Refactor staging job for mem loop and COM declare

- Move rRUN, mem list, and COM declares inside python/yaml - Move mem loop inside python - Add path_exists checks to some initial conditions - Create dicts for replace_tmpl COM declares Refs NOAA-EMC#2475
KateFriedman-NOAA · Aug 12, 2024 · b74e696 · b74e696
1 parent 2913b58
commit b74e696
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diff --git a/jobs/JGLOBAL_STAGE_IC b/jobs/JGLOBAL_STAGE_IC
@@ -3,12 +3,6 @@
 source "${HOMEgfs}/ush/preamble.sh"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "stage_ic" -c "base stage_ic"
 
-# Restart conditions for GFS cycle come from GDAS
-# shellcheck disable=SC2153
-rRUN=${RUN}
-# shellcheck disable=SC2153
-[[ ${RUN} == "gfs" ]] && rRUN="gdas"
-
 # Define significant cycles
 # shellcheck disable=SC2153
 half_window=$(( assim_freq / 2 ))
@@ -30,56 +24,11 @@ else
 fi
 export current_cycle previous_cycle current_cycle_offset model_start_date_current_cycle
 
-# Define MEMDIR_ARRAY
-MEMDIR_ARRAY=()
-if [[ "${RUN:-}" = "enkfgdas" || "${RUN:-}" = "gefs" ]]; then
-  if [[ "${RUN:-}" = "gefs" ]]; then
-    ii_start=0
-  elif [[ "${RUN:-}" = "enkfgdas" ]]; then
-    ii_start=1
-  fi
-  # Populate the member_dirs array based on the value of NMEM_ENS
-  for ((ii = "${ii_start}"; ii <= "${NMEM_ENS:-0}"; ii++)); do
-    MEMDIR_ARRAY+=("mem$(printf "%03d" "${ii}")")
-  done
-else
-  MEMDIR_ARRAY+=("")
-fi
-
 # Initialize return code
 err=0
 
-###############################################################
-for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
-
-  # Declare COMs
-  if [[ "${MODE}" = "cycled" && "${RUN}" = "gdas" ]]; then
-    YMD=${current_cycle:0:8} HH=${current_cycle:8:2} declare_from_tmpl -x COMOUT_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL
-  fi
-
-  if [[ ${EXP_WARM_START:-".false."} = ".true." ]]; then
-    MEMDIR=${MEMDIR} RUN=${rRUN} YMD=${previous_cycle:0:8} HH=${previous_cycle:8:2} declare_from_tmpl -x COMOUT_ATMOS_RESTART_PREV:COM_ATMOS_RESTART_TMPL
-    MEMDIR=${MEMDIR} RUN=${rRUN} YMD=${previous_cycle:0:8} HH=${previous_cycle:8:2} declare_from_tmpl -x COMOUT_MED_RESTART_PREV:COM_MED_RESTART_TMPL
-  else
-    MEMDIR=${MEMDIR} YMD=${current_cycle:0:8} HH=${current_cycle:8:2} declare_from_tmpl -x COMOUT_ATMOS_INPUT:COM_ATMOS_INPUT_TMPL
-  fi
-  if [[ "${DO_OCN:-}" = "YES" ]]; then
-    MEMDIR=${MEMDIR} RUN=${rRUN} YMD=${previous_cycle:0:8} HH=${previous_cycle:8:2} declare_from_tmpl -x COMOUT_OCEAN_RESTART_PREV:COM_OCEAN_RESTART_TMPL
-    if [[ "${REPLAY_ICS:-NO}" = "YES" ]]; then
-      MEMDIR=${MEMDIR} YMD=${current_cycle:0:8} HH=${current_cycle:8:2} declare_from_tmpl -x COMOUT_OCEAN_ANALYSIS:COM_OCEAN_ANALYSIS_TMPL
-    fi
-  fi
-  if [[ "${DO_ICE:-}" = "YES" ]]; then
-    MEMDIR=${MEMDIR} RUN=${rRUN} YMD=${previous_cycle:0:8} HH=${previous_cycle:8:2} declare_from_tmpl -x COMOUT_ICE_RESTART_PREV:COM_ICE_RESTART_TMPL
-  fi
-  if [[ "${DO_WAVE:-}" = "YES" ]]; then
-    MEMDIR=${MEMDIR} YMD=${previous_cycle:0:8} HH=${previous_cycle:8:2} declare_from_tmpl -x COMOUT_WAVE_RESTART_PREV:COM_WAVE_RESTART_TMPL
-  fi
-
-  # Execute staging
-  "${SCRgfs}/exglobal_stage_ic.py"
-
-done # for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
+# Execute staging
+"${SCRgfs}/exglobal_stage_ic.py"
 
 ###############################################################
 # Check for errors and exit if any of the above failed

diff --git a/parm/stage/stage.yaml.j2 b/parm/stage/stage.yaml.j2
@@ -19,43 +19,77 @@
 #############################################################
 
 # Set variables used below
-{% set cycle_HH = current_cycle | strftime("%H") %}
+{% set current_cycle_YMD = current_cycle | to_YMD %}
+{% set current_cycle_HH = current_cycle | strftime("%H") %}
+{% set previous_cycle_YMD = previous_cycle | to_YMD %}
+{% set previous_cycle_HH = previous_cycle | strftime("%H") %}
 {% set m_prefix = model_start_date_current_cycle | to_YMD + "." + model_start_date_current_cycle | strftime("%H") + "0000" %}
 {% set o_prefix = current_cycle_offset | to_YMD + "." + current_cycle_offset | strftime("%H") + "0000" %}
 {% set p_prefix = previous_cycle | to_YMD + "." + previous_cycle | strftime("%H") + "0000" %}
 
-#############################################################
+####################################################################
 # Initial condition to stage
+####################################################################
+
+# Declare a dict of search and replace terms to run on each template
+
+{% if mem >= 0 %}
+  {% set mem_char = 'mem%03d' | format(mem) %}
+{% else %}
+  {% set mem_char = '' %}
+{% endif %}
+{% set current_dict = ({ '${ROTDIR}':ROTDIR,
+                         '${RUN}':RUN,
+                         '${YMD}':current_cycle_YMD,
+                         '${HH}':current_cycle_HH,
+                         '${MEMDIR}': mem_char }) %}
+{% set previous_dict = ({ '${ROTDIR}':ROTDIR,
+                          '${RUN}':rRUN,
+                          '${YMD}':previous_cycle_YMD,
+                          '${HH}':previous_cycle_HH,
+                          '${MEMDIR}': mem_char }) %}
+{% set previous_run_dict = ({ '${ROTDIR}':ROTDIR,
+                              '${RUN}':RUN,
+                              '${YMD}':previous_cycle_YMD,
+                              '${HH}':previous_cycle_HH,
+                              '${MEMDIR}': mem_char }) %}
+
+# Initial condition definitions
 
 {% if MODE == "cycled" and RUN == "gdas" %}
+{% set COMOUT_ATMOS_ANALYSIS = COM_ATMOS_ANALYSIS_TMPL | replace_tmpl(current_dict) %}
 analysis:
     mkdir:
         - "{{ COMOUT_ATMOS_ANALYSIS }}"
     copy:
         {% for ftype in ["abias", "abias_air", "abias_int", "abias_pc", "atminc.nc", "radstat"] %}
-        {% if path_exists(ICSDIR ~ "/" ~ COMOUT_ATMOS_ANALYSIS | relpath(ROTDIR) ~ "/" ~ RUN ~ ".t" ~ cycle_HH ~ "z." ~ ftype) %}
-        - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ RUN }}.t{{ cycle_HH }}z.{{ ftype }}", "{{ COMOUT_ATMOS_ANALYSIS }}"]
+        {% if path_exists(ICSDIR ~ "/" ~ COMOUT_ATMOS_ANALYSIS | relpath(ROTDIR) ~ "/" ~ RUN ~ ".t" ~ current_cycle_HH ~ "z." ~ ftype) %}
+        - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ RUN }}.t{{ current_cycle_HH }}z.{{ ftype }}", "{{ COMOUT_ATMOS_ANALYSIS }}"]
         {% endif %}
         {% endfor %}
 {% endif %}
 
 {% if EXP_WARM_START == True %}
+{% set COMOUT_ATMOS_RESTART_PREV = COM_ATMOS_RESTART_TMPL | replace_tmpl(previous_dict) %}
 atmosphere_warm:
     mkdir:
         - "{{ COMOUT_ATMOS_RESTART_PREV }}"
     copy:
         {% for ftype in ["coupler.res", "fv_core.res.nc"] %}
-        - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV | relpath(ROTDIR) }}/{{ o_prefix }}.{{ ftype }}", "{{ COMOUT_ATMOS_RESTART_PREV }}"]
+        - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV | relpath(ROTDIR) }}/{{ m_prefix }}.{{ ftype }}", "{{ COMOUT_ATMOS_RESTART_PREV }}"]
         {% endfor %}
         {% for ftype in ["ca_data", "fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
             {% for ntile in range(1, ntiles + 1) %}
-        - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV | relpath(ROTDIR) }}/{{ o_prefix }}.{{ ftype }}.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_RESTART_PREV }}"]
+        - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV | relpath(ROTDIR) }}/{{ m_prefix }}.{{ ftype }}.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_RESTART_PREV }}"]
             {% endfor %} # ntile
         {% endfor %} # ftype
         {% for ntile in range(1, ntiles + 1) %}
+        {% if path_exists(ICSDIR ~ "/" ~ COMOUT_ATMOS_RESTART_PREV | relpath(ROTDIR) ~ "/" ~ p_prefix ~ ".sfcanl_data.tile" ~ ntile ~ ".nc") %}
         - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV | relpath(ROTDIR) }}/{{ p_prefix }}.sfcanl_data.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_RESTART_PREV }}"]
+        {% endif %} # path_exists
         {% endfor %} # ntile
-{% else %}
+{% else %} # cold start
+{% set COMOUT_ATMOS_INPUT = COM_ATMOS_INPUT_TMPL | replace_tmpl(current_dict) %}
 atmosphere_cold:
     mkdir:
         - "{{ COMOUT_ATMOS_INPUT }}"
@@ -69,31 +103,38 @@ atmosphere_cold:
 {% endif %}
 
 {% if REPLAY_ICS == "YES" %}
+{% set COMOUT_ATMOS_ANALYSIS = COM_ATMOS_ANALYSIS_TMPL | replace_tmpl(current_dict) %}
 atmosphere_perturbation:
     mkdir:
         - "{{ COMOUT_ATMOS_ANALYSIS }}"
     copy:
-        - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ m_prefix }}.fv3_perturbation.nc", "{{ COMOUT_ATMOS_ANALYSIS }}/{{ RUN }}.t{{ cycle_HH }}z.atminc.nc"]
+        - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ m_prefix }}.fv3_perturbation.nc", "{{ COMOUT_ATMOS_ANALYSIS }}/{{ RUN }}.t{{ current_cycle_HH }}z.atminc.nc"]
 {% endif %}
 
 {% if DO_NEST %}
 atmosphere_nest:
-    {% set ntile = 7 %}
+  {% set ntile = 7 %}
+  {% if EXP_WARM_START == True %}
+    {% set COMOUT_ATMOS_RESTART_PREV = COM_ATMOS_RESTART_TMPL | replace_tmpl(previous_dict) %}
     mkdir:
         - "{{ COMOUT_ATMOS_RESTART_PREV }}"
     copy:
-        {% if EXP_WARM_START == True %}
-            {% for ftype in ["ca_data", "fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
+        {% for ftype in ["ca_data", "fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
         - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV | relpath(ROTDIR) }}/{{ o_prefix }}.{{ ftype }}.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_RESTART_PREV }}/{{ o_prefix }}.{{ ftype }}.nest0{{ ntile-5 }}.tile{{ ntile }}.nc"]
-            {% endfor %} # ftype
-        {% else %}
-            {% for ftype in ["gfs_data", "sfc_data"] %}
+        {% endfor %}
+  {% else %} # cold start
+    {% set COMOUT_ATMOS_INPUT = COM_ATMOS_INPUT_TMPL | replace_tmpl(current_dict) %}
+    mkdir:
+        - "{{ COMOUT_ATMOS_INPUT }}"
+    copy:
+        {% for ftype in ["gfs_data", "sfc_data"] %}
         - ["{{ COMOUT_ATMOS_INPUT }}/{{ ftype }}.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_INPUT }}/{{ ftype }}.nest0{{ ntile-5 }}.tile{{ ntile }}.nc"]
-            {% endfor %} # ftype
-        {% endif %} # cold-start
+        {% endfor %}
+  {% endif %}
 {% endif %}
 
 {% if DO_ICE %}
+{% set COMOUT_ICE_RESTART_PREV = COM_ICE_RESTART_TMPL | replace_tmpl(previous_dict) %}
 ice:
     mkdir:
         - "{{ COMOUT_ICE_RESTART_PREV }}"
@@ -102,6 +143,7 @@ ice:
 {% endif %}
 
 {% if DO_OCN %}
+{% set COMOUT_OCEAN_RESTART_PREV = COM_OCEAN_RESTART_TMPL | replace_tmpl(previous_dict) %}
 ocean:
     mkdir:
         - "{{ COMOUT_OCEAN_RESTART_PREV }}"
@@ -114,6 +156,7 @@ ocean:
         {% endif %}
 
 {% if REPLAY_ICS == "YES" %}
+{% set COMOUT_OCEAN_ANALYSIS = COM_OCEAN_ANALYSIS_TMPL | replace_tmpl(current_dict) %}
 replay:
     mkdir:
         - "{{ COMOUT_OCEAN_ANALYSIS }}"
@@ -122,6 +165,7 @@ replay:
 {% endif %}
 
 {% if EXP_WARM_START == True %}
+{% set COMOUT_MED_RESTART_PREV = COM_MED_RESTART_TMPL | replace_tmpl(previous_dict) %}
 {% if path_exists(ICSDIR ~ "/" ~ COMOUT_MED_RESTART_PREV | relpath(ROTDIR) ~ "/" ~ m_prefix ~ ".ufs.cpld.cpl.r.nc") %}
 mediator:
     mkdir:
@@ -134,6 +178,7 @@ mediator:
 {% endif %} # DO_OCN=YES
 
 {% if DO_WAVE %}
+{% set COMOUT_WAVE_RESTART_PREV = COM_WAVE_RESTART_TMPL | replace_tmpl(previous_run_dict) %}
 wave:
     mkdir:
         - "{{ COMOUT_WAVE_RESTART_PREV }}"

diff --git a/scripts/exglobal_stage_ic.py b/scripts/exglobal_stage_ic.py
@@ -18,7 +18,7 @@ def main():
     stage = Stage(config)
 
     # Pull out all the configuration keys needed to run stage job
-    keys = ['RUN', 'MODE', 'EXP_WARM_START',
+    keys = ['RUN', 'MODE', 'EXP_WARM_START', 'NMEM_ENS',
             'previous_cycle', 'current_cycle',
             'current_cycle_offset', 'model_start_date_current_cycle',
             'ROTDIR', 'ICSDIR', 'STAGE_IC_YAML_TMPL',

diff --git a/ush/python/pygfs/task/stage.py b/ush/python/pygfs/task/stage.py
@@ -56,9 +56,31 @@ def execute_stage(self, stage_dict: Dict[str, Any]) -> None:
         # Add the os.path.exists function to the dict for yaml parsing
         stage_dict['path_exists'] = os.path.exists
 
-        stage_set = parse_j2yaml(self.task_config.STAGE_IC_YAML_TMPL, stage_dict,
-                                 allow_missing=False)
-
-        # Copy files to ROTDIR
-        for key in stage_set.keys():
-            FileHandler(stage_set[key]).sync()
+        # Determine restart RUN
+        rRUN = self.task_config.RUN
+        if self.task_config.RUN == "gfs":
+            rRUN = "gdas"
+        stage_dict['rRUN'] = rRUN
+
+        # Determine ensemble member settings
+        MEM_START = -1 # Deterministic default, no members
+        if self.task_config.NMEM_ENS > 0:
+            if self.task_config.RUN == "gefs":
+                MEM_START = 0
+            elif self.task_config.RUN == "enkfgdas":
+                MEM_START = 1
+
+        if MEM_START >= 0: # Ensemble RUN
+            first_mem = MEM_START
+            last_mem = self.task_config.NMEM_ENS
+        else: # Deteministic RUN
+            first_mem = MEM_START
+            last_mem = MEM_START
+
+        # Loop over members
+        for mem in range(first_mem, last_mem + 1):
+            stage_dict['mem'] = mem
+            stage_set = parse_j2yaml(self.task_config.STAGE_IC_YAML_TMPL, stage_dict, allow_missing=False)
+            # Copy files to ROTDIR
+            for key in stage_set.keys():
+                FileHandler(stage_set[key]).sync()