NOAA-EMC · WalterKolczynski-NOAA · Apr 24, 2023 · Jan 31, 2023 · Jan 31, 2023 · Jan 31, 2023
diff --git a/.shellcheckrc b/.shellcheckrc
@@ -11,3 +11,6 @@ disable=SC1090
 
 # Disable non-existent binary
 disable=SC1091
+
+# Disable -p -m only applies to deepest directory
+disable=SC2174
diff --git a/env/ORION.env b/env/ORION.env
@@ -41,7 +41,8 @@ if [[ "${step}" = "prep" ]] || [[ "${step}" = "prepbufr" ]]; then
     export sys_tp="ORION"
     export launcher_PREP="srun"
 
-elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}" = "wavepostsbs" ]] || [[ "${step}" = "wavepostbndpnt" ]] || [[ "${step}" = "wavepostbndpntbll" ]]|| [[ "${step}" = "wavepostpnt" ]]; then
+elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}" = "wavepostsbs" ]] || \
+    [[ "${step}" = "wavepostbndpnt" ]] || [[ "${step}" = "wavepostpnt" ]] || [[ "${step}" == "wavepostbndpntbll" ]]; then
 
     export CFP_MP="YES"
     if [[ "${step}" = "waveprep" ]]; then export MP_PULSE=0 ; fi

@@ -7,56 +7,29 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "anal" -c "base anal analdiag"
 ##############################################
 # Set variables used in the script
 ##############################################
-export CDATE=${CDATE:-${PDY}${cyc}}
-export CDUMP=${CDUMP:-${RUN:-"gfs"}}
+export CDUMP="${RUN/enkf}"
 export DO_CALC_ANALYSIS=${DO_CALC_ANALYSIS:-"YES"}
 
 
 ##############################################
 # Begin JOB SPECIFIC work
 ##############################################
 
-GDATE=$(${NDATE} -${assim_freq} ${CDATE})
-gPDY=$(echo ${GDATE} | cut -c1-8)
-gcyc=$(echo ${GDATE} | cut -c9-10)
-GDUMP=${GDUMP:-"gdas"}
+# Ignore possible spelling error (nothing is misspelled)
+# shellcheck disable=SC2153
+GDATE=$(${NDATE} -${assim_freq} ${PDY}${cyc})
+# shellcheck disable=
+export gPDY=${GDATE:0:8}
+export gcyc=${GDATE:8:2}
+export GDUMP="gdas"
+export GDUMP_ENS="enkf${GDUMP}"
 
 export OPREFIX="${CDUMP}.t${cyc}z."
 export GPREFIX="${GDUMP}.t${gcyc}z."
-export APREFIX="${CDUMP}.t${cyc}z."
-export GPREFIX_ENS="enkf${GDUMP}.t${gcyc}z."
-
-
-if [ ${RUN_ENVIR} = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
-    export COMOUT=${COMOUT:-${ROTDIR}/${RUN}.${PDY}/${cyc}/atmos}
-    export COMIN_OBS=${COMIN_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/${RUN}.${PDY}/${cyc}/atmos}
-    export COMIN_GES_OBS=${COMIN_GES_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/${GDUMP}.${gPDY}/${gcyc}/atmos}
-else
-    export COMOUT="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/atmos"
-    export COMIN_OBS="${COMIN_OBS:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/obs}"
-    export COMIN_GES_OBS="${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/obs"
-fi
-mkdir -m 775 -p ${COMOUT}
-# COMIN_GES and COMIN_GES_ENS are used in script
-export COMIN_GES="${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/atmos"
-export COMIN_GES_ENS="${ROTDIR}/enkfgdas.${gPDY}/${gcyc}"
-
-
-export ATMGES="${COMIN_GES}/${GPREFIX}atmf006.nc"
-if [ ! -f ${ATMGES} ]; then
-    echo "FATAL ERROR: FILE MISSING: ATMGES = ${ATMGES}"
-    exit 1
-fi
-
-
-if [ ${DOHYBVAR} = "YES" ]; then
-    export ATMGES_ENSMEAN="${COMIN_GES_ENS}/${GPREFIX_ENS}atmf006.ensmean.nc"
-    if [ ! -f ${ATMGES_ENSMEAN} ]; then
-        echo "FATAL ERROR: FILE MISSING: ATMGES_ENSMEAN = ${ATMGES_ENSMEAN}"
-        exit 2
-    fi
-fi
+export APREFIX="${RUN}.t${cyc}z."
 
+YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_ANALYSIS
+mkdir -m 775 -p "${COM_ATMOS_ANALYSIS}"
 
 ###############################################################
 # Run relevant script

@@ -7,29 +7,19 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "anal" -c "base anal echgres"
 ##############################################
 # Set variables used in the script
 ##############################################
-export CDATE=${CDATE:-${PDY}${cyc}}
-export CDUMP=${CDUMP:-${RUN:-"gfs"}}
-export COMPONENT="atmos"
+export CDUMP=${RUN/enkf}
 export DO_CALC_ANALYSIS=${DO_CALC_ANALYSIS:-"YES"}
 
 
 ##############################################
 # Begin JOB SPECIFIC work
 ##############################################
 
-export APREFIX="${CDUMP/enkf}.t${cyc}z."
-export APREFIX_ENS="${CDUMP}.t${cyc}z."
+export APREFIX="${CDUMP}.t${cyc}z."
+export APREFIX_ENS="${RUN}.t${cyc}z."
 
-if [ ${RUN_ENVIR} = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
-    export COMOUT=${COMOUT:-${ROTDIR}/${RUN/enkf}.${PDY}/${cyc}/atmos}
-    export COMOUT_ENS=${COMOUT_ENS:-${ROTDIR}/${RUN}.${PDY}/${cyc}}
-else
-    export COMOUT="${ROTDIR}/${RUN/enkf}.${PDY}/${cyc}/atmos"
-    export COMOUT_ENS="${ROTDIR}/${RUN}.${PDY}/${cyc}"
-fi
-mkdir -m 775 -p ${COMOUT}
-
-export ATMFCST_ENSRES="${COMOUT_ENS}/mem001/atmos/${APREFIX_ENS}atmf006.nc"
+RUN=${CDUMP} YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_HISTORY
+MEMDIR="mem001" YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_HISTORY_MEM:COM_ATMOS_HISTORY_TMPL
 
 ###############################################################
 # Run relevant script

@@ -35,32 +35,37 @@ export DBNROOT=${DBNROOT:-${UTILROOT}/fakedbn}
 # Specify NET and RUN Name and model
 ####################################
 export model=${model:-gdas}
-export COMPONENT="atmos"
 
 ##############################################
 # 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}/${RUN}.${PDY})/${cyc}/${COMPONENT}/gempak}
+for grid in 0p25 0p50 1p00; do
+  GRID=${grid} YMD=${PDY} HH=${cyc} generate_com -rx "COM_ATMOS_GRIB_${grid}:COM_ATMOS_GRIB_TMPL"
+done
 
-if [ ${SENDCOM} = YES ] ; then
-  mkdir -m 775 -p ${COMOUT}
-fi
+for grid in 1p00 0p25; do
+  prod_dir="COM_ATMOS_GEMPAK_${grid}"
+  GRID=${grid} YMD=${PDY} HH=${cyc} generate_com -rx "COM_ATMOS_GEMPAK_${grid}:COM_ATMOS_GEMPAK_TMPL"
+
+  if [[ ${SENDCOM} == YES && ! -d "${!prod_dir}" ]] ; then
+    mkdir -m 775 -p "${!prod_dir}"
+  fi
+done
 
 
-# TODO: These actions belong in an ex-script not a j-job (#1219)
-if [ -f ${DATA}/poescript ]; then
-   rm ${DATA}/poescript
+# TODO: These actions belong in an ex-script not a j-job
+if [[ -f poescript ]]; then
+   rm -f poescript
 fi
 
 ########################################################
 # Execute the script.
-echo "${SRCgfs}/exgdas_atmos_nawips.sh gdas 009 GDAS_GEMPAK " >> poescript
+echo "${SRCgfs}/exgdas_atmos_nawips.sh gdas 009 GDAS_GEMPAK ${COM_ATMOS_GEMPAK_1p00}" >> poescript
 ########################################################
 
 ########################################################
 # Execute the script for quater-degree grib
-echo "${SRCgfs}/exgdas_atmos_nawips.sh gdas_0p25 009 GDAS_GEMPAK " >>poescript
+echo "${SRCgfs}/exgdas_atmos_nawips.sh gdas_0p25 009 GDAS_GEMPAK ${COM_ATMOS_GEMPAK_0p25}" >> poescript
 ########################################################
 
 cat poescript
@@ -76,9 +81,8 @@ export OMP_NUM_THREADS=${threads}
 APRUN="mpiexec -l -np ${ntasks} --cpu-bind verbose,core cfp"
 
 APRUN_GEMPAKCFP=${APRUN_GEMPAKCFP:-${APRUN}}
-APRUNCFP=$(eval echo ${APRUN_GEMPAKCFP})
 
-${APRUNCFP} ${DATA}/poescript
+${APRUN_GEMPAKCFP} ${DATA}/poescript
 export err=$?; err_chk
 
 ############################################

@@ -6,12 +6,6 @@
 source "${HOMEgfs}/ush/preamble.sh"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "vrfy" -c "base vrfy"
 
-
-###############################
-# Specify NET, RUN, and COMPONENT name
-##############################
-export COMPONENT="atmos"
-
 export OZNMON_SUFFIX=${OZNMON_SUFFIX:-${NET}}
 
 #---------------------------------------------
@@ -39,20 +33,20 @@ export USHoznmon=${USHoznmon:-${HOMEoznmon}/ush}
 #  determine PDY and cyc for previous cycle
 #############################################
 
-cdate=$(${NDATE} -6 ${PDY}${cyc})
-echo 'pdate = ${pdate}'
+pdate=$(${NDATE} -6 ${PDY}${cyc})
+echo "pdate = ${pdate}"
 
-export P_PDY=$(echo ${cdate} | cut -c1-8)
-export p_cyc=$(echo ${cdate} | cut -c9-10)
+export P_PDY=${pdate:0:8}
+export p_cyc=${pdate:8:2}
 
 #---------------------------------------------
 # OZN_TANKDIR - WHERE OUTPUT DATA WILL RESIDE
 #
 export OZN_TANKDIR=${OZN_TANKDIR:-$(compath.py ${envir}/${NET}/${gfs_ver})}
-export TANKverf_ozn=${TANKverf_ozn:-${OZN_TANKDIR}/${RUN}.${PDY}/${cyc}/${COMPONENT}/oznmon}
-export TANKverf_oznM1=${TANKverf_oznM1:-${OZN_TANKDIR}/${RUN}.${P_PDY}/${p_cyc}/${COMPONENT}/oznmon}
-export COM_IN=${COM_IN:-$(compath.py ${envir}/${NET}/${gfs_ver})}
-export COMIN=${COMIN:-${COM_IN}/${RUN}.${PDY}/${cyc}/${COMPONENT}}
+export TANKverf_ozn=${TANKverf_ozn:-${OZN_TANKDIR}/${RUN}.${PDY}/${cyc}/atmos/oznmon}
+export TANKverf_oznM1=${TANKverf_oznM1:-${OZN_TANKDIR}/${RUN}.${P_PDY}/${p_cyc}/atmos/oznmon}
+
+YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_ANALYSIS
 
 if [[ ! -d ${TANKverf_ozn} ]]; then
    mkdir -p -m 775 ${TANKverf_ozn}
@@ -69,7 +63,7 @@ fi
 # Set necessary environment variables
 #
 export OZN_AREA=${OZN_AREA:-glb}
-export oznstat=${oznstat:-${COMIN}/gdas.t${cyc}z.oznstat}
+export oznstat=${oznstat:-${COM_ATMOS_ANALYSIS}/gdas.t${cyc}z.oznstat}
 
 
 #-------------------------------------------------------

@@ -42,31 +42,21 @@ parm_file=${parm_file:-${PARMmon}/da_mon.parm}
 #  determine PDY and cyc for previous cycle
 #############################################
 
-cdate=$(${NDATE} -6 ${PDY}${cyc})
-echo 'pdate = ${pdate}'
+pdate=$(${NDATE} -6 ${PDY}${cyc})
+echo "pdate = ${pdate}"
 
-export P_PDY=$(echo ${cdate} | cut -c1-8)
-export p_cyc=$(echo ${cdate} | cut -c9-10)
+export P_PDY=${pdate:0:8}
+export p_cyc=${pdate:8:2}
 
 #############################################
 # COMOUT - WHERE GSI OUTPUT RESIDES
 # TANKverf - WHERE OUTPUT DATA WILL RESIDE
 #############################################
 export TANKverf=${TANKverf:-$(compath.py ${envir}/${NET}/${gfs_ver})}
-export TANKverf_rad=${TANKverf_rad:-${TANKverf}/${RUN}.${PDY}/${cyc}/${COMPONENT}/radmon}
-export TANKverf_radM1=${TANKverf_radM1:-${TANKverf}/${RUN}.${P_PDY}/${p_cyc}/${COMPONENT}/radmon}
-export COM_IN=${COM_IN:-$(compath.py ${envir}/${NET}/${gfs_ver})}
-export COMIN=${COMIN:-${COM_IN}/${RUN}.${PDY}/${cyc}/${COMPONENT}}
-
-################################
-#  backwards compatibility for
-#  gfs v15 which doesn't have
-#  a $COMPONENT in output path
-################################
-if [[ ! -d ${COMIN} ]]; then
-   export COMIN=${COM_IN}/${RUN}.${PDY}/${cyc}
-fi
+export TANKverf_rad=${TANKverf_rad:-${TANKverf}/${RUN}.${PDY}/${cyc}/atmos/radmon}
+export TANKverf_radM1=${TANKverf_radM1:-${TANKverf}/${RUN}.${P_PDY}/${p_cyc}/atmos/radmon}
 
+YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_ANALYSIS
 
 mkdir -p -m 775 ${TANKverf_rad}
 
@@ -75,8 +65,8 @@ mkdir -p -m 775 ${TANKverf_rad}
 ########################################
 export RAD_AREA=${RAD_AREA:-glb}
 
-export biascr=${biascr:-${COMIN}/gdas.t${cyc}z.abias}
-export radstat=${radstat:-${COMIN}/gdas.t${cyc}z.radstat}
+export biascr=${biascr:-${COM_ATMOS_ANALYSIS}/gdas.t${cyc}z.abias}
+export radstat=${radstat:-${COM_ATMOS_ANALYSIS}/gdas.t${cyc}z.radstat}
 
 echo " "
 echo "JOB HAS STARTED"

diff --git a/jobs/JGDAS_ATMOS_VMINMON b/jobs/JGDAS_ATMOS_VMINMON
@@ -6,8 +6,6 @@
 source "${HOMEgfs}/ush/preamble.sh"
 source "${HOMEgfs}/ush/jjob_header.sh" -e "vrfy" -c "base vrfy"
 
-export COMPONENT="atmos"
-
 ###########################################################
 # obtain unique process id (pid) and make temp directories
 ###########################################################
@@ -32,32 +30,29 @@ export USHminmon=${USHminmon:-${HOMEminmon}/ush}
 #  determine PDY and cyc for previous cycle
 #############################################
 
-cdate=$(${NDATE} -6 ${PDY}${cyc})
-echo 'pdate = ${pdate}'
+pdate=$(${NDATE} -6 ${PDY}${cyc})
+echo "pdate = ${pdate}"
 
-export P_PDY=$(echo ${cdate} | cut -c1-8)
-export p_cyc=$(echo ${cdate} | cut -c9-10)
+export P_PDY=${pdate:0:8}
+export p_cyc=${pdate:8:2}
 
 
 #############################################
 # TANKverf - WHERE OUTPUT DATA WILL RESIDE
 #############################################
-export COM_IN=${COM_IN:-$(compath.py ${envir}/${NET}/${gfs_ver})}
-
-export M_TANKverf=${M_TANKverf:-${COM_IN}/${RUN}.${PDY}/${cyc}/${COMPONENT}/minmon}
-export M_TANKverfM1=${M_TANKverfM1:-${COM_IN}/${RUN}.${P_PDY}/${p_cyc}/${COMPONENT}/minmon}
+export M_TANKverf=${M_TANKverf:-${COM_IN}/${RUN}.${PDY}/${cyc}/atmos/minmon}
+export M_TANKverfM1=${M_TANKverfM1:-${COM_IN}/${RUN}.${P_PDY}/${p_cyc}/atmos/minmon}
 
-export COMIN=${COMIN:-${COM_IN}/${RUN}.${PDY}/${cyc}/${COMPONENT}}
+YMD=${PDY} HH=${cyc} generate_com -rx COM_ATMOS_ANALYSIS
 
 mkdir -p -m 775 ${M_TANKverf}
 
 
-
 ########################################
 # Set necessary environment variables
 ########################################
 export CYCLE_INTERVAL=6
-export gsistat=${gsistat:-${COMIN}/gdas.t${cyc}z.gsistat}
+export gsistat=${gsistat:-${COM_ATMOS_ANALYSIS}/gdas.t${cyc}z.gsistat}
 
 
 ########################################################

@@ -7,8 +7,11 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "earc" -c "base earc"
 ##############################################
 # Set variables used in the script
 ##############################################
-export CDATE=${CDATE:-${PDY}${cyc}}
-export CDUMP=${CDUMP:-${RUN:-"gdas"}}
+export CDUMP=${RUN/enkf}
+
+YMD=${PDY} HH=${cyc} generate_com -rx COM_TOP
+MEMDIR="ensstat" YMD=${PDY} HH=${cyc} generate_com -rx \
+  COM_ATMOS_ANALYSIS_ENSSTAT:COM_ATMOS_ANALYSIS_TMPL
 
 ###############################################################
 # Run archive script