GitHub Issue NOAA-EMC#120. merge GFS v16.1.1 DA changes into master

AndrewEichmann-NOAA · Jun 1, 2021 · d199ed5 · d199ed5
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diff --git a/doc/Release_Notes.gfsda.v16.1.0.txt b/doc/Release_Notes.gfsda.v16.1.0.txt
@@ -0,0 +1,121 @@
+GFSDA.v16.1.0 RELEASE NOTES
+
+
+PRELUDE
+
+* The tag gfsda.v16.1.0 was created in the NOAA-EMC/GSI repository to 
+  support the GFSv16.1 implementation and is included as a part of the 
+  NOAA-EMC/global-workflow tag EMC-v16.1.0.  See release notes
+  docs/Release_Notes.gfs.v16.1.0.txt in the NOAA-EMC/global-workflow 
+  tag for more details on the motivation, workflow changes, and 
+  implementation instructions.
+
+
+FIX CHANGES
+
+* fix/
+  * global_convinfo.txt: Change GeoOptics (SAID=265) from -1 to 1 
+    for active assimilation
+
+
+SCRIPTS CHANGES
+
+* scripts/
+  * exgdas_atmos_chgres_forenkf.sh: Addresses GFSv16 bugzilla #1198
+  * exgdas_enkf_ecen.sh:  Addresses GFSv16 bugzilla #1198
+  * exgdas_enkf_fcst.sh:  Addresses GFSv16 bugzilla #1198
+  * exgdas_enkf_post.sh:  Addresses GFSv16 bugzilla #1198
+  * exgdas_enkf_select_obs.sh:  Addresses GFSv16 bugzilla #1198
+  * exgdas_enkf_sfc.sh:  Addresses GFSv16 bugzilla #1198
+  * exgdas_enkf_update.sh:  Addresses GFSv16 bugzilla #1198
+  * exglobal_atmos_analysis.sh:  Addresses GFSv16 bugzilla #1198, 
+    adds default values for commercial RO parameters
+  * exglobal_atmos_analysis_calc.sh:  Addresses GFSv16 bugzilla #1198
+  * exglobal_diag.sh:  Addresses GFSv16 bugzilla #1198
+
+
+SRC CHANGES
+
+* src/
+  * enkf/
+     * gridio_gfs.f90: Changes delz calculation to negative definite
+
+  * fv3gfs_ncio/
+    *  module_fv3gfs_ncio.f90: Addresses GFSv16 bugzilla #1196
+
+  * gsi/
+    * cplr_gfs_ensmod.f90: Addresses GFSv16 bugzilla #1196
+    * genstats_gps.f90: GPSRO bugfix 
+    * gesinfo.F90: Addresses GFSv16 bugzilla #1196
+    * gsimod.F90: Add commercial RO parameters
+    * guess_grids.F90: Add commercial RO parameters
+    * ncepnems_io.f90:  Changes delz calculation to negative definite
+    * netcdfgfs_io.f90: Addresses GFSv16 bugzilla #1196 and delz sign bugfix
+    * read_files.f90: Addresses GFSv16 bugzilla #1196
+    * read_fl_hdob.f90: Addresses GFSv16 bugzilla #1205
+    * setupbend.f90: New QC and error inflation for commercial RO
+    * setuprad.f90:  Bugfix for radiance diags 
+    * stop1.f90: Addresses GFSv16 bugzilla #1196
+    * write_incr.f90: Delz bugfix
+
+
+USH CHANGES
+
+* ush/
+  * build_all_cmake.sh: Addresses DA aspects of GFSv16 bugzillas 
+    #216, #1218, and #1222
+  * prune_4nco_global.sh: New script to address DA aspects of GFSv16 
+    bugzillas #216 and #1222
+
+
+UTIL CHANGES
+
+* util/Radiance_Monitor/nwprod/gdas_radmon.v3.0.0/scripts/exgdas_atmos_verfrad.sh: 
+  chgrp Megha-Tropiques SAPHIR radiance diagnostic file to rsptrod since 
+  this is a restricted data type, partially address DA aspects of GFSv16 
+  bugzilla #1221.
+
+
+IMPLEMENTATION INSTRUCTIONS
+
+* The GFS DA v16.1 tag must be installed in conjunction with the entire 
+  GFS v16.1 package.  See release notes docs/Release_Notes.gfs.v16.1.0.txt 
+  in the NOAA-EMC/global-workflow tag EMC-v16.1.0 tag for instructions.
+
+
+PRE-IMPLEMENTATION TESTING REQUIREMENTS
+
+* Which production jobs should be tested as part of this implementation?
+  * The GFS DA package needs to be tested with the entire GFS suite.
+
+* Does this change require a 30-day evaluation?
+  * No.
+
+
+DISSEMINATION INFORMATION
+
+* Where should this output be sent?
+  * No change from GFS v16.0
+
+* Who are the users?
+  * No change from GFS v16.0
+
+* Which output files should be transferred from PROD WCOSS to DEV WCOSS?
+  * No change from GFS v16.0
+
+* Directory changes
+  * No change from GFS v16.0
+
+* File changes
+  * No change from GFS v16.0
+
+
+HPSS ARCHIVE
+
+* No change from GFS v16.0
+
+
+JOB DEPENDENCIES & FLOW DIAGRAM
+
+* No change from GFSv16.0
+
diff --git a/fix b/fix
diff --git a/scripts/exgdas_atmos_chgres_forenkf.sh b/scripts/exgdas_atmos_chgres_forenkf.sh
@@ -48,7 +48,6 @@ export NMV=${NMV:-"/bin/mv"}
 export NLN=${NLN:-"/bin/ln -sf"}
 export CHGRP_CMD=${CHGRP_CMD:-"chgrp ${group_name:-rstprod}"}
 export NCLEN=${NCLEN:-$HOMEgfs/ush/getncdimlen}
-export ERRSCRIPT=${ERRSCRIPT:-'eval [[ $err = 0 ]]'}
 
 # IAU
 DOIAU=${DOIAU:-"NO"}
@@ -176,10 +175,7 @@ EOF
          . prep_step
 
 	 $APRUN_CHGRES $CHGRESNCEXEC chgres_nc_gauss0$FHR.nml
-	 rc=$?
-	 export ERR=$rc
-	 export err=$ERR
-	 $ERRSCRIPT || exit 1
+         export err=$?; err_chk
      fi
    done
 
@@ -194,9 +190,7 @@ EOF
          . prep_step
 
          $APRUNCFP_CHGRES $DATA/mp_chgres.sh
-         export ERR=$?
-         export err=$ERR
-         $ERRSCRIPT || exit 3
+         export err=$?; err_chk
       fi
    fi
 

diff --git a/scripts/exgdas_enkf_ecen.sh b/scripts/exgdas_enkf_ecen.sh
@@ -34,7 +34,6 @@ export CASE=${CASE:-384}
 ntiles=${ntiles:-6}
 
 # Utilities
-ERRSCRIPT=${ERRSCRIPT:-'eval [[ $err = 0 ]]'}
 NCP=${NCP:-"/bin/cp -p"}
 NLN=${NLN:-"/bin/ln -sf"}
 NEMSIOGET=${NEMSIOGET:-${NWPROD}/exec/nemsio_get}
@@ -164,11 +163,7 @@ if [ $DO_CALC_INCREMENT = "YES" ]; then
 
    $NCP $GETATMENSMEANEXEC $DATA
    $APRUN_ECEN ${DATA}/$(basename $GETATMENSMEANEXEC) $DATAPATH $ATMANLMEANNAME $ATMANLNAME $NMEM_ENKF
-   rc=$?
-
-   export ERR=$rc
-   export err=$ERR
-   $ERRSCRIPT || exit 2
+   export err=$?; err_chk
 else
    # Link ensemble mean increment
    if [ $FHR -eq 6 ]; then
@@ -188,11 +183,7 @@ else
 
    $NCP $GETATMENSMEANEXEC $DATA
    $APRUN_ECEN ${DATA}/$(basename $GETATMENSMEANEXEC) $DATAPATH $ATMINCMEANNAME $ATMINCNAME $NMEM_ENKF
-   rc=$?
-
-   export ERR=$rc
-   export err=$ERR
-   $ERRSCRIPT || exit 2
+   export err=$?; err_chk
 
    # If available, link to ensemble mean guess.  Otherwise, compute ensemble mean guess
    if [ -s $COMIN_GES_ENS/${GPREFIX}atmf00${FHR}.ensmean$GSUFFIX ]; then
@@ -208,11 +199,7 @@ else
 
        $NCP $GETATMENSMEANEXEC $DATA
        $APRUN_ECEN ${DATA}/$(basename $GETATMENSMEANEXEC) $DATAPATH $ATMGESMEANNAME $ATMGESNAME $NMEM_ENKF
-       rc=$?
-
-       export ERR=$rc
-       export err=$ERR
-       $ERRSCRIPT || exit 2
+       export err=$?; err_chk
    fi
 fi
 
@@ -284,12 +271,7 @@ if [ $RECENTER_ENKF = "YES" ]; then
 EOF
       cat $chgresnml
       $APRUN_CHGRES ./chgres.x
-      rc=$?
-
-      export ERR=$rc
-      export err=$ERR
-      $ERRSCRIPT || exit 3
-
+      export err=$?; err_chk
    fi
 
    if [ $DO_CALC_INCREMENT = "YES" ]; then
@@ -307,12 +289,7 @@ EOF
 
       $NCP $RECENATMEXEC $DATA
       $APRUN_ECEN ${DATA}/$(basename $RECENATMEXEC) $FILENAMEIN $FILENAME_MEANIN $FILENAME_MEANOUT $FILENAMEOUT $NMEM_ENKF
-      rc=$?
-
-      export ERR=$rc
-      export err=$ERR
-      $ERRSCRIPT || exit 2
-
+      export err=$?; err_chk
    else
       ################################################################################
       # Recenter ensemble member atmospheric increments about hires analysis
@@ -340,12 +317,7 @@ cat recenter.nml
 
       $NCP $RECENATMEXEC $DATA
       $APRUN_ECEN ${DATA}/$(basename $RECENATMEXEC) $FILENAMEIN $FILENAME_INCMEANIN $FILENAME_GSIDET $FILENAMEOUT $NMEM_ENKF $FILENAME_GESMEANIN
-      rc=$?
-
-      export ERR=$rc
-      export err=$ERR
-      $ERRSCRIPT || exit 2
-
+      export err=$?; err_chk
    fi
 fi
 
@@ -388,11 +360,7 @@ EOF
 cat calc_increment.nml
 
    $APRUN_CALCINC ${DATA}/$(basename $CALCINCEXEC)
-   rc=$?
-
-   export ERR=$rc
-   export err=$rc
-   $ERRSCRIPT || exit 4
+   export err=$?; err_chk
 fi
 done # loop over analysis times in window
 

diff --git a/scripts/exgdas_enkf_fcst.sh b/scripts/exgdas_enkf_fcst.sh
@@ -34,8 +34,6 @@ export FIX_AM=${FIX_AM:-$FIX_DIR/fix_am}
 export NCP=${NCP:-"/bin/cp -p"}
 export NMV=${NMV:-"/bin/mv"}
 export NLN=${NLN:-"/bin/ln -sf"}
-export ERRSCRIPT=${ERRSCRIPT:-'eval [[ $err = 0 ]]'}
-export NDATE=${NDATE:-/$NWPROD/util/exec/ndate}
 
 # Scripts.
 FORECASTSH=${FORECASTSH:-$HOMEgfs/scripts/exglobal_forecast.sh}
@@ -170,15 +168,13 @@ for imem in $(seq $ENSBEG $ENSEND); do
       export MEMBER=$imem
       export DATA=$DATATOP/$memchar
       if [ -d $DATA ]; then rm -rf $DATA; fi
+      mkdir -p $DATA
       $FORECASTSH
       ra=$?
 
       # Notify a member forecast failed and abort
       if [ $ra -ne 0 ]; then
-         msg="FATAL ERROR:  forecast of member $cmem FAILED.  Aborting job"
-         print $msg
-         export err=$ra
-         $ERRSCRIPT || exit 2
+         err_exit "FATAL ERROR:  forecast of member $cmem FAILED.  Aborting job"
       fi
 
       ((rc+=ra))
@@ -226,9 +222,7 @@ cat $EFCSGRP
 
 ################################################################################
 # If any members failed, error out
-export ERR=$rc
-export err=$ERR
-$ERRSCRIPT || exit 2
+export err=$rc; err_chk
 
 ################################################################################
 #  Postprocessing

diff --git a/scripts/exgdas_enkf_post.sh b/scripts/exgdas_enkf_post.sh
@@ -28,7 +28,6 @@ fi
 pwd=$(pwd)
 
 # Utilities
-ERRSCRIPT=${ERRSCRIPT:-'eval [[ $err = 0 ]]'}
 NCP=${NCP:-"/bin/cp"}
 NLN=${NLN:-"/bin/ln -sf"}
 
@@ -127,10 +126,7 @@ for fhr in $(seq $FHMIN $FHOUT $FHMAX); do
    ra=$?
    ((rc+=ra))
 done
-
-export ERR=$rc
-export err=$ERR
-$ERRSCRIPT || exit 2
+export err=$rc; err_chk
 
 ################################################################################
 # If smoothing on but no smoothing output, copy smoothed ensemble atmospheric files

diff --git a/scripts/exgdas_enkf_select_obs.sh b/scripts/exgdas_enkf_select_obs.sh
@@ -29,7 +29,6 @@ pwd=$(pwd)
 
 # Utilities
 export NLN=${NLN:-"/bin/ln -sf"}
-export ERRSCRIPT=${ERRSCRIPT:-'eval [[ $err = 0 ]]'}
 
 # Scripts.
 ANALYSISSH=${ANALYSISSH:-$HOMEgfs/scripts/exglobal_atmos_analysis.sh}
@@ -115,10 +114,7 @@ export CHEM="$CHEM_INVOBS"
 # Execute GSI as a forward operator
 
 $ANALYSISSH
-
-export ERR=$?
-export err=$ERR
-$ERRSCRIPT || exit 2
+export err=$?; err_chk
 
 ################################################################################
 # Postprocessing

diff --git a/scripts/exgdas_enkf_sfc.sh b/scripts/exgdas_enkf_sfc.sh
@@ -35,7 +35,6 @@ export CASE=${CASE:-384}
 ntiles=${ntiles:-6}
 
 # Utilities
-ERRSCRIPT=${ERRSCRIPT:-'eval [[ $err = 0 ]]'}
 NCP=${NCP:-"/bin/cp -p"}
 NLN=${NLN:-"/bin/ln -sf"}
 NEMSIOGET=${NEMSIOGET:-${NWPROD}/exec/nemsio_get}
@@ -163,10 +162,7 @@ if [ $DOIAU = "YES" ]; then
         done
 
         $CYCLESH
-        rc=$?
-        export ERR=$rc
-        export err=$ERR
-        $ERRSCRIPT || exit 11
+        export err=$?; err_chk
 
     done
 
@@ -192,10 +188,7 @@ if [ $DOSFCANL_ENKF = "YES" ]; then
     done
 
     $CYCLESH
-    rc=$?
-    export ERR=$rc
-    export err=$ERR
-    $ERRSCRIPT || exit 11
+    export err=$?; err_chk
 
  done
 fi

diff --git a/scripts/exgdas_enkf_update.sh b/scripts/exgdas_enkf_update.sh
@@ -30,7 +30,6 @@ pwd=$(pwd)
 # Utilities
 NCP=${NCP:-"/bin/cp -p"}
 NLN=${NLN:-"/bin/ln -sf"}
-ERRSCRIPT=${ERRSCRIPT:-'eval [[ $err = 0 ]]'}
 NEMSIOGET=${NEMSIOGET:-$NWPROD/utils/exec/nemsio_get}
 NCLEN=${NCLEN:-$HOMEgfs/ush/getncdimlen}
 USE_CFP=${USE_CFP:-"NO"}
@@ -245,9 +244,7 @@ if [ $USE_CFP = "YES" ]; then
       ncmd_max=$((ncmd < npe_node_max ? ncmd : npe_node_max))
       APRUNCFP=$(eval echo $APRUNCFP)
       $APRUNCFP $DATA/mp_untar.sh
-      export ERR=$?
-      export err=$ERR
-      $ERRSCRIPT || exit 3
+      export err=$?; err_chk
    fi
 fi
 
@@ -378,11 +375,7 @@ export pgm=$ENKFEXEC
 
 $NCP $ENKFEXEC $DATA
 $APRUN_ENKF ${DATA}/$(basename $ENKFEXEC) 1>stdout 2>stderr
-rc=$?
-
-export ERR=$rc
-export err=$ERR
-$ERRSCRIPT || exit 2
+export err=$?; err_chk
 
 # Cat runtime output files.
 cat stdout stderr > $COMOUT_ANL_ENS/$ENKFSTAT