Merge branch 'NOAA-EMC:develop' into develop

kayeekayee · Jan 2, 2024 · a75e73e · a75e73e
2 parents 5adc47b + 9d901db
commit a75e73e
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Showing 36 changed files with 413 additions and 419 deletions.
diff --git a/jobs/JGFS_ATMOS_GEMPAK_PGRB2_SPEC b/jobs/JGFS_ATMOS_GEMPAK_PGRB2_SPEC
@@ -1,7 +1,5 @@
 #! /usr/bin/env bash
 
-# TODO (#1222) This job is not part of the rocoto suite
-
 ############################################
 # GFS_PGRB2_SPEC_GEMPAK PRODUCT GENERATION
 ############################################
@@ -12,12 +10,12 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "gempak_spec" -c "base"
 ################################
 # Set up the HOME directory
 ################################
-export EXECgfs=${EXECgfs:-${HOMEgfs}/exec}
-export PARMgfs=${PARMgfs:-${HOMEgfs}/parm}
-export EXPDIR=${EXPDIR:-${HOMEgfs}/parm/config}
-export FIXgempak=${FIXgempak:-${HOMEgfs}/gempak/fix}
-export USHgempak=${USHgempak:-${HOMEgfs}/gempak/ush}
-export SRCgfs=${SRCgfs:-${HOMEgfs}/scripts}
+export EXECgfs="${EXECgfs:-${HOMEgfs}/exec}"
+export PARMgfs="${PARMgfs:-${HOMEgfs}/parm}"
+export EXPDIR="${EXPDIR:-${HOMEgfs}/parm/config}"
+export FIXgempak="${FIXgempak:-${HOMEgfs}/gempak/fix}"
+export USHgempak="${USHgempak:-${HOMEgfs}/gempak/ush}"
+export SRCgfs="${SRCgfs:-${HOMEgfs}/scripts}"
 
 # For half-degree P Grib files
 #export DO_HD_PGRB=YES
@@ -33,25 +31,20 @@ export EXT=""
 ##############################################
 # Define COM directories
 ##############################################
-export COMIN=${COMIN:-$(compath.py ${envir}/${NET}/${gfs_ver})/${RUN}.${PDY}/${cyc}/${COMPONENT}}
-export COMOUT=${COMOUT:-$(compath.py -o ${NET}/${gfs_ver}/${NET}.${PDY})/${cyc}/${COMPONENT}/gempak}
-
-export SENDDBN=${SENDDBN:-NO}
-export DBNROOT=${DBNROOT:-${UTILROOT}/fakedbn}
-
-mkdir -m 775 -p ${COMOUT}
-
+export COMIN="${COMIN:-$(compath.py "${envir}"/"${NET}"/"${gfs_ver}")/${RUN}.${PDY}/${cyc}/${COMPONENT}}"
+export COMOUT="${COMOUT:-$(compath.py -o "${NET}"/"${gfs_ver}"/"${NET}"."${PDY}")/${cyc}/${COMPONENT}/gempak}"
 
-# TODO - Assess what is going on with overwriting $DATA here (#1224)
+export SENDDBN="${SENDDBN:-NO}"
+export DBNROOT="${DBNROOT:-${UTILROOT}/fakedbn}"
 
-export DATA_HOLD=${DATA}
+mkdir -m 775 -p "${COMOUT}"
 
 #################################################################
 # Execute the script for the regular grib
 #################################################################
-export DATA=${DATA_HOLD}/SPECIAL
-mkdir -p ${DATA}
-cd ${DATA}
+export DATA_SPECIAL="${DATA}/SPECIAL"
+mkdir -p "${DATA_SPECIAL}"
+cd "${DATA_SPECIAL}" || exit 1
 
 export DBN_ALERT_TYPE=GFS_GOESSIM_GEMPAK
 export RUN2=gfs_goessim
@@ -65,14 +58,14 @@ echo "RUNS the Program"
 
 ########################################################
 # Execute the script.
-${SRCgfs}/exgfs_atmos_goes_nawips.sh
+"${SRCgfs}/exgfs_atmos_goes_nawips.sh"
 
 #################################################################
 # Execute the script for the 221 grib
 
-export DATA=${DATA_HOLD}/SPECIAL221
-mkdir -p ${DATA}
-cd ${DATA}
+export DATA_SPECIAL221="${DATA}/SPECIAL221"
+mkdir -p "${DATA_SPECIAL221}"
+cd "${DATA_SPECIAL221}" || exit 1
 
 export DBN_ALERT_TYPE=GFS_GOESSIM221_GEMPAK
 export RUN2=gfs_goessim221
@@ -86,27 +79,27 @@ echo "RUNS the Program"
 
 ########################################################
 # Execute the script.
-${SRCgfs}/exgfs_atmos_goes_nawips.sh
+"${SRCgfs}/exgfs_atmos_goes_nawips.sh"
 export err=$?; err_chk
 ########################################################
 
 echo "end of program"
-cd ${DATA_HOLD}
+cd "${DATA}" || exit 1
 echo "######################################"
 echo "  SPECIAL.OUT "
 echo "######################################"
 
 ############################################
 # print exec I/O output
 ############################################
-if [ -e "${pgmout}" ] ; then
-  cat ${pgmout}
+if [[ -e "${pgmout}" ]] ; then
+  cat "${pgmout}"
 fi
 
 ###################################
 # Remove temp directories
 ###################################
-if [ "${KEEPDATA}" != "YES" ] ; then
+if [[ "${KEEPDATA}" != "YES" ]] ; then
   rm -rf "${DATA}"
 fi
 
diff --git a/jobs/JGFS_ATMOS_PGRB2_SPEC_NPOESS b/jobs/JGFS_ATMOS_PGRB2_SPEC_NPOESS
@@ -10,7 +10,6 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "npoess" -c "base"
 
 export OMP_NUM_THREADS=${OMP_NUM_THREADS:-1}
 
-
 ################################
 # Set up the HOME directory
 ################################
@@ -38,47 +37,6 @@ GRID="0p50" YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_GRIB_0p50:COM_ATMOS_
 
 mkdir -m 775 -p "${COM_ATMOS_GOES}"
 
-# TODO - This should be in the ex-script (#1226)
-
-####################################
-# Specify Forecast Hour Range
-####################################
-export SHOUR=000
-export FHOUR=180
-export FHINC=003
-
-####################################
-# Specify Timeout Behavior of Post
-#
-# SLEEP_TIME - Amount of time to wait for
-#              a restart file before exiting
-# SLEEP_INT  - Amount of time to wait between
-#              checking for restart files
-####################################
-export SLEEP_TIME=900
-export SLEEP_INT=5
-
-####################################
-# Check if this is a restart
-####################################
-if [[ -f "${COM_ATMOS_GOES}/${RUN}.t${cyc}z.control.goessimpgrb2" ]]; then
-   modelrecvy=$(cat < "${COM_ATMOS_GOES}/${RUN}.t${cyc}z.control.goessimpgrb")
-   recvy_cyc="${modelrecvy:8:2}"
-   recvy_shour="${modelrecvy:10:13}"
-
-   if [[ ${RERUN} == "NO" ]]; then
-      NEW_SHOUR=$(( recvy_shour + FHINC ))
-      if (( NEW_SHOUR >= SHOUR )); then
-         export SHOUR=${NEW_SHOUR}
-      fi
-      if (( recvy_shour >= FHOUR )); then
-         echo "Forecast Pgrb Generation Already Completed to ${FHOUR}"
-      else
-         echo "Starting: PDY=${PDY} cycle=t${recvy_cyc}z SHOUR=${SHOUR}"
-      fi
-   fi
-fi
-
 #############################################################
 # Execute the script
 "${HOMEgfs}/scripts/exgfs_atmos_grib2_special_npoess.sh"

diff --git a/jobs/JGLOBAL_WAVE_INIT b/jobs/JGLOBAL_WAVE_INIT
@@ -10,7 +10,7 @@ export errchk=${errchk:-err_chk}
 export MP_PULSE=0
 
 # Path to HOME Directory
-export FIXwave=${FIXwave:-${HOMEgfs}/fix/fix_wave_${NET}}
+export FIXwave=${FIXwave:-${HOMEgfs}/fix/wave}
 export PARMwave=${PARMwave:-${HOMEgfs}/parm/wave}
 export USHwave=${USHwave:-${HOMEgfs}/ush}
 export EXECwave=${EXECwave:-${HOMEgfs}/exec}

diff --git a/jobs/JGLOBAL_WAVE_POST_BNDPNT b/jobs/JGLOBAL_WAVE_POST_BNDPNT
@@ -9,7 +9,7 @@ export errchk=${errchk:-err_chk}
 export MP_PULSE=0
 
 # Path to HOME Directory
-export FIXwave=${FIXwave:-${HOMEgfs}/fix/fix_wave_${NET}}
+export FIXwave=${FIXwave:-${HOMEgfs}/fix/wave}
 export PARMwave=${PARMwave:-${HOMEgfs}/parm/wave}
 export USHwave=${USHwave:-${HOMEgfs}/ush}
 export EXECwave=${EXECwave:-${HOMEgfs}/exec}

diff --git a/jobs/JGLOBAL_WAVE_POST_BNDPNTBLL b/jobs/JGLOBAL_WAVE_POST_BNDPNTBLL
@@ -13,7 +13,7 @@ export CDATE=${PDY}${cyc}
 export MP_PULSE=0
 
 # Path to HOME Directory
-export FIXwave=${FIXwave:-${HOMEgfs}/fix/fix_wave_${NET}}
+export FIXwave=${FIXwave:-${HOMEgfs}/fix/wave}
 export PARMwave=${PARMwave:-${HOMEgfs}/parm/wave}
 export USHwave=${USHwave:-${HOMEgfs}/ush}
 export EXECwave=${EXECwave:-${HOMEgfs}/exec}

diff --git a/jobs/JGLOBAL_WAVE_POST_PNT b/jobs/JGLOBAL_WAVE_POST_PNT
@@ -9,7 +9,7 @@ export errchk=${errchk:-err_chk}
 export MP_PULSE=0
 
 # Path to HOME Directory
-export FIXwave=${FIXwave:-${HOMEgfs}/fix/fix_wave_${NET}}
+export FIXwave=${FIXwave:-${HOMEgfs}/fix/wave}
 export PARMwave=${PARMwave:-${HOMEgfs}/parm/wave}
 export USHwave=${USHwave:-${HOMEgfs}/ush}
 export EXECwave=${EXECwave:-${HOMEgfs}/exec}

diff --git a/jobs/JGLOBAL_WAVE_POST_SBS b/jobs/JGLOBAL_WAVE_POST_SBS
@@ -9,7 +9,7 @@ export errchk=${errchk:-err_chk}
 export MP_PULSE=0
 
 # Path to HOME Directory
-export FIXwave=${FIXwave:-${HOMEgfs}/fix/fix_wave_${NET}}
+export FIXwave=${FIXwave:-${HOMEgfs}/fix/wave}
 export PARMwave=${PARMwave:-${HOMEgfs}/parm/wave}
 export USHwave=${USHwave:-${HOMEgfs}/ush}
 export EXECwave=${EXECwave:-${HOMEgfs}/exec}

diff --git a/jobs/JGLOBAL_WAVE_PREP b/jobs/JGLOBAL_WAVE_PREP
@@ -17,7 +17,7 @@ export MP_PULSE=0
 export CDO=${CDO_ROOT}/bin/cdo
 
 # Path to HOME Directory
-export FIXwave=${FIXwave:-${HOMEgfs}/fix/fix_wave_${NET}}
+export FIXwave=${FIXwave:-${HOMEgfs}/fix/wave}
 export PARMwave=${PARMwave:-${HOMEgfs}/parm/wave}
 export USHwave=${USHwave:-${HOMEgfs}/ush}
 export EXECwave=${EXECwave:-${HOMEgfs}/exec}

diff --git a/parm/config/gefs/config.base.emc.dyn b/parm/config/gefs/config.base.emc.dyn
@@ -30,9 +30,15 @@ export UTILgfs=${HOMEgfs}/util
 export EXECgfs=${HOMEgfs}/exec
 export SCRgfs=${HOMEgfs}/scripts
 
-export FIXcice=${HOMEgfs}/fix/cice
-export FIXmom=${HOMEgfs}/fix/mom6
-export FIXreg2grb2=${HOMEgfs}/fix/reg2grb2
+export FIXam="${FIXgfs}/am"
+export FIXaer="${FIXgfs}/aer"
+export FIXcpl="${FIXgfs}/cpl"
+export FIXlut="${FIXgfs}/lut"
+export FIXorog="${FIXgfs}/orog"
+export FIXcice="${FIXgfs}/cice"
+export FIXmom="${FIXgfs}/mom6"
+export FIXreg2grb2="${FIXgfs}/reg2grb2"
+export FIXugwd="${FIXgfs}/ugwd"
 
 ########################################################################
 

diff --git a/parm/config/gfs/config.aeroanl b/parm/config/gfs/config.aeroanl
@@ -10,8 +10,8 @@ export OBS_YAML_DIR=${HOMEgfs}/sorc/gdas.cd/parm/aero/obs/config/
 export OBS_LIST=${HOMEgfs}/sorc/gdas.cd/parm/aero/obs/lists/gdas_aero_prototype.yaml
 export STATICB_TYPE='identity'
 export BERROR_YAML=${HOMEgfs}/sorc/gdas.cd/parm/aero/berror/staticb_${STATICB_TYPE}.yaml
-export FV3JEDI_FIX=${HOMEgfs}/fix/gdas
-export BERROR_DATA_DIR=${FV3JEDI_FIX}/bump/aero/${CASE_ANL}/
+export FIXgdas=${HOMEgfs}/fix/gdas
+export BERROR_DATA_DIR=${FIXgdas}/bump/aero/${CASE_ANL}/
 export BERROR_DATE="20160630.000000"
 
 export io_layout_x=@IO_LAYOUT_X@

diff --git a/parm/config/gfs/config.base.emc.dyn b/parm/config/gfs/config.base.emc.dyn
@@ -23,16 +23,22 @@ export HPSS_PROJECT="@HPSS_PROJECT@"
 
 # Directories relative to installation areas:
 export HOMEgfs=@HOMEgfs@
-export PARMgfs=${HOMEgfs}/parm
-export FIXgfs=${HOMEgfs}/fix
-export USHgfs=${HOMEgfs}/ush
-export UTILgfs=${HOMEgfs}/util
-export EXECgfs=${HOMEgfs}/exec
-export SCRgfs=${HOMEgfs}/scripts
-
-export FIXcice=${HOMEgfs}/fix/cice
-export FIXmom=${HOMEgfs}/fix/mom6
-export FIXreg2grb2=${HOMEgfs}/fix/reg2grb2
+export PARMgfs="${HOMEgfs}/parm"
+export FIXgfs="${HOMEgfs}/fix"
+export USHgfs="${HOMEgfs}/ush"
+export UTILgfs="${HOMEgfs}/util"
+export EXECgfs="${HOMEgfs}/exec"
+export SCRgfs="${HOMEgfs}/scripts"
+
+export FIXam="${FIXgfs}/am"
+export FIXaer="${FIXgfs}/aer"
+export FIXcpl="${FIXgfs}/cpl"
+export FIXlut="${FIXgfs}/lut"
+export FIXorog="${FIXgfs}/orog"
+export FIXcice="${FIXgfs}/cice"
+export FIXmom="${FIXgfs}/mom6"
+export FIXreg2grb2="${FIXgfs}/reg2grb2"
+export FIXugwd="${FIXgfs}/ugwd"
 
 ########################################################################
 

diff --git a/parm/gdas/aero_jedi_fix.yaml b/parm/gdas/aero_jedi_fix.yaml
@@ -1,11 +1,11 @@
 mkdir:
 - !ENV ${DATA}/fv3jedi
 copy:
-- - !ENV ${FV3JEDI_FIX}/fv3jedi/fv3files/akbk$(npz).nc4
+- - !ENV ${FIXgdas}/fv3jedi/fv3files/akbk$(npz).nc4
   - !ENV ${DATA}/fv3jedi/akbk.nc4
-- - !ENV ${FV3JEDI_FIX}/fv3jedi/fv3files/fmsmpp.nml
+- - !ENV ${FIXgdas}/fv3jedi/fv3files/fmsmpp.nml
   - !ENV ${DATA}/fv3jedi/fmsmpp.nml
-- - !ENV ${FV3JEDI_FIX}/fv3jedi/fv3files/field_table_gfdl
+- - !ENV ${FIXgdas}/fv3jedi/fv3files/field_table_gfdl
   - !ENV ${DATA}/fv3jedi/field_table
 - - !ENV $(HOMEgfs)/sorc/gdas.cd/parm/io/fv3jedi_fieldmetadata_restart.yaml
   - !ENV ${DATA}/fv3jedi/fv3jedi_fieldmetadata_restart.yaml