Use err_chk in GSI J-Jobs and scripts

jobs/JGDAS_ATMOS_ANALYSIS_DIAG

@@ -32,12 +32,9 @@ mkdir -m 775 -p "${COMOUT_ATMOS_ANALYSIS}"
 
 ###############################################################
 # Run relevant script
-${ANALDIAGSH:-${SCRgfs}/exglobal_diag.sh}
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${ANALDIAGSH:-${SCRgfs}/exglobal_diag.sh} && true
+export err=$?
+err_chk
 
 ##############################################
 # End JOB SPECIFIC work

jobs/JGDAS_ATMOS_CHGRES_FORENKF

@@ -25,12 +25,9 @@ MEMDIR="mem001" YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
 
 ###############################################################
 # Run relevant script
-${CHGRESFCSTSH:-${SCRgfs}/exgdas_atmos_chgres_forenkf.sh}
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${CHGRESFCSTSH:-${SCRgfs}/exgdas_atmos_chgres_forenkf.sh} && true
+export err=$?
+err_chk
 
 ##############################################
 # End JOB SPECIFIC work

jobs/JGDAS_ATMOS_VERFOZN

@@ -29,12 +29,9 @@ if [[ ! -d ${TANKverf_ozn} ]]; then mkdir -p ${TANKverf_ozn} ; fi
 #-------------------------------------------------------
 # Execute the script.
 #
-"${SCRgfs}/exgdas_atmos_verfozn.sh"
-err=$?
-if (( err != 0 )); then
-    exit "${err}"
-fi
-
+"${SCRgfs}/exgdas_atmos_verfozn.sh" && true
+export err=$?
+err_chk
 
 ################################
 # Remove the Working Directory

jobs/JGDAS_ATMOS_VERFRAD

@@ -33,11 +33,9 @@ if [[ ! -d ${TANKverf_rad} ]]; then mkdir -p ${TANKverf_rad} ; fi
 
 ########################################################
 # Execute the script.
-"${SCRgfs}/exgdas_atmos_verfrad.sh"
-err=$?
-if (( err != 0 )); then
-    exit "${err}"
-fi
+"${SCRgfs}/exgdas_atmos_verfrad.sh" && true
+export err=$?
+err_chk
 
 ################################
 # Remove the Working Directory

jobs/JGDAS_ENKF_DIAG

@@ -44,8 +44,8 @@ MEMDIR="ensstat" RUN=${GDUMP_ENS} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
 
 export ATMGES_ENSMEAN="${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf006.ensmean.nc"
 if [ ! -f ${ATMGES_ENSMEAN} ]; then
-    echo "FATAL ERROR: FILE MISSING: ATMGES_ENSMEAN = ${ATMGES_ENSMEAN}"
-    exit 1
+    export err=1
+    err_chk "FATAL ERROR: FILE MISSING: ATMGES_ENSMEAN = ${ATMGES_ENSMEAN}"
 fi
 
 # Link observational data
@@ -99,12 +99,9 @@ done
 ###############################################################
 # Run relevant script
 
-${ANALDIAGSH:-${SCRgfs}/exglobal_diag.sh}
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${ANALDIAGSH:-${SCRgfs}/exglobal_diag.sh} && true
+export err=$?
+err_chk
 
 ##############################################
 # End JOB SPECIFIC work

jobs/JGDAS_ENKF_ECEN

@@ -40,12 +40,9 @@ MEMDIR="ensstat" RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
 ###############################################################
 # Run relevant script
 
-${ENKFRECENSH:-${SCRgfs}/exgdas_enkf_ecen.sh}
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${ENKFRECENSH:-${SCRgfs}/exgdas_enkf_ecen.sh} && true
+export err=$?
+err_chk
 
 ##############################################
 # End JOB SPECIFIC work

jobs/JGDAS_ENKF_POST

@@ -21,12 +21,9 @@ export LEVS=$((LEVS-1))
 ###############################################################
 # Run relevant script
 
-${ENKFPOSTSH:-${SCRgfs}/exgdas_enkf_post.sh}
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${ENKFPOSTSH:-${SCRgfs}/exgdas_enkf_post.sh} && true
+export err=$?
+err_chk
 
 ##############################################
 # End JOB SPECIFIC work

jobs/JGDAS_ENKF_SELECT_OBS

@@ -51,18 +51,14 @@ mkdir -p "${COMOUT_ATMOS_ANALYSIS}"
 
 export ATMGES_ENSMEAN="${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf006${GSUFFIX}"
 if [[ ! -f ${ATMGES_ENSMEAN} ]]; then
-    echo "FATAL ERROR: FILE MISSING: ATMGES_ENSMEAN = ${ATMGES_ENSMEAN}"
-    exit 1
+    export err=1
+    err_chk "FATAL ERROR: FILE MISSING: ATMGES_ENSMEAN = ${ATMGES_ENSMEAN}"
 fi
 
-# Ignore masking of chained commands and possible misspelling warning
-# shellcheck disable=SC2153,SC2312
-LEVS=$(${NCDUMP} -h "${ATMGES_ENSMEAN}" | grep -i "pfull" | head -1 | awk -F" = " '{print $2}' | awk -F" " '{print $1}') # get LEVS
-# shellcheck disable=
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
+LEVS=$(${NCLEN} ${ATMGES} pfull) && true
+export err=$?
+set_strict
+
 export LEVS
 
 # Link observational data
@@ -121,12 +117,9 @@ done
 ###############################################################
 # Run relevant script
 
-${INVOBSSH:-${SCRgfs}/exgdas_enkf_select_obs.sh}
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${INVOBSSH:-${SCRgfs}/exgdas_enkf_select_obs.sh} && true
+export err=$?
+err_chk
 
 ##############################################
 # Send Alerts
@@ -144,7 +137,7 @@ fi
 # Final processing
 ##############################################
 if [[ -e "${pgmout}" ]] ; then
-  cat ${pgmout}
+  cat "${pgmout}"
 fi
 
 ##########################################

jobs/JGDAS_ENKF_SFC

@@ -42,12 +42,9 @@ RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
 ###############################################################
 # Run relevant script
 
-${ENKFRESFCSH:-${SCRgfs}/exgdas_enkf_sfc.sh}
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${ENKFRESFCSH:-${SCRgfs}/exgdas_enkf_sfc.sh} && true
+export err=$?
+err_chk
 
 ##############################################
 # End JOB SPECIFIC work

jobs/JGDAS_ENKF_UPDATE

@@ -36,12 +36,9 @@ MEMDIR="ensstat" RUN="enkfgdas" YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
 ###############################################################
 # Run relevant script
 
-${ENKFUPDSH:-${SCRgfs}/exgdas_enkf_update.sh}
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${ENKFUPDSH:-${SCRgfs}/exgdas_enkf_update.sh} && true
+export err=$?
+err_chk
 
 ##############################################
 # Send Alerts

jobs/JGLOBAL_ARCHIVE_TARS

@@ -75,7 +75,10 @@ fi
 
 set +eu
 ${GLOBALARCHIVESH:-${SCRgfs}/exglobal_archive_tars.py}
-export err=$?; err_chk "FATAL ERROR: failed to archive the COM structure"
+export err=$?
+set +x
+err_chk "FATAL ERROR: failed to archive the COM structure"
+set_trace
 set_strict
 
 ##############################################

jobs/JGLOBAL_ATMOS_ANALYSIS

@@ -45,23 +45,20 @@ mkdir -p "${COMOUT_ATMOS_ANALYSIS}"
 
 export ATMGES="${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf006.nc"
 if [ ! -f ${ATMGES} ]; then
-    echo "FATAL ERROR: FILE MISSING: ATMGES = ${ATMGES}"
-    exit 1
+    export err=1
+    err_chk "FATAL ERROR: FILE MISSING: ATMGES = ${ATMGES}"
 fi
 
 # Get LEVS
-export LEVS=$(${NCLEN} ${ATMGES} pfull)
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+export LEVS=$(${NCLEN} ${ATMGES} pfull) && true
+export err=$?
+err_chk
 
 if [ ${DOHYBVAR} = "YES" ]; then
     export ATMGES_ENSMEAN="${COMIN_ATMOS_HISTORY_ENS_PREV}/${GPREFIX_ENS}atmf006.ensmean.nc"
     if [ ! -f ${ATMGES_ENSMEAN} ]; then
-        echo "FATAL ERROR: FILE MISSING: ATMGES_ENSMEAN = ${ATMGES_ENSMEAN}"
-        exit 2
+        export err=2
+        err_chk "FATAL ERROR: FILE MISSING: ATMGES_ENSMEAN = ${ATMGES_ENSMEAN}"
     fi
 fi
 
@@ -89,12 +86,9 @@ fi
 ###############################################################
 # Run relevant script
 
-${ANALYSISSH:-${SCRgfs}/exglobal_atmos_analysis.sh}
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${ANALYSISSH:-${SCRgfs}/exglobal_atmos_analysis.sh} && true
+export err=$?
+err_chk
 
 ##############################################
 # Send Alerts

jobs/JGLOBAL_ATMOS_ANALYSIS_CALC

@@ -41,17 +41,14 @@ RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
 
 export ATMGES="${COMIN_ATMOS_HISTORY_PREV}/${GPREFIX}atmf006.nc"
 if [ ! -f ${ATMGES} ]; then
-    echo "FATAL ERROR: FILE MISSING: ATMGES = ${ATMGES}"
-    exit 1
+    export err=1
+    err_chk "FATAL ERROR: FILE MISSING: ATMGES = ${ATMGES}"
 fi
 
 # Get LEVS
-export LEVS=$(${NCLEN} ${ATMGES} pfull)
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+export LEVS=$(${NCLEN} ${ATMGES} pfull) && true
+export err=$?
+err_chk
 
 # Generate Gaussian surface analysis  # TODO: Should this be removed now that sfcanl is its own job?
 export DOGAUSFCANL=${DOGAUSFCANL:-"YES"}
@@ -60,12 +57,9 @@ export DOGAUSFCANL=${DOGAUSFCANL:-"YES"}
 ###############################################################
 # Run relevant script
 
-${ANALCALCSH:-${SCRgfs}/exglobal_atmos_analysis_calc.sh}
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${ANALCALCSH:-${SCRgfs}/exglobal_atmos_analysis_calc.sh} && true
+export err=$?
+err_chk
 
 ##############################################
 # End JOB SPECIFIC work

jobs/JGLOBAL_ATMOS_SFCANL

@@ -32,12 +32,9 @@ mkdir -p "${COMOUT_ATMOS_RESTART}"
 ###############################################################
 # Run relevant script
 
-${SFCANALSH:-${SCRgfs}/exglobal_atmos_sfcanl.sh}
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${SFCANALSH:-${SCRgfs}/exglobal_atmos_sfcanl.sh} && true
+export err=$?
+err_chk
 
 ##############################################
 # End JOB SPECIFIC work

jobs/JGLOBAL_ATMOS_VMINMON

@@ -31,11 +31,9 @@ if [[ ! -d ${M_TANKverf} ]]; then mkdir -p "${M_TANKverf}" ; fi
 
 ########################################################
 # Execute the script.
-"${SCRgfs}/exglobal_atmos_vminmon.sh"
-err=$?
-if (( err != 0 )); then
-    exit "${err}"
-fi
+"${SCRgfs}/exglobal_atmos_vminmon.sh" && true
+export err=$?
+err_chk
 
 ################################
 # Remove the Working Directory

jobs/JGLOBAL_ENS_ARCHIVE_TARS

@@ -21,7 +21,10 @@ if [[ ! -d ${COMOUT_CONF} ]]; then mkdir -p "${COMOUT_CONF}"; fi
 # Calls an external bash command; do not fail on unassigned/error
 set +eu
 "${SCRgfs}/exgdas_enkf_earc_tars.py"
-export err=$?; err_chk "FATAL ERROR Failed to archive the ensemble COM structure"
+export err=$?
+set +x
+err_chk "FATAL ERROR Failed to archive the ensemble COM structure"
+set_trace
 set_strict
 
 ###############################################################

scripts/exgdas_atmos_chgres_forenkf.sh

@@ -154,8 +154,9 @@ EOF
          export pgm=$CHGRESNCEXEC
          . prep_step
 
-         $APRUN_CHGRES $CHGRESNCEXEC chgres_nc_gauss0$FHR.nml
-         export err=$?; err_chk
+         ${APRUN_CHGRES} "${CHGRESNCEXEC}" "chgres_nc_gauss0${FHR}.nml" && true
+         export err=$?
+         err_chk
      fi
    done
 
@@ -169,8 +170,9 @@ EOF
          export pgm=$CHGRESNCEXEC
          . prep_step
 
-         $APRUNCFP_CHGRES $DATA/mp_chgres.sh
-         export err=$?; err_chk
+         ${APRUNCFP_CHGRES} "${DATA}/mp_chgres.sh" && true
+         export err=$?
+         err_chk
       fi
    fi
 

scripts/exgdas_atmos_verfozn.sh

@@ -7,7 +7,7 @@
 # (OznMon) DA package.
 #
 ################################################################################
-err=0
+export err=0
 
 data_available=0
 
@@ -36,13 +36,13 @@ if [[ -s ${oznstat} ]]; then
 
    export OZNMON_NETCDF=${netcdf}
 
-   "${USHgfs}/ozn_xtrct.sh"
-   err=$?
+   "${USHgfs}/ozn_xtrct.sh" && true
+   export err=$?
 
 else
    # oznstat file not found
-   err=1
+   export err=1
 fi
 
-exit ${err}
-
+err_chk
+exit 0