Update bash ex-scripts to be linter compliant

jobs/JGDAS_AERO_ANALYSIS_GENERATE_BMATRIX

@@ -16,7 +16,6 @@ YMD=${PDY} HH=${cyc} declare_from_tmpl -rx COMIN_OBS:COM_OBS_TMPL \
     COMIN_ATMOS_RESTART:COM_ATMOS_RESTART_TMPL \
     COMOUT_CONF:COM_CONF_TMPL
 
-
 mkdir -p "${COMOUT_CHEM_BMAT}"
 mkdir -p "${COMOUT_CONF}"
 

jobs/JGDAS_ENKF_SFC

@@ -37,7 +37,7 @@ RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
     COMIN_ATMOS_ANALYSIS_DET_PREV:COM_ATMOS_ANALYSIS_TMPL
 
 # Use CFP to stage and save files in parallel
- export USE_CFP=YES
+export USE_CFP=YES
 
 ###############################################################
 # Run relevant script

jobs/JGDAS_ENKF_UPDATE

@@ -40,8 +40,8 @@ fi
 ##############################################
 # Send Alerts
 ##############################################
-if [[ "${SENDDBN}" == "YES" ]] ; then
-   "${DBNROOT}/bin/dbn_alert" "MODEL" "ENKF1_MSC_enkfstat" "${job}" "${COMOUT_ATMOS_ANALYSIS_STAT}/${APREFIX}enkfstat.txt"
+if [[ "${SENDDBN}" == "YES" ]]; then
+    "${DBNROOT}/bin/dbn_alert" "MODEL" "ENKF1_MSC_enkfstat" "${job}" "${COMOUT_ATMOS_ANALYSIS_STAT}/${APREFIX}enkfstat.txt"
 fi
 
 ##############################################

jobs/JGLOBAL_ATMOS_ANALYSIS_CALC_FV3JEDI

@@ -26,9 +26,9 @@ YMD=${PDY} HH=${cyc} RUN=${RUN} declare_from_tmpl -rx \
 YMD=${PDY} HH=${cyc} RUN=${RUN} declare_from_tmpl -rx \
     COMOUT_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL
 RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
-   COMIN_ATMOS_HISTORY_PREV:COM_ATMOS_HISTORY_TMPL
+    COMIN_ATMOS_HISTORY_PREV:COM_ATMOS_HISTORY_TMPL
 YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
-   COMOUT_CONF:COM_CONF_TMPL
+    COMOUT_CONF:COM_CONF_TMPL
 
 mkdir -m 775 -p "${COMOUT_CONF}"
 

jobs/JGLOBAL_ATMOS_SFCANL

@@ -33,7 +33,7 @@ RUN="enkfgdas" MEMDIR="ensstat" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
 mkdir -p "${COMOUT_ATMOS_RESTART}"
 
 # Use CFP to stage and save files in parallel
- export USE_CFP=YES
+export USE_CFP=YES
 
 ###############################################################
 # Run relevant script

scripts/exgdas_atmos_chgres_forenkf.sh

@@ -26,9 +26,10 @@ GDUMP=${GDUMP:-"gdas"}
 # Derived base variables
 # shellcheck disable=SC2153
 GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
+export GDATE
 BDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - 3 hours")
-bPDY=${BDATE:0:8}
-bcyc=${BDATE:8:2}
+export bPDY=${BDATE:0:8}
+export bcyc=${BDATE:8:2}
 
 # Utilities
 export CHGRP_CMD=${CHGRP_CMD:-"chgrp ${group_name:-rstprod}"}
@@ -73,111 +74,80 @@ DOHYBVAR=${DOHYBVAR:-"NO"}
 lrun_subdirs=${lrun_subdirs:-".true."}
 USE_CFP=${USE_CFP:-"NO"}
 CFP_MP=${CFP_MP:-"NO"}
-nm=""
-if [ $CFP_MP = "YES" ]; then
-    nm=0
-fi
-if [ $DOHYBVAR = "YES" ]; then
-   l_hyb_ens=.true.
-   export l4densvar=${l4densvar:-".false."}
-   export lwrite4danl=${lwrite4danl:-".false."}
+
+if [[ "${DOHYBVAR}" == "YES" ]]; then
+    export l_hyb_ens=.true.
+    export l4densvar=${l4densvar:-".false."}
+    export lwrite4danl=${lwrite4danl:-".false."}
 else
-   echo "DOHYBVAR != YES, this script will exit without regridding deterministic forecast"
-   exit 0
+    echo "DOHYBVAR != YES, this script will exit without regridding deterministic forecast"
+    exit 0
 fi
 
 ################################################################################
 ################################################################################
 
 # get resolution information
-LONB_ENKF=${LONB_ENKF:-$($NCLEN $ATMFCST_ENSRES grid_xt)} # get LONB_ENKF
-LATB_ENKF=${LATB_ENKF:-$($NCLEN $ATMFCST_ENSRES grid_yt)} # get LATB_ENFK
-LEVS_ENKF=${LEVS_ENKF:-$($NCLEN $ATMFCST_ENSRES pfull)} # get LATB_ENFK
+LONB_ENKF=${LONB_ENKF:-$(${NCLEN} "${ATMFCST_ENSRES}" grid_xt)} # get LONB_ENKF
+LATB_ENKF=${LATB_ENKF:-$(${NCLEN} "${ATMFCST_ENSRES}" grid_yt)} # get LATB_ENFK
+LEVS_ENKF=${LEVS_ENKF:-$(${NCLEN} "${ATMFCST_ENSRES}" pfull)}   # get LATB_ENFK
 
 ##############################################################
 # If analysis increment is written by GSI, regrid forecasts to increment resolution
-if [ $DO_CALC_ANALYSIS == "YES" ]; then
-   $NLN $ATMF06 fcst.06
-   $NLN $ATMF06ENS fcst.ensres.06
-   $NLN $ATMFCST_ENSRES atmens_fcst
-   if [ $DOHYBVAR = "YES" -a $l4densvar = ".true." -a $lwrite4danl = ".true." ]; then
-      $NLN $ATMF03     fcst.03
-      $NLN $ATMF03ENS  fcst.ensres.03
-      $NLN $ATMF04     fcst.04
-      $NLN $ATMF04ENS  fcst.ensres.04
-      $NLN $ATMF05     fcst.05
-      $NLN $ATMF05ENS  fcst.ensres.05
-      $NLN $ATMF07     fcst.07
-      $NLN $ATMF07ENS  fcst.ensres.07
-      $NLN $ATMF08     fcst.08
-      $NLN $ATMF08ENS  fcst.ensres.08
-      $NLN $ATMF09     fcst.09
-      $NLN $ATMF09ENS  fcst.ensres.09
-   fi
-   export OMP_NUM_THREADS=$NTHREADS_CHGRES
-   SIGLEVEL=${SIGLEVEL:-${FIXgfs}/am/global_hyblev.l${LEVS_ENKF}.txt}
-
-   if [[ "${USE_CFP}" == "YES" ]]; then
-       rm -f "${DATA}/mp_chgres.sh"
-   fi
-
-   nfhrs=$(echo "${IAUFHRS_ENKF}" | sed 's/,/ /g')
-   for FHR in $nfhrs; do
-     echo "Regridding deterministic forecast for forecast hour $FHR"
-     rm -f chgres_nc_gauss0$FHR.nml
-cat > chgres_nc_gauss0$FHR.nml << EOF
+if [[ ${DO_CALC_ANALYSIS} == "YES" ]]; then
+    ${NLN} "${ATMF06}" fcst.06
+    ${NLN} "${ATMF06ENS}" fcst.ensres.06
+    ${NLN} "${ATMFCST_ENSRES}" atmens_fcst
+    if [[ "${DOHYBVAR}" == "YES" ]] && [[ "${l4densvar}" == ".true." ]] && [[ "${lwrite4danl}" == ".true." ]]; then
+        ${NLN} "${ATMF03}" fcst.03
+        ${NLN} "${ATMF03ENS}" fcst.ensres.03
+        ${NLN} "${ATMF04}" fcst.04
+        ${NLN} "${ATMF04ENS}" fcst.ensres.04
+        ${NLN} "${ATMF05}" fcst.05
+        ${NLN} "${ATMF05ENS}" fcst.ensres.05
+        ${NLN} "${ATMF07}" fcst.07
+        ${NLN} "${ATMF07ENS}" fcst.ensres.07
+        ${NLN} "${ATMF08}" fcst.08
+        ${NLN} "${ATMF08ENS}" fcst.ensres.08
+        ${NLN} "${ATMF09}" fcst.09
+        ${NLN} "${ATMF09ENS}" fcst.ensres.09
+    fi
+    export OMP_NUM_THREADS=${NTHREADS_CHGRES}
+    SIGLEVEL=${SIGLEVEL:-${FIXgfs}/am/global_hyblev.l${LEVS_ENKF}.txt}
+
+    if [[ "${USE_CFP}" == "YES" ]]; then
+        rm -f "${DATA}/mp_chgres.sh"
+    fi
+
+    nfhrs="${IAUFHRS_ENKF//,/ }"
+    for FHR in ${nfhrs}; do
+        echo "Regridding deterministic forecast for forecast hour ${FHR}"
+        rm -f "chgres_nc_gauss0${FHR}.nml"
+        cat > "chgres_nc_gauss0${FHR}.nml" << EOF
 &chgres_setup
-i_output=$LONB_ENKF
-j_output=$LATB_ENKF
-input_file="fcst.0$FHR"
-output_file="fcst.ensres.0$FHR"
-terrain_file="atmens_fcst"
-ref_file="atmens_fcst"
+   i_output=${LONB_ENKF}
+   j_output=${LATB_ENKF}
+   input_file="fcst.0${FHR}"
+   output_file="fcst.ensres.0${FHR}"
+   terrain_file="atmens_fcst"
+   ref_file="atmens_fcst"
 /
 EOF
-     if [[ $USE_CFP == "YES" ]]; then
-          echo "$nm $APRUN_CHGRES $CHGRESNCEXEC chgres_nc_gauss0$FHR.nml" | tee -a $DATA/mp_chgres.sh
-          if [[ ${CFP_MP:-"NO"} = "YES" ]]; then
-              nm=$((nm+1))
-          fi
-     else
-
-         export pgm=$CHGRESNCEXEC
-         . prep_step
-
-         ${APRUN_CHGRES} "${CHGRESNCEXEC}" "chgres_nc_gauss0${FHR}.nml" && true
-         export err=$?
-         if [[ ${err} -ne 0 ]]; then
-            err_exit
-         fi
-     fi
-   done
-
-   if [[ ${USE_CFP} == "YES" ]]; then
-      chmod 755 ${DATA}/mp_chgres.sh
-      ncmd=$(wc -l < "${DATA}/mp_chgres.sh")
-      if [[ ${ncmd} -gt 0 ]]; then
-         ncmd_max=$((ncmd < max_tasks_per_node ? ncmd : max_tasks_per_node))
-         APRUNCFP_CHGRES=$(eval echo "${APRUNCFP}")
-
-         export pgm=${CHGRESNCEXEC}
-         source prep_step
-
-         ${APRUNCFP_CHGRES} "${DATA}/mp_chgres.sh" && true
-         export err=$?
-         if [[ ${err} -ne 0 ]]; then
-           err_exit
-         fi
-      fi
-   fi
 
+        echo "${APRUN_CHGRES} ${CHGRESNCEXEC} chgres_nc_gauss0${FHR}.nml" | tee -a "${DATA}/mp_chgres.sh"
+
+    done
+
+    # Run with MPMD
+    "${USHgfs}/run_mpmd.sh" "${DATA}/mp_chgres.sh" && true
+    export err=$?
+    if [[ ${err} -ne 0 ]]; then
+        err_exit
+    fi
 else
-   echo "DO_CALC_ANALYSIS != YES, doing nothing"
+    echo "DO_CALC_ANALYSIS != YES, doing nothing"
 fi
 
+cd "${pwd}" || exit
 
-################################################################################
-# Postprocessing
-cd $pwd
-
-exit $err
+exit "${err}"

scripts/exgdas_atmos_gempak_gif_ncdc.sh

@@ -18,17 +18,17 @@ if [[ ${MODEL} == GDAS ]]; then
     export fhr3
     for fhr3 in ${fcsthrs}; do
         gempak_file="${COMIN_ATMOS_GEMPAK_1p00}/${RUN}_1p00_${PDY}${cyc}f${fhr3}"
-        if ! wait_for_file "${gempak_file}" "${sleep_interval}" "${max_tries}" ; then
+        if ! wait_for_file "${gempak_file}" "${sleep_interval}" "${max_tries}"; then
             export err=10
             if [[ ${err} -ne 0 ]]; then
-              err_exit "${gempak_file} not found after ${max_tries} iterations"
+                err_exit "${gempak_file} not found after ${max_tries} iterations"
             fi
         fi
 
         if [[ ! -f "${gempak_file}" ]]; then
             export err=1
             if [[ ${err} -ne 0 ]]; then
-              err_exit "Could not copy ${gempak_file}"
+                err_exit "Could not copy ${gempak_file}"
             fi
         fi
 
@@ -37,7 +37,7 @@ if [[ ${MODEL} == GDAS ]]; then
         "${HOMEgfs}/gempak/ush/gempak_${RUN}_f${fhr3}_gif.sh" && true
         export err=$?
         if [[ ${err} -ne 0 ]]; then
-          err_exit
+            err_exit
         fi
     done
 fi

scripts/exgdas_atmos_nawips.sh

@@ -18,11 +18,11 @@ cd "${DATA_RUN}" || exit 1
 source "${USHgfs}/product_functions.sh"
 
 for table in g2varswmo2.tbl g2vcrdwmo2.tbl g2varsncep1.tbl g2vcrdncep1.tbl; do
-  source_table="${HOMEgfs}/gempak/fix/${table}"
-  if [[ ! -f "${source_table}" ]]; then
-    err_exit "${table} is missing"
-  fi
-  cpreq "${source_table}" "${table}"
+    source_table="${HOMEgfs}/gempak/fix/${table}"
+    if [[ ! -f "${source_table}" ]]; then
+        err_exit "${table} is missing"
+    fi
+    cpreq "${source_table}" "${table}"
 done
 
 NAGRIB="${GEMEXE}/nagrib2"
@@ -37,15 +37,13 @@ proj=
 output=T
 pdsext=no
 
-
-
 GEMGRD="${RUN}_${grid}_${PDY}${cyc}f${fhr3}"
 source_dirvar="COMOUT_ATMOS_GRIB_${grid}"
 export GRIBIN="${!source_dirvar}/${RUN}.${cycle}.pres_a.${grid}.f${fhr3}.grib2"
 GRIBIN_chk="${GRIBIN}.idx"
 
 if [[ ! -r "${GRIBIN_chk}" ]]; then
-  err_exit "GRIB index file ${GRIBIN_chk} not found!"
+    err_exit "GRIB index file ${GRIBIN_chk} not found!"
 fi
 
 cpreq "${GRIBIN}" "grib${fhr3}"
@@ -73,13 +71,13 @@ EOF
 
 export err=$?
 if [[ ${err} -ne 0 ]]; then
-  err_exit "${NAGRIB} failed to create ${GEMGRD}!"
+    err_exit "${NAGRIB} failed to create ${GEMGRD}!"
 fi
 
 cpfs "${GEMGRD}" "${destination}/${GEMGRD}"
-if [[ "${SENDDBN}" == "YES" ]] ; then
-  "${DBNROOT}/bin/dbn_alert" MODEL "${DBN_ALERT_TYPE}" "${job}" \
-    "${destination}/${GEMGRD}"
+if [[ "${SENDDBN}" == "YES" ]]; then
+    "${DBNROOT}/bin/dbn_alert" MODEL "${DBN_ALERT_TYPE}" "${job}" \
+        "${destination}/${GEMGRD}"
 fi
 
 "${GEMEXE}/gpend"

scripts/exgdas_atmos_verfozn.sh

@@ -9,42 +9,35 @@
 ################################################################################
 export err=0
 
-data_available=0
+if [[ -s "${oznstat}" ]]; then
+    #------------------------------------------------------------------
+    #  Copy data files file to local data directory.
+    #  Untar oznstat file.
+    #------------------------------------------------------------------
 
-if [[ -s ${oznstat} ]]; then
-   data_available=1
+    cpreq "${oznstat}" "./oznstat.${PDY}${cyc}"
 
-   #------------------------------------------------------------------
-   #  Copy data files file to local data directory.
-   #  Untar oznstat file.
-   #------------------------------------------------------------------
+    tar -xvf "oznstat.${PDY}${cyc}"
+    rm -f "oznstat.${PDY}${cyc}"
 
-   cpreq "${oznstat}" "./oznstat.${PDY}${cyc}"
+    netcdf=0
+    for filenc4 in diag*nc4.gz; do
+        netcdf=1
+        file=$(echo "${filenc4}" | cut -d'.' -f1-2).gz
+        mv "${filenc4}" "${file}"
+    done
 
-   tar -xvf "oznstat.${PDY}${cyc}"
-   rm -f "oznstat.${PDY}${cyc}"
+    export OZNMON_NETCDF=${netcdf}
 
-   netcdf=0
-   count=$(ls diag* | grep ".nc4" | wc -l)
-   if [ "${count}" -gt 0 ] ; then
-      netcdf=1
-      for filenc4 in $(ls diag*nc4.gz); do
-         file=$(echo "${filenc4}" | cut -d'.' -f1-2).gz
-         mv "${filenc4}" "${file}"
-      done
-   fi
-
-   export OZNMON_NETCDF=${netcdf}
-
-   "${USHgfs}/ozn_xtrct.sh" && true
-   export err=$?
-   if [[ ${err} -ne 0 ]]; then
-     err_exit "ozn_xtrct.sh failed!"
-   fi
+    "${USHgfs}/ozn_xtrct.sh" && true
+    export err=$?
+    if [[ ${err} -ne 0 ]]; then
+        err_exit "ozn_xtrct.sh failed!"
+    fi
 
 else
-   # oznstat file not found
-   export err=1
-   err_exit "${oznstat} does not exist!"
+    # oznstat file not found
+    export err=1
+    err_exit "${oznstat} does not exist!"
 fi
 exit 0