Merge branch 'NOAA-EMC:develop' into aws-forecast-only

ci/cases/yamls/gfs_extended_ci.yaml

@@ -9,5 +9,6 @@ base:
   DO_AWIPS: "NO"
   DO_NPOESS: "YES"
   DO_GENESIS_FSU: "NO"
+  FCST_BREAKPOINTS: 192
   FHMAX_GFS: 384
   FHMAX_HF_GFS: 120

jobs/JGLOBAL_FORECAST

@@ -116,6 +116,17 @@ fi
 # Remove the Temporary working directory
 ##########################################
 cd "${DATAROOT}" || true
-[[ "${KEEPDATA}" == "NO" ]] && rm -rf "${DATA}" "${DATArestart}"  # do not remove DATAjob. It contains DATAoutput
+# do not remove DATAjob. It contains DATAoutput
+if [[ "${KEEPDATA}" == "NO" ]]; then
+  rm -rf "${DATA}"
+
+  # Determine if this is the last segment
+  commas="${FCST_SEGMENTS//[^,]}"
+  n_segs=${#commas}
+  if (( n_segs - 1 == ${FCST_SEGMENT:-0} )); then
+    # Only delete temporary restarts if it is the last segment
+    rm -rf "${DATArestart}"
+  fi
+fi
 
 exit 0

parm/archive/enkf.yaml.j2

@@ -11,7 +11,7 @@ enkf:
         {% endfor %}
         - "logs/{{ cycle_YMDH }}/{{ RUN }}echgres.log"
         - "logs/{{ cycle_YMDH }}/{{ RUN }}esfc.log"
-        {% for grp in range(iaufhrs | length) %}
+        {% for grp in range(IAUFHRS | length) %}
         - "logs/{{ cycle_YMDH }}/{{ RUN }}ecen{{ '%03d' % grp }}.log"
         {% endfor %}
 
@@ -68,7 +68,7 @@ enkf:
         {% if DOIAU %}
         # IAU increments/analyses
 
-        {% for fhr in iaufhrs if fhr != 6 %}
+        {% for fhr in IAUFHRS if fhr != 6 %}
         {% if do_calc_increment %}
         # Store analyses instead of increments
         - "{{ COMIN_ATMOS_ANALYSIS_ENSSTAT | relpath(ROTDIR) }}/{{ head }}atma{{ '%03d' % fhr }}.ensmean.nc"

parm/archive/enkf_restarta_grp.yaml.j2

@@ -36,14 +36,14 @@ enkf_restarta_grp:
         {% endif %}
 
         # Member increments
-        {% for iaufhr in iaufhrs if iaufhr != 6 %}
+        {% for iaufhr in IAUFHRS if iaufhr != 6 %}
         {% set iaufhr = iaufhr %}
         {% if do_calc_increment %}
         - "{{ COMIN_ATMOS_ANALYSIS_MEM | relpath(ROTDIR) }}/{{ head }}atma{{ '%03d' % iaufhr }}.nc"
         {% else %}
         - "{{ COMIN_ATMOS_ANALYSIS_MEM | relpath(ROTDIR) }}/{{ head }}ratmi{{ '%03d' % iaufhr }}.nc"
         {% endif %}
-        {% endfor %}  # iaufhr in iaufhrs
+        {% endfor %}  # iaufhr in IAUFHRS
 
         # Conventional data
         {% if not lobsdiag_forenkf and not DO_JEDIATMENS %}

parm/archive/gdas.yaml.j2

@@ -49,7 +49,7 @@ gdas:
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}atmanl.ensres.nc"
                 {% if DOIAU %}
         # Ensemble IAU analysis residuals
-                    {% for fhr in iaufhrs if fhr != 6 %}
+                    {% for fhr in IAUFHRS if fhr != 6 %}
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}atma{{ '%03d' % fhr }}.ensres.nc"
                     {% endfor %}
                 {% endif %}
@@ -108,7 +108,7 @@ gdas:
         {% endif %}  # End of cycled data
 
         # Forecast and post logs
-        - "logs/{{ cycle_YMDH }}/{{ RUN }}fcst.log"
+        - "logs/{{ cycle_YMDH }}/{{ RUN }}fcst_seg0.log"
 
         {% for fhr in range(0, FHMAX + 1, 3) %}
             {% set fhr3 = '%03d' % fhr %}

parm/archive/gdas_restarta.yaml.j2

@@ -6,7 +6,7 @@ gdas_restarta:
         # Deterministic analysis increments
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}atminc.nc"
         # IAU increments
-        {% for iaufhr in iaufhrs if iaufhr != 6 %}
+        {% for iaufhr in IAUFHRS if iaufhr != 6 %}
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}atmi{{ "%03d" % iaufhr }}.nc"
         {% endfor %}
 

parm/archive/gfs_netcdfa.yaml.j2

@@ -6,7 +6,7 @@ gfs_netcdfa:
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}atmanl.nc"
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}sfcanl.nc"
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}atminc.nc"
-        {% for iauhr in iaufhrs if iauhr != 6 %}
+        {% for iauhr in IAUFHRS if iauhr != 6 %}
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}atmi{{ "%03d" % iauhr }}.nc"
         {% endfor %}
     optional:

parm/archive/master_enkf.yaml.j2

@@ -4,28 +4,6 @@
 {% set cycle_YMDH = current_cycle | to_YMDH %}
 {% set head = RUN + ".t" + cycle_HH + "z." %}
 
-# Split IAUFHRS into a list; typically either "3,6,9" or 6 (integer)
-{% if IAUFHRS is string %}
-    # "3,6,9"
-    {% set iaufhrs = [] %}
-    {% for iaufhr in IAUFHRS.split(",") %}
-        {% do iaufhrs.append(iaufhr | int) %}
-    {% endfor %}
-{% else %}
-    # 6 (integer)
-    {% set iaufhrs = [IAUFHRS] %}
-{% endif %}
-
-# Repeat for IAUFHRS_ENKF
-{% if IAUFHRS_ENKF is string %}
-    {% set iaufhrs_enkf = [] %}
-    {% for iaufhr in IAUFHRS_ENKF.split(",") %}
-        {% do iaufhrs_enkf.append(iaufhr | int) %}
-    {% endfor %}
-{% else %}
-    {% set iaufhrs_enkf = [IAUFHRS_ENKF] %}
-{% endif %}
-
 # Determine which data to archive
 datasets:
 {% if ENSGRP == 0 %}

parm/archive/master_gdas.yaml.j2

@@ -3,16 +3,6 @@
 {% set cycle_YMDH = current_cycle | to_YMDH %}
 {% set head = "gdas.t" + cycle_HH + "z." %}
 
-# Split IAUFHRS into a list; typically either "3,6,9" or 6 (integer)
-{% if IAUFHRS is string %}
-    {% set iaufhrs = [] %}
-    {% for iaufhr in IAUFHRS.split(",") %}
-        {% do iaufhrs.append(iaufhr | int) %}
-    {% endfor %}
-{% else %}
-    {% set iaufhrs = [IAUFHRS] %}
-{% endif %}
-
 datasets:
 # Always archive atmosphere forecast/analysis data
 {% filter indent(width=4) %}

parm/archive/master_gfs.yaml.j2

@@ -3,18 +3,6 @@
 {% set cycle_YMD = current_cycle | to_YMD %}
 {% set cycle_YMDH = current_cycle | to_YMDH %}
 
-# Split IAUFHRS into a list; typically either "3,6,9" or 6 (integer)
-{% if IAUFHRS is string %}
-    # "3,6,9"
-    {% set iaufhrs = [] %}
-    {% for iaufhr in IAUFHRS.split(",") %}
-        {% do iaufhrs.append(iaufhr | int) %}
-    {% endfor %}
-{% else %}
-    # 6 (integer)
-    {% set iaufhrs = [IAUFHRS] %}
-{% endif %}
-
 # Determine which data to archive
 datasets:
 # Always archive atmosphere forecast/analysis data

parm/config/gefs/config.base

@@ -229,8 +229,11 @@ export gfs_cyc=@gfs_cyc@ # 0: no GFS cycle, 1: 00Z only, 2: 00Z and 12Z only, 4:
 
 # GFS output and frequency
 export FHMIN_GFS=0
-export FHMIN=${FHMIN_GFS}
-export FHMAX_GFS=@FHMAX_GFS@
+export FHMAX_GFS="@FHMAX_GFS@"
+# Intermediate times to stop forecast when running in segments
+breakpnts="@FCST_BREAKPOINTS@"
+export FCST_SEGMENTS="${FHMIN_GFS},${breakpnts:+${breakpnts},}${FHMAX_GFS}"
+
 export FHOUT_GFS=6
 export FHMAX_HF_GFS=@FHMAX_HF_GFS@
 export FHOUT_HF_GFS=1

parm/config/gefs/config.fcst

@@ -30,14 +30,19 @@ string="--fv3 ${CASE}"
 # shellcheck disable=SC2086
 source "${EXPDIR}/config.ufs" ${string}
 
-# shellcheck disable=SC2153
-export FHMAX=${FHMAX_GFS}
+# Convert comma-separated string into bash array
+IFS=', ' read -ra segments <<< "${FCST_SEGMENTS}"
+# Determine MIN and MAX based on the forecast segment
+export FHMIN=${segments[${FCST_SEGMENT}]}
+export FHMAX=${segments[${FCST_SEGMENT}+1]}
+# Cap other FHMAX variables at FHMAX for the segment
+export FHMAX_HF=$(( FHMAX_HF_GFS > FHMAX ? FHMAX : FHMAX_HF_GFS ))
+export FHMAX_WAV=$(( FHMAX_WAV > FHMAX ? FHMAX : FHMAX_WAV ))
 # shellcheck disable=SC2153
 export FHOUT=${FHOUT_GFS}
-export FHMAX_HF=${FHMAX_HF_GFS}
 export FHOUT_HF=${FHOUT_HF_GFS}
 export FHOUT_OCN=${FHOUT_OCN_GFS}
-export FHOUT_ICE=${FHOUT_ICE_GFS} 
+export FHOUT_ICE=${FHOUT_ICE_GFS}
 
 # Get task specific resources
 source "${EXPDIR}/config.resources" fcst

parm/config/gefs/yaml/defaults.yaml

@@ -11,5 +11,6 @@ base:
   DO_EXTRACTVARS: "NO"
   FHMAX_GFS: 120
   FHMAX_HF_GFS: 0
+  FCST_BREAKPOINTS: "48"
   REPLAY_ICS: "NO"
   USE_OCN_PERTURB_FILES: "false"

parm/config/gfs/config.aeroanl

@@ -24,7 +24,7 @@ if [[ "${DOIAU}" == "YES" ]]; then
   export aero_bkg_times="3,6,9"
   export JEDIYAML="${PARMgfs}/gdas/aero/variational/3dvar_fgat_gfs_aero.yaml.j2"
 else
-  export aero_bkg_times="6"
+  export aero_bkg_times="6," # Trailing comma is necessary so this is treated as a list
   export JEDIYAML="${PARMgfs}/gdas/aero/variational/3dvar_gfs_aero.yaml.j2"
 fi
 

parm/config/gfs/config.base

@@ -285,7 +285,10 @@ export gfs_cyc=@gfs_cyc@ # 0: no GFS cycle, 1: 00Z only, 2: 00Z and 12Z only, 4:
 
 # GFS output and frequency
 export FHMIN_GFS=0
-export FHMAX_GFS=@FHMAX_GFS@
+export FHMAX_GFS="@FHMAX_GFS@"
+# Intermediate times to stop forecast when running in segments
+breakpnts="@FCST_BREAKPOINTS@"
+export FCST_SEGMENTS="${FHMIN_GFS},${breakpnts:+${breakpnts},}${FHMAX_GFS}"
 export FHOUT_GFS=3 # 3 for ops
 export FHMAX_HF_GFS=@FHMAX_HF_GFS@
 export FHOUT_HF_GFS=1
@@ -384,10 +387,10 @@ fi
 
 # if 3DVAR and IAU
 if [[ ${DOHYBVAR} == "NO" && ${DOIAU} == "YES"  ]]; then
-    export IAUFHRS="6"
+    export IAUFHRS="6,"
     export IAU_FHROT="3"
     export IAU_FILTER_INCREMENTS=".true."
-    export IAUFHRS_ENKF="6"
+    export IAUFHRS_ENKF="6,"
 fi
 
 # Generate post-processing ensemble spread files
@@ -397,10 +400,10 @@ export ENKF_SPREAD="YES"
 if [[ "${MODE}" = "cycled" && "${SDATE}" = "${PDY}${cyc}" && ${EXP_WARM_START} = ".false." ]] || [[ "${DOIAU}" = "NO" ]] || [[ "${MODE}" = "forecast-only" && ${EXP_WARM_START} = ".false." ]] ; then
   export IAU_OFFSET=0
   export IAU_FHROT=0
-  export IAUFHRS="6"
+  export IAUFHRS="6,"
 fi
 
-if [[ "${DOIAU_ENKF}" = "NO" ]]; then export IAUFHRS_ENKF="6"; fi
+if [[ "${DOIAU_ENKF}" = "NO" ]]; then export IAUFHRS_ENKF="6,"; fi
 
 # Determine restart intervals
 # For IAU, write restarts at beginning of window also

parm/config/gfs/config.fcst

@@ -33,11 +33,16 @@ source "${EXPDIR}/config.ufs" ${string}
 # Forecast length for GFS forecast
 case ${RUN} in
   *gfs)
-    # shellcheck disable=SC2153
-    export FHMAX=${FHMAX_GFS}
+    # Convert comma-separated string into bash array
+    IFS=', ' read -ra segments <<< "${FCST_SEGMENTS}"
+    # Determine MIN and MAX based on the forecast segment
+    export FHMIN=${segments[${FCST_SEGMENT}]}
+    export FHMAX=${segments[${FCST_SEGMENT}+1]}
+    # Cap other FHMAX variables at FHMAX for the segment
+    export FHMAX_HF=$(( FHMAX_HF_GFS > FHMAX ? FHMAX : FHMAX_HF_GFS ))
+    export FHMAX_WAV=$(( FHMAX_WAV > FHMAX ? FHMAX : FHMAX_WAV ))
     # shellcheck disable=SC2153
     export FHOUT=${FHOUT_GFS}
-    export FHMAX_HF=${FHMAX_HF_GFS}
     export FHOUT_HF=${FHOUT_HF_GFS}
     export FHOUT_OCN=${FHOUT_OCN_GFS}
     export FHOUT_ICE=${FHOUT_ICE_GFS}

parm/config/gfs/yaml/defaults.yaml

@@ -16,6 +16,7 @@ base:
   DO_METP: "YES"
   FHMAX_GFS: 120
   FHMAX_HF_GFS: 0
+  FCST_BREAKPOINTS: ""
   DO_VRFY_OCEANDA: "NO"
   GSI_SOILANAL: "NO"
   EUPD_CYC: "gdas"

ush/calcanl_gfs.py

@@ -11,6 +11,7 @@
 import gsi_utils
 from collections import OrderedDict
 import datetime
+from wxflow import cast_as_dtype
 
 python2fortran_bool = {True: '.true.', False: '.false.'}
 
@@ -358,7 +359,7 @@ def calcanl_gfs(DoIAU, l4DEnsVar, Write4Danl, ComOut, APrefix,
     ExecAnl = os.getenv('CALCANLEXEC', './calc_analysis.x')
     ExecChgresInc = os.getenv('CHGRESINCEXEC', './interp_inc.x')
     NEMSGet = os.getenv('NEMSIOGET', 'nemsio_get')
-    IAUHrs = list(map(int, os.getenv('IAUFHRS', '6').split(',')))
+    IAUHrs = cast_as_dtype(os.getenv('IAUFHRS', '6,'))
     Run = os.getenv('RUN', 'gdas')
     JEDI = gsi_utils.isTrue(os.getenv('DO_JEDIATMVAR', 'YES'))
 

ush/forecast_predet.sh

@@ -77,6 +77,7 @@ common_predet(){
 
   CDATE=${CDATE:-"${PDY}${cyc}"}
   ENSMEM=${ENSMEM:-000}
+  MEMBER=$(( 10#${ENSMEM:-"-1"} )) # -1: control, 0: ensemble mean, >0: ensemble member $MEMBER
 
   # Define significant cycles
   half_window=$(( assim_freq / 2 ))
@@ -154,7 +155,6 @@ FV3_predet(){
   FV3_OUTPUT_FH="${FV3_OUTPUT_FH} $(seq -s ' ' "${fhr}" "${FHOUT}" "${FHMAX}")"
 
   # Other options
-  MEMBER=$(( 10#${ENSMEM:-"-1"} )) # -1: control, 0: ensemble mean, >0: ensemble member $MEMBER
   PREFIX_ATMINC=${PREFIX_ATMINC:-""} # allow ensemble to use recentered increment
 
   # IAU options

ush/python/pygfs/task/aero_analysis.py

@@ -46,7 +46,7 @@ def __init__(self, config):
                 'npz_anl': self.task_config['LEVS'] - 1,
                 'AERO_WINDOW_BEGIN': _window_begin,
                 'AERO_WINDOW_LENGTH': f"PT{self.task_config['assim_freq']}H",
-                'aero_bkg_fhr': map(int, str(self.task_config['aero_bkg_times']).split(',')),
+                'aero_bkg_fhr': self.task_config['aero_bkg_times'],
                 'OPREFIX': f"{self.task_config.RUN}.t{self.task_config.cyc:02d}z.",
                 'APREFIX': f"{self.task_config.RUN}.t{self.task_config.cyc:02d}z.",
                 'GPREFIX': f"gdas.t{self.task_config.previous_cycle.hour:02d}z.",

ush/python/pygfs/task/aero_prepobs.py

@@ -31,7 +31,7 @@ def __init__(self, config: Dict[str, Any]) -> None:
             {
                 'window_begin': _window_begin,
                 'window_end': _window_end,
-                'sensors': str(self.task_config['SENSORS']).split(','),
+                'sensors': self.task_config['SENSORS'],
                 'data_dir': self.task_config['VIIRS_DATA_DIR'],
                 'input_files': '',
                 'OPREFIX': f"{self.task_config.RUN}.t{self.task_config.cyc:02d}z.",

workflow/applications/applications.py

@@ -75,6 +75,10 @@ def __init__(self, conf: Configuration) -> None:
         self.do_hpssarch = _base.get('HPSSARCH', False)
 
         self.nens = _base.get('NMEM_ENS', 0)
+        self.fcst_segments = _base.get('FCST_SEGMENTS', None)
+
+        if not AppConfig.is_monotonic(self.fcst_segments):
+            raise ValueError(f'Forecast segments do not increase monotonically: {",".join(self.fcst_segments)}')
 
         self.wave_runs = None
         if self.do_wave:
@@ -208,3 +212,26 @@ def get_gfs_interval(gfs_cyc: int) -> timedelta:
             return to_timedelta(gfs_internal_map[str(gfs_cyc)])
         except KeyError:
             raise KeyError(f'Invalid gfs_cyc = {gfs_cyc}')
+
+    @staticmethod
+    def is_monotonic(test_list: List, check_decreasing: bool = False) -> bool:
+        """
+        Determine if an array is monotonically increasing or decreasing
+
+        TODO: Move this into wxflow somewhere
+
+        Inputs
+          test_list: List
+            A list of comparable values to check
+          check_decreasing: bool [default: False]
+            Check whether list is monotonically decreasing
+
+        Returns
+          bool: Whether the list is monotonically increasing (if check_decreasing
+                if False) or decreasing (if check_decreasing is True)
+
+        """
+        if check_decreasing:
+            return all(x > y for x, y in zip(test_list, test_list[1:]))
+        else:
+            return all(x < y for x, y in zip(test_list, test_list[1:]))