Implement fix reorg and remove gfs-utils code

.gitignore

@@ -17,8 +17,23 @@ install*/
 # Ignore fix directory symlinks
 #------------------------------
 fix/0readme
-fix/fix_*
-fix/gdas/
+fix/aer
+fix/am
+fix/chem
+fix/cice
+fix/cpl
+fix/datm
+fix/gdas
+fix/gldas
+fix/gsi
+fix/lut
+fix/mom6
+fix/orog
+fix/reg2grb2
+fix/sfc_climo
+fix/ugwd
+fix/verif
+fix/wave
 fix/wafs
 
 # Ignore parm file symlinks
@@ -75,62 +90,8 @@ parm/wafs
 #--------------------------------------------
 sorc/*log
 sorc/logs
-sorc/ufs_model.fd
-sorc/gfs_post.fd
-sorc/gfs_wafs.fd
-sorc/gldas.fd
-sorc/gsi_enkf.fd
-sorc/gsi.fd
-sorc/enkf.fd
-sorc/gdas.cd
-sorc/gsi_utils.fd
-sorc/gsi_monitor.fd
-sorc/ufs_utils.fd
-sorc/verif-global.fd
-
-# Ignore sorc symlinks
-#---------------------
-sorc/calc_analysis.fd
-sorc/calc_increment_ens.fd
-sorc/calc_increment_ens_ncio.fd
-sorc/emcsfc_ice_blend.fd
-sorc/emcsfc_snow2mdl.fd
-sorc/fregrid.fd
-sorc/gdas2gldas.fd
-sorc/getsfcensmeanp.fd
-sorc/getsigensmeanp_smooth.fd
-sorc/getsigensstatp.fd
-sorc/gfs_ncep_post.fd
-sorc/gldas2gdas.fd
-sorc/gldas_forcing.fd
-sorc/gldas_model.fd
-sorc/gldas_post.fd
-sorc/gldas_rst.fd
-sorc/global_chgres.fd
-sorc/global_cycle.fd
-sorc/global_enkf.fd
-sorc/global_gsi.fd
-sorc/interp_inc.fd
-sorc/make_hgrid.fd
-sorc/make_solo_mosaic.fd
-sorc/ncdiag_cat.fd
-sorc/nst_tf_chg.fd
-sorc/oznmon_horiz.fd
-sorc/oznmon_time.fd
-sorc/radmon_angle.fd
-sorc/radmon_bcoef.fd
-sorc/radmon_bcor.fd
-sorc/radmon_time.fd
-sorc/recentersigp.fd
-sorc/upp.fd
-sorc/wafs_awc_wafavn.fd
-sorc/wafs_blending.fd
-sorc/wafs_blending_0p25.fd
-sorc/wafs_cnvgrib2.fd
-sorc/wafs_gcip.fd
-sorc/wafs_grib2_0p25.fd
-sorc/wafs_makewafs.fd
-sorc/wafs_setmissing.fd
+sorc/*.cd
+sorc/*.fd
 
 # Ignore scripts from externals
 #------------------------------

Externals.cfg

@@ -7,8 +7,15 @@ repo_url = https://github.com/ufs-community/ufs-weather-model.git
 protocol = git
 required = True
 
+[gfs-utils]
+hash = 93898e1
+local_path = sorc/gfs_utils.fd
+repo_url = https://github.com/NOAA-EMC/gfs-utils
+protocol = git
+required = True
+
 [UFS-Utils]
-hash = ufs_utils_1_8_0
+hash = 8b990c0
 local_path = sorc/ufs_utils.fd
 repo_url = https://github.com/NOAA-EMC/UFS_UTILS.git
 protocol = git

jobs/JGDAS_ATMOS_GLDAS

@@ -83,7 +83,7 @@ export COMPONENT=${COMPONENT:-atmos}
 ##############################################
 export gldas_ver=${gldas_ver:-v2.3.0}
 export HOMEgldas=${HOMEgldas:-${HOMEgfs}}
-export FIXgldas=${FIXgldas:-${HOMEgldas}/fix/fix_gldas}
+export FIXgldas=${FIXgldas:-${HOMEgldas}/fix/gldas}
 export PARMgldas=${PARMgldas:-${HOMEgldas}/parm/gldas}
 export EXECgldas=${EXECgldas:-${HOMEgldas}/exec}
 export USHgldas=${USHgldas:-${HOMEgldas}/ush}

parm/config/config.aeroanl

@@ -9,7 +9,7 @@ export OBS_YAML_DIR=$HOMEgfs/sorc/gdas.cd/parm/aero/obs/config/
 export OBS_LIST=$HOMEgfs/sorc/gdas.cd/parm/aero/obs/lists/aero_prototype.yaml
 export AEROVARYAML=$HOMEgfs/sorc/gdas.cd/parm/aero/variational/3dvar_dripcg.yaml
 export BERROR_YAML=$HOMEgfs/sorc/gdas.cd/parm/aero/berror/static_bump.yaml
-export FV3JEDI_FIX=$HOMEgfs/fix/fix_jedi
+export FV3JEDI_FIX=$HOMEgfs/fix/gdas
 
 export io_layout_x=1
 export io_layout_y=1

parm/config/config.atmanal

@@ -9,7 +9,7 @@ export OBS_YAML_DIR=$HOMEgfs/sorc/gdas.cd/parm/atm/obs/config/
 export OBS_LIST=$HOMEgfs/sorc/gdas.cd/parm/atm/obs/lists/gdas_prototype.yaml
 export ATMVARYAML=$HOMEgfs/sorc/gdas.cd/parm/atm/variational/3dvar_dripcg.yaml
 export BERROR_YAML=$HOMEgfs/sorc/gdas.cd/parm/atm/berror/hybvar_bump.yaml
-export FV3JEDI_FIX=$HOMEgfs/fix/fix_jedi
+export FV3JEDI_FIX=$HOMEgfs/fix/gdas
 export R2D2_OBS_DB='ufsda_test'
 export R2D2_OBS_DUMP='oper_gdas'
 export R2D2_OBS_SRC='ncdiag'

parm/config/config.atmensanal

@@ -9,7 +9,7 @@ export OBS_YAML_DIR=$HOMEgfs/sorc/gdas.cd/parm/atm/obs/config/
 export OBS_LIST=$HOMEgfs/sorc/gdas.cd/parm/atm/obs/lists/lgetkf_prototype.yaml
 export BERROR_YAML=$HOMEgfs/sorc/gdas.cd/parm/atm/berror/hybvar_bump.yaml
 export ATMENSYAML=$HOMEgfs/sorc/gdas.cd/parm/atm/lgetkf/lgetkf.yaml
-export FV3JEDI_FIX=$HOMEgfs/fix/fix_jedi
+export FV3JEDI_FIX=$HOMEgfs/fix/gdas
 export R2D2_OBS_DB='ufsda_test'
 export R2D2_OBS_DUMP='oper_gdas'
 export R2D2_OBS_SRC='ncdiag'

parm/config/config.base.emc.dyn

@@ -29,9 +29,9 @@ export UTILgfs=$HOMEgfs/util
 export EXECgfs=$HOMEgfs/exec
 export SCRgfs=$HOMEgfs/scripts
 
-export FIXcice=$HOMEgfs/fix/fix_cice
-export FIXmom=$HOMEgfs/fix/fix_mom6
-export FIXreg2grb2=$HOMEgfs/fix/fix_reg2grb2
+export FIXcice=$HOMEgfs/fix/cice
+export FIXmom=$HOMEgfs/fix/mom6
+export FIXreg2grb2=$HOMEgfs/fix/reg2grb2
 
 ########################################################################
 
@@ -74,7 +74,7 @@ export MODE="@MODE@" # cycled/forecast-only
 # CLEAR
 ####################################################
 # Build paths relative to $HOMEgfs
-export FIXgsi="$HOMEgfs/fix/fix_gsi"
+export FIXgsi="$HOMEgfs/fix/gsi"
 export HOMEfv3gfs="$HOMEgfs/sorc/fv3gfs.fd"
 export HOMEpost="$HOMEgfs"
 export HOMEobsproc_prep="$BASE_GIT/obsproc/obsproc_prep.v5.5.0_hpc-stack"

parm/config/config.base.nco.static

@@ -62,7 +62,7 @@ export REALTIME="YES"
 # CLEAR
 ####################################################
 # Build paths relative to $HOMEgfs
-export FIXgsi="$HOMEgfs/fix/fix_gsi"
+export FIXgsi="$HOMEgfs/fix/gsi"
 export HOMEfv3gfs="$HOMEgfs/sorc/fv3gfs.fd"
 export HOMEpost="$HOMEgfs"
 export HOMEobsproc_prep="$NWPROD/obsproc_prep.v5.5.0"

parm/config/config.prep

@@ -21,7 +21,7 @@ export COMINsyn=${COMINsyn:-$(compath.py ${envir}/com/gfs/${gfs_ver})/syndat}
 
 export HOMERELO=$HOMEgfs
 export EXECRELO=${HOMERELO}/exec
-export FIXRELO=${HOMERELO}/fix/fix_am
+export FIXRELO=${HOMERELO}/fix/am
 export USHRELO=${HOMERELO}/ush
 
 # Adjust observation error for GFS v16 parallels

parm/config/config.vrfy

@@ -30,8 +30,8 @@ if [ $VRFYFITS = "YES" ]; then
 
     export fit_ver="newm.1.3"
     export fitdir="$BASE_GIT/verif/global/Fit2Obs/${fit_ver}/batrun"
-    export PRVT=$HOMEgfs/fix/fix_gsi/prepobs_errtable.global
-    export HYBLEVS=$HOMEgfs/fix/fix_am/global_hyblev.l${LEVS}.txt
+    export PRVT=$HOMEgfs/fix/gsi/prepobs_errtable.global
+    export HYBLEVS=$HOMEgfs/fix/am/global_hyblev.l${LEVS}.txt
     export CUE2RUN=$QUEUE
 
     export VBACKUP_FITS=24

parm/config/config.wave

@@ -11,7 +11,7 @@ echo "BEGIN: config.wave"
 export wave_sys_ver=v1.0.0
 
 export EXECwave="$HOMEgfs/exec"
-export FIXwave="$HOMEgfs/fix/fix_wave"
+export FIXwave="$HOMEgfs/fix/wave"
 export PARMwave="$HOMEgfs/parm/wave"
 export USHwave="$HOMEgfs/ush"
 

scripts/exgdas_atmos_chgres_forenkf.sh

@@ -21,7 +21,7 @@ source "$HOMEgfs/ush/preamble.sh"
 
 #  Directories.
 pwd=$(pwd)
-export FIXgsm=${FIXgsm:-$HOMEgfs/fix/fix_am}
+export FIXgsm=${FIXgsm:-$HOMEgfs/fix/am}
 
 # Base variables
 CDATE=${CDATE:-"2001010100"}

scripts/exgdas_atmos_gldas.sh

@@ -60,8 +60,8 @@ nlat=$((2*res))
 nlon=$((4*res))
 
 export USHgldas=${USHgldas:?}
-export FIXgldas=${FIXgldas:-${HOMEgfs}/fix/fix_gldas}
-export topodir=${topodir:-${HOMEgfs}/fix/fix_fv3_gmted2010/${CASE}/}
+export FIXgldas=${FIXgldas:-${HOMEgfs}/fix/gldas}
+export topodir=${topodir:-${HOMEgfs}/fix/orog/${CASE}}
 
 DATA=${DATA:-${pwd}/gldastmp$$}
 mkdata=NO

scripts/exgdas_enkf_ecen.sh

@@ -75,8 +75,8 @@ CYCLESH=${CYCLESH:-$HOMEgfs/ush/global_cycle.sh}
 export CYCLEXEC=${CYCLEXEC:-$HOMEgfs/exec/global_cycle}
 APRUN_CYCLE=${APRUN_CYCLE:-${APRUN:-""}}
 NTHREADS_CYCLE=${NTHREADS_CYCLE:-${NTHREADS:-1}}
-export FIXfv3=${FIXfv3:-$HOMEgfs/fix/fix_fv3_gmted2010}
-export FIXgsm=${FIXgsm:-$HOMEgfs/fix/fix_am}
+export FIXfv3=${FIXfv3:-$HOMEgfs/fix/orog}
+export FIXgsm=${FIXgsm:-$HOMEgfs/fix/am}
 export CYCLVARS=${CYCLVARS:-"FSNOL=-2.,FSNOS=99999.,"}
 export FHOUR=${FHOUR:-0}
 export DELTSFC=${DELTSFC:-6}

scripts/exgdas_enkf_fcst.sh

@@ -23,7 +23,7 @@ source "$HOMEgfs/ush/preamble.sh"
 # Directories.
 pwd=$(pwd)
 export FIX_DIR=${FIX_DIR:-$HOMEgfs/fix}
-export FIX_AM=${FIX_AM:-$FIX_DIR/fix_am}
+export FIX_AM=${FIX_AM:-$FIX_DIR/am}
 
 # Utilities
 export NCP=${NCP:-"/bin/cp -p"}

scripts/exgdas_enkf_sfc.sh

@@ -57,8 +57,8 @@ CYCLESH=${CYCLESH:-$HOMEgfs/ush/global_cycle.sh}
 export CYCLEXEC=${CYCLEXEC:-$HOMEgfs/exec/global_cycle}
 APRUN_CYCLE=${APRUN_CYCLE:-${APRUN:-""}}
 NTHREADS_CYCLE=${NTHREADS_CYCLE:-${NTHREADS:-1}}
-export FIXfv3=${FIXfv3:-$HOMEgfs/fix/fix_fv3_gmted2010}
-export FIXgsm=${FIXgsm:-$HOMEgfs/fix/fix_am}
+export FIXfv3=${FIXfv3:-$HOMEgfs/fix/orog}
+export FIXgsm=${FIXgsm:-$HOMEgfs/fix/am}
 export CYCLVARS=${CYCLVARS:-"FSNOL=-2.,FSNOS=99999.,"}
 export FHOUR=${FHOUR:-0}
 export DELTSFC=${DELTSFC:-6}

scripts/exglobal_atmos_analysis_calc.sh

@@ -23,7 +23,7 @@ source "$HOMEgfs/ush/preamble.sh"
 
 #  Directories.
 pwd=$(pwd)
-export FIXgsm=${FIXgsm:-$HOMEgfs/fix/fix_am}
+export FIXgsm=${FIXgsm:-$HOMEgfs/fix/am}
 
 # Base variables
 CDATE=${CDATE:-"2001010100"}
@@ -72,7 +72,7 @@ CALCANLPY=${CALCANLPY:-$HOMEgfs/ush/calcanl_gfs.py}
 
 DOGAUSFCANL=${DOGAUSFCANL-"NO"}
 GAUSFCANLSH=${GAUSFCANLSH:-$HOMEgfs/ush/gaussian_sfcanl.sh}
-export GAUSFCANLEXE=${GAUSFCANLEXE:-$HOMEgfs/exec/gaussian_sfcanl.exe}
+export GAUSFCANLEXE=${GAUSFCANLEXE:-$HOMEgfs/exec/gaussian_sfcanl.x}
 NTHREADS_GAUSFCANL=${NTHREADS_GAUSFCANL:-1}
 APRUN_GAUSFCANL=${APRUN_GAUSFCANL:-${APRUN:-""}}
 

scripts/exglobal_atmos_sfcanl.sh

@@ -61,8 +61,8 @@ export SNOW_NUDGE_COEFF=${SNOW_NUDGE_COEFF:-'-2.'}
 export CYCLVARS=${CYCLVARS:-""}
 export FHOUR=${FHOUR:-0}
 export DELTSFC=${DELTSFC:-6}
-export FIXgsm=${FIXgsm:-$HOMEgfs/fix/fix_am}
-export FIXfv3=${FIXfv3:-$HOMEgfs/fix/fix_fv3_gmted2010}
+export FIXgsm=${FIXgsm:-$HOMEgfs/fix/am}
+export FIXfv3=${FIXfv3:-$HOMEgfs/fix/orog}
 
 # FV3 specific info (required for global_cycle)
 export CASE=${CASE:-"C384"}

scripts/run_reg2grb2.sh

@@ -5,7 +5,7 @@ source "$HOMEgfs/ush/preamble.sh"
 #requires grib_util module 
 
 MOM6REGRID=${MOM6REGRID:-$HOMEgfs}
-export mask_file=$MOM6REGRID/fix/fix_reg2grb2/mask.0p25x0p25.grb2
+export mask_file=$MOM6REGRID/fix/reg2grb2/mask.0p25x0p25.grb2
 
 # offline testing:
 #export DATA=