Merge with May 10 version

commit 6a9c137 (HEAD -> develop, origin/develop, origin/HEAD) Author: TerrenceMcGuinness-NOAA <[email protected]> Date: Fri May 10 14:17:13 2024 -0400 Do not use BUILT_semphore to force rebuilds when re-run (NOAA-EMC#2593) Remove the placement of the `BUILT_semaphore` file after the build in the Jenkins Pipeline and force it to rebuild any changes after a PR is re-ran.
zhanglikate · May 13, 2024 · c196670 · c196670
1 parent df0e471
commit c196670
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diff --git a/scripts/exgfs_atmos_grib2_special_npoess.sh b/scripts/exgfs_atmos_grib2_special_npoess.sh
@@ -153,7 +153,8 @@ for (( fhr=SHOUR; fhr <= FHOUR; fhr = fhr + FHINC )); do
    # existence of the restart files
    ###############################
    export pgm="postcheck"
-   grib_file="${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.goesmasterf${fhr3}.grb2"
+   # grib_file="${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.goesmasterf${fhr3}.grb2"
+   grib_file="${COM_ATMOS_MASTER}/${RUN}.t${cyc}z.special.grb2f${fhr3}"
    if ! wait_for_file "${grib_file}" "${SLEEP_INT}" "${SLEEP_LOOP_MAX}"; then
       echo "FATAL ERROR: GOES master grib file ${grib_file} not available after max sleep time"
       export err=9

diff --git a/scripts/exglobal_archive.sh b/scripts/exglobal_archive.sh
@@ -237,7 +237,10 @@ if [[ ${HPSSARCH} = "YES" || ${LOCALARCH} = "YES" ]]; then
 
         #gdasocean
         if [ "${DO_OCN}" = "YES" ]; then
-            targrp_list="${targrp_list} gdasocean gdasocean_analysis"
+            targrp_list="${targrp_list} gdasocean"	  
+            if [[ "${DO_JEDIOCNVAR}" == "YES" ]]; then
+                targrp_list="${targrp_list} gdasocean_analysis"
+            fi 
         fi
 
         #gdasice

diff --git a/scripts/exglobal_prep_emissions.py b/scripts/exglobal_prep_emissions.py
@@ -0,0 +1,25 @@
+#!/usr/bin/env python3
+# exglobal_prep_emissions.py
+# This script creates a emissions object
+# which perform the pre-processing for aerosol emissions
+import os
+
+from wxflow import Logger, cast_strdict_as_dtypedict
+from pygfs import AerosolEmissions
+
+
+# Initialize root logger
+logger = Logger(level=os.environ.get("LOGGING_LEVEL", "DEBUG"), colored_log=True)
+
+
+if __name__ == '__main__':
+
+    # Take configuration from environment and cast it as python dictionary
+    config = cast_strdict_as_dtypedict(os.environ)
+
+    # Instantiate the emissions pre-processing task
+    emissions = AerosolEmissions(config)
+    emissions.initialize()
+    emissions.configure()
+    emissions.execute(emissions.task_config.DATA, emissions.task_config.APRUN)
+    emissions.finalize()
diff --git a/ush/forecast_det.sh b/ush/forecast_det.sh
@@ -6,15 +6,9 @@ UFS_det(){
   echo "SUB ${FUNCNAME[0]}: Run type determination for UFS"
 
   # Determine if the current cycle is a warm start (based on the availability of restarts)
-  if [[ "${DOIAU:-}" == "YES" ]]; then
-    if [[ -f "${COM_ATMOS_RESTART_PREV}/${current_cycle_begin:0:8}.${current_cycle_begin:8:2}0000.coupler.res" ]]; then
-      warm_start=".true."
-    fi
-  else
-    if [[ -f "${COM_ATMOS_RESTART_PREV}/${current_cycle:0:8}.${current_cycle:8:2}0000.coupler.res" ]]; then
-      warm_start=".true."
-    fi
-  fi
+  if [[ -f "${COM_ATMOS_RESTART_PREV}/${model_start_date_current_cycle:0:8}.${model_start_date_current_cycle:8:2}0000.coupler.res" ]]; then
+    warm_start=".true."
+  fi 
 
   # If restarts were not available, this is likely a cold start
   if [[ "${warm_start}" == ".false." ]]; then
@@ -30,6 +24,7 @@ UFS_det(){
     # Since warm start is false, we cannot do IAU
     DOIAU="NO"
     IAU_OFFSET=0
+    model_start_date_current_cycle=${current_cycle}
 
     # It is still possible that a restart is available from a previous forecast attempt
     # So we have to continue checking for restarts

diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
@@ -48,11 +48,7 @@ FV3_postdet() {
       restart_date="${RERUN_DATE}"
       restart_dir="${DATArestart}/FV3_RESTART"
     else  # "${RERUN}" == "NO"
-      if [[ "${DOIAU}" == "YES" ]]; then
-        restart_date="${current_cycle_begin}"
-      else
-        restart_date="${current_cycle}"
-      fi
+      restart_date="${model_start_date_current_cycle}"
       restart_dir="${COM_ATMOS_RESTART_PREV}"
     fi
 
@@ -92,11 +88,10 @@ FV3_postdet() {
       # Need a coupler.res that is consistent with the model start time
       if [[ "${DOIAU}" == "YES" ]]; then
         local model_start_time="${previous_cycle}"
-        local model_current_time="${current_cycle_begin}"
       else
         local model_start_time="${current_cycle}"
-        local model_current_time="${current_cycle}"
       fi
+      local model_current_time="${model_start_date_current_cycle}"
       rm -f "${DATA}/INPUT/coupler.res"
       cat >> "${DATA}/INPUT/coupler.res" << EOF
       3        (Calendar: no_calendar=0, thirty_day_months=1, julian=2, gregorian=3, noleap=4)
@@ -258,13 +253,15 @@ FV3_out() {
   # Copy the final restart files at the end of the forecast segment
   # The final restart written at the end of the forecast does not include the valid date
   # TODO: verify the above statement since RM found that it did!
-  echo "Copying FV3 restarts for 'RUN=${RUN}' at the end of the forecast segment: ${forecast_end_cycle}"
-  for fv3_restart_file in "${fv3_restart_files[@]}"; do
-    restart_file="${forecast_end_cycle:0:8}.${forecast_end_cycle:8:2}0000.${fv3_restart_file}"
-    ${NCP} "${DATArestart}/FV3_RESTART/${restart_file}" \
-           "${COM_ATMOS_RESTART}/${restart_file}"
-  done
-
+  # TODO: For other components, this is only for gfs/gefs - check to see if this should also have this 
+  if [[ "${COPY_FINAL_RESTARTS}" == "YES" ]]; then 
+    echo "Copying FV3 restarts for 'RUN=${RUN}' at the end of the forecast segment: ${forecast_end_cycle}"
+    for fv3_restart_file in "${fv3_restart_files[@]}"; do
+      restart_file="${forecast_end_cycle:0:8}.${forecast_end_cycle:8:2}0000.${fv3_restart_file}"
+      ${NCP} "${DATArestart}/FV3_RESTART/${restart_file}" \
+             "${COM_ATMOS_RESTART}/${restart_file}"
+    done
+  fi 
   echo "SUB ${FUNCNAME[0]}: Output data for FV3 copied"
 }
 
@@ -281,11 +278,7 @@ WW3_postdet() {
       restart_date="${RERUN_DATE}"
       restart_dir="${DATArestart}/WW3_RESTART"
     else
-      if [[ "${DOIAU}" == "YES" ]]; then
-        restart_date="${current_cycle_begin}"
-      else
-        restart_date="${current_cycle}"
-      fi
+      restart_date="${model_start_date_current_cycle}"
       restart_dir="${COM_WAVE_RESTART_PREV}"
     fi
     echo "Copying WW3 restarts for 'RUN=${RUN}' at '${restart_date}' from '${restart_dir}'"
@@ -384,11 +377,7 @@ MOM6_postdet() {
     restart_date="${RERUN_DATE}"
   else  # "${RERUN}" == "NO"
     restart_dir="${COM_OCEAN_RESTART_PREV}"
-    if [[ "${DOIAU}" == "YES" ]]; then
-      restart_date="${current_cycle_begin}"
-    else
-      restart_date="${current_cycle}"
-    fi
+    restart_date="${model_start_date_current_cycle}"
   fi
 
   # Copy MOM6 ICs
@@ -489,44 +478,41 @@ MOM6_out() {
   # Coarser than 1/2 degree has a single MOM restart
   local mom6_restart_files mom6_restart_file restart_file
   mom6_restart_files=(MOM.res.nc)
-  # 1/4 degree resolution has 4 additional restarts
+  # 1/4 degree resolution has 3 additional restarts
   case "${OCNRES}" in
     "025")
       local nn
-      for (( nn = 1; nn <= 4; nn++ )); do
+      for (( nn = 1; nn <= 3; nn++ )); do
         mom6_restart_files+=("MOM.res_${nn}.nc")
       done
       ;;
     *) ;;
   esac
 
   # Copy MOM6 restarts at the end of the forecast segment to COM for RUN=gfs|gefs
-  local restart_file
-  if [[ "${RUN}" == "gfs" || "${RUN}" == "gefs" ]]; then
-    echo "Copying MOM6 restarts for 'RUN=${RUN}' at ${forecast_end_cycle}"
-    for mom6_restart_file in "${mom6_restart_files[@]}"; do
-      restart_file="${forecast_end_cycle:0:8}.${forecast_end_cycle:8:2}0000.${mom6_restart_file}"
-      ${NCP} "${DATArestart}/MOM6_RESTART/${restart_file}" \
-             "${COM_OCEAN_RESTART}/${restart_file}"
-    done
+  if [[ "${COPY_FINAL_RESTARTS}" == "YES" ]]; then
+    local restart_file
+    if [[ "${RUN}" == "gfs" || "${RUN}" == "gefs" ]]; then
+      echo "Copying MOM6 restarts for 'RUN=${RUN}' at ${forecast_end_cycle}"
+      for mom6_restart_file in "${mom6_restart_files[@]}"; do
+        restart_file="${forecast_end_cycle:0:8}.${forecast_end_cycle:8:2}0000.${mom6_restart_file}"
+        ${NCP} "${DATArestart}/MOM6_RESTART/${restart_file}" \
+               "${COM_OCEAN_RESTART}/${restart_file}"
+      done
+    fi 
   fi
 
-  # Copy restarts at the beginning/middle of the next assimilation cycle to COM for RUN=gdas|enkfgdas|enkfgfs
+  # Copy restarts for the next cycle for RUN=gdas|enkfgdas|enkfgfs
   if [[ "${RUN}" =~ "gdas" || "${RUN}" == "enkfgfs" ]]; then
     local restart_date
-    if [[ "${DOIAU}" == "YES" ]]; then  # Copy restarts at the beginning of the next cycle from DATA to COM
-      restart_date="${next_cycle_begin}"
-    else  # Copy restarts at the middle of the next cycle from DATA to COM
-      restart_date="${next_cycle}"
-    fi
+    restart_date="${model_start_date_next_cycle}"
     echo "Copying MOM6 restarts for 'RUN=${RUN}' at ${restart_date}"
     for mom6_restart_file in "${mom6_restart_files[@]}"; do
       restart_file="${restart_date:0:8}.${restart_date:8:2}0000.${mom6_restart_file}"
       ${NCP} "${DATArestart}/MOM6_RESTART/${restart_file}" \
              "${COM_OCEAN_RESTART}/${restart_file}"
     done
   fi
-
 }
 
 CICE_postdet() {
@@ -539,11 +525,7 @@ CICE_postdet() {
     seconds=$(to_seconds "${restart_date:8:2}0000")  # convert HHMMSS to seconds
     cice_restart_file="${DATArestart}/CICE_RESTART/cice_model.res.${restart_date:0:4}-${restart_date:4:2}-${restart_date:6:2}-${seconds}.nc"
   else  # "${RERUN}" == "NO"
-    if [[ "${DOIAU}" == "YES" ]]; then
-      restart_date="${current_cycle_begin}"
-    else
-      restart_date="${current_cycle}"
-    fi
+    restart_date="${model_start_date_current_cycle}"
     cice_restart_file="${COM_ICE_RESTART_PREV}/${restart_date:0:8}.${restart_date:8:2}0000.cice_model.res.nc"
   fi
 
@@ -554,8 +536,8 @@ CICE_postdet() {
   # Link iceh_ic file to COM.  This is the initial condition file from CICE (f000)
   # TODO: Is this file needed in COM? Is this going to be used for generating any products?
   local vdate seconds vdatestr fhr fhr3 interval last_fhr
-  seconds=$(to_seconds "${current_cycle:8:2}0000")  # convert HHMMSS to seconds
-  vdatestr="${current_cycle:0:4}-${current_cycle:4:2}-${current_cycle:6:2}-${seconds}"
+  seconds=$(to_seconds "${model_start_date_current_cycle:8:2}0000")  # convert HHMMSS to seconds
+  vdatestr="${model_start_date_current_cycle:0:4}-${model_start_date_current_cycle:4:2}-${model_start_date_current_cycle:6:2}-${seconds}"
   ${NLN} "${COM_ICE_HISTORY}/${RUN}.ice.t${cyc}z.ic.nc" "${DATA}/CICE_OUTPUT/iceh_ic.${vdatestr}.nc"
 
   # Link CICE forecast output files from DATA/CICE_OUTPUT to COM
@@ -601,24 +583,22 @@ CICE_out() {
   ${NCP} "${DATA}/ice_in" "${COM_CONF}/ufs.ice_in"
 
   # Copy CICE restarts at the end of the forecast segment to COM for RUN=gfs|gefs
-  local seconds source_file target_file
-  if [[ "${RUN}" == "gfs" || "${RUN}" == "gefs" ]]; then
-    echo "Copying CICE restarts for 'RUN=${RUN}' at ${forecast_end_cycle}"
-    seconds=$(to_seconds "${forecast_end_cycle:8:2}0000")  # convert HHMMSS to seconds
-    source_file="cice_model.res.${forecast_end_cycle:0:4}-${forecast_end_cycle:4:2}-${forecast_end_cycle:6:2}-${seconds}.nc"
-    target_file="${forecast_end_cycle:0:8}.${forecast_end_cycle:8:2}0000.cice_model.res.nc"
-    ${NCP} "${DATArestart}/CICE_RESTART/${source_file}" \
-           "${COM_ICE_RESTART}/${target_file}"
+  if [[ "${COPY_FINAL_RESTARTS}" == "YES" ]]; then
+    local seconds source_file target_file
+    if [[ "${RUN}" == "gfs" || "${RUN}" == "gefs" ]]; then
+      echo "Copying CICE restarts for 'RUN=${RUN}' at ${forecast_end_cycle}"
+      seconds=$(to_seconds "${forecast_end_cycle:8:2}0000")  # convert HHMMSS to seconds
+      source_file="cice_model.res.${forecast_end_cycle:0:4}-${forecast_end_cycle:4:2}-${forecast_end_cycle:6:2}-${seconds}.nc"
+      target_file="${forecast_end_cycle:0:8}.${forecast_end_cycle:8:2}0000.cice_model.res.nc"
+      ${NCP} "${DATArestart}/CICE_RESTART/${source_file}" \
+             "${COM_ICE_RESTART}/${target_file}"
+    fi 
   fi
 
-  # Copy restarts at the beginning/middle of the next assimilation cycle to COM for RUN=gdas|enkfgdas|enkfgfs
+  # Copy restarts for next cycle for RUN=gdas|enkfgdas|enkfgfs
   if [[ "${RUN}" =~ "gdas" || "${RUN}" == "enkfgfs" ]]; then
     local restart_date
-    if [[ "${DOIAU}" == "YES" ]]; then  # Copy restarts at the beginning of the next cycle from DATA to COM
-      restart_date="${next_cycle_begin}"
-    else  # Copy restarts at the middle of the next cycle from DATA to COM
-      restart_date="${next_cycle}"
-    fi
+    restart_date="${model_start_date_next_cycle}"
     echo "Copying CICE restarts for 'RUN=${RUN}' at ${restart_date}"
     seconds=$(to_seconds "${restart_date:8:2}0000")  # convert HHMMSS to seconds
     source_file="cice_model.res.${restart_date:0:4}-${restart_date:4:2}-${restart_date:6:2}-${seconds}.nc"
@@ -713,11 +693,7 @@ CMEPS_postdet() {
       seconds=$(to_seconds "${restart_date:8:2}0000")  # convert HHMMSS to seconds
       cmeps_restart_file="${DATArestart}/CMEPS_RESTART/ufs.cpld.cpl.r.${restart_date:0:4}-${restart_date:4:2}-${restart_date:6:2}-${seconds}.nc"
     else  # "${RERUN}" == "NO"
-      if [[ "${DOIAU}" == "YES" ]]; then
-        restart_date="${current_cycle_begin}"
-      else
-        restart_date="${current_cycle}"
-      fi
+      restart_date="${model_start_date_current_cycle}"
       cmeps_restart_file="${COM_MED_RESTART_PREV}/${restart_date:0:8}.${restart_date:8:2}0000.ufs.cpld.cpl.r.nc"
     fi
 
@@ -747,26 +723,24 @@ CMEPS_out() {
   echo "SUB ${FUNCNAME[0]}: Copying output data for CMEPS mediator"
 
   # Copy mediator restarts at the end of the forecast segment to COM for RUN=gfs|gefs
-  echo "Copying mediator restarts for 'RUN=${RUN}' at ${forecast_end_cycle}"
-  local seconds source_file target_file
-  seconds=$(to_seconds "${forecast_end_cycle:8:2}"0000)
-  source_file="ufs.cpld.cpl.r.${forecast_end_cycle:0:4}-${forecast_end_cycle:4:2}-${forecast_end_cycle:6:2}-${seconds}.nc"
-  target_file="${forecast_end_cycle:0:8}.${forecast_end_cycle:8:2}0000.ufs.cpld.cpl.r.nc"
-  if [[ -f "${DATArestart}/CMEPS_RESTART/${source_file}" ]]; then
-    ${NCP} "${DATArestart}/CMEPS_RESTART/${source_file}" \
-           "${COM_MED_RESTART}/${target_file}"
-  else
-    echo "Mediator restart '${DATArestart}/CMEPS_RESTART/${source_file}' not found."
-  fi
+  if [[ "${COPY_FINAL_RESTARTS}" == "YES" ]]; then
+    echo "Copying mediator restarts for 'RUN=${RUN}' at ${forecast_end_cycle}"
+    local seconds source_file target_file
+    seconds=$(to_seconds "${forecast_end_cycle:8:2}"0000)
+    source_file="ufs.cpld.cpl.r.${forecast_end_cycle:0:4}-${forecast_end_cycle:4:2}-${forecast_end_cycle:6:2}-${seconds}.nc"
+    target_file="${forecast_end_cycle:0:8}.${forecast_end_cycle:8:2}0000.ufs.cpld.cpl.r.nc"
+    if [[ -f "${DATArestart}/CMEPS_RESTART/${source_file}" ]]; then
+      ${NCP} "${DATArestart}/CMEPS_RESTART/${source_file}" \
+             "${COM_MED_RESTART}/${target_file}"
+    else
+      echo "Mediator restart '${DATArestart}/CMEPS_RESTART/${source_file}' not found."
+    fi
+  fi 
 
-  # Copy restarts at the beginning/middle of the next assimilation cycle to COM for RUN=gdas|enkfgdas|enkfgfs
+  # Copy restarts for the next cycle to COM for RUN=gdas|enkfgdas|enkfgfs
   if [[ "${RUN}" =~ "gdas" || "${RUN}" == "enkfgfs" ]]; then
     local restart_date
-    if [[ "${DOIAU}" == "YES" ]]; then  # Copy restarts at the beginning of the next cycle from DATA to COM
-      restart_date="${next_cycle_begin}"
-    else  # Copy restarts at the middle of the next cycle from DATA to COM
-      restart_date="${next_cycle}"
-    fi
+    restart_date="${model_start_date_next_cycle}"
     echo "Copying mediator restarts for 'RUN=${RUN}' at ${restart_date}"
     seconds=$(to_seconds "${restart_date:8:2}"0000)
     source_file="ufs.cpld.cpl.r.${restart_date:0:4}-${restart_date:4:2}-${restart_date:6:2}-${seconds}.nc"

diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
@@ -54,7 +54,14 @@ common_predet(){
   current_cycle_begin=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} - ${half_window} hours" +%Y%m%d%H)
   current_cycle_end=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${half_window} hours" +%Y%m%d%H)
   next_cycle_begin=$(date --utc -d "${next_cycle:0:8} ${next_cycle:8:2} - ${half_window} hours" +%Y%m%d%H)
-  next_cycle_end=$(date --utc -d "${next_cycle:0:8} ${next_cycle:8:2} + ${half_window} hours" +%Y%m%d%H)
+  #Define model start date for current_cycle and next_cycle as the time the forecast will start
+  if [[ "${DOIAU:-}" == "YES" ]]; then
+    model_start_date_current_cycle="${current_cycle_begin}"
+    model_start_date_next_cycle="${next_cycle_begin}"
+  else
+    model_start_date_current_cycle=${current_cycle} 
+    model_start_date_next_cycle=${next_cycle}
+  fi 
   forecast_end_cycle=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${FHMAX} hours" +%Y%m%d%H)
 
   FHMIN=${FHMIN:-0}

diff --git a/ush/hpssarch_gen.sh b/ush/hpssarch_gen.sh
@@ -560,13 +560,14 @@ if [[ ${type} == "gdas" ]]; then
       echo "${COM_MED_RESTART/${ROTDIR}\//}/*"
     } >> "${DATA}/gdasocean_restart.txt"
 
-    {
-      echo "${COM_OCEAN_ANALYSIS/${ROTDIR}\//}/${head}*"
-      echo "${COM_OCEAN_ANALYSIS/${ROTDIR}\//}/gdas.t??z.ocngrid.nc"
-      echo "${COM_OCEAN_ANALYSIS/${ROTDIR}\//}/diags"
-      echo "${COM_OCEAN_ANALYSIS/${ROTDIR}\//}/yaml"
-    } >> "${DATA}/gdasocean_analysis.txt"
-
+    if [[ ${DO_JEDIOCNVAR} = "YES" ]]; then
+      {
+        echo "${COM_OCEAN_ANALYSIS/${ROTDIR}\//}/${head}*"
+        echo "${COM_OCEAN_ANALYSIS/${ROTDIR}\//}/gdas.t??z.ocngrid.nc"
+        echo "${COM_OCEAN_ANALYSIS/${ROTDIR}\//}/diags"
+        echo "${COM_OCEAN_ANALYSIS/${ROTDIR}\//}/yaml"
+      } >> "${DATA}/gdasocean_analysis.txt"
+    fi
   fi
 
   if [[ ${DO_ICE} = "YES" ]]; then