Enable metplus and fit2obs jobs on Jet. NOAA-EMC#357

Also fix a multitude of shellcheck warnings in related scripts.
DavidHuber-NOAA · Mar 21, 2023 · 8b98e18 · 8b98e18
1 parent 822bf71
commit 8b98e18
Show file tree

Hide file tree

Showing 4 changed files with 106 additions and 108 deletions.
diff --git a/jobs/rocoto/vrfy.sh b/jobs/rocoto/vrfy.sh
@@ -17,33 +17,36 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "vrfy" -c "base vrfy"
 
 ###############################################################
 export COMPONENT="atmos"
-export CDATEm1=$(${NDATE} -24 ${CDATE})
-export PDYm1=$(echo ${CDATEm1} | cut -c1-8)
+CDATEm1=$(${NDATE} -24 "${CDATE}")
+export CDATEm1
+PDYm1=$(echo "${CDATEm1}" | cut -c1-8)
+export PDYm1
 
-CDATEm1c=$(${NDATE} -06 ${CDATE})
-PDYm1c=$(echo ${CDATEm1c} | cut -c1-8)
-pcyc=$(echo ${CDATEm1c} | cut -c9-10)
+CDATEm1c=$(${NDATE} -06 "${CDATE}")
+PDYm1c=$(echo "${CDATEm1c}" | cut -c1-8)
+pcyc=$(echo "${CDATEm1c}" | cut -c9-10)
 
 export COMIN="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/${COMPONENT}"
 
 
 ###############################################################
 echo
 echo "=============== START TO GENERATE QUARTER DEGREE GRIB1 FILES ==============="
-if [ ${MKPGB4PRCP} = "YES" -a ${CDUMP} = "gfs" ]; then
-    if [ ! -d ${ARCDIR} ]; then mkdir -p ${ARCDIR} ; fi
+if [[ ${MKPGB4PRCP} = "YES" && ${CDUMP} = "gfs" ]]; then
+    if [[ ! -d "${ARCDIR}" ]]; then mkdir -p "${ARCDIR}" ; fi
     nthreads_env=${OMP_NUM_THREADS:-1} # get threads set in env
     export OMP_NUM_THREADS=1
-    cd ${COMIN}
+    set -e
+    cd "${COMIN}"
     fhmax=${vhr_rain:-${FHMAX_GFS}}
     fhr=0
-    while [ ${fhr} -le ${fhmax} ]; do
-       fhr2=$(printf %02i ${fhr})
-       fhr3=$(printf %03i ${fhr})
+    while [[ ${fhr} -le ${fhmax} ]]; do
+       fhr2=$(printf %02i "${fhr}")
+       fhr3=$(printf %03i "${fhr}")
        fname=${CDUMP}.t${cyc}z.sfluxgrbf${fhr3}.grib2
        fileout=${ARCDIR}/pgbq${fhr2}.${CDUMP}.${CDATE}.grib2
-       ${WGRIB2} ${fname} -match "(:PRATE:surface:)|(:TMP:2 m above ground:)" -grib ${fileout}
-       (( fhr = ${fhr} + 6 ))
+       ${WGRIB2} "${fname}" -match "(:PRATE:surface:)|(:TMP:2 m above ground:)" -grib "${fileout}"
+       (( fhr = fhr + 6 ))
     done
     export OMP_NUM_THREADS=${nthreads_env} # revert to threads set in env
 fi
@@ -52,32 +55,34 @@ fi
 ###############################################################
 echo
 echo "=============== START TO RUN MOS ==============="
-if [ ${RUNMOS} = "YES" -a ${CDUMP} = "gfs" ]; then
-    ${RUNGFSMOSSH} ${PDY}${cyc}
+if [[ ${RUNMOS} = "YES" && ${CDUMP} = "gfs" ]]; then
+    ${RUNGFSMOSSH} "${PDY}${cyc}"
 fi
 
 
 ###############################################################
 echo
 echo "=============== START TO RUN FIT2OBS VERIFICATION ==============="
-if [ ${VRFYFITS} = "YES" -a ${CDUMP} = ${CDFNL} -a ${CDATE} != ${SDATE} ]; then
+if [[ ${VRFYFITS} = "YES" && ${CDUMP} = "${CDFNL}" && ${CDATE} != "${SDATE}" ]]; then
 
     export CDUMPFCST=${VDUMP}
     export TMPDIR="${RUNDIR}/${CDATE}/${CDUMP}"
-    [[ ! -d ${TMPDIR} ]] && mkdir -p ${TMPDIR}
+    [[ ! -d ${TMPDIR} ]] && mkdir -p "${TMPDIR}"
 
-    xdate=$(${NDATE} -${VBACKUP_FITS} ${CDATE})
+    xdate=$(${NDATE} -"${VBACKUP_FITS} ${CDATE}")
 
-    export vday=$(echo ${xdate} | cut -c1-8)
-    export vcyc=$(echo ${xdate} | cut -c9-10)
+    vday=$(echo "${xdate}" | cut -c1-8)
+    export vday
+    vcyc=$(echo "${xdate}" | cut -c9-10)
+    export vcyc
     export COMDAY=${ROTDIR}/logs/${xdate}
     export COM_INA=${ROTDIR}/gdas.${vday}/${vcyc}/atmos
-    export COM_INF='$ROTDIR/vrfyarch/gfs.$fdy/$fzz'
-    export COM_PRP='$ROTDIR/gdas.$pdy/$cyc/obs'
+    export COM_INF="${ROTDIR}/vrfyarch/gfs.${fdy}/${fzz}"
+    export COM_PRP="${ROTDIR}/gdas.${pdy}/${cyc}/obs"
 
     export OUTPUT_FILETYPE_SAVE=${OUTPUT_FILETYPE}
 
-    ${PREPQFITSH} ${PSLOT} ${xdate} ${ROTDIR} ${ARCDIR} ${TMPDIR}
+    ${PREPQFITSH} "${PSLOT} ${xdate} ${ROTDIR} ${ARCDIR} ${TMPDIR}"
 
     export OUTPUT_FILETYPE=${OUTPUT_FILETYPE_SAVE}
 
@@ -87,7 +92,7 @@ fi
 ###############################################################
 echo
 echo "=============== START TO RUN RADMON DATA EXTRACTION ==============="
-if [ ${VRFYRAD} = "YES" -a "${CDUMP}" = "${CDFNL}" -a "${CDATE}" != "${SDATE}" ]; then
+if [[ ${VRFYRAD} = "YES" && ${CDUMP} = "${CDFNL}" && ${CDATE} != "${SDATE}" ]]; then
 
     export EXP=${PSLOT}
     export COMOUT="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/${COMPONENT}"
@@ -103,7 +108,7 @@ fi
 ###############################################################
 echo
 echo "=============== START TO RUN OZMON DATA EXTRACTION ==============="
-if [ "${VRFYOZN}" = "YES" -a "${CDUMP}" = "${CDFNL}" -a "${CDATE}" != "${SDATE}" ]; then
+if [[ ${VRFYOZN} = "YES" && ${CDUMP} = "${CDFNL}" && ${CDATE} != "${SDATE}" ]]; then
 
     export EXP=${PSLOT}
     export COMOUT="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/${COMPONENT}"
@@ -119,7 +124,7 @@ fi
 ###############################################################
 echo
 echo "=============== START TO RUN MINMON ==============="
-if [ "${VRFYMINMON}" = "YES" -a "${CDATE}" != "${SDATE}" ]; then
+if [[ ${VRFYMINMON} = "YES" && ${CDATE} != "${SDATE}" ]]; then
 
     export COMOUT="${ROTDIR}/${CDUMP}.${PDY}/${cyc}/${COMPONENT}"
     export M_TANKverfM0="${M_TANKverf}/stats/${PSLOT}/${CDUMP}.${PDY}/${cyc}"
@@ -134,9 +139,10 @@ fi
 ################################################################################
 echo
 echo "=============== START TO RUN CYCLONE TRACK VERIFICATION ==============="
-if [ ${VRFYTRAK} = "YES" ]; then
+if [[ ${VRFYTRAK} = "YES" ]]; then
 
-    export COMINsyn=${COMINsyn:-$(compath.py ${envir}/com/gfs/${gfs_ver})/syndat}
+    COMINsyn=${COMINsyn:-$(compath.py "${envir}/com/gfs/${gfs_ver}")/syndat}
+    export COMINsyn
 
     ${TRACKERSH}
 fi
@@ -145,23 +151,23 @@ fi
 ################################################################################
 echo
 echo "=============== START TO RUN CYCLONE GENESIS VERIFICATION ==============="
-if [ ${VRFYGENESIS} = "YES" -a "${CDUMP}" = "gfs" ]; then
+if [[ ${VRFYGENESIS} = "YES" && "${CDUMP}" = "gfs" ]]; then
     ${GENESISSH}
 fi
 
 
 ################################################################################
 echo
 echo "=============== START TO RUN CYCLONE GENESIS VERIFICATION (FSU) ==============="
-if [ ${VRFYFSU} = "YES" -a "${CDUMP}" = "gfs" ]; then
+if [[ ${VRFYFSU} = "YES" && "${CDUMP}" = "gfs" ]]; then
     ${GENESISFSU}
 fi
 
 
 ###############################################################
 # Force Exit out cleanly
-cd ${DATAROOT}
-if [ ${KEEPDATA:-"NO"} = "NO" ] ; then rm -rf ${DATA} ; fi
+cd "${DATAROOT}"
+if [[ ${KEEPDATA:-"NO"} = "NO" ]] ; then rm -rf "${DATA}" ; fi
 
 
 exit 0
diff --git a/parm/config/config.metp b/parm/config/config.metp
@@ -6,33 +6,27 @@
 echo "BEGIN: config.metp"
 
 # Get task specific resources
-. $EXPDIR/config.resources metp
+. "${EXPDIR}"/config.resources metp
 
-if [[ $machine == "JET" ]]; then
-   export RUN_GRID2GRID_STEP1="NO"
-   export RUN_GRID2OBS_STEP1="NO"
-   export RUN_PRECIP_STEP1="NO"
-else
-   export RUN_GRID2GRID_STEP1="YES" # Run grid-to-grid verification using METplus
-   export RUN_GRID2OBS_STEP1="YES"  # Run grid-to-obs verification using METplus
-   export RUN_PRECIP_STEP1="YES"    # Run precip verification using METplus
-fi
+export RUN_GRID2GRID_STEP1="YES" # Run grid-to-grid verification using METplus
+export RUN_GRID2OBS_STEP1="YES"  # Run grid-to-obs verification using METplus
+export RUN_PRECIP_STEP1="YES"    # Run precip verification using METplus
 
 
 #----------------------------------------------------------
 # METplus: Verify grid-to-grid, grid-to-obs, precipitation options
 #----------------------------------------------------------
 ## EMC_VERIF_GLOBAL SETTINGS
 export HOMEverif_global=${HOMEgfs}/sorc/verif-global.fd
-export VERIF_GLOBALSH=$HOMEverif_global/ush/run_verif_global_in_global_workflow.sh
+export VERIF_GLOBALSH=${HOMEverif_global}/ush/run_verif_global_in_global_workflow.sh
 ## INPUT DATA SETTINGS
-export model=$PSLOT
+export model=${PSLOT}
 export model_file_format="pgbf{lead?fmt=%2H}.${CDUMP}.{init?fmt=%Y%m%d%H}.grib2"
-export model_hpss_dir=$ATARDIR/.. 
+export model_hpss_dir=${ATARDIR}/..
 export get_data_from_hpss="NO"
 export hpss_walltime="10"
 ## OUTPUT SETTINGS
-export model_stat_dir=$ARCDIR/..
+export model_stat_dir=${ARCDIR}/..
 export make_met_data_by="VALID"
 export SENDMETVIEWER="NO"
 ## DATE SETTINGS
@@ -45,20 +39,20 @@ export log_MET_output_to_METplus="yes"
 export g2g1_type_list="anom pres sfc"
 export g2g1_anom_truth_name="self_anl"
 export g2g1_anom_truth_file_format="pgbanl.${CDUMP}.{valid?fmt=%Y%m%d%H}.grib2"
-export g2g1_anom_fhr_min=$FHMIN_GFS
-export g2g1_anom_fhr_max=$FHMAX_GFS
+export g2g1_anom_fhr_min=${FHMIN_GFS}
+export g2g1_anom_fhr_max=${FHMAX_GFS}
 export g2g1_anom_grid="G002"
 export g2g1_anom_gather_by="VSDB"
 export g2g1_pres_truth_name="self_anl"
 export g2g1_pres_truth_file_format="pgbanl.${CDUMP}.{valid?fmt=%Y%m%d%H}.grib2"
-export g2g1_pres_fhr_min=$FHMIN_GFS
-export g2g1_pres_fhr_max=$FHMAX_GFS
+export g2g1_pres_fhr_min=${FHMIN_GFS}
+export g2g1_pres_fhr_max=${FHMAX_GFS}
 export g2g1_pres_grid="G002"
 export g2g1_pres_gather_by="VSDB"
 export g2g1_sfc_truth_name="self_f00"
 export g2g1_sfc_truth_file_format="pgbf00.${CDUMP}.{valid?fmt=%Y%m%d%H}.grib2"
-export g2g1_sfc_fhr_min=$FHMIN_GFS
-export g2g1_sfc_fhr_max=$FHMAX_GFS
+export g2g1_sfc_fhr_min=${FHMIN_GFS}
+export g2g1_sfc_fhr_max=${FHMAX_GFS}
 export g2g1_sfc_grid="G002"
 export g2g1_sfc_gather_by="VSDB"
 export g2g1_mv_database_name="mv_${PSLOT}_grid2grid_metplus"
@@ -68,19 +62,19 @@ export g2g1_mv_database_desc="Grid-to-grid METplus data for global workflow expe
 export g2o1_type_list="upper_air conus_sfc"
 export g2o1_upper_air_msg_type_list="ADPUPA"
 export g2o1_upper_air_vhr_list="00 06 12 18"
-export g2o1_upper_air_fhr_min=$FHMIN_GFS
+export g2o1_upper_air_fhr_min=${FHMIN_GFS}
 export g2o1_upper_air_fhr_max="240"
 export g2o1_upper_air_grid="G003"
 export g2o1_upper_air_gather_by="VSDB"
 export g2o1_conus_sfc_msg_type_list="ONLYSF ADPUPA"
 export g2o1_conus_sfc_vhr_list="00 03 06 09 12 15 18 21"
-export g2o1_conus_sfc_fhr_min=$FHMIN_GFS
+export g2o1_conus_sfc_fhr_min=${FHMIN_GFS}
 export g2o1_conus_sfc_fhr_max="240"
 export g2o1_conus_sfc_grid="G104"
 export g2o1_conus_sfc_gather_by="VSDB"
 export g2o1_polar_sfc_msg_type_list="IABP"
 export g2o1_polar_sfc_vhr_list="00 03 06 09 12 15 18 21"
-export g2o1_polar_sfc_fhr_min=$FHMIN_GFS
+export g2o1_polar_sfc_fhr_min=${FHMIN_GFS}
 export g2o1_polar_sfc_fhr_max="240"
 export g2o1_polar_sfc_grid="G219"
 export g2o1_polar_sfc_gather_by="VSDB"
@@ -93,7 +87,7 @@ export precip1_type_list="ccpa_accum24hr"
 export precip1_ccpa_accum24hr_model_bucket="06"
 export precip1_ccpa_accum24hr_model_var="APCP"
 export precip1_ccpa_accum24hr_model_file_format="pgbf{lead?fmt=%2H}.${CDUMP}.{init?fmt=%Y%m%d%H}.grib2"
-export precip1_ccpa_accum24hr_fhr_min="$FHMIN_GFS"
+export precip1_ccpa_accum24hr_fhr_min=${FHMIN_GFS}
 export precip1_ccpa_accum24hr_fhr_max="180"
 export precip1_ccpa_accum24hr_grid="G211"
 export precip1_ccpa_accum24hr_gather_by="VSDB"