Add fixes to products for when REPLAY IC's are used (#2755)

This PR fixes a couple issues that arise when replay initial conditions are used. These issues only occur when `REPLAY_ICS` is set to `YES` and `OFFSET_START_HOUR` is greater than `0`. The following items are addressed in this PR. 1. Fix issue that causes ocean_prod tasks not to be triggered (issue [#2725](#2725)). A new diag_table was added (called `diag_table_replay`) that is used only when `REPLAY_ICS` is set to `YES`. This diag_table accounts for the offset that occurs when using replay IC's. 2. Fix issue that causes atmos_prod tasks not to be triggered for the first lead time (e.g. f003) (issue [#2754](#2754)). When `OFFSET_START_HOUR` is greater than `0`, the first `fhr` is `${OFFSET_START_HOUR}+(${DELTIM}/3600)`, which is defined in `forecast_predet.sh` and will allow data for the first lead time to be generated. The filename with this lead time will still be labelled with `OFFSET_START_HOUR`. 3. Minor modifications were made to the extractvars task so that atmos data from replay cases can be processed. This PR was split from PR #2680. Refs #2725, #2754 --------- Co-authored-by: Walter Kolczynski - NOAA <[email protected]>
NOAA-EMC · Aug 13, 2024 · 5699167 · 5699167
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diff --git a/parm/config/gefs/config.extractvars b/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

diff --git a/parm/config/gefs/config.fcst b/parm/config/gefs/config.fcst
@@ -247,7 +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}

diff --git a/parm/config/gefs/config.resources b/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}"

diff --git a/parm/post/oceanice_products_gefs.yaml b/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 %}
diff --git a/parm/ufs/fv3/diag_table_replay b/parm/ufs/fv3/diag_table_replay
diff --git a/ush/atmos_extractvars.sh b/ush/atmos_extractvars.sh
@@ -31,7 +31,16 @@ for outtype in "f2d" "f3d"; do
   outdirpre="${subdata}/${outtype}"
   [[ -d "${outdirpre}" ]] || mkdir -p "${outdirpre}"
 
-  nh=${FHMIN}
+  if [[ "${REPLAY_ICS:-NO}" == "YES" ]]; then
+    if [[ "${outtype}" == "f2d" ]]; then
+      nh=${OFFSET_START_HOUR}
+    elif [[ "${outtype}" == "f3d" ]]; then
+      nh=${FHOUT_GFS}
+    fi
+  else
+    nh=${FHMIN}
+  fi
+
   while (( nh <= FHMAX_GFS )); do
     fnh=$(printf "%3.3d" "${nh}")
 
@@ -45,11 +54,15 @@ for outtype in "f2d" "f3d"; do
       outres="1p00"
     fi
 
-    if (( nh <= FHMAX_HF_GFS )); then
-      outfreq=${FHOUT_HF_GFS}
-    else
-      outfreq=${FHOUT_GFS}
-    fi                                      
+    if [[ "${outtype}" == "f2d" ]]; then
+      if (( nh < FHMAX_HF_GFS )); then
+        outfreq=${FHOUT_HF_GFS}
+      else
+        outfreq=${FHOUT_GFS}
+      fi
+    elif [[ "${outtype}" == "f3d" ]]; then
+     outfreq=${FHOUT_GFS}
+    fi
 
     com_var="COMIN_ATMOS_GRIB_${outres}"
     infile1="${!com_var}/${RUN}.t${cyc}z.pgrb2.${outres}.f${fnh}"

diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
@@ -206,11 +206,24 @@ EOF
     for fhr in ${FV3_OUTPUT_FH}; do
       FH3=$(printf %03i "${fhr}")
       FH2=$(printf %02i "${fhr}")
-      ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.atmf${FH3}.nc" "atmf${FH3}.nc"
-      ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.sfcf${FH3}.nc" "sfcf${FH3}.nc"
-      ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.atm.logf${FH3}.txt" "log.atm.f${FH3}"
-      ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.cubed_sphere_grid_atmf${FH3}.nc" "cubed_sphere_grid_atmf${FH3}.nc"
-      ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.cubed_sphere_grid_sfcf${FH3}.nc" "cubed_sphere_grid_sfcf${FH3}.nc"
+      # When replaying, the time format outputted by model in filename is HH-MM-SS
+      # because first fhr is a decimal number
+      if [[ ${REPLAY_ICS:-NO} == "YES" ]] && (( fhr >= OFFSET_START_HOUR )); then
+        local hhmmss_substring=${FV3_OUTPUT_FH_hhmmss/" ${FH3}-"*/} # Extract substring that contains all lead times up to the one space before target lead HHH-MM-SS
+        local hhmmss_substring_len=$(( ${#hhmmss_substring} + 1 )) # Get the size of the substring and add 1 to account for space
+        local f_hhmmss=${FV3_OUTPUT_FH_hhmmss:${hhmmss_substring_len}:9} # extract HHH-MM-SS for target lead time
+        ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.atmf${FH3}.nc" "atmf${f_hhmmss}.nc"
+        ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.sfcf${FH3}.nc" "sfcf${f_hhmmss}.nc"
+        ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.atm.logf${FH3}.txt" "log.atm.f${f_hhmmss}"
+        ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.cubed_sphere_grid_atmf${FH3}.nc" "cubed_sphere_grid_atmf${f_hhmmss}.nc"
+        ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.cubed_sphere_grid_sfcf${FH3}.nc" "cubed_sphere_grid_sfcf${f_hhmmss}.nc"
+      else
+        ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.atmf${FH3}.nc" "atmf${FH3}.nc"
+        ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.sfcf${FH3}.nc" "sfcf${FH3}.nc"
+        ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.atm.logf${FH3}.txt" "log.atm.f${FH3}"
+        ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.cubed_sphere_grid_atmf${FH3}.nc" "cubed_sphere_grid_atmf${FH3}.nc"
+        ${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.cubed_sphere_grid_sfcf${FH3}.nc" "cubed_sphere_grid_sfcf${FH3}.nc"
+      fi
       if [[ "${WRITE_DOPOST}" == ".true." ]]; then
         ${NLN} "${COMOUT_ATMOS_MASTER}/${RUN}.t${cyc}z.master.grb2f${FH3}" "GFSPRS.GrbF${FH2}"
         ${NLN} "${COMOUT_ATMOS_MASTER}/${RUN}.t${cyc}z.sfluxgrbf${FH3}.grib2" "GFSFLX.GrbF${FH2}"
@@ -454,10 +467,19 @@ MOM6_postdet() {
       (( midpoint = last_fhr + interval/2 ))
 
       vdate=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${fhr} hours" +%Y%m%d%H)
-      vdate_mid=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${midpoint} hours" +%Y%m%d%H)
+      #If OFFSET_START_HOUR is greater than 0, OFFSET_START_HOUR should be added to the midpoint for first lead time
+      if (( OFFSET_START_HOUR > 0 )) &&  (( fhr == FHOUT_OCN ));then
+        vdate_mid=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + $(( midpoint + OFFSET_START_HOUR )) hours" +%Y%m%d%H)
+      else
+        vdate_mid=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${midpoint} hours" +%Y%m%d%H)
+      fi
 
       # Native model output uses window midpoint in the filename, but we are mapping that to the end of the period for COM
-      source_file="ocn_${vdate_mid:0:4}_${vdate_mid:4:2}_${vdate_mid:6:2}_${vdate_mid:8:2}.nc"
+      if (( OFFSET_START_HOUR > 0 )) &&  (( fhr == FHOUT_OCN ));then
+        source_file="ocn_lead1_${vdate_mid:0:4}_${vdate_mid:4:2}_${vdate_mid:6:2}_${vdate_mid:8:2}.nc"
+      else
+        source_file="ocn_${vdate_mid:0:4}_${vdate_mid:4:2}_${vdate_mid:6:2}_${vdate_mid:8:2}.nc"
+      fi
       dest_file="${RUN}.ocean.t${cyc}z.${interval}hr_avg.f${fhr3}.nc"
       ${NLN} "${COMOUT_OCEAN_HISTORY}/${dest_file}" "${DATA}/MOM6_OUTPUT/${source_file}"
 

diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
@@ -146,6 +146,7 @@ FV3_predet(){
   fi
 
   # Convert output settings into an explicit list for FV3
+  # Create an FV3 fhr list to be used in the filenames
   FV3_OUTPUT_FH=""
   local fhr=${FHMIN}
   if (( FHOUT_HF > 0 && FHMAX_HF > 0 )); then
@@ -154,6 +155,35 @@ FV3_predet(){
   fi
   FV3_OUTPUT_FH="${FV3_OUTPUT_FH} $(seq -s ' ' "${fhr}" "${FHOUT}" "${FHMAX}")"
 
+  # Create an FV3 fhr list to be used in the namelist
+  # The FV3 fhr list for the namelist and the FV3 fhr list for the filenames
+  # are only different when REPLAY_ICS is set to YES
+  if [[ "${REPLAY_ICS:-NO}" == "YES"  ]]; then
+    local FV3_OUTPUT_FH_s
+    FV3_OUTPUT_FH_NML="$(echo "scale=5; ${OFFSET_START_HOUR}+(${DELTIM}/3600)" | bc -l)"
+    FV3_OUTPUT_FH_s=$(( OFFSET_START_HOUR * 3600 + DELTIM ))
+    local fhr=${FHOUT}
+    if (( FHOUT_HF > 0 && FHMAX_HF > 0 )); then
+      FV3_OUTPUT_FH_NML="${FV3_OUTPUT_FH_NML} $(seq -s ' ' "$(( OFFSET_START_HOUR + FHOUT_HF ))" "${FHOUT_HF}" "${FHMAX_HF}")"
+      FV3_OUTPUT_FH_s="${FV3_OUTPUT_FH_s} $(seq -s ' ' "$(( OFFSET_START_HOUR * 3600 + FHOUT_HF * 3600 ))" "$(( FHOUT_HF * 3600 ))" "$(( FHMAX_HF * 3600 ))")"
+      fhr=${FHMAX_HF}
+    fi
+    FV3_OUTPUT_FH_NML="${FV3_OUTPUT_FH_NML} $(seq -s ' ' "${fhr}" "${FHOUT}" "${FHMAX}")"
+    FV3_OUTPUT_FH_s="${FV3_OUTPUT_FH_s} $(seq -s ' ' "$(( fhr * 3600 ))" "$(( FHOUT * 3600 ))" "$(( FHMAX * 3600 ))")"
+    local hh mm ss s_total
+    FV3_OUTPUT_FH_hhmmss=""
+    for s_total in ${FV3_OUTPUT_FH_s}; do
+      # Convert seconds to HHH:MM:SS
+      (( ss = s_total, mm = ss / 60, ss %= 60, hh = mm / 60, mm %= 60 )) || true
+      FV3_OUTPUT_FH_hhmmss="${FV3_OUTPUT_FH_hhmmss} $(printf "%03d-%02d-%02d" "${hh}" "${mm}" "${ss}")"
+    done
+    # Create a string from an array
+  else # If non-replay ICs are being used
+    # The FV3 fhr list for the namelist and the FV3 fhr list for the filenames
+    # are identical when REPLAY_ICS is set to NO
+    FV3_OUTPUT_FH_NML="${FV3_OUTPUT_FH}"
+  fi
+
   # Other options
   PREFIX_ATMINC=${PREFIX_ATMINC:-""} # allow ensemble to use recentered increment
 

diff --git a/ush/ocnice_extractvars.sh b/ush/ocnice_extractvars.sh
@@ -25,11 +25,11 @@ for (( nh = FHMIN_GFS; nh <= FHMAX_GFS; nh = nh + fhout_ocnice )); do
   fnh=$(printf "%3.3d" "${nh}")
 
   if [[ ${component_name} == "ocn" ]]; then
-    infile=${COMIN_OCEAN_NETCDF}/${RUN}.ocean.t${cyc}z.${datares}.f${fnh}.nc
+    infile=${COMIN_OCEAN_NETCDF}/${datares}/${RUN}.ocean.t${cyc}z.${datares}.f${fnh}.nc
     # For ocean products, add an argument to extract a subset of levels
     otherargs=(-d "${depthvar_name},""${zmin},""${zmax}")
   elif [[ ${component_name} == "ice" ]]; then
-    infile=${COMIN_ICE_NETCDF}/${RUN}.ice.t${cyc}z.${datares}.f${fnh}.nc
+    infile=${COMIN_ICE_NETCDF}/${datares}/${RUN}.ice.t${cyc}z.${datares}.f${fnh}.nc
     otherargs=()
   fi
   outfile=${subdata}/${RUN}.${component_name}.t${cyc}z.${datares}.f${fnh}.nc

diff --git a/ush/parsing_model_configure_FV3.sh b/ush/parsing_model_configure_FV3.sh
@@ -48,7 +48,7 @@ local JCHUNK3D=$((2*restile))
 local KCHUNK3D=1
 local IMO=${LONB_IMO}
 local JMO=${LATB_JMO}
-local OUTPUT_FH=${FV3_OUTPUT_FH}
+local OUTPUT_FH=${FV3_OUTPUT_FH_NML}
 local IAU_OFFSET=${IAU_OFFSET:-0}
 
 # Ensure the template exists

diff --git a/ush/parsing_namelists_FV3.sh b/ush/parsing_namelists_FV3.sh
@@ -42,6 +42,18 @@ local SDAY=${current_cycle:6:2}
 local CHOUR=${current_cycle:8:2}
 local MOM6_OUTPUT_DIR="./MOM6_OUTPUT"
 
+if [[ "${REPLAY_ICS:-NO}" == "YES" ]]; then
+  local current_cycle_p1 
+  current_cycle_p1=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${FHOUT_OCN} hours" +%Y%m%d%H)
+  local current_cycle_offset
+  current_cycle_offset=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${OFFSET_START_HOUR} hours" +%Y%m%d%H)
+  local SYEAR1=${current_cycle_p1:0:4}
+  local SMONTH1=${current_cycle_p1:4:2}
+  local SDAY1=${current_cycle_p1:6:2}
+  local CHOUR1=${current_cycle_p1:8:2}
+  local CHOUR_offset=${current_cycle_offset:8:2}
+fi
+
 atparse < "${template}" >> "diag_table"