From 06bce0edcb32844f9a07b7bee291be49c6971d99 Mon Sep 17 00:00:00 2001
From: WenMeng-NOAA <48260754+WenMeng-NOAA@users.noreply.github.com>
Date: Mon, 14 Sep 2020 20:08:42 -0400
Subject: [PATCH] Update workflow scripts for gfs v16 EE2 review (#183)

* Add changes in workflow scripts based on Eric's EE2 review.

* Update gfs_transfer.sh for GFS V16.
---
 scripts/exgdas_nceppost.sh | 25 +++++++++++--------------
 scripts/exgfs_nceppost.sh  | 25 ++++++++++++-------------
 scripts/exglobal_pmgr.sh   |  2 +-
 ush/gfs_nceppost.sh        |  1 +
 ush/gfs_transfer.sh        |  7 ++++---
 5 files changed, 29 insertions(+), 31 deletions(-)

diff --git a/scripts/exgdas_nceppost.sh b/scripts/exgdas_nceppost.sh
index a4da491f9..862c18b4a 100755
--- a/scripts/exgdas_nceppost.sh
+++ b/scripts/exgdas_nceppost.sh
@@ -15,6 +15,7 @@ echo "                 from j-job script."
 echo " Feb 18 - Meng - Removed legacy setting for generating grib1 data"
 echo "                 and reading sigio model outputs."
 echo " Aug 20 - Meng - Remove .ecf extentsion per EE2 review."
+echo " Sep 20 - Meng - Update clean up files per EE2 review."
 echo "-----------------------------------------------------"
 #####################################################################
 
@@ -63,7 +64,6 @@ export machine=${machine:-WCOSS_C}
 ###########################
 # Specify Output layers
 ###########################
-#export POSTGPVARS="KPO=50,PO=1000.,975.,950.,925.,900.,875.,850.,825.,800.,775.,750.,725.,700.,675.,650.,625.,600.,575.,550.,525.,500.,475.,450.,425.,400.,375.,350.,325.,300.,275.,250.,225.,200.,175.,150.,125.,100.,70.,50.,40.,30.,20.,15.,10.,7.,5.,3.,2.,1.,0.4,"
 export POSTGPVARS="KPO=57,PO=1000.,975.,950.,925.,900.,875.,850.,825.,800.,775.,750.,725.,700.,675.,650.,625.,600.,575.,550.,525.,500.,475.,450.,425.,400.,375.,350.,325.,300.,275.,250.,225.,200.,175.,150.,125.,100.,70.,50.,40.,30.,20.,15.,10.,7.,5.,3.,2.,1.,0.7,0.4,0.2,0.1,0.07,0.04,0.02,0.01,"
 
 ##########################################################
@@ -114,17 +114,19 @@ then
      export CTLFILE=$PARMpost/postcntrl_gfs_anl.xml
    fi
 
-   rm sigfile sfcfile nemsfile
+   [[ -f flxfile ]] && rm flxfile ; [[ -f nemsfile ]] && rm nemsfile
    if [ $OUTTYP -eq 4 ] ; then
-      export NEMSINP=$COMIN/${PREFIX}atmanl${SUFFIX}
-      export FLXINP=$COMIN/${PREFIX}sfcanl${SUFFIX}
+      ln -fs $COMIN/${PREFIX}atmanl${SUFFIX} nemsfile
+      export NEMSINP=nemsfile
+      ln -fs $COMIN/${PREFIX}sfcanl${SUFFIX} flxfile
+      export FLXINP=flxfile
    fi
    export PGBOUT=pgbfile
    export PGIOUT=pgifile
    export PGBOUT2=pgbfile.grib2
    export PGIOUT2=pgifile.grib2.idx
    export IGEN=$IGEN_ANL
-   export FILTER=1  
+   export FILTER=0  
 
  #specify fhr even for analysis because postgp uses it    
 #   export fhr=00
@@ -173,7 +175,7 @@ then
       fi
 
    fi
-   rm pgbfile pgifile pgbfile.grib2 tfile prmsl h5wav
+   rm pgbfile.grib2 
 fi
 
 #----------------------------------
@@ -211,7 +213,7 @@ do
        ###############################
        if [ $ic -eq $SLEEP_LOOP_MAX ]
        then
-          echo " *** FATA ERROR: No model output in nemsio for f${fhr} "
+          echo " *** FATAL ERROR: No model output in nemsio for f${fhr} "
           export err=9
           err_chk
        fi
@@ -225,7 +227,7 @@ do
     # Put restart files into /nwges 
     # for backup to start Model Fcst
     ###############################
-    rm -f sigfile sfcfile flxfile nemsfile
+    [[ -f flxfile ]] && rm flxfile ; [[ -f nemsfile ]] && rm nemsfile
     if [ $OUTTYP -eq 4 ] ; then
       ln -sf $COMIN/${PREFIX}atmf$fhr${SUFFIX} nemsfile
       export NEMSINP=nemsfile
@@ -318,13 +320,8 @@ do
       $DBNROOT/bin/dbn_alert MODEL ${run}_PGB2_0P25_WIDX $job $COMOUT/${PREFIX}pgrb2.0p25.f${fhr}.idx
       $DBNROOT/bin/dbn_alert MODEL ${run}_PGB_GB2 $job $COMOUT/${PREFIX}pgrb2.1p00.f${fhr}
       $DBNROOT/bin/dbn_alert MODEL ${run}_PGB_GB2_WIDX $job $COMOUT/${PREFIX}pgrb2.1p00.f${fhr}.idx
-#      $DBNROOT/bin/dbn_alert MODEL ${run}_PGB_GB2 $job $COMOUT/${RUN}.${cycle}.pgrb2.0p50.f${fhr3}
-#      $DBNROOT/bin/dbn_alert MODEL ${run}_PGB_GB2_WIDX $job $COMOUT/${RUN}.${cycle}.pgrb2.0p50.f${fhr3}.idx
-#      $DBNROOT/bin/dbn_alert MODEL ${run}_PGB $job $COMOUT/${PREFIX}pgrbf${fhr}
-#      $DBNROOT/bin/dbn_alert MODEL ${run}_PGBI $job $COMOUT/${PREFIX}pgrbif${fhr}
     fi
     
-#    echo "$PDY$cyc$fhr" > $COMOUT/${RUN}.t${cyc}z.${RUN_FLAG}control
  
     if test $SENDCOM = 'YES'
     then
@@ -371,7 +368,7 @@ do
       fi
     fi 
 
-    rm pgbfile pgifile pgbfile.grib2 flxfile flxifile flxfile.grib2 flxfile.grib2.idx tfile prmsl h5wav
+    [[ -f pgbfile.grib2 ]] && rm pgbfile.grib2 ; [[ -f flxfile ]] && rm flxfile
 
 done 
 
diff --git a/scripts/exgfs_nceppost.sh b/scripts/exgfs_nceppost.sh
index 750d55cb5..53a065527 100755
--- a/scripts/exgfs_nceppost.sh
+++ b/scripts/exgfs_nceppost.sh
@@ -24,6 +24,7 @@ echo "                 from j-job script."
 echo " Feb 18 - Meng - Removed legacy setting for generating grib1 data"
 echo "                 and reading sigio model outputs."
 echo " Aug 20 - Meng - Remove .ecf extentsion per EE2 review."
+echo " Sep 20 - Meng - Update clean up files per EE2 review."
 echo "-----------------------------------------------------"
 #####################################################################
 
@@ -74,7 +75,6 @@ export machine=${machine:-WCOSS_C}
 ###########################
 # Specify Output layers
 ###########################
-#export POSTGPVARS="KPO=50,PO=1000.,975.,950.,925.,900.,875.,850.,825.,800.,775.,750.,725.,700.,675.,650.,625.,600.,575.,550.,525.,500.,475.,450.,425.,400.,375.,350.,325.,300.,275.,250.,225.,200.,175.,150.,125.,100.,70.,50.,40.,30.,20.,15.,10.,7.,5.,3.,2.,1.,0.4,"
 export POSTGPVARS="KPO=57,PO=1000.,975.,950.,925.,900.,875.,850.,825.,800.,775.,750.,725.,700.,675.,650.,625.,600.,575.,550.,525.,500.,475.,450.,425.,400.,375.,350.,325.,300.,275.,250.,225.,200.,175.,150.,125.,100.,70.,50.,40.,30.,20.,15.,10.,7.,5.,3.,2.,1.,0.7,0.4,0.2,0.1,0.07,0.04,0.02,0.01,"
 
 ##########################################################
@@ -117,7 +117,7 @@ then
      export CTLFILE=$PARMpost/postcntrl_gfs_anl.xml
    fi
 
-   rm sigfile sfcfile nemsfile
+   [[ -f flxfile ]] && rm flxfile ; [[ -f nemsfile ]] && rm nemsfile
    if [ $OUTTYP -eq 4 ] ; then
      ln -fs $COMIN/${PREFIX}atmanl${SUFFIX} nemsfile
      export NEMSINP=nemsfile
@@ -130,14 +130,14 @@ then
    export PGBOUT2=pgbfile.grib2
    export PGIOUT2=pgifile.grib2.idx
    export IGEN=$IGEN_ANL
-   export FILTER=1
+   export FILTER=0
 
    $POSTGPSH
    export err=$?; err_chk
    
    if test $GRIBVERSION = 'grib2'
    then
-     cp $PGBOUT $PGBOUT2
+     mv $PGBOUT $PGBOUT2
    fi
 
 #  Process pgb files
@@ -185,7 +185,7 @@ then
      fi 
 
    fi
-   rm pgbfile pgifile pgbfile.grib2 tfile prmsl h5wav
+   [[ -f pgbfile.grib2 ]] && rm pgbfile.grib2 
 #   ecflow_client --event release_pgrb2_anl
 
 ##########################  WAFS U/V/T analysis start ##########################
@@ -265,7 +265,7 @@ do
        ###############################
        if [ $ic -eq $SLEEP_LOOP_MAX ]
        then
-          echo " *** FATA ERROR: No model output in nemsio for f${fhr} "
+          echo " *** FATAL ERROR: No model output in nemsio for f${fhr} "
           export err=9
           err_chk
        fi
@@ -279,7 +279,7 @@ do
     # Put restart files into /nwges 
     # for backup to start Model Fcst
     ###############################
-    rm sigfile sfcfile flxfile nemsfile
+    [[ -f flxfile ]] && rm flxfile ; [[ -f nemsfile ]] && rm nemsfile
     if [ $OUTTYP -eq 4 ] ; then
       ln -fs $COMIN/${PREFIX}atmf${fhr}${SUFFIX} nemsfile
       export NEMSINP=nemsfile
@@ -326,7 +326,6 @@ do
           export CTLFILE=${CTLFILEGFS:-$PARMpost/postcntrl_gfs.xml}
         fi
       fi
-#      export CTL=`basename $CTLFILE1`
     fi
     
     export FLXIOUT=flxifile
@@ -363,7 +362,6 @@ do
 
     if test $SENDCOM = "YES"
     then
-	#      echo "$PDY$cyc$pad$fhr" > $COMOUT/${RUN}.t${cyc}z.master.control
 	if [ $GRIBVERSION = 'grib2' ] ; then
             if [ $INLINE_POST = ".false." ]; then 
               cp $PGBOUT2 $COMOUT/${MASTERFL} 
@@ -408,7 +406,7 @@ do
 	$USHgfs/gfs_transfer.sh
 	#      fi
     fi
-    rm pgbfile* pgifile* tfile prmsl h5wav
+    [[ -f pgbfile.grib2 ]] && rm pgbfile.grib2
 
 # use post to generate GFS Grib2 Flux file as model generated Flux file
 # will be in nemsio format after FY17 upgrade.
@@ -490,8 +488,6 @@ do
        mv goesifile $COMOUT/${SPECIALFLIDX}f$fhr
 
     fi
-   # rm flxfile flxifile goesfile goesifile    
-    rm flxifile goesfile goesifile    
     fi
 # end of satellite processing
 
@@ -529,16 +525,19 @@ do
 
           export err=$?; err_chk
 
+          if [ -e $PGBOUT ]
+          then
           if test $SENDCOM = "YES"
           then
               cp $PGBOUT $COMOUT/${PREFIX}wafs.grb2f$fhr
               cp $PGIOUT $COMOUT/${PREFIX}wafs.grb2if$fhr
           fi
+          fi
       fi
+      [[ -f wafsfile ]] && rm wafsfile ; [[ -f wafsifile ]] && rm wafsifile
     fi
 ###########################  WAFS  end ###########################
 
-    rm flxfile flxifile wafsfile wafsifile
 
 done
 
diff --git a/scripts/exglobal_pmgr.sh b/scripts/exglobal_pmgr.sh
index a9bcb4251..58784241c 100755
--- a/scripts/exglobal_pmgr.sh
+++ b/scripts/exglobal_pmgr.sh
@@ -67,7 +67,7 @@ do
 
   sleep 10
   icnt=$((icnt + 1))
-  if [ $icnt -ge 1080 ]
+  if [ $icnt -ge 1001 ]
   then
     msg="ABORTING after 3 hours of waiting for ${RUN} FCST hours $postjobs."
     err_exit $msg
diff --git a/ush/gfs_nceppost.sh b/ush/gfs_nceppost.sh
index 7e8bc361b..409163739 100755
--- a/ush/gfs_nceppost.sh
+++ b/ush/gfs_nceppost.sh
@@ -379,6 +379,7 @@ if [ $GRIBVERSION = grib2 ]; then
 #cat $PGBOUT prmsl h5wav >> $PGBOUT
 #wm
 #  cat  prmsl h5wav >> $PGBOUT
+[[ -f prmsl ]] && rm prmsl ; [[ -f h5wav ]] && rm h5wav ; [[ -f tfile ]] && rm tfile  
 
 fi
 
diff --git a/ush/gfs_transfer.sh b/ush/gfs_transfer.sh
index f6ff4c721..028004d90 100755
--- a/ush/gfs_transfer.sh
+++ b/ush/gfs_transfer.sh
@@ -11,6 +11,7 @@ echo " History - "
 echo "    Cooke   - 04/21/05 - Inital version, based off of"
 echo "                         global_transfer.sh"
 echo "    Meng    - 01/04/18 - Remove writing data file to /nwges."
+echo "    Meng    - 09/14/20 - Update model output format to netcdf for GFS V16"
 echo "-----------------------------------------------------"
 #####################################################################
 set -xa
@@ -67,16 +68,16 @@ then
   #fi
 
   fhr=`printf "%03d" $fhr`
-  $DBNROOT/bin/dbn_alert MODEL GFS_SF $job $COMOUT/${RUN}.t${cyc}z.atmf$fhr.nemsio
+  $DBNROOT/bin/dbn_alert MODEL GFS_SF $job $COMOUT/${RUN}.t${cyc}z.atmf$fhr.nc
 
  
   if [[ $fhr -gt 0  && $fhr -le 84  ]]
   then
-     $DBNROOT/bin/dbn_alert MODEL GFS_BF $job $COMOUT/${RUN}.t${cyc}z.sfcf$fhr.nemsio
+     $DBNROOT/bin/dbn_alert MODEL GFS_BF $job $COMOUT/${RUN}.t${cyc}z.sfcf$fhr.nc
   fi
   if [[ $fhr -eq 120  ]]
   then
-     $DBNROOT/bin/dbn_alert MODEL GFS_BF $job $COMOUT/${RUN}.t${cyc}z.sfcf$fhr.nemsio
+     $DBNROOT/bin/dbn_alert MODEL GFS_BF $job $COMOUT/${RUN}.t${cyc}z.sfcf$fhr.nc
   fi
 fi