICSDIR ~ '/' ~ 'enkfgdas.' ~ previous_cycle_YMD ~ '/' ~ previous_cycle_HH ~ '/' ~ 'mem%03d' | format(gfs_member) ~ '/model/atmos/restart/' ~ previous_cycle_YMD ~ '.' ~ mid_cyc ~ '.' %}
         {% set increment_mem_path = ICSDIR ~ '/' ~ 'enkfgfs.' ~ current_cycle_YMD ~ '/' ~ current_cycle_HH ~ '/' ~ 'mem%03d' | format(gfs_member) ~ '/analysis/atmos/enkfgfs.t' ~ current_cycle_HH ~ 'z.' %}
-        {% set restart_destination_path = COMOUT_ATMOS_RESTART_PREV_MEM %}
-        {% set increment_destination_path = COMOUT_ATMOS_ANALYSIS_MEM %}
 
         # Include increment files
         # TODO: make these filenames the same after RE-staging inputs with EE2-compliant filenames
@@ -24,15 +22,15 @@ atmosphere_warm_RT:
 
         {% if path_exists(ICSDIR) %}
             {% set file = restart_mem_path ~ 'coupler.res' %}
-        - ["{{ file }}", "{{ restart_destination_path }}"]
+        - ["{{ file }}", "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}"]
             {% set file = restart_mem_path ~ 'fv_core.res.nc' %}
-        - ["{{ file }}", "{{ restart_destination_path }}"]
+        - ["{{ file }}", "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}"]
             {% set ntiles = 6 %}
             {% for ftype in ["fv_core.res", "fv_srf_wnd.res", "phy_data", "sfc_data"] %}
                 # Include restart tile files (e.g., .tile1 to .tile6)
                 {% for tile in range(1, ntiles + 1) %}
                     {% set file = restart_mem_path ~ ftype ~ '.tile' ~ tile ~ '.nc' %}
-        - ["{{ file }}", "{{ restart_destination_path }}"]
+        - ["{{ file }}", "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}"]
                 {% endfor %}
             {% endfor %}
         {% endif %}

parm/stage/ice.yaml.j2

@@ -1,35 +1,14 @@
-{% set START_ICE_FROM_ANA = False %}
-{% if DO_JEDIOCNVAR == True and RUN == 'gdas' %}
-    {% set START_ICE_FROM_ANA = True %}
-{% endif %}
-{% if DO_STARTMEM_FROM_JEDIICE == True and RUN == 'enkfgdas' %}
-    {% set START_ICE_FROM_ANA = True %}
-{% endif %}
 ice:
     {% if START_ICE_FROM_ANA == True %}
     mkdir:
-        {% for mem in range(first_mem, last_mem + 1) %}
-        {% set imem = mem - first_mem %}
-        {% set COMOUT_ICE_ANALYSIS_MEM = COMOUT_ICE_ANALYSIS_MEM_list[imem] %}
         - "{{ COMOUT_ICE_ANALYSIS_MEM }}"
-        {% endfor %} # mem loop
     link_req:
-        {% for mem in range(first_mem, last_mem + 1) %}
-        {% set imem = mem - first_mem %}
-        {% set COMOUT_ICE_ANALYSIS_MEM = COMOUT_ICE_ANALYSIS_MEM_list[imem] %}
-        - ["{{ ICSDIR }}/{{ COMOUT_ICE_ANALYSIS_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.cice_model_anl.res.nc", "{{ COMOUT_ICE_ANALYSIS_MEM }}/{{ m_prefix }}.analysis.cice_model.res.nc"]
-        {% endfor %} # mem loop
+    {% set COMOUT_ICE_ANALYSIS_MEM = COMOUT_ICE_ANALYSIS_MEM %}
+        - ["{{ ICSDIR }}/{{ COMOUT_ICE_ANALYSIS_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.cice_model_anl.res.nc",
+           "{{ COMOUT_ICE_ANALYSIS_MEM }}/{{ m_prefix }}.analysis.cice_model.res.nc"]
     {% else %}
     mkdir:
-        {% for mem in range(first_mem, last_mem + 1) %}
-        {% set imem = mem - first_mem %}
-        {% set COMOUT_ICE_RESTART_PREV_MEM = COMOUT_ICE_RESTART_PREV_MEM_list[imem] %}
         - "{{ COMOUT_ICE_RESTART_PREV_MEM }}"
-        {% endfor %} # mem loop
     link_req:
-        {% for mem in range(first_mem, last_mem + 1) %}
-        {% set imem = mem - first_mem %}
-        {% set COMOUT_ICE_RESTART_PREV_MEM = COMOUT_ICE_RESTART_PREV_MEM_list[imem] %}
         - ["{{ ICSDIR }}/{{ COMOUT_ICE_RESTART_PREV_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.cice_model.res.nc", "{{ COMOUT_ICE_RESTART_PREV_MEM }}"]
-        {% endfor %} # mem loop
     {% endif %}

parm/stage/ice_RT.yaml.j2

@@ -8,5 +8,4 @@ ice_RT:
         {% set increment_destination_path = COMOUT_ICE_ANALYSIS_MEM %}
 
         # Include increment files
-        {% set file = increment_mem_path %}
-        - ["{{ file }}", "{{ increment_destination_path }}"]
+        - ["{{ increment_mem_file }}", "{{ COMOUT_ICE_ANALYSIS_MEM }}"]