turn off checksum for restart of ufs_model

jobs/JLANDDA_ANALYSIS

@@ -75,8 +75,8 @@ export COMOUThofx="${COMOUThofx:-${COMOUT}/hofx}"
 mkdir -p ${COMOUThofx}
 
 # Create a teomporary share directory
-export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}}"
-mkdir -p ${DATA_SHARE}
+export DATA_RESTART="${DATA_RESTART:-${DATAROOT}/DATA_SHARE/RESTART}"
+mkdir -p ${DATA_RESTART}
 export DATA_HOFX="${DATA_HOFX:-${DATAROOT}/DATA_SHARE/hofx}"
 mkdir -p ${DATA_HOFX}
 

jobs/JLANDDA_FCST_IC

@@ -65,23 +65,17 @@ setpdy.sh
 if [ "${MACHINE}" = "WCOSS2" ]; then
   export COMIN="${COMIN:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY})}"
   export COMOUT="${COMOUT:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDY})}"
-  export COMINm1="${COMINm1:-$(compath.py -o ${NET}/${model_ver}/${RUN}.${PDYm1})}"
   export COMINgdas="${COMINgdas:-$(compath.py ${envir}/gdas/${gdas_ver})}"
   export COMINgfs="${COMINgfs:-$(compath.py ${envir}/gfs/${gfs_ver})}"
 else
   export COMIN="${COMIN:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}}"
   export COMOUT="${COMOUT:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDY}}"
-  export COMINm1="${COMINm1:-${COMROOT}/${NET}/${model_ver}/${RUN}.${PDYm1}}"
   export COMINgdas="${COMINgdas:-${FIXlandda}/DATA_gdas}"
   export COMINgfs="${COMINgfs:-${FIXlandda}/DATA_gfs}"
 fi
 
 mkdir -p ${COMOUT}
 
-# Create a teomporary share directory
-export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}}"
-mkdir -p ${DATA_SHARE}
-
 #
 #-----------------------------------------------------------------------
 #

jobs/JLANDDA_FORECAST

@@ -81,8 +81,6 @@ export COMOUTplot="${COMOUTplot:-${COMOUT}/plot}"
 mkdir -p ${COMOUTplot}
 
 # Create a teomporary share directory
-export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}}"
-mkdir -p ${DATA_SHARE}
 export DATA_RESTART="${DATA_RESTART:-${DATAROOT}/DATA_SHARE/RESTART}"
 mkdir -p ${DATA_RESTART}
 

jobs/JLANDDA_PLOT_STATS

@@ -75,8 +75,6 @@ export COMOUTplot="${COMOUTplot:-${COMOUT}/plot}"
 mkdir -p ${COMOUTplot}
 
 # Create a teomporary share directory
-export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}}"
-mkdir -p ${DATA_SHARE}
 export DATA_HOFX="${DATA_HOFX:-${DATAROOT}/DATA_SHARE/hofx}"
 mkdir -p ${DATA_HOFX}
 

jobs/JLANDDA_POST_ANAL

@@ -73,8 +73,8 @@ fi
 mkdir -p ${COMOUT}
 
 # Create a teomporary share directory
-export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}}"
-mkdir -p ${DATA_SHARE}
+export DATA_RESTART="${DATA_RESTART:-${DATAROOT}/DATA_SHARE/RESTART}"
+mkdir -p ${DATA_RESTART}
 
 #
 #-----------------------------------------------------------------------

jobs/JLANDDA_PREP_OBS

@@ -76,10 +76,6 @@ mkdir -p ${COMOUTobs}
 export COMOUTplot="${COMOUTplot:-${COMOUT}/plot}"
 mkdir -p ${COMOUTplot}
 
-# Create a teomporary share directory
-export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}}"
-mkdir -p ${DATA_SHARE}
-
 #
 #-----------------------------------------------------------------------
 #

jobs/JLANDDA_PRE_ANAL

@@ -73,8 +73,6 @@ fi
 mkdir -p ${COMOUT}
 
 # Create a teomporary share directory
-export DATA_SHARE="${DATA_SHARE:-${DATAROOT}/DATA_SHARE/${PDY}}"
-mkdir -p ${DATA_SHARE}
 export DATA_RESTART="${DATA_RESTART:-${DATAROOT}/DATA_SHARE/RESTART}"
 mkdir -p ${DATA_RESTART}
 

parm/templates/template.ATML.input.nml.FV3_GFS_v17_p8

@@ -3,6 +3,7 @@
   chksum_debug = .false.
   dycore_only = .false.
   ccpp_suite = '{{ ccpp_suite }}'
+  ignore_rst_cksum = .true.
 /
 
 &diag_manager_nml

parm/templates/template.land_analysis.yaml

@@ -81,6 +81,7 @@ workflow:
     DATADEP_FILE1: "<cyclestr>&DATAROOT;/DATA_SHARE/RESTART/ufs_land_restart.@Y-@m-@[email protected]</cyclestr>"
     DATADEP_FILE2: "<cyclestr>&WARMSTART_DIR;/ufs_land_restart.@Y-@m-@[email protected]</cyclestr>"
     DATADEP_COLDSTART: "<cyclestr>&EXP_BASEDIR;/exp_case/&EXP_CASE_NAME;/task_skip_coldstart_@Y@m@[email protected]</cyclestr>"
+    DATADEP_SFCDATA: "<cyclestr>&DATAROOT;/DATA_SHARE/RESTART/@Y@m@[email protected]_data.tile6.nc</cyclestr>" 
   log: "&LOGDIR;/workflow.log"
   tasks:
     task_prep_obs:
@@ -144,6 +145,7 @@ workflow:
       join: "&LOGDIR;/fcst_ic&LOGFN_SUFFIX;"
       memory: 128G
 {%- endif %}
+{%- if app == "LND" %}
     task_pre_anal:
       attrs:
 {%- if coldstart == "YES" %}
@@ -184,6 +186,7 @@ workflow:
             attrs:
               age: 5
             value: "&DATADEP_FILE2;"
+{%- endif %}
 {%- endif %}
     task_analysis:
       attrs:
@@ -226,9 +229,16 @@ workflow:
           taskdep_prep_obs:
             attrs:
               task: prep_obs
+{%- if app == "LND" %}
           taskdep_pre_anal:
             attrs:
               task: pre_anal
+{%- else %}
+          datadep_sfcdata:
+            attrs:
+              age: 5
+            value: "&DATADEP_SFCDATA;"
+{%- endif %}
     task_post_anal:
       attrs:
 {%- if coldstart == "YES" %}

scripts/exlandda_analysis.sh

@@ -40,7 +40,7 @@ B=30 # back ground error std for LETKFOI
 # Import input files
 for itile in {1..6}
 do
-  cp ${DATA_SHARE}/${FILEDATE}.sfc_data.tile${itile}.nc .
+  cp ${DATA_RESTART}/${FILEDATE}.sfc_data.tile${itile}.nc .
 done
 ln -nsf ${COMIN}/obs/GHCN_${YYYY}${MM}${DD}${HH}.nc .
 
@@ -70,7 +70,7 @@ if [ $GFSv17 == "YES" ]; then
 else
   SNOWDEPTHVAR="snwdph"
   # replace field overwrite file
-  cp ${PARMlandda}/jedi/gfs-land.yaml ${DATA}/gfs-land.yaml
+  cp -p ${PARMlandda}/jedi/gfs-land.yaml ${DATA}/gfs-land.yaml
 fi
 # FOR LETKFOI, CREATE THE PSEUDO-ENSEMBLE
 for ens in pos neg
@@ -79,8 +79,8 @@ do
     rm -r $DATA/mem_${ens}
   fi
   mkdir -p $DATA/mem_${ens}
-  cp ${FILEDATE}.sfc_data.tile*.nc ${DATA}/mem_${ens}
-  cp ${DATA}/${FILEDATE}.coupler.res ${DATA}/mem_${ens}/${FILEDATE}.coupler.res
+  cp -p ${FILEDATE}.sfc_data.tile*.nc ${DATA}/mem_${ens}
+  cp -p ${DATA}/${FILEDATE}.coupler.res ${DATA}/mem_${ens}/${FILEDATE}.coupler.res
 done
 
 # using ioda mods to get a python version with netCDF4
@@ -207,8 +207,8 @@ if [[ $do_DA == "YES" ]]; then
 cat << EOF > apply_incr_nml
 &noahmp_snow
  date_str=${YYYY}${MM}${DD}
- hour_str=$HH
- res=$RES
+ hour_str=${HH}
+ res=${RES}
  frac_grid=$GFSv17
  orog_path="${FIXlandda}/FV3_fix_tiled/C${RES}"
  otype="C${RES}_oro_data"
@@ -237,21 +237,21 @@ do
   cp -p ${DATA}/${FILEDATE}.sfc_data.tile${itile}.nc ${COMOUT}
 done
 
-if [[ -d output/DA/hofx ]]; then
+if [ -d output/DA/hofx ]; then
   cp -p output/DA/hofx/* ${COMOUThofx}
   ln -nsf ${COMOUThofx}/* ${DATA_HOFX}
 fi
 
 ###########################################################
 # WE2E test
 ###########################################################
-if [[ "${WE2E_TEST}" == "YES" ]]; then
+if [ "${WE2E_TEST}" == "YES" ]; then
   path_fbase="${FIXlandda}/test_base/we2e_com/${RUN}.${PDY}"
   fn_sfc="${FILEDATE}.sfc_data.tile"
   fn_inc="${FILEDATE}.xainc.sfc_data.tile"
   fn_hofx="letkf_hofx_ghcn_${PDY}${cyc}.nc"
   we2e_log_fp="${LOGDIR}/${WE2E_LOG_FN}"
-  if [[ ! -e "${we2e_log_fp}" ]]; then
+  if [ ! -f "${we2e_log_fp}" ]; then
     touch ${we2e_log_fp}
   fi
   # surface data tiles

scripts/exlandda_forecast.sh

@@ -175,9 +175,9 @@ ${USHlandda}/fill_jinja_template.py -u "${settings}" -t "${fp_template}" -o "${f
 if [ "${APP}" = "LND" ]; then
   # CDEPS restart and pointer files for DATM (LND)
   rfile2="ufs.cpld.datm.r.${YYYY}-${MM}-${DD}-${HHsec_5d}.nc"
-  if [[ -e "${COMINm1}/${rfile2}" ]]; then
+  if [ -f "${COMINm1}/${rfile2}" ]; then
     ln -nsf "${COMINm1}/${rfile2}" .
-  elif [[ -e "${WARMSTART_DIR}/${rfile2}" ]]; then
+  elif [ -f "${WARMSTART_DIR}/${rfile2}" ]; then
     ln -nsf "${WARMSTART_DIR}/${rfile2}" .
   else
     ln -nsf ${FIXlandda}/restarts/${ATMOS_FORC}/${rfile2} .
@@ -266,31 +266,44 @@ if [ "${APP}" = "ATML" ]; then
   if [ "${COLDSTART}" = "NO" ] || [ "${PDY}${cyc}" != "${DATE_FIRST_CYCLE:0:10}" ]; then
     # Set path to directory where restart files exist
     if [ "${COLDSTART}" = "NO" ] && [ "${PDY}${cyc}" = "${DATE_FIRST_CYCLE:0:10}" ]; then
-      data_dir="${WARMSTART_DIR}"
+      data_dir="${WARMSTART_DIR}/RESTART"
     else
-      data_dir="${COMINm1}"
+      data_dir="${COMINm1}/RESTART"
     fi
 
-    rst_fns=( "ca_data" "fv_core.res" "fv_srf_wnd.res" "fv_tracer.res" "phy_data" "sfc_data" )
+    rst_fns=( "ca_data" "fv_core.res" "fv_srf_wnd.res" "fv_tracer.res" "phy_data" )
     for ifn in "${rst_fns[@]}" ; do
       for itile in {1..6};
       do
-        r_fp="${data_dir}/RESTART/${YYYY}${MM}${DD}.${HH}0000.${ifn}.tile${itile}.nc"
+        r_fp="${data_dir}/${YYYY}${MM}${DD}.${HH}0000.${ifn}.tile${itile}.nc"
         if [ -f "${r_fp}" ]; then
           ln -nsf "${r_fp}" "${ifn}.tile${itile}.nc"
         else
           err_exit "${r_fp} file does not exist."
         fi
       done
       if [ "${ifn}" = "fv_core.res" ]; then
-        r_fp="${data_dir}/RESTART/${YYYY}${MM}${DD}.${HH}0000.${ifn}.nc"
+        r_fp="${data_dir}/${YYYY}${MM}${DD}.${HH}0000.${ifn}.nc"
         if [ -f "${r_fp}" ]; then
           ln -nsf "${r_fp}" "${ifn}.nc"
         else
           err_exit "${r_fp} file does not exist."
         fi
       fi
     done
+    # link sfc_data from COMIN because they were upated by JEDI Analysis task
+    if [ "${PDY}${cyc}" != "${DATE_FIRST_CYCLE:0:10}" ]; then
+      data_dir="${COMIN}"
+    fi
+    for itile in {1..6};
+    do
+      r_fp="${data_dir}/${YYYY}${MM}${DD}.${HH}0000.sfc_data.tile${itile}.nc"
+      if [ -f "${r_fp}" ]; then
+        ln -nsf "${r_fp}" "sfc_data.tile${itile}.nc"
+      else
+        err_exit "${r_fp} file does not exist."
+      fi
+    done
 
     # update coupler.res file
     settings="\
@@ -395,18 +408,23 @@ elif [ "${APP}" = "ATML" ]; then
       cp -p "${DATA}/RESTART/${nYYYY}${nMM}${nDD}.${nHH}0000.${ifn}.tile${itile}.nc" ${COMOUT}/RESTART/.
     done
   done
+  # Set sfc_data to DATA_RESTART to trigger ANALYSIS task in next cycle
+  for itile in {1..6};
+  do
+    cp -p "${COMOUT}/RESTART/${nYYYY}${nMM}${nDD}.${nHH}0000.sfc_data.tile${itile}.nc" ${DATA_RESTART}/.
+  done
 fi
 
 
 ###########################################################
 # WE2E test
 ###########################################################
-if [[ "${WE2E_TEST}" == "YES" ]]; then
+if [ "${WE2E_TEST}" == "YES" ]; then
   path_fbase="${FIXlandda}/test_base/we2e_com/${RUN}.${PDY}/RESTART"
   fn_res="ufs_land_restart.${nYYYY}-${nMM}-${nDD}_${nHH}-00-00.tile"
   we2e_log_fp="${LOGDIR}/${WE2E_LOG_FN}"
 
-  if [[ ! -e "${we2e_log_fp}" ]]; then
+  if [ ! -f "${we2e_log_fp}" ]; then
     touch ${we2e_log_fp}
   fi
   # restart files

scripts/exlandda_post_anal.sh

@@ -38,16 +38,24 @@ esac
 FILEDATE=${YYYY}${MM}${DD}.${HH}0000
 for itile in {1..6}
 do
-  cp ${DATA_SHARE}/${FILEDATE}.sfc_data.tile${itile}.nc .
+  cp -p ${COMIN}/${FILEDATE}.sfc_data.tile${itile}.nc .
 done
 
 #  convert back to UFS tile 
 echo '************************************************'
 echo 'calling tile2tile' 
 
+# copy restarts into work directory
 for itile in {1..6}
 do
-  cp ${DATA_SHARE}/ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc .
+  rst_fn="ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc"
+  if [ -f ${DATA_RESTART}/${rst_fn} ]; then
+    cp ${DATA_RESTART}/${rst_fn} .
+  elif [ -f ${WARMSTART_DIR}/${rst_fn} ]; then
+    cp ${WARMSTART_DIR}/${rst_fn} .
+  else
+    err_exit "Initial restart files do not exist"
+  fi
 done
 
 # update tile2tile namelist
@@ -81,11 +89,11 @@ do
 done
 
 # WE2E test
-if [[ "${WE2E_TEST}" == "YES" ]]; then
+if [ "${WE2E_TEST}" == "YES" ]; then
   path_fbase="${FIXlandda}/test_base/we2e_com/${RUN}.${PDY}"
   fn_res="ufs_land_restart.anal.${YYYY}-${MM}-${DD}_${HH}-00-00.tile"
   we2e_log_fp="${LOGDIR}/${WE2E_LOG_FN}"
-  if [[ ! -e "${we2e_log_fp}" ]]; then
+  if [ ! -f "${we2e_log_fp}" ]; then
     touch ${we2e_log_fp}
   fi
   # restart files

scripts/exlandda_pre_anal.sh

@@ -13,15 +13,13 @@ FILEDATE=${YYYY}${MM}${DD}.${HH}0000
 for itile in {1..6}
 do
   rst_fn="ufs_land_restart.${YYYY}-${MM}-${DD}_${HH}-00-00.tile${itile}.nc"
-  if [[ -e ${DATA_RESTART}/${rst_fn} ]]; then
+  if [ -f ${DATA_RESTART}/${rst_fn} ]; then
     cp ${DATA_RESTART}/${rst_fn} .
-  elif [[ -e ${WARMSTART_DIR}/${rst_fn} ]]; then
+  elif [ -f ${WARMSTART_DIR}/${rst_fn} ]; then
     cp ${WARMSTART_DIR}/${rst_fn} .
   else
     err_exit "Initial restart files do not exist"
   fi
-  # copy restart to data share dir for post_anal
-  cp -p ${rst_fn} ${DATA_SHARE}
 done
 
 # update tile2tile namelist
@@ -52,6 +50,6 @@ fi
 #stage restarts for applying JEDI update to intermediate directory
 for itile in {1..6}
 do
-  cp -p ${DATA}/${FILEDATE}.sfc_data.tile${itile}.nc ${DATA_SHARE}/${FILEDATE}.sfc_data.tile${itile}.nc
+  cp -p ${DATA}/${FILEDATE}.sfc_data.tile${itile}.nc ${DATA_RESTART}/${FILEDATE}.sfc_data.tile${itile}.nc
 done