Merge branch 'NOAA-EMC:develop' into develop

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.extractvars

@@ -9,12 +9,12 @@ echo "BEGIN: config.extractvars"
 
 export COMPRSCMD=${COMPRSCMD:-bzip2}
 
-export compress_ocn=0 #1: Compress extracted ocean product, 0: Do not compress extracted ocean product
-export compress_ice=0 #1: Compress extracted ice product, 0: Do not compress extracted ice product
+export compress_ocn=1 #1: Compress extracted ocean product, 0: Do not compress extracted ocean product
+export compress_ice=1 #1: Compress extracted ice product, 0: Do not compress extracted ice product
 
-export ocnres="5p00" # Resolution of ocean products
-export iceres="5p00" # Resolution of ice products
-export wavres="5p00" # Resolution of wave products
+export ocnres="1p00" # Resolution of ocean products
+export iceres="native" # Resolution of ice products
+export wavres="0p25" # Resolution of wave products
 
 export depthvar_name="z_l" # Name of depth variable in NetCDF ocean products
 export zmin="0." # Minimum depth to extract from NetCDF ocean products

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
@@ -242,7 +247,11 @@ export FSICS="0"
 
 #---------------------------------------------------------------------
 # Write more variables to output
-export DIAG_TABLE="${PARMgfs}/ufs/fv3/diag_table"
+if [[ "${REPLAY_ICS:-NO}" == "YES" ]]; then
+  export DIAG_TABLE="${PARMgfs}/ufs/fv3/diag_table_replay"
+else
+  export DIAG_TABLE="${PARMgfs}/ufs/fv3/diag_table"
+fi
 
 # Write gfs restart files to rerun fcst from any break point
 export restart_interval=${restart_interval_gfs:-12}

parm/config/gefs/config.resources

@@ -272,7 +272,7 @@ case ${step} in
     export walltime_gefs="00:30:00"
     export ntasks_gefs=1
     export threads_per_task_gefs=1
-    export tasks_per_node_gefs="${ntasks}"
+    export tasks_per_node_gefs="${ntasks_gefs}"
     export walltime_gfs="${walltime_gefs}"
     export ntasks_gfs="${ntasks_gefs}"
     export threads_per_tasks_gfs="${threads_per_task_gefs}"

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"

parm/post/oceanice_products_gefs.yaml

@@ -39,14 +39,15 @@ ocean:
       - ["{{ COM_OCEAN_HISTORY }}/{{ RUN }}.ocean.t{{ current_cycle | strftime('%H') }}z.{{ interval }}hr_avg.f{{ '%03d' % forecast_hour }}.nc", "{{ DATA }}/ocean.nc"]
   data_out:
     mkdir:
-      - "{{ COM_OCEAN_NETCDF }}"
+      - "{{ COM_OCEAN_NETCDF }}/native"
       {% for grid in product_grids %}
+      - "{{ COM_OCEAN_NETCDF }}/{{ grid }}"
       - "{{ COM_OCEAN_GRIB }}/{{ grid }}"
       {% endfor %}
     copy:
-      - ["{{ DATA }}/ocean_subset.nc", "{{ COM_OCEAN_NETCDF }}/{{ RUN }}.ocean.t{{ current_cycle | strftime('%H') }}z.native.f{{ '%03d' % forecast_hour }}.nc"]
+      - ["{{ DATA }}/ocean_subset.nc", "{{ COM_OCEAN_NETCDF }}/native/{{ RUN }}.ocean.t{{ current_cycle | strftime('%H') }}z.native.f{{ '%03d' % forecast_hour }}.nc"]
       {% for grid in product_grids %}
-      - ["{{ DATA }}/ocean.{{ grid }}.nc", "{{ COM_OCEAN_NETCDF }}/{{ RUN }}.ocean.t{{ current_cycle | strftime('%H') }}z.{{ grid }}.f{{ '%03d' % forecast_hour }}.nc"]
+      - ["{{ DATA }}/ocean.{{ grid }}.nc", "{{ COM_OCEAN_NETCDF }}/{{ grid }}/{{ RUN }}.ocean.t{{ current_cycle | strftime('%H') }}z.{{ grid }}.f{{ '%03d' % forecast_hour }}.nc"]
       {% endfor %}
 
 ice:
@@ -62,12 +63,13 @@ ice:
       - ["{{ COM_ICE_HISTORY }}/{{ RUN }}.ice.t{{ current_cycle | strftime('%H') }}z.{{ interval }}hr_avg.f{{ '%03d' % forecast_hour }}.nc", "{{ DATA }}/ice.nc"]
   data_out:
     mkdir:
-      - "{{ COM_ICE_NETCDF }}"
+      - "{{ COM_ICE_NETCDF }}/native"
       {% for grid in product_grids %}
+      - "{{ COM_ICE_NETCDF }}/{{ grid }}"
       - "{{ COM_ICE_GRIB }}/{{ grid }}"
       {% endfor %}
     copy:
-      - ["{{ DATA }}/ice_subset.nc", "{{ COM_ICE_NETCDF }}/{{ RUN }}.ice.t{{ current_cycle | strftime('%H') }}z.native.f{{ '%03d' % forecast_hour }}.nc"]
+      - ["{{ DATA }}/ice_subset.nc", "{{ COM_ICE_NETCDF }}/native/{{ RUN }}.ice.t{{ current_cycle | strftime('%H') }}z.native.f{{ '%03d' % forecast_hour }}.nc"]
       {% for grid in product_grids %}
-      - ["{{ DATA }}/ice.{{ grid }}.nc", "{{ COM_ICE_NETCDF }}/{{ RUN }}.ice.t{{ current_cycle | strftime('%H') }}z.{{ grid }}.f{{ '%03d' % forecast_hour }}.nc"]
+      - ["{{ DATA }}/ice.{{ grid }}.nc", "{{ COM_ICE_NETCDF }}/{{ grid }}/{{ RUN }}.ice.t{{ current_cycle | strftime('%H') }}z.{{ grid }}.f{{ '%03d' % forecast_hour }}.nc"]
       {% endfor %}