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Update fit2obs for COM refactor #1719

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merged 8 commits into from
Jul 14, 2023
+11 −7
Merged

Update fit2obs for COM refactor #1719

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2fbe399
Update fit2obs for COM refactor
WalterKolczynski-NOAA Jun 28, 2023
415455f
Shellcheck updates for fit2obs j-job
WalterKolczynski-NOAA Jun 29, 2023
fd0aef6
Fix path of history files for fit2obs archive
WalterKolczynski-NOAA Jul 8, 2023
404fd0d
Turn fit2obs back on by default
WalterKolczynski-NOAA Jul 8, 2023
50ab97b
Add comment about why fit2obs variable name not updated
WalterKolczynski-NOAA Jul 12, 2023
8147d5e
Remove intermediary COM variables in fit2obs
WalterKolczynski-NOAA Jul 13, 2023
62c6533
Fix shellcheck complaint
WalterKolczynski-NOAA Jul 13, 2023
fee5e03
Ignore shellcheck complaint
WalterKolczynski-NOAA Jul 13, 2023
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12 changes: 8 additions & 4 deletions jobs/JGDAS_FIT2OBS
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Original file line number Diff line number Diff line change
Expand Up @@ -17,11 +17,15 @@ export CDATE
vday=${CDATE:0:8}
vcyc=${CDATE:8:2}

export COM_INA=${ROTDIR}/gdas.${vday}/${vcyc}/atmos
YMD=${vday} HH=${vcyc} generate_com -rx COM_ATMOS_ANALYSIS_VERIF:COM_ATMOS_ANALYSIS_TMPL
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Is COM_ATMOS_ANALYSIS_VERIF used in the fit2obs scripts? Or is it being used to set COM_INA on line 24?
Same with COM_OBS_VERIF

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Just to set COM_INA and COM_PRP below. We can cut out the middle man if you want, but I believe I followed this same pattern in other j-jobs that had to set variables for external packages.

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Just to set COM_INA and COM_PRP below. We can cut out the middle man if you want, but I believe I followed this same pattern in other j-jobs that had to set variables for external packages.

Then we should atleast eliminate -x.
I would rather directly set COM_INA and COM_PRP and cut out the middle man. There is no reason to call 2 things with the same name.

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Done

RUN=${CDUMP} YMD=${vday} HH=${vcyc} generate_com -rx COM_OBS_VERIF:COM_OBS_TMPL

# These are used by fit2obs, so we can't change them to the standard COM variable names
export COM_INA=${COM_ATMOS_ANALYSIS_VERIF}
# We want to defer variable expansion, so ignore warning about single quotes
# shellcheck disable=SC2016
export COM_INF='$ROTDIR/vrfyarch/gfs.$fdy/$fzz'
export COM_PRP=${ROTDIR}/gdas.${vday}/${vcyc}/obs
export COM_PRP=${COM_OBS_VERIF}

export PRPI=${COM_PRP}/${RUN}.t${vcyc}z.prepbufr
export sig1=${COM_INA}/${RUN}.t${vcyc}z.atmanl.nc
Expand All @@ -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
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2 changes: 1 addition & 1 deletion parm/config/gfs/config.base.emc.dyn
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Expand Up @@ -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
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4 changes: 2 additions & 2 deletions scripts/exglobal_archive.sh
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Expand Up @@ -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 ))
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