GitHub Issue #118. Merging updated master with PR branch

CMakeLists.txt

@@ -175,8 +175,8 @@ project(GSI)
     find_package( LAPACK )
   endif()
 # build the WRF I/O libraries
-  if(DEFINED ENV{GSIWRF_LIB})
-    set(wrflib "$ENV{GSIWRF_LIB}" CACHE INTERNAL "WRFIO library" )
+  if(DEFINED ENV{WRF_IO_LIB})
+    set(wrflib "$ENV{WRF_IO_LIB}" CACHE INTERNAL "WRFIO library" )
   elseif(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/libsrc/wrflib)
     add_subdirectory(libsrc/wrflib)
   else()
@@ -260,8 +260,8 @@ project(GSI)
   endif(BUILD_ENKF) 
   if(BUILD_UTIL)
     add_subdirectory(util/EnKF/gfs/src)
-    add_subdirectory(util/Ozone_Monitor/nwprod/oznmon_shared.v2.0.0/sorc/oznmon_horiz.fd)
-    add_subdirectory(util/Ozone_Monitor/nwprod/oznmon_shared.v2.0.0/sorc/oznmon_time.fd)
+    add_subdirectory(util/Ozone_Monitor/nwprod/oznmon_shared/sorc/oznmon_horiz.fd)
+    add_subdirectory(util/Ozone_Monitor/nwprod/oznmon_shared/sorc/oznmon_time.fd)
     add_subdirectory(util/Radiance_Monitor/nwprod/radmon_shared/sorc/verf_radang.fd)
     add_subdirectory(util/Radiance_Monitor/nwprod/radmon_shared/sorc/verf_radbcoef.fd)
     add_subdirectory(util/Radiance_Monitor/nwprod/radmon_shared/sorc/verf_radbcor.fd)

cmake/Modules/FindBUFR.cmake

@@ -11,8 +11,8 @@ endif()
 
 set( NO_DEFAULT_PATH )
 if(NOT BUILD_BUFR )
-  if(DEFINED ENV{BUFR_LIBd} )
-    set(BUFR_LIBRARY $ENV{BUFR_LIBd} )
+  if(DEFINED ENV{BUFR_LIBd_DA} )
+    set(BUFR_LIBRARY $ENV{BUFR_LIBd_DA} )
     message("BUFR library ${BUFR_LIBRARY} set via Environment variable")
   else()
   find_library( BUFR_LIBRARY 

cmake/Modules/FindCORELIBS.cmake

@@ -102,8 +102,8 @@ else()
     set( w3nco "w3nco${libsuffix}")
 endif()
 if(NOT  BUILD_BUFR  )
-  if(DEFINED ENV{BUFR_LIBd} )
-    set(BUFR_LIBRARY $ENV{BUFR_LIBd} )
+  if(DEFINED ENV{BUFR_LIBd_DA} )
+    set(BUFR_LIBRARY $ENV{BUFR_LIBd_DA} )
   else()
   find_library( BUFR_LIBRARY 
     NAMES libbufr.a libbufr_d_64.a libbufr_i4r8.a libbufr_v${BUFR_VER}_d_64.a

cmake/Modules/platforms/Generic.cmake

@@ -20,5 +20,6 @@ macro (setGeneric)
   set(BUILD_SP "OFF" CACHE INTERNAL "Build the SP library" )
   set(BUILD_CRTM "OFF" CACHE INTERNAL "Build the CRTM library" )
   set(BUILD_W3EMC "OFF" CACHE INTERNAL "Build the EMC library" )
+  set(BUILD_W3NCO "OFF" CACHE INTERNAL "Build the EMC library" )
   set(BUILD_NCO "OFF" CACHE INTERNAL "Build the NCO library" )
 endmacro()

cmake/Modules/setHOST.cmake

@@ -33,8 +33,7 @@ macro( setHOST )
   string(REGEX MATCH "discover" HOST-Discover ${HOSTNAME} )
   string(REGEX MATCH "cheyenne" HOST-Cheyenne ${HOSTNAME}  )
   message("done figuring out host--${HOSTNAME}")
-  if ( BUILD_CORELIBS )
-    MESSAGE(STATUS "BUILD_CORELIBS manually-specified as ON")
+  if ( COMGSI )
     set( host "GENERIC"  )
     set( HOST-Generic "TRUE"  )
     setGeneric()

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
+

jobs/JGDAS_EFSOI

@@ -0,0 +1,133 @@
+#!/bin/ksh
+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 efsoi"
+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 efsoi
+
+
+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.${pid}"
+export pgmerr=errfile
+
+
+##############################################
+# Set variables used in the exglobal script
+##############################################
+export CDATE=${CDATE:-${PDY}${cyc}}
+export CDUMP=${CDUMP:-${RUN:-"gdas"}}
+export COMPONENT=${COMPONENT:-atmos}
+if [ $RUN_ENVIR = "nco" ]; then
+    export ROTDIR=${COMROOT:?}/$NET/$envir
+fi
+
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+GDATE=$($NDATE -$assim_freq $CDATE)
+gPDY=$(echo $GDATE | cut -c1-8)
+export gcyc=$(echo $GDATE | cut -c9-10) # needed in namelist
+
+VDATE=$($NDATE 24 $CDATE)
+vPDY=$(echo $VDATE | cut -c1-8)
+vcyc=$(echo $VDATE | cut -c9-10)
+
+export APREFIX="${CDUMP}.t${cyc}z."
+export GPREFIX="gdas.t${gcyc}z."
+export ASUFFIX=${ASUFFIX:-$SUFFIX}
+export GSUFFIX=${GSUFFIX:-$SUFFIX}
+
+
+
+# COMIN_GES_ENS and COMOUT_ANL_ENS are used in script
+export COMIN_GES_ENS="$ROTDIR/efsoigdas.$gPDY/$gcyc/$COMPONENT"
+export COMOUT_ANL_ENS="$ROTDIR/enkf$CDUMP.$PDY/$cyc/$COMPONENT"
+export COMIN_ANL="$ROTDIR/$CDUMP.$vPDY/$vcyc/$COMPONENT"
+export COMOUT_ANL_ENSFSOI="$ROTDIR/efsoi$CDUMP.$PDY/$cyc/$COMPONENT"
+export OSENSE_SAVE_DIR="$ROTDIR/osense"
+mkdir -p $OSENSE_SAVE_DIR
+# ========================================================
+
+###############################################################
+# Run relevant exglobal script
+env
+msg="HAS BEGUN on `hostname`"
+postmsg "$jlogfile" "$msg"
+$LOGSCRIPT
+
+${EFSOIUPDSH:-$SCRgfs/exgdas_efsoi.sh}
+status=$?
+[[ $status -ne 0 ]] && exit $status
+
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [ -e "$pgmout" ] ; then
+  cat $pgmout
+fi
+
+
+msg="ENDED NORMALLY."
+postmsg "$jlogfile" "$msg"
+
+
+##########################################
+# Remove the Temporary working directory
+##########################################
+cd $DATAROOT
+
+[[ $KEEPDATA = "NO" ]] && rm -rf $DATA
+
+date
+exit 0