Call err_chk/err_exit for fatal errors in post JJobs/ex-scripts

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -43,6 +43,8 @@ body:
         - All or N/A
         - WCOSS2
         - Hera
+        - Gaea-C5
+        - Gaea-C6
         - Orion
         - Hercules
         - Jet

.github/ISSUE_TEMPLATE/dump_request.yml

@@ -14,8 +14,9 @@ body:
       options:
         - WCOSS2
         - Hera/Ursa
+        - Gaea-C5
+        - Gaea-C6
         - Orion/Hercules
-        - Jet
       multiple: true
     validations:
       required: true

dev/jobs/arch_tars.sh

@@ -10,11 +10,6 @@ if [[ ${status} -ne 0 ]]; then
     exit "${status}"
 fi
 
-###############################################################
-# setup python path for workflow utilities and tasks
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${HOMEgfs}/ush/python"
-export PYTHONPATH
-
 export job="arch_tars"
 export jobid="${job}.$$"
 

dev/jobs/arch_vrfy.sh

@@ -10,11 +10,6 @@ if [[ ${status} -ne 0 ]]; then
     exit "${status}"
 fi
 
-###############################################################
-# setup python path for workflow utilities and tasks
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${HOMEgfs}/ush/python"
-export PYTHONPATH
-
 export job="arch_vrfy"
 export jobid="${job}.$$"
 

dev/jobs/earc_tars.sh

@@ -10,11 +10,6 @@ if [[ ${status} -ne 0 ]]; then
     exit "${status}"
 fi
 
-###############################################################
-# setup python path for workflow utilities and tasks
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${HOMEgfs}/ush/python"
-export PYTHONPATH
-
 export job="earc_tars"
 export jobid="${job}.$$"
 

dev/jobs/earc_vrfy.sh

@@ -10,11 +10,6 @@ if [[ ${status} -ne 0 ]]; then
     exit "${status}"
 fi
 
-###############################################################
-# setup python path for workflow utilities and tasks
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${HOMEgfs}/ush/python"
-export PYTHONPATH
-
 export job="earc_vrfy"
 export jobid="${job}.$$"
 

dev/jobs/esnowanl.sh

@@ -11,14 +11,6 @@ fi
 export job="esnowanl"
 export jobid="${job}.$$"
 
-###############################################################
-# setup python path for ioda utilities
-# shellcheck disable=SC2311
-pyiodaPATH="${HOMEgfs}/sorc/gdas.cd/build/lib/python${PYTHON_VERSION}/"
-gdasappPATH="${HOMEgfs}/sorc/gdas.cd/sorc/iodaconv/src:${pyiodaPATH}"
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}:${gdasappPATH}"
-export PYTHONPATH
-
 ###############################################################
 # Execute the JJOB
 "${HOMEgfs}/jobs/JGLOBAL_SNOWENS_ANALYSIS"

dev/jobs/globus_arch.sh

@@ -8,11 +8,6 @@ set -x
 status=$?
 [[ ${status} -ne 0 ]] && exit "${status}"
 
-###############################################################
-# setup python path for workflow utilities and tasks
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${HOMEgfs}/ush/python"
-export PYTHONPATH
-
 export job="globus_arch"
 export jobid="${job}.$$"
 

dev/jobs/globus_earc.sh

@@ -8,11 +8,6 @@ set -x
 status=$?
 if [[ ${status} -ne 0 ]]; then exit "${status}"; fi
 
-###############################################################
-# setup python path for workflow utilities and tasks
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${HOMEgfs}/ush/python"
-export PYTHONPATH
-
 export job="globus_earc"
 export jobid="${job}.$$"
 

dev/jobs/marineanlletkf.sh

@@ -13,11 +13,6 @@ fi
 export job="marineanlletkf"
 export jobid="${job}.$$"
 
-###############################################################
-# Setup Python path for GDASApp ush
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${HOMEgfs}/ush/python"
-export PYTHONPATH
-
 ###############################################################
 # Execute the JJOB
 "${HOMEgfs}/jobs/JGLOBAL_MARINE_ANALYSIS_LETKF"

dev/jobs/prep_emissions.sh

@@ -11,11 +11,6 @@ status=$?
 export job="prep_emissions"
 export jobid="${job}.$$"
 
-###############################################################
-# setup python path for workflow utilities and tasks
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${HOMEgfs}/ush/python"
-export PYTHONPATH
-
 ###############################################################
 # Execute the JJOB
 "${HOMEgfs}/jobs/JGLOBAL_PREP_EMISSIONS"

dev/jobs/prepatmiodaobs.sh

@@ -11,13 +11,6 @@ fi
 export job="prepatmobs"
 export jobid="${job}.$$"
 
-###############################################################
-# setup python path for ioda utilities
-# shellcheck disable=SC2311
-pyiodaPATH="${HOMEgfs}/sorc/gdas.cd/build/lib/python${PYTHON_VERSION}/"
-PYTHONPATH="${pyiodaPATH}:${PYTHONPATH}"
-export PYTHONPATH
-
 ###############################################################
 # Execute the JJOB
 "${HOMEgfs}/jobs/JGLOBAL_ATM_PREP_IODA_OBS"

dev/jobs/prepoceanobs.sh

@@ -13,13 +13,6 @@ fi
 export job="prepoceanobs"
 export jobid="${job}.$$"
 
-###############################################################
-# setup python path for class defs and utils
-# shellcheck disable=SC2311
-pyiodaPATH="${HOMEgfs}/sorc/gdas.cd/build/lib/python${PYTHON_VERSION}/"
-PYTHONPATH="${pyiodaPATH}:${PYTHONPATH}"
-export PYTHONPATH
-
 ###############################################################
 # Execute the JJOB
 "${HOMEgfs}"/jobs/JGLOBAL_PREP_OCEAN_OBS

dev/jobs/snowanl.sh

@@ -11,14 +11,6 @@ fi
 export job="snowanl"
 export jobid="${job}.$$"
 
-###############################################################
-# setup python path for ioda utilities
-# shellcheck disable=SC2311
-pyiodaPATH="${HOMEgfs}/sorc/gdas.cd/build/lib/python${PYTHON_VERSION}/"
-gdasappPATH="${HOMEgfs}/sorc/gdas.cd/sorc/iodaconv/src:${pyiodaPATH}"
-PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}:${gdasappPATH}"
-export PYTHONPATH
-
 ###############################################################
 # Execute the JJOB
 "${HOMEgfs}/jobs/JGLOBAL_SNOW_ANALYSIS"

jobs/JGDAS_ATMOS_GEMPAK

@@ -33,13 +33,15 @@ done
 # Execute the script for one degree grib
 ########################################################
 
-"${SCRgfs}/exgdas_atmos_nawips.sh" "1p00" "${FHR3}" "GDAS_GEMPAK" "${COMOUT_ATMOS_GEMPAK_1p00}"
+"${SCRgfs}/exgdas_atmos_nawips.sh" "1p00" "${FHR3}" "GDAS_GEMPAK" "${COMOUT_ATMOS_GEMPAK_1p00}" && true
+
+export err=$?; err_chk
 
 ########################################################
 # Execute the script for quater-degree grib
 ########################################################
 
-"${SCRgfs}/exgdas_atmos_nawips.sh" "0p25" "${FHR3}" "GDAS_GEMPAK" "${COMOUT_ATMOS_GEMPAK_0p25}"
+"${SCRgfs}/exgdas_atmos_nawips.sh" "0p25" "${FHR3}" "GDAS_GEMPAK" "${COMOUT_ATMOS_GEMPAK_0p25}" && true
 
 export err=$?; err_chk
 

jobs/JGDAS_ATMOS_GEMPAK_META_NCDC

@@ -54,14 +54,17 @@ export pgmout=OUTPUT.$$
 
 ########################################################
 # Execute the script.
-"${HOMEgfs}/gempak/ush/gdas_meta_na.sh"
+"${HOMEgfs}/gempak/ush/gdas_meta_na.sh" && true
 export err=$?; err_chk
-"${HOMEgfs}/gempak/ush/gdas_meta_loop.sh"
+
+"${HOMEgfs}/gempak/ush/gdas_meta_loop.sh" && true
 export err=$?; err_chk
+
 if [[ "${cyc}" == '06' ]]; then
-  "${HOMEgfs}/gempak/ush/gdas_ecmwf_meta_ver.sh"
+  "${HOMEgfs}/gempak/ush/gdas_ecmwf_meta_ver.sh" && true
   export err=$?; err_chk
-  "${HOMEgfs}/gempak/ush/gdas_ukmet_meta_ver.sh"
+
+  "${HOMEgfs}/gempak/ush/gdas_ukmet_meta_ver.sh" && true
   export err=$?; err_chk
 fi
 ########################################################
@@ -73,7 +76,7 @@ fi
 ########################################################
 # Execute the script.
 if (( cyc%12 == 0 )); then
-  "${SCRgfs}/exgdas_atmos_gempak_gif_ncdc.sh"
+  "${SCRgfs}/exgdas_atmos_gempak_gif_ncdc.sh" && true
 fi
 export err=$?; err_chk
 ########################################################
@@ -91,4 +94,3 @@ fi
 if [[ "${KEEPDATA}" != "YES" ]] ; then
   rm -rf "${DATA}"
 fi
-

jobs/JGDAS_FIT2OBS

@@ -65,6 +65,8 @@ if [[ ${CDATE} -gt ${SDATE} ]]; then
   # RUN FIT2OBS VERIFICATION
   ##############################################
 
+  # Un-export SHELLOPTS before going into the Fit2Obs package (let that package handle logging/errors)
+  export -n SHELLOPTS
   "${SCRIPTSfit2obs}/excfs_gdas_vrfyfits.sh"
   err=$?
   if [[ ${err} -ne 0 ]]; then

jobs/JGFS_ATMOS_AWIPS_20KM_1P0DEG

@@ -37,7 +37,7 @@ export pgmout=OUTPUT.$$
 
 ########################################################
 # Execute the script.
-"${SCRgfs}/exgfs_atmos_awips_20km_1p0deg.sh" "${fcsthrs}"
+"${SCRgfs}/exgfs_atmos_awips_20km_1p0deg.sh" "${fcsthrs}" && true
 export err=$?; err_chk
 ########################################################
 

jobs/JGFS_ATMOS_FBWIND

@@ -29,7 +29,7 @@ export DBNROOT=${DBNROOT:-${UTILROOT}/fakedbn}
 
 ########################################################
 # Execute the script.
-"${SCRgfs}/exgfs_atmos_fbwind.sh"
+"${SCRgfs}/exgfs_atmos_fbwind.sh" && true
 export err=$?;err_chk
 ########################################################
 

jobs/JGFS_ATMOS_GEMPAK

@@ -45,15 +45,17 @@ fhmin=0
 fhmax=240
 if (( fhr >= fhmin && fhr <= fhmax )); then
   if ((fhr % 3 == 0)); then
-    "${SCRgfs}/exgfs_atmos_nawips.sh" "1p00" "${FHR3}" "GFS_GEMPAK" "${COMOUT_ATMOS_GEMPAK_1p00}"
+    "${SCRgfs}/exgfs_atmos_nawips.sh" "1p00" "${FHR3}" "GFS_GEMPAK" "${COMOUT_ATMOS_GEMPAK_1p00}" && true
+    export err=$?; err_chk
   fi
 fi
 
 fhmin=252
 fhmax=384
 if (( fhr >= fhmin && fhr <= fhmax )); then
   if ((fhr % 12 == 0)); then
-    "${SCRgfs}/exgfs_atmos_nawips.sh" "1p00" "${FHR3}" "GFS_GEMPAK" "${COMOUT_ATMOS_GEMPAK_1p00}"
+    "${SCRgfs}/exgfs_atmos_nawips.sh" "1p00" "${FHR3}" "GFS_GEMPAK" "${COMOUT_ATMOS_GEMPAK_1p00}" && true
+    export err=$?; err_chk
   fi
 fi
 
@@ -64,23 +66,26 @@ fhmin=0
 fhmax=240
 if (( fhr >= fhmin && fhr <= fhmax )); then
   if ((fhr % 3 == 0)); then
-    "${SCRgfs}/exgfs_atmos_nawips.sh" "0p50" "${FHR3}" "GFS_GEMPAK" "${COMOUT_ATMOS_GEMPAK_0p50}"
+    "${SCRgfs}/exgfs_atmos_nawips.sh" "0p50" "${FHR3}" "GFS_GEMPAK" "${COMOUT_ATMOS_GEMPAK_0p50}" && true
+    export err=$?; err_chk
   fi
 fi
 
 fhmin=246
 fhmax=276
 if (( fhr >= fhmin && fhr <= fhmax )); then
   if ((fhr % 6 == 0)); then
-    "${SCRgfs}/exgfs_atmos_nawips.sh" "0p50" "${FHR3}" "GFS_GEMPAK" "${COMOUT_ATMOS_GEMPAK_0p50}"
+    "${SCRgfs}/exgfs_atmos_nawips.sh" "0p50" "${FHR3}" "GFS_GEMPAK" "${COMOUT_ATMOS_GEMPAK_0p50}" && true
+    export err=$?; err_chk
   fi
 fi
 
 fhmin=288
 fhmax=384
 if (( fhr >= fhmin && fhr <= fhmax )); then
   if ((fhr % 12 == 0)); then
-    "${SCRgfs}/exgfs_atmos_nawips.sh" "0p50" "${FHR3}" "GFS_GEMPAK" "${COMOUT_ATMOS_GEMPAK_0p50}"
+    "${SCRgfs}/exgfs_atmos_nawips.sh" "0p50" "${FHR3}" "GFS_GEMPAK" "${COMOUT_ATMOS_GEMPAK_0p50}" && true
+    export err=$?; err_chk
   fi
 fi
 
@@ -91,23 +96,26 @@ fhmin=0
 fhmax=120
 if (( fhr >= fhmin && fhr <= fhmax )); then
   if ((fhr % 1 == 0)); then
-    "${SCRgfs}/exgfs_atmos_nawips.sh" "0p25" "${FHR3}" "GFS_GEMPAK" "${COMOUT_ATMOS_GEMPAK_0p25}"
+    "${SCRgfs}/exgfs_atmos_nawips.sh" "0p25" "${FHR3}" "GFS_GEMPAK" "${COMOUT_ATMOS_GEMPAK_0p25}" && true
+    export err=$?; err_chk
   fi
 fi
 
 fhmin=123
 fhmax=240
 if (( fhr >= fhmin && fhr <= fhmax )); then
   if ((fhr % 3 == 0)); then
-    "${SCRgfs}/exgfs_atmos_nawips.sh" "0p25" "${FHR3}" "GFS_GEMPAK" "${COMOUT_ATMOS_GEMPAK_0p25}"
+    "${SCRgfs}/exgfs_atmos_nawips.sh" "0p25" "${FHR3}" "GFS_GEMPAK" "${COMOUT_ATMOS_GEMPAK_0p25}" && true
+    export err=$?; err_chk
   fi
 fi
 
 fhmin=252
 fhmax=384
 if (( fhr >= fhmin && fhr <= fhmax )); then
   if ((fhr % 12 == 0)); then
-    "${SCRgfs}/exgfs_atmos_nawips.sh" "0p25" "${FHR3}" "GFS_GEMPAK" "${COMOUT_ATMOS_GEMPAK_0p25}"
+    "${SCRgfs}/exgfs_atmos_nawips.sh" "0p25" "${FHR3}" "GFS_GEMPAK" "${COMOUT_ATMOS_GEMPAK_0p25}" && true
+    export err=$?; err_chk
   fi
 fi
 
@@ -118,16 +126,17 @@ fhmin=0
 fhmax="${ocean_domain_max}"
 if (( fhr >= fhmin && fhr <= fhmax )); then
   if ((fhr % 3 == 0)); then
-    "${SCRgfs}/exgfs_atmos_nawips.sh" "35km_pac" "${FHR3}" "GFS_GEMPAK_WWB" "${COMOUT_ATMOS_GEMPAK_35km_pac}"
+    "${SCRgfs}/exgfs_atmos_nawips.sh" "35km_pac" "${FHR3}" "GFS_GEMPAK_WWB" "${COMOUT_ATMOS_GEMPAK_35km_pac}" && true
+    export err=$?; err_chk
 
-    "${SCRgfs}/exgfs_atmos_nawips.sh" "35km_atl" "${FHR3}" "GFS_GEMPAK_WWB" "${COMOUT_ATMOS_GEMPAK_35km_atl}"
+    "${SCRgfs}/exgfs_atmos_nawips.sh" "35km_atl" "${FHR3}" "GFS_GEMPAK_WWB" "${COMOUT_ATMOS_GEMPAK_35km_atl}" && true
+    export err=$?; err_chk
 
-    "${SCRgfs}/exgfs_atmos_nawips.sh" "40km" "${FHR3}" "GFS_GEMPAK_WWB" "${COMOUT_ATMOS_GEMPAK_40km}"
+    "${SCRgfs}/exgfs_atmos_nawips.sh" "40km" "${FHR3}" "GFS_GEMPAK_WWB" "${COMOUT_ATMOS_GEMPAK_40km}" && true
+    export err=$?; err_chk
   fi
 fi
 
-export err=$?; err_chk
-
 ############################################
 # print exec I/O output
 ############################################

jobs/JGFS_ATMOS_GEMPAK_META

@@ -60,7 +60,7 @@ fi
 
 ########################################################
 # Execute the script.
-"${SCRgfs}/exgfs_atmos_gempak_meta.sh"
+"${SCRgfs}/exgfs_atmos_gempak_meta.sh" && true
 export err=$?; err_chk
 ########################################################
 

jobs/JGFS_ATMOS_GEMPAK_PGRB2_SPEC

@@ -47,7 +47,7 @@ export RUN2=gfs_goessim221
 export GRIB=goessimpgrb2f
 export EXT=".grd221"
 
-"${SCRgfs}/exgfs_atmos_goes_nawips.sh" "${FHR3}"
+"${SCRgfs}/exgfs_atmos_goes_nawips.sh" "${FHR3}" && true
 
 export err=$?; err_chk
 

jobs/JGFS_ATMOS_PGRB2_SPEC_NPOESS

@@ -30,7 +30,7 @@ mkdir -m 775 -p "${COMOUT_ATMOS_GOES}"
 
 #############################################################
 # Execute the script
-"${SCRgfs}/exgfs_atmos_grib2_special_npoess.sh"
+"${SCRgfs}/exgfs_atmos_grib2_special_npoess.sh" && true
 export err=$?;err_chk
 #############################################################
 

jobs/JGFS_ATMOS_POSTSND

@@ -39,12 +39,8 @@ fi
 
 ########################################################
 # Execute the script.
-${SCRgfs}/exgfs_atmos_postsnd.sh
-err=$?
-if [[ ${err} -ne 0 ]]; then
-    exit "${err}"
-fi
-
+${SCRgfs}/exgfs_atmos_postsnd.sh && true
+export err=$?; err_chk
 
 ##############################################
 # End JOB SPECIFIC work