Implement the ICs part to generate ICs for real-time and retro run

env/HERA.env

@@ -250,6 +250,10 @@ elif [[ "${step}" = "epos" ]]; then
     [[ ${NTHREADS_EPOS} -gt ${nth_max} ]] && export NTHREADS_EPOS=${nth_max}
     export APRUN_EPOS="${launcher} -n ${npe_epos} --cpus-per-task=${NTHREADS_EPOS}"
 
+elif [[ "${step}" = "init" ]]; then
+
+    export APRUN="${launcher} -n ${npe_init}"
+
 elif [[ "${step}" = "postsnd" ]]; then
 
     export CFP_MP="YES"

jobs/rocoto/archive_fv3ics.ksh

@@ -0,0 +1,33 @@
+#!/bin/ksh -l
+
+# this file archives FV3 ICs to the mass store, /BMC/fim/5year/FV3ICS
+#    input is operational GFS initial conditions  
+
+module load hpss
+module list
+
+# initialize
+#inpDir=/scratch4/BMC/rtfim/rtruns/FV3GFS/FV3ICS
+#mssDir=FV3ICS
+#CDUMP=gfs
+#CASE=C384
+#yyyymmddhh=$1
+echo "****************************"
+echo ICSDIR:   $ICSDIR
+echo mssDIR:   $mssDir
+echo CDUMP:    $CDUMP
+echo CASE:     $CASE
+echo DATE:     $yyyymmddhh
+
+# for each directory, archive FV3 ICs to mass store in monthly directories
+#    /scratch4/BMC/rtfim/rtruns/FV3ICS/2017111012/gfs/C384/INPUT
+echo "in $ICSDIR....."
+echo "Archiving ${yyyymmddhh} to mss"
+cd $ICSDIR
+cmd="htar -cPvf /BMC/fim/5year/${mssDir}/${yyyymmddhh}_${CASE}.tar ${CDUMP}/${CASE}/INPUT/*"
+$cmd
+status=$?
+if [ $status != 0 ] ; then
+  printf "Error : [%d] when executing htar command: '$cmd'" $status
+  exit $status
+fi

jobs/rocoto/getic.sh

@@ -0,0 +1,65 @@
+#! /usr/bin/env bash
+
+source "$HOMEgfs/ush/preamble.sh"
+
+## this script makes links to FV3GFS netcdf files under /public 
+##   /home/rtfim/UFS_CAMSUITE/FV3GFSrun/FV3ICS/YYYYMMDDHH/gfs
+##     gfs.tHHz.sfcanl.nc -> /public/data/grids/gfs/netcdf/YYDDDHH00.gfs.tHHz.sfcanl.nc
+##     gfs.tHHz.atmanl.nc -> /public/data/grids/gfs/netcdf/YYDDDHH00.gfs.tHHz.atmanl.nc
+
+echo
+echo "CDATE = $CDATE"
+echo "CDUMP = $CDUMP"
+echo "COMPONENT = $COMPONENT"
+echo "ICSDIR = $ICSDIR"
+echo "PUBDIR = $PUBDIR"
+echo "RETRODIR = $RETRODIR"
+echo "ROTDIR = $ROTDIR"
+echo "PSLOT = $PSLOT"
+echo
+
+## initialize
+yyyymmdd=`echo $CDATE | cut -c1-8`
+hh=`echo $CDATE | cut -c9-10`
+yyddd=`date +%y%j -u -d $yyyymmdd`
+fv3ic_dir=${ROTDIR}/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}
+
+## create links in FV3ICS directory
+mkdir -p $fv3ic_dir
+cd $fv3ic_dir
+echo "making link to netcdf files under $fv3ic_dir"
+
+pubsfc_file=${yyddd}${hh}00.${CDUMP}.t${hh}z.sfcanl.nc
+sfc_file=`echo $pubsfc_file | cut -d. -f2-`
+pubatm_file=${yyddd}${hh}00.${CDUMP}.t${hh}z.atmanl.nc
+atm_file=`echo $pubatm_file | cut -d. -f2-`
+
+echo "pubsfc_file:  $pubsfc_file"
+echo "pubatm_file:  $pubatm_file"
+
+if  [[ -f $RETRODIR/${pubatm_file} ]]; then
+  echo "linking $RETRODIR...."
+  echo "pubsfc_file:  $pubsfc_file"
+  echo "pubatm_file:  $pubatm_file"
+  ln -fs $RETRODIR/${pubsfc_file} $sfc_file
+  ln -fs $RETRODIR/${pubatm_file} $atm_file 
+elif [[ -f $PUBDIR/${pubatm_file} ]]; then
+  echo "linking $PUBDIR...."
+  ln -fs $PUBDIR/${pubsfc_file} $sfc_file
+  ln -fs $PUBDIR/${pubatm_file} $atm_file
+elif  [[ -f $EMCDIR/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}/${atm_file} ]]; then
+  echo "linking $EMCDIR/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}..."
+  echo "sfc_file:  $sfc_file"
+  echo "atm_file:  $atm_file"
+  ln -s $EMCDIR/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}/${sfc_file}
+  ln -s $EMCDIR/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}/${atm_file}
+elif  [[ -f $RETRODIR/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}/${atm_file} ]]; then
+  echo "linking $RETRODIR/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}..."
+  echo "sfc_file:  $sfc_file"
+  echo "atm_file:  $atm_file"
+  ln -s $RETRODIR/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}/${sfc_file}
+  ln -s $RETRODIR/${CDUMP}.${yyyymmdd}/${hh}/${COMPONENT}/${atm_file}
+else
+  echo "missing input files!"
+  exit 1
+fi

jobs/rocoto/init.sh

@@ -0,0 +1,85 @@
+#! /usr/bin/env bash
+
+source "$HOMEgfs/ush/preamble.sh"
+
+###############################################################
+## Abstract:
+## Get GFS intitial conditions
+## RUN_ENVIR : runtime environment (emc | nco)
+## HOMEgfs   : /full/path/to/workflow
+## EXPDIR : /full/path/to/config/files
+## CDATE  : current date (YYYYMMDDHH)
+## CDUMP  : cycle name (gdas / gfs)
+## PDY    : current date (YYYYMMDD)
+## cyc    : current cycle (HH)
+###############################################################
+
+###############################################################
+# Source FV3GFS workflow modules
+#. $HOMEgfs/ush/load_fv3gfs_modules.sh
+#status=$?
+#[[ $status -ne 0 ]] && exit $status
+
+#JKH load ufs-utils modules
+#module use /scratch1/BMC/gsd-fv3/rtruns/modulefiles
+#module load build.hera.intel.lua.gfsinit
+module purge
+module use $HOMEgfs/sorc/ufs_utils.fd/modulefiles
+module load build.hera.intel
+module list
+
+###############################################################
+# Source relevant configs
+configs="base getic init"
+for config in $configs; do
+    . $EXPDIR/config.${config}
+    status=$?
+    [[ $status -ne 0 ]] && exit $status
+done
+
+###############################################################
+# Source machine runtime environment
+. $BASE_ENV/${machine}.env init
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+###############################################################
+# Set script and dependency variables
+
+export yy=$(echo $CDATE | cut -c1-4)
+export mm=$(echo $CDATE | cut -c5-6)
+export dd=$(echo $CDATE | cut -c7-8)
+export hh=${cyc:-$(echo $CDATE | cut -c9-10)}
+
+export DATA=${DATA:-${DATAROOT}/init_$CDATE}
+export EXTRACT_DIR=${EXTRACT_DIR:-$ROTDIR}
+export WORKDIR=${WORKDIR:-$DATA}
+export OUTDIR=${OUTDIR:-$ROTDIR}
+export COMPONENT="atmos"
+export gfs_ver=${gfs_ver:-"v16"}
+export OPS_RES=${OPS_RES:-"C768"}
+export RUNICSH=${RUNICSH:-${GDASINIT_DIR}/run_v16.chgres.sh}
+
+# Check if init is needed and run if so
+if [[ $gfs_ver = "v16" && $EXP_WARM_START = ".true." && $CASE = $OPS_RES ]]; then
+  echo "Detected v16 $OPS_RES warm starts, will not run init. Exiting..."
+
+else
+  # Run chgres_cube
+  if [ ! -d $OUTDIR ]; then mkdir -p $OUTDIR ; fi
+  sh ${RUNICSH} ${CDUMP}
+  status=$?
+  [[ $status -ne 0 ]] && exit $status
+fi
+
+##########################################
+# Remove the Temporary working directory
+##########################################
+cd $DATAROOT
+[[ $KEEPDATA = "NO" ]] && rm -rf $DATA
+
+###############################################################
+# Exit out cleanly
+
+
+exit 0

parm/config/gfs/config.getic

@@ -0,0 +1,66 @@
+#! /usr/bin/env bash
+
+########## config.getic ##########
+# Fetching GFS initial conditions specific
+
+echo "BEGIN: config.getic"
+
+# Get task specific resources
+. $EXPDIR/config.resources getic
+
+export RETRO="NO" # YES = Pull v16 inputs from retrospective parallels; NO = use operational inputs
+export gfs_ver="v16" # Default = v16
+export OPS_RES=${OPS_RES:-"C768"} # Operational resolution
+
+export UFS_DIR=${HOMEgfs}/sorc/ufs_utils.fd
+export GDAS_INIT_DIR=${UFS_DIR}/util/gdas_init
+
+export PRODHPSSDIR=/NCEPPROD/hpssprod/runhistory
+export GETICSH=${GDAS_INIT_DIR}/get_v16.data.sh
+
+if [ ${RETRO:-"NO"} = "YES" ]; then # Retrospective parallel input
+  export GETICSH=${GDAS_INIT_DIR}/get_v16retro.data.sh
+  if [[ "$CDATE" -lt "2019060106" ]]; then
+    HPSSDIR=/NCEPDEV/emc-global/5year/emc.glopara/WCOSS_D/gfsv16/v16retro0e
+  elif [[ "$CDATE" -lt "2019090100" ]]; then
+    HPSSDIR=/NCEPDEV/emc-global/5year/emc.glopara/WCOSS_D/gfsv16/v16retro1e
+  elif [[ "$CDATE" -lt "2019101706" ]]; then
+    HPSSDIR=/NCEPDEV/emc-global/5year/emc.glopara/WCOSS_D/gfsv16/v16retro2e
+  elif [[ "$CDATE" -lt "2020122200" ]]; then
+    HPSSDIR=/NCEPDEV/emc-global/5year/emc.glopara/WCOSS_D/gfsv16/v16rt2
+  elif [[ "$CDATE" -le "2021032506" ]]; then
+    HPSSDIR=/NCEPDEV/emc-global/5year/emc.glopara/WCOSS_D/gfsv16/v16rt2n
+  else
+    set +x
+    echo NO DATA FOR $CDATE
+    exit 3
+  fi
+elif [ ${RETRO:-"NO"} = "NO" ]; then # Operational input
+  # No ENKF data prior to 2012/05/21/00z
+  if [[ "$CDATE" -lt "2012052100" ]]; then
+    set +x
+    echo FATAL ERROR: SCRIPTS DO NOT SUPPORT OLD GFS DATA
+  elif [[ "$CDATE" -lt "2016051000" ]]; then
+    export gfs_ver=v12
+    export GETICSH=${GDAS_INIT_DIR}/get_pre-v14.data.sh
+  elif [[ "$CDATE" -lt "2017072000" ]]; then
+    export gfs_ver=v13
+    export GETICSH=${GDAS_INIT_DIR}/get_pre-v14.data.sh
+  elif [[ "$CDATE" -lt "2019061200" ]]; then
+    export gfs_ver=v14
+    export GETICSH=${GDAS_INIT_DIR}/get_${gfs_ver}.data.sh
+  elif [[ "$CDATE" -lt "2021032100" ]]; then
+    export gfs_ver=v15
+    export GETICSH=${GDAS_INIT_DIR}/get_${gfs_ver}.data.sh
+  elif [[ "$CDATE" -lt "2021032106" ]]; then
+    # The way the v16 switch over was done, there is no complete
+    # set of v16 or v15 data for 2021032100.  And although
+    # v16 was officially implemented 2021032212, the v16 prod
+    # tarballs were archived starting 2021032106.
+    set +x
+    echo FATAL ERROR: NO V15 OR V16 DATA FOR 2021032100
+    exit 1
+  fi
+fi
+
+echo "END: config.getic"

parm/config/gfs/config.init

@@ -0,0 +1,55 @@
+#! /usr/bin/env bash
+
+########## config.init ##########
+# Prepare initial conditions 
+
+echo "BEGIN: config.init"
+
+# Get task specific resources
+. $EXPDIR/config.resources init
+
+# Get task specific resources
+. $EXPDIR/config.getic
+
+export UFS_DIR=${HOMEgfs}/sorc/ufs_utils.fd
+export GDAS_INIT_DIR=${UFS_DIR}/util/gdas_init
+export EXEC_DIR=${UFS_DIR}/exec
+
+export CRES_HIRES=$CASE
+export CRES_ENKF=""
+export FRAC_ORO="yes"
+
+export RUNICSH=${GDAS_INIT_DIR}/run_v16.chgres.sh
+if [ "${RETRO:-"NO"}" = "YES" ] || [ "$CDUMP" = "gdas" ]; then
+  export RUNICSH=${GDAS_INIT_DIR}/run_v16retro.chgres.sh
+fi
+
+if [ ${RETRO:-"NO"} = "NO" ]; then # Operational input
+  # No ENKF data prior to 2012/05/21/00z
+  if [[ "$CDATE" -lt "2012052100" ]]; then
+    set +x
+    echo FATAL ERROR: SCRIPTS DO NOT SUPPORT OLD GFS DATA
+  elif [[ "$CDATE" -lt "2016051000" ]]; then
+    export gfs_ver=v12
+    export RUNICSH=${GDAS_INIT_DIR}/run_pre-v14.chgres.sh
+  elif [[ "$CDATE" -lt "2017072000" ]]; then
+    export gfs_ver=v13
+    export RUNICSH=${GDAS_INIT_DIR}/run_pre-v14.chgres.sh
+  elif [[ "$CDATE" -lt "2019061200" ]]; then
+    export gfs_ver=v14
+    export RUNICSH=${GDAS_INIT_DIR}/run_${gfs_ver}.chgres.sh
+  elif [[ "$CDATE" -lt "2021032100" ]]; then
+    export gfs_ver=v15
+    export RUNICSH=${GDAS_INIT_DIR}/run_${gfs_ver}.chgres.gfs.sh
+  elif [[ "$CDATE" -lt "2021032106" ]]; then
+    # The way the v16 switch over was done, there is no complete
+    # set of v16 or v15 data for 2021032100.  And although
+    # v16 was officially implemented 2021032212, the v16 prod
+    # tarballs were archived starting 2021032106.
+    set +x
+    echo FATAL ERROR: NO V15 OR V16 DATA FOR 2021032100
+    exit 1
+  fi
+fi
+
+echo "END: config.init"

sorc/link_workflow.sh

@@ -120,6 +120,10 @@ do
   ${LINK_OR_COPY} "${FIX_DIR}/${dir}/${!fix_ver}" "${dir}"
 done
 
+if [[ -d "${HOMEgfs}/sorc/ufs_utils.fd" ]]; then
+  cd "${HOMEgfs}/sorc/ufs_utils.fd/fix" || exit 1
+  ./link_fixdirs.sh "${RUN_ENVIR}" "${machine}" 2> /dev/null
+fi
 
 #---------------------------------------
 #--add files from external repositories

workflow/ccpp-chem-C384-ics.sh

@@ -0,0 +1,22 @@
+USER=Kate.Zhang
+
+
+BASEDIR=/scratch2/BMC/gsd-fv3-dev/lzhang/UFS-dev/global-workflow
+STMP=/scratch1/NCEPDEV/stmp2/$USER/RUNDIRS
+IDATE=2024040500
+EDATE=2016040500
+APP=ATM
+PSLOT=rt_c384ics
+RES=384
+GFS_CYC=1
+START=cold
+COMROT=/scratch1/BMC/gsd-fv3-dev/NCEPDEV/global/$USER/fv3gfs/comrot
+EXPDIR=/scratch2/BMC/gsd-fv3-dev/NCEPDEV/global/$USER/fv3gfs/expdir
+ICSDIR=$COMROT/$PSLOT
+
+
+./setup_expt.py gfs forecast-only --idate $IDATE --edate $EDATE --app $APP --gfs_cyc $GFS_CYC --resdetatmos $RES --pslot $PSLOT --comroot $COMROT --expdir $EXPDIR 
+
+
+./setup_xml.py $EXPDIR/$PSLOT
+

workflow/ccpp-chem-C96-ics.sh

@@ -0,0 +1,22 @@
+USER=Kate.Zhang
+
+
+BASEDIR=/scratch2/BMC/gsd-fv3-dev/lzhang/UFS-dev/global-workflow
+STMP=/scratch1/NCEPDEV/stmp2/$USER/RUNDIRS
+IDATE=2016071500
+EDATE=2016071500
+APP=ATM
+PSLOT=CAT_C96_CCPP
+RES=96
+GFS_CYC=1
+START=cold
+COMROT=/scratch1/BMC/gsd-fv3-dev/NCEPDEV/global/$USER/fv3gfs/comrot
+EXPDIR=/scratch2/BMC/gsd-fv3-dev/NCEPDEV/global/$USER/fv3gfs/expdir
+ICSDIR=$COMROT/$PSLOT
+
+
+./setup_expt.py gfs forecast-only --idate $IDATE --edate $EDATE --app $APP --gfs_cyc $GFS_CYC --resdetatmos $RES --pslot $PSLOT --comroot $COMROT --expdir $EXPDIR 
+
+
+./setup_xml.py $EXPDIR/$PSLOT
+