Merge branch 'develop' into feature/dev-wcoss2

* develop:
  Update UFS_UTILS tag to `ufs_utils_1_8_0` (#1001)
  Fix preamble id (#996)
  Add missing "atmos" into job dependencies (#998)
  Bugfix in arch.sh to remove hardwired "htar" (#992)
  Add in stubs for aerosol DA tasks + bugfix for setup_expt where cycled and ATMA are used (#990)
  Add GSI monitor scripts (#969)
  Fix product generation at some fcst hrs (#988)

.gitignore

@@ -136,10 +136,6 @@ sorc/wafs_setmissing.fd
 #------------------------------
 # jobs symlinks
 jobs/JGDAS_ATMOS_GLDAS
-jobs/JGDAS_ATMOS_VERFOZN
-jobs/JGDAS_ATMOS_VERFRAD
-jobs/JGDAS_ATMOS_VMINMON
-jobs/JGFS_ATMOS_VMINMON
 jobs/JGFS_ATMOS_WAFS
 jobs/JGFS_ATMOS_WAFS_BLENDING
 jobs/JGFS_ATMOS_WAFS_BLENDING_0P25
@@ -149,10 +145,6 @@ jobs/JGFS_ATMOS_WAFS_GRIB2_0P25
 # scripts symlinks
 scripts/exemcsfc_global_sfc_prep.sh
 scripts/exgdas_atmos_gldas.sh
-scripts/exgdas_atmos_verfozn.sh
-scripts/exgdas_atmos_verfrad.sh
-scripts/exgdas_atmos_vminmon.sh
-scripts/exgfs_atmos_vminmon.sh
 scripts/exgfs_atmos_wafs_blending.sh
 scripts/exgfs_atmos_wafs_blending_0p25.sh
 scripts/exgfs_atmos_wafs_gcip.sh
@@ -178,19 +170,8 @@ ush/global_chgres.sh
 ush/global_chgres_driver.sh
 ush/global_cycle.sh
 ush/global_cycle_driver.sh
-ush/minmon_xtrct_costs.pl
-ush/minmon_xtrct_gnorms.pl
-ush/minmon_xtrct_reduct.pl
 ush/mkwfsgbl.sh
-ush/ozn_xtrct.sh
-ush/radmon_ck_stdout.sh
-ush/radmon_err_rpt.sh
-ush/radmon_verf_angle.sh
-ush/radmon_verf_bcoef.sh
-ush/radmon_verf_bcor.sh
-ush/radmon_verf_time.sh
 ush/ufsda
-ush/rstprod.sh
 ush/wafs_blending.sh
 ush/wafs_grib2.regrid.sh
 ush/wafs_intdsk.sh

Externals.cfg

@@ -8,7 +8,7 @@ protocol = git
 required = True
 
 [UFS-Utils]
-hash = a2b0817
+hash = ufs_utils_1_8_0
 local_path = sorc/ufs_utils.fd
 repo_url = https://github.com/NOAA-EMC/UFS_UTILS.git
 protocol = git

jobs/JGDAS_ATMOS_VERFOZN

@@ -0,0 +1,110 @@
+#! /usr/bin/env bash
+
+#############################################################
+# Set up environment for GDAS Ozone Monitor job
+#############################################################
+source "$HOMEgfs/ush/preamble.sh"
+
+###############################
+# Specify NET, RUN, and COMPONENT name
+##############################
+export NET=${NET:-gfs}
+export RUN=${RUN:-gdas}
+export COMPONENT=${COMPONENT:-atmos}
+
+###########################################################
+# obtain unique process id (pid) and make temp directories
+###########################################################
+export pid=$$
+export outid=${outid:-"LL$job"}
+export DATA=${DATA:-${DATAROOT}/${jobid:?}}
+
+export OZNMON_SUFFIX=${OZNMON_SUFFIX:-${NET}}
+
+mkdir -p ${DATA}
+cd ${DATA}
+
+
+####################################
+# Determine Job Output Name on System
+####################################
+export pgmout="OUTPUT.${pid}"
+export pgmerr=errfile
+export cycle=t${cyc}z
+
+
+#---------------------------------------------
+# Specify Execution Areas
+#
+export HOMEgfs_ozn=${HOMEgfs:-${NWROOT}/gfs.${gfs_ver}}
+export HOMEgdas_ozn=${HOMEgfs_ozn:-${NWROOT}/gfs.${gfs_ver}}
+export PARMgdas_ozn=${PARMgfs_ozn:-$HOMEgfs_ozn/parm/mon}
+export SCRgdas_ozn=${SCRgfs_ozn:-$HOMEgfs_ozn/scripts}
+export FIXgdas_ozn=${FIXgfs_ozn:-$HOMEgfs_ozn/fix/gdas}
+
+export HOMEoznmon=${HOMEoznmon:-${HOMEgfs_ozn}}
+export EXECoznmon=${EXECoznmon:-$HOMEoznmon/exec}
+export FIXoznmon=${FIXoznmon:-${HOMEoznmon}/fix}
+export USHoznmon=${USHoznmon:-$HOMEoznmon/ush}
+
+
+#-----------------------------------
+# source the parm file
+#
+.  ${PARMgdas_ozn}/gdas_oznmon.parm
+
+
+#############################################
+#  determine PDY and cyc for previous cycle
+#############################################
+
+cdate=$(${NDATE} -6 ${PDY}${cyc})
+echo 'pdate = ${pdate}'
+
+export P_PDY=$(echo ${cdate} | cut -c1-8)
+export p_cyc=$(echo ${cdate} | cut -c9-10)
+
+#---------------------------------------------
+# OZN_TANKDIR - WHERE OUTPUT DATA WILL RESIDE
+#
+export OZN_TANKDIR=${OZN_TANKDIR:-$(compath.py ${envir}/${NET}/${gfs_ver})}
+export TANKverf_ozn=${TANKverf_ozn:-${OZN_TANKDIR}/${RUN}.${PDY}/${cyc}/${COMPONENT}/oznmon}
+export TANKverf_oznM1=${TANKverf_oznM1:-${OZN_TANKDIR}/${RUN}.${P_PDY}/${p_cyc}/${COMPONENT}/oznmon}
+export COM_IN=${COM_IN:-$(compath.py ${envir}/${NET}/${gfs_ver})}
+export COMIN=${COMIN:-${COM_IN}/${RUN}.${PDY}/${cyc}/${COMPONENT}}
+
+if [[ ! -d ${TANKverf_ozn} ]]; then
+   mkdir -p -m 775 ${TANKverf_ozn}
+fi
+
+#---------------------------------------
+#  set up validation file
+#
+if [[ ${VALIDATE_DATA} -eq 1 ]]; then
+   export ozn_val_file=${ozn_val_file:-${FIXgdas_ozn}/gdas_oznmon_base.tar}
+fi
+
+#---------------------------------------
+# Set necessary environment variables
+#
+export OZN_AREA=${OZN_AREA:-glb}
+export oznstat=${oznstat:-$COMIN/gdas.t${cyc}z.oznstat}
+
+
+#-------------------------------------------------------
+# Execute the script.
+#
+${OZNMONSH:-${SCRgdas_ozn}/exgdas_atmos_verfozn.sh} ${PDY} ${cyc}
+err=$?
+[[ $err -ne 0 ]] && exit $err
+
+
+################################
+# Remove the Working Directory
+################################
+KEEPDATA=${KEEPDATA:-YES}
+cd $DATAROOT
+if [ ${KEEPDATA} = NO ] ; then
+  rm -rf $DATA
+fi
+

jobs/JGDAS_ATMOS_VERFRAD

@@ -0,0 +1,131 @@
+#! /usr/bin/env bash
+
+#############################################################
+# Set up environment for GDAS Radiance Monitor job
+#############################################################
+source "$HOMEgfs/ush/preamble.sh"
+
+###############################
+# Specify NET, RUN, and COMPONENT name
+##############################
+export NET=${NET:-gfs}
+export RUN=${RUN:-gdas}
+export COMPONENT=${COMPONENT:-atmos}
+
+########################################################### 
+# obtain unique process id (pid) and make temp directories
+###########################################################
+export pid=$$
+export outid=${outid:-"LL$job"}
+export RAD_DATA_IN=${RAD_DATA_IN:-${DATAROOT}/${jobid:?}}
+
+export RADMON_SUFFIX=${RADMON_SUFFIX:-${RUN}}
+export CYCLE_INTERVAL=${CYCLE_INTERVAL:-6}
+
+mkdir -p $RAD_DATA_IN
+cd $RAD_DATA_IN
+
+####################################
+# Determine Job Output Name on System
+####################################
+export pgmout="OUTPUT.${pid}"
+export pgmerr=errfile
+export cycle=t${cyc}z
+
+##############################################
+# Specify Execution Areas
+##############################################
+export HOMEgfs=${HOMEgfs:-${NWROOT}/gfs.${gfs_ver}}
+export SCRgfs=${SCRgfs:-$HOMEgfs/scripts}
+
+export FIXgdas=${FIXgdas:-$HOMEgfs/fix/gdas}
+export PARMmon=${PARMmon:-$HOMEgfs/parm/mon}
+
+export HOMEradmon=${HOMEradmon:-${HOMEgfs}}
+export EXECradmon=${EXECradmon:-$HOMEradmon/exec}
+export FIXradmon=${FIXradmon:-${FIXgfs}}
+export USHradmon=${USHradmon:-$HOMEradmon/ush}
+
+
+###################################
+# source the parm file
+###################################
+parm_file=${parm_file:-${PARMmon}/da_mon.parm}
+.  ${parm_file}
+
+
+#############################################
+# Run setpdy and initialize PDY variables
+#############################################
+if [[ $MY_MACHINE != "HERA" && $MY_MACHINE != "hera" ]]; then
+   setpdy.sh
+   . ./PDY
+fi   
+
+#############################################
+#  determine PDY and cyc for previous cycle
+#############################################
+
+cdate=$(${NDATE} -6 ${PDY}${cyc})
+echo 'pdate = ${pdate}'
+
+export P_PDY=$(echo ${cdate} | cut -c1-8)
+export p_cyc=$(echo ${cdate} | cut -c9-10)
+
+#############################################
+# COMOUT - WHERE GSI OUTPUT RESIDES
+# TANKverf - WHERE OUTPUT DATA WILL RESIDE
+#############################################
+export TANKverf=${TANKverf:-$(compath.py ${envir}/${NET}/${gfs_ver})}
+export TANKverf_rad=${TANKverf_rad:-${TANKverf}/${RUN}.${PDY}/${cyc}/$COMPONENT/radmon}
+export TANKverf_radM1=${TANKverf_radM1:-${TANKverf}/${RUN}.${P_PDY}/${p_cyc}/$COMPONENT/radmon}
+export COM_IN=${COM_IN:-$(compath.py ${envir}/${NET}/${gfs_ver})}
+export COMIN=${COMIN:-${COM_IN}/${RUN}.${PDY}/${cyc}/$COMPONENT}
+
+################################
+#  backwards compatibility for
+#  gfs v15 which doesn't have 
+#  a $COMPONENT in output path 
+################################
+if [[ ! -d ${COMIN} ]]; then
+   export COMIN=${COM_IN}/${RUN}.${PDY}/${cyc}
+fi
+
+
+mkdir -p -m 775 $TANKverf_rad
+
+########################################
+# Set necessary environment variables
+########################################
+export RAD_AREA=${RAD_AREA:-glb}
+
+export biascr=${biascr:-$COMIN/gdas.t${cyc}z.abias}
+export radstat=${radstat:-$COMIN/gdas.t${cyc}z.radstat}
+
+echo " "
+echo "JOB HAS STARTED"
+echo " "
+
+
+########################################################
+# Execute the script.
+${RADMONSH:-${SCRgfs}/exgdas_atmos_verfrad.sh} ${PDY} ${cyc}
+err=$?
+
+if [[ $err -ne 0 ]] ; then
+   exit $err
+else
+   echo " "
+   echo "JOB HAS COMPLETED NORMALLY"
+   echo " "
+fi
+
+################################
+# Remove the Working Directory
+################################
+KEEPDATA=${KEEPDATA:-YES}
+cd $DATAROOT
+if [ ${KEEPDATA} = NO ] ; then 
+  rm -rf $RAD_DATA_IN
+fi
+

jobs/JGDAS_ATMOS_VMINMON

@@ -0,0 +1,95 @@
+#! /usr/bin/env bash
+
+###########################################################
+# GDAS Minimization Monitor (MinMon) job
+###########################################################
+source "$HOMEgfs/ush/preamble.sh"
+
+###############################
+# Specify NET, RUN, and COMPONENT name
+##############################
+export NET=${NET:-gfs}
+export RUN=${RUN:-gdas}
+export COMPONENT=${COMPONENT:-atmos}
+
+###########################################################
+# obtain unique process id (pid) and make temp directories
+###########################################################
+export pid=$$
+export outid=${outid:-"LL$job"}
+
+export DATA=${DATA:-${DATAROOT}/${jobid:?}}
+mkdir -p $DATA
+cd $DATA
+
+
+########################################################### 
+# obtain unique process id (pid) and make temp directories
+###########################################################
+export MINMON_SUFFIX=${MINMON_SUFFIX:-${NET}}
+export m_job=${m_job:-${MINMON_SUFFIX}_mmDE}
+
+
+##############################################
+# Specify Package Areas
+##############################################
+export HOMEgfs=${HOMEgfs:-${NWROOT}/gfs.${gfs_ver}}
+export SCRgfs=${SCRgfs:-$HOMEgfs/scripts}
+
+export M_FIXgdas=${M_FIXgdas:-$HOMEgfs/fix/gdas}
+
+export HOMEminmon=${HOMEminmon:-${HOMEgfs}}
+export EXECminmon=${EXECminmon:-$HOMEminmon/exec}
+export USHminmon=${USHminmon:-$HOMEminmon/ush}
+
+
+#############################################
+#  determine PDY and cyc for previous cycle
+#############################################
+
+cdate=$(${NDATE} -6 ${PDY}${cyc})
+echo 'pdate = ${pdate}'
+
+export P_PDY=$(echo ${cdate} | cut -c1-8)
+export p_cyc=$(echo ${cdate} | cut -c9-10)
+
+
+#############################################
+# TANKverf - WHERE OUTPUT DATA WILL RESIDE
+#############################################
+export COM_IN=${COM_IN:-$(compath.py ${envir}/${NET}/${gfs_ver})}
+
+export M_TANKverf=${M_TANKverf:-${COM_IN}/${RUN}.${PDY}/${cyc}/${COMPONENT}/minmon}
+export M_TANKverfM1=${M_TANKverfM1:-${COM_IN}/${RUN}.${P_PDY}/${p_cyc}/${COMPONENT}/minmon}
+
+export COMIN=${COMIN:-$COM_IN/${RUN}.${PDY}/${cyc}/$COMPONENT}
+
+mkdir -p -m 775 $M_TANKverf
+
+
+
+########################################
+# Set necessary environment variables
+########################################
+export CYCLE_INTERVAL=6
+export gsistat=${gsistat:-${COMIN}/gdas.t${cyc}z.gsistat}
+
+
+########################################################
+# Execute the script.
+${GMONSH:-$SCRgfs/exgdas_atmos_vminmon.sh} ${PDY} ${cyc}
+err=$?
+[[ $err -ne 0 ]] && exit $err
+
+
+################################
+# Remove the Working Directory
+################################
+KEEPDATA=${KEEPDATA:-NO}
+cd ${DATAROOT}
+
+if [ ${KEEPDATA} = NO ] ; then
+  rm -rf ${DATA}
+fi
+
+