Update operational workflow to work with GSI develop branch

.gitignore

@@ -94,59 +94,28 @@ sorc/wafs_setmissing.fd
 # Ignore scripts from externals
 #------------------------------
 # jobs symlinks
-jobs/JGDAS_ATMOS_ANALYSIS_DIAG
-jobs/JGDAS_ATMOS_CHGRES_FORENKF
 jobs/JGDAS_ATMOS_GLDAS
-jobs/JGDAS_ATMOS_VERFOZN
-jobs/JGDAS_ATMOS_VERFRAD
-jobs/JGDAS_ATMOS_VMINMON
-jobs/JGDAS_ENKF_DIAG
-jobs/JGDAS_ENKF_ECEN
-jobs/JGDAS_ENKF_FCST
-jobs/JGDAS_ENKF_POST
-jobs/JGDAS_ENKF_SELECT_OBS
-jobs/JGDAS_ENKF_SFC
-jobs/JGDAS_ENKF_UPDATE
-jobs/JGFS_ATMOS_VMINMON
 jobs/JGFS_ATMOS_WAFS
 jobs/JGFS_ATMOS_WAFS_BLENDING
 jobs/JGFS_ATMOS_WAFS_BLENDING_0P25
 jobs/JGFS_ATMOS_WAFS_GCIP
 jobs/JGFS_ATMOS_WAFS_GRIB2
 jobs/JGFS_ATMOS_WAFS_GRIB2_0P25
-jobs/JGLOBAL_ATMOS_ANALYSIS
-jobs/JGLOBAL_ATMOS_ANALYSIS_CALC
 jobs/JGLOBAL_ATMOS_NCEPPOST
 jobs/JGLOBAL_ATMOS_POST_MANAGER
 # scripts symlinks
 scripts/exemcsfc_global_sfc_prep.sh
-scripts/exgdas_atmos_chgres_forenkf.sh
 scripts/exgdas_atmos_gldas.sh
 scripts/exgdas_atmos_nceppost.sh
-scripts/exgdas_atmos_verfozn.sh
-scripts/exgdas_atmos_verfrad.sh
-scripts/exgdas_atmos_vminmon.sh
-scripts/exgdas_enkf_ecen.sh
-scripts/exgdas_enkf_fcst.sh
-scripts/exgdas_enkf_post.sh
-scripts/exgdas_enkf_select_obs.sh
-scripts/exgdas_enkf_sfc.sh
-scripts/exgdas_enkf_update.sh
 scripts/exgfs_atmos_nceppost.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
 scripts/exgfs_atmos_wafs_grib.sh
 scripts/exgfs_atmos_wafs_grib2.sh
 scripts/exgfs_atmos_wafs_grib2_0p25.sh
-scripts/exglobal_atmos_analysis.sh
-scripts/exglobal_atmos_analysis_calc.sh
 scripts/exglobal_atmos_pmgr.sh
-scripts/exglobal_diag.sh
 # ush symlinks
-ush/calcanl_gfs.py
-ush/calcinc_gfs.py
 ush/emcsfc_ice_blend.sh
 ush/emcsfc_snow.sh
 ush/fix_precip.sh
@@ -157,7 +126,6 @@ ush/fv3gfs_dwn_nems.sh
 ush/fv3gfs_filter_topo.sh
 ush/fv3gfs_make_grid.sh
 ush/fv3gfs_make_orog.sh
-ush/getncdimlen
 ush/gfs_nceppost.sh
 ush/gfs_transfer.sh
 ush/gldas_archive.sh
@@ -170,20 +138,11 @@ ush/global_chgres.sh
 ush/global_chgres_driver.sh
 ush/global_cycle.sh
 ush/global_cycle_driver.sh
-ush/gsi_utils.py
 ush/link_crtm_fix.sh
-ush/minmon_xtrct_costs.pl
-ush/minmon_xtrct_gnorms.pl
-ush/minmon_xtrct_reduct.pl
 ush/mkwfsgbl.sh
 ush/mod_icec.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/trim_rh.sh
 ush/wafs_blending.sh
 ush/wafs_grib2.regrid.sh

ecf/scripts/gdas/atmos/analysis/jgdas_atmos_analysis_calc.ecf

@@ -29,6 +29,7 @@ module load cray-pals/${cray_pals_ver}
 module load python/${python_ver}
 module load hdf5/${hdf5_ver}
 module load netcdf/${netcdf_ver}
+module load ncdiag/${ncdiag_ver}
 
 module list
 

jobs/JGDAS_ATMOS_ANALYSIS_DIAG

@@ -0,0 +1,156 @@
+#!/bin/bash
+set -x
+
+export RUN_ENVIR=${RUN_ENVIR:-"nco"}
+export PS4='$SECONDS + '
+date
+
+
+#############################
+# Source relevant config files
+#############################
+export EXPDIR=${EXPDIR:-$HOMEgfs/parm/config}
+configs="base anal analdiag"
+config_path=${EXPDIR:-$NWROOT/gfs.${gfs_ver}/parm/config}
+for config in $configs; do
+    . $config_path/config.$config
+    status=$?
+    [[ $status -ne 0 ]] && exit $status
+done
+
+
+##########################################
+# Source machine runtime environment
+##########################################
+. $HOMEgfs/env/${machine}.env anal
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+
+##############################################
+# Obtain unique process id (pid) and make temp directory
+##############################################
+export pid=${pid:-$$}
+export outid=${outid:-"LL$job"}
+
+export DATA=${DATA:-${DATAROOT}/${jobid:?}}
+mkdir -p $DATA
+cd $DATA
+
+
+##############################################
+# Run setpdy and initialize PDY variables
+##############################################
+export cycle="t${cyc}z"
+setpdy.sh
+. ./PDY
+
+
+##############################################
+# Determine Job Output Name on System
+##############################################
+export pgmout="OUTPUT.${pid}"
+export pgmerr=errfile
+
+
+##############################################
+# Set variables used in the script
+##############################################
+export CDATE=${CDATE:-${PDY}${cyc}}
+export CDUMP=${CDUMP:-${RUN:-"gfs"}}
+export COMPONENT=${COMPONENT:-atmos}
+export DO_CALC_ANALYSIS=${DO_CALC_ANALYSIS:-"YES"} 
+
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+GDATE=$($NDATE -$assim_freq $CDATE)
+gPDY=$(echo $GDATE | cut -c1-8)
+gcyc=$(echo $GDATE | cut -c9-10)
+GDUMP=${GDUMP:-"gdas"}
+
+export OPREFIX="${CDUMP}.t${cyc}z."
+export GPREFIX="${GDUMP}.t${gcyc}z."
+export APREFIX="${CDUMP}.t${cyc}z."
+export GSUFFIX=${GSUFFIX:-$SUFFIX}
+export ASUFFIX=${ASUFFIX:-$SUFFIX}
+
+
+if [ $RUN_ENVIR = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
+    export COMIN=${COMIN:-$ROTDIR/$RUN.$PDY/$cyc/$COMPONENT}
+    export COMOUT=${COMOUT:-$ROTDIR/$RUN.$PDY/$cyc/$COMPONENT}
+    export COMIN_OBS=${COMIN_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/$RUN.$PDY/$cyc/$COMPONENT}
+    export COMIN_GES_OBS=${COMIN_GES_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/$GDUMP.$gPDY/$gcyc/$COMPONENT}
+else
+    export COMOUT="$ROTDIR/$CDUMP.$PDY/$cyc/$COMPONENT"
+    export COMIN_OBS="$DMPDIR/$CDUMP.$PDY/$cyc/$COMPONENT"
+    export COMIN_GES_OBS="$DMPDIR/$GDUMP.$gPDY/$gcyc/$COMPONENT"
+fi
+mkdir -m 775 -p $COMOUT
+# COMIN_GES and COMIN_GES_ENS are used in script
+export COMIN_GES="$ROTDIR/$GDUMP.$gPDY/$gcyc/$COMPONENT"
+export COMIN_GES_ENS="$ROTDIR/enkfgdas.$gPDY/$gcyc/$COMPONENT"
+
+
+export ATMGES="$COMIN_GES/${GPREFIX}atmf006${GSUFFIX}"
+if [ ! -f $ATMGES ]; then
+    echo "FATAL ERROR: FILE MISSING: ATMGES = $ATMGES"
+    exit 1
+fi
+
+
+if [ $DOHYBVAR = "YES" ]; then
+    export ATMGES_ENSMEAN="$COMIN_GES_ENS/${GPREFIX}atmf006.ensmean$GSUFFIX"
+    if [ ! -f $ATMGES_ENSMEAN ]; then
+        echo "FATAL ERROR: FILE MISSING: ATMGES_ENSMEAN = $ATMGES_ENSMEAN"
+        exit 2
+    fi
+fi
+
+
+
+# Update surface fields with global_cycle
+export DOGCYCLE=${DOGCYCLE:-"YES"}
+
+
+# Generate Gaussian surface analysis
+export DOGAUSFCANL=${DOGAUSFCANL:-"YES"}
+
+
+###############################################################
+# Run relevant script
+env
+echo "HAS BEGUN on $(hostname)"
+$LOGSCRIPT
+
+
+${ANALDIAGSH:-$SCRgfs/exglobal_diag.sh}
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [ -e "$pgmout" ] ; then
+  cat $pgmout
+fi
+
+
+echo "ENDED NORMALLY."
+
+
+##########################################
+# Remove the Temporary working directory
+##########################################
+cd $DATAROOT
+[[ $KEEPDATA = "NO" ]] && rm -rf $DATA
+
+date
+exit 0

jobs/JGDAS_ATMOS_CHGRES_FORENKF

@@ -0,0 +1,132 @@
+#!/bin/bash
+set -x
+
+export RUN_ENVIR=${RUN_ENVIR:-"nco"}
+export PS4='$SECONDS + '
+date
+
+
+#############################
+# Source relevant config files
+#############################
+export EXPDIR=${EXPDIR:-$HOMEgfs/parm/config}
+configs="base anal echgres"
+config_path=${EXPDIR:-$NWROOT/gfs.${gfs_ver}/parm/config}
+for config in $configs; do
+    . $config_path/config.$config
+    status=$?
+    [[ $status -ne 0 ]] && exit $status
+done
+
+
+##########################################
+# Source machine runtime environment
+##########################################
+. $HOMEgfs/env/${machine}.env anal
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+
+##############################################
+# Obtain unique process id (pid) and make temp directory
+##############################################
+export pid=${pid:-$$}
+export outid=${outid:-"LL$job"}
+
+export DATA=${DATA:-${DATAROOT}/${jobid:?}}
+mkdir -p $DATA
+cd $DATA
+
+
+##############################################
+# Run setpdy and initialize PDY variables
+##############################################
+export cycle="t${cyc}z"
+setpdy.sh
+. ./PDY
+
+
+##############################################
+# Determine Job Output Name on System
+##############################################
+export pgmout="OUTPUT.${pid}"
+export pgmerr=errfile
+
+
+##############################################
+# Set variables used in the script
+##############################################
+export CDATE=${CDATE:-${PDY}${cyc}}
+export CDUMP=${CDUMP:-${RUN:-"gfs"}}
+export COMPONENT=${COMPONENT:-atmos}
+export DO_CALC_ANALYSIS=${DO_CALC_ANALYSIS:-"YES"}
+
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+GDATE=$($NDATE -$assim_freq $CDATE)
+gPDY=$(echo $GDATE | cut -c1-8)
+gcyc=$(echo $GDATE | cut -c9-10)
+GDUMP=${GDUMP:-"gdas"}
+
+export OPREFIX="${CDUMP}.t${cyc}z."
+export GPREFIX="${GDUMP}.t${gcyc}z."
+export APREFIX="${CDUMP}.t${cyc}z."
+export GSUFFIX=${GSUFFIX:-$SUFFIX}
+export ASUFFIX=${ASUFFIX:-$SUFFIX}
+
+
+if [ $RUN_ENVIR = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
+    export COMIN=${COMIN:-$ROTDIR/$RUN.$PDY/$cyc/$COMPONENT}
+    export COMOUT=${COMOUT:-$ROTDIR/$RUN.$PDY/$cyc/$COMPONENT}
+    export COMOUT_ENS=${COMOUT_ENS:-$ROTDIR/enkfgdas.$PDY/$cyc/$COMPONENT}
+    export COMIN_OBS=${COMIN_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/$RUN.$PDY/$cyc/$COMPONENT}
+    export COMIN_GES_OBS=${COMIN_GES_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/$GDUMP.$gPDY/$gcyc/$COMPONENT}
+else
+    export COMOUT="$ROTDIR/$CDUMP.$PDY/$cyc/$COMPONENT"
+    export COMOUT_ENS="$ROTDIR/enkfgdas.$PDY/$cyc/$COMPONENT"
+    export COMIN_OBS="$DMPDIR/$CDUMP.$PDY/$cyc/$COMPONENT"
+    export COMIN_GES_OBS="$DMPDIR/$GDUMP.$gPDY/$gcyc/$COMPONENT"
+fi
+mkdir -m 775 -p $COMOUT
+# COMIN_GES and COMIN_GES_ENS are used in script
+export COMIN_GES="$ROTDIR/$GDUMP.$gPDY/$gcyc/$COMPONENT"
+export COMIN_GES_ENS="$ROTDIR/enkfgdas.$gPDY/$gcyc/$COMPONENT"
+
+###############################################################
+# Run relevant script
+env
+echo "HAS BEGUN on $(hostname)"
+$LOGSCRIPT
+
+
+${CHGRESFCSTSH:-$SCRgfs/exgdas_atmos_chgres_forenkf.sh}
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [ -e "$pgmout" ] ; then
+  cat $pgmout
+fi
+
+
+echo "ENDED NORMALLY."
+
+
+##########################################
+# Remove the Temporary working directory
+##########################################
+cd $DATAROOT
+[[ $KEEPDATA = "NO" ]] && rm -rf $DATA
+
+date
+exit 0