Update fit2obs for COM refactor (#1719)

Fixes #1486

* Turn fit2obs back on by default

Fit2obs had been turned off during the COM refactor because it had
not yet been updated for the new paths. Now that the job has been
updated, it can be turned back on.

jobs/JGDAS_FIT2OBS

@@ -17,13 +17,17 @@ export CDATE
 vday=${CDATE:0:8}
 vcyc=${CDATE:8:2}
 
-export COM_INA=${ROTDIR}/gdas.${vday}/${vcyc}/atmos
+# These are used by fit2obs, so we can't change them to the standard COM variable names
+# shellcheck disable=SC2153
+YMD=${vday} HH=${vcyc} generate_com -rx COM_INA:COM_ATMOS_ANALYSIS_TMPL
+RUN=${CDUMP} YMD=${vday} HH=${vcyc} generate_com -rx COM_PRP:COM_OBS_TMPL
+
 # We want to defer variable expansion, so ignore warning about single quotes
 # shellcheck disable=SC2016
 export COM_INF='$ROTDIR/vrfyarch/gfs.$fdy/$fzz'
-export COM_PRP=${ROTDIR}/gdas.${vday}/${vcyc}/obs
 
 export PRPI=${COM_PRP}/${RUN}.t${vcyc}z.prepbufr
+# shellcheck disable=SC2153
 export sig1=${COM_INA}/${RUN}.t${vcyc}z.atmanl.nc
 export sfc1=${COM_INA}/${RUN}.t${vcyc}z.atmanl.nc
 export CNVS=${COM_INA}/${RUN}.t${vcyc}z.cnvstat
@@ -37,8 +41,8 @@ export HORZ_DIR=${ARCDIR}/horiz
 export COMLOX=${DATA}/fitx
 [[ ! -d "${COMLOX}" ]] && mkdir -p "${COMLOX}"
 
-echo "echo err_chk">"${DATA}"/err_chk; chmod 755 "${DATA}"/err_chk
-echo "echo postmsg">"${DATA}"/postmsg; chmod 755 "${DATA}"/postmsg
+echo "echo err_chk">"${DATA}/err_chk"; chmod 755 "${DATA}/err_chk"
+echo "echo postmsg">"${DATA}/postmsg"; chmod 755 "${DATA}/postmsg"
 
 ##############################################
 # Check spinup and available inputs

parm/config/gfs/config.base.emc.dyn

@@ -384,7 +384,7 @@ export binary_diag=".false."
 
 # Verification options
 export DO_METP="YES"         # Run METPLUS jobs - set METPLUS settings in config.metp
-export DO_FIT2OBS="NO"      # Run fit to observations package
+export DO_FIT2OBS="YES"      # Run fit to observations package
 
 # Archiving options
 export HPSSARCH="@HPSSARCH@"        # save data to HPSS archive

scripts/exglobal_archive.sh

@@ -103,8 +103,8 @@ if [[ "${RUN}" == "gfs" ]] && [[ "${FITSARC}" = "YES" ]]; then
     fhr=0
     while [[ ${fhr} -le ${fhmax} ]]; do
         fhr3=$(printf %03i "${fhr}")
-        sfcfile="${COM_ATMOS_MASTER}/${prefix}.sfcf${fhr3}.nc"
-        sigfile="${COM_ATMOS_MASTER}/${prefix}.atmf${fhr3}.nc"
+        sfcfile="${COM_ATMOS_HISTORY}/${prefix}.sfcf${fhr3}.nc"
+        sigfile="${COM_ATMOS_HISTORY}/${prefix}.atmf${fhr3}.nc"
         nb_copy "${sfcfile}" "${VFYARC}/${RUN}.${PDY}/${cyc}/"
         nb_copy "${sigfile}" "${VFYARC}/${RUN}.${PDY}/${cyc}/"
         (( fhr = 10#${fhr} + 6 ))