Add GSI monitor scripts (#969)

As part of the overarching goal of moving global workflow scripts out of component repositories and under global workflow, all of the scripts currently linked in GSI monitor are added to global workflow. Scripts have been updated to reflect standardization already made to other workflow scripts (preamble, no backticks, etc.). See 7aa637 for those modifications specifically.

Related GSI-Montitor issue: NOAA-EMC/GSI-Monitor/pull/23

Fixes #967

.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

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
+
+