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Restructure the bufr sounding job #2853

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merged 11 commits into from
Sep 7, 2024
Merged

Restructure the bufr sounding job #2853

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c734f41
Add restart capability to job JGFS_ATMOS_POSTSND
BoCui-NOAA Jun 20, 2024
bb89562
Merge branch 'NOAA-EMC:develop' into develop
BoCui-NOAA Jun 28, 2024
8e42d49
Merge branch 'NOAA-EMC:develop' into develop
BoCui-NOAA Aug 21, 2024
b0637b7
Convert bufr to handle one forecast at a time
BoCui-NOAA Aug 21, 2024
c4f0399
update to fix shellcheck warning
BoCui-NOAA Aug 21, 2024
f711c3f
fix shellcheck issue
BoCui-NOAA Aug 21, 2024
202c449
Updated gfs_utils hash
BoCui-NOAA Aug 29, 2024
133755a
20240903 gfsv17 bufr package update
BoCui-NOAA Sep 3, 2024
e293370
Update env/WCOSS2.env
BoCui-NOAA Sep 4, 2024
0e94d92
Update scripts/exgfs_atmos_postsnd.sh
BoCui-NOAA Sep 4, 2024
5f5e542
Add new bufr table for GFS C96 output
BoCui-NOAA Sep 6, 2024
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141 changes: 108 additions & 33 deletions scripts/exgfs_atmos_postsnd.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -18,10 +18,15 @@
# 7) 2018-07-18 Guang Ping Lou Generalize this version to other platforms
# 8) 2019-10-18 Guang Ping Lou Transition to reading in NetCDF model data
# 9) 2019-12-18 Guang Ping Lou generalizing to reading in NetCDF or nemsio
# 10) 2024-08-08 Bo Cui Update to handle one forecast at a time
# For GFSv17 bufr, total number of forecast hours is 141(num_hours=141)
# it requires 7 nodes & allocate 21 processes per node(num_ppn=21)
################################################################

source "${USHgfs}/preamble.sh"

runscript=${USHgfs}/gfs_bufr.sh

cd $DATA

########################################
Expand All @@ -44,47 +49,116 @@

rm -f -r "${COM_ATMOS_BUFR}"
mkdir -p "${COM_ATMOS_BUFR}"
export COM_ATMOS_BUFR="${COM_ATMOS_BUFR}"
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GETDIM="${USHgfs}/getncdimlen"
LEVS=$(${GETDIM} "${COM_ATMOS_HISTORY}/${RUN}.${cycle}.atmf000.${atmfm}" pfull)
export LEVS=$(${GETDIM} "${COM_ATMOS_HISTORY}/${RUN}.${cycle}.atmf000.${atmfm}" pfull)
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declare -x LEVS

### Loop for the hour and wait for the sigma and surface flux file:
export FSTART=$STARTHOUR
### wait for the sigma and surface flux file:
sleep_interval=10
max_tries=360
#
while [ $FSTART -lt $ENDHOUR ]
do
export FINT=$NINT1
# Define the end hour for the input
export FEND=$(expr $FSTART + $INCREMENT)
if test $FEND -lt 100; then FEND=0$FEND; fi
if [ $FSTART -eq 00 ]
then
export F00FLAG=YES
else
export F00FLAG=NO
fi

if [ $FEND -eq $ENDHOUR ]
then
export MAKEBUFR=YES
fi

filename="${COM_ATMOS_HISTORY}/${RUN}.${cycle}.atm.logf${FEND}.${logfm}"
if ! wait_for_file "${filename}" "${sleep_interval}" "${max_tries}"; then
err_exit "FATAL ERROR: logf${FEND} not found after waiting $((sleep_interval * ( max_tries - 1) )) secs"
fi

## 1-hourly output before $NEND1, 3-hourly output after
if [[ $((10#$FEND)) -gt $((10#$NEND1)) ]]; then
export FINT=$NINT3
fi
${USHgfs}/gfs_bufr.sh
export FSTART="${FEND}"
# Initialize an empty list to store the hours
hour_list=()

# Generate hours from 0 to NEND1 with interval NINT1
# Convert ENDHOUR to decimal through $((10#$ENDHOUR)) to avoid it is thought as octal number
for (( hour=0; hour<=$((10#$NEND1)) && hour<=$((10#$ENDHOUR)); hour+=$((10#$NINT1)) )); do
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hour_list+=($(printf "%03d" $hour))
Fixed Show fixed Hide fixed
done

# Generate hours from NEND1 + NINT3 to ENDHOUR with interval NINT3
for (( hour=$((10#$NEND1))+$((10#$NINT3)); hour<=$((10#$ENDHOUR)); hour+=$((10#$NINT3)) )); do
hour_list+=($(printf "%03d" $hour))
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done

# Print the hour list
echo "Hour List: ${hour_list[@]}"
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# Count the number of elements in the hour_list
num_hours=${#hour_list[@]}

# Print the total number of hours
echo "Total number of hours: $num_hours"

# allocate 21 processes per node
# don't allocate more processes, or it might have memory issue
num_ppn=21
export APRUN="mpiexec -np "${num_hours}" -ppn "${num_ppn}" --cpu-bind core cfp "
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if [ -s "${DATA}/poescript_bufr" ]; then
rm ${DATA}/poescript_bufr
fi

for fhr in ${hour_list[@]}; do
Fixed Show fixed Hide fixed

if [ ! -s "${DATA}/${fhr}" ]; then mkdir -p ${DATA}/${fhr}; fi
export fhr=${fhr}
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export FINT=${NINT1}
## 1-hourly output before $NEND1, 3-hourly output after
if [[ $((10#${fhr})) -gt $((10#${NEND1})) ]]; then
export FINT=${NINT3}
fi
if [ ${fhr} -eq 000 ]; then
export F00FLAG="YES"
else
export F00FLAG="NO"
fi

# Convert fhr to integer
fhr_int=$((10#$fhr))

# Get previous hour
if (( fhr_int == STARTHOUR )); then
fhr_p=${fhr_int}
else
fhr_p=$(( fhr_int - FINT ))
fi

# Format fhr_p with leading zeros
fhr_p=$(printf "%03d" $fhr_p)
Fixed Show fixed Hide fixed

filename="${COM_ATMOS_HISTORY}/${RUN}.${cycle}.atm.logf${fhr}.${logfm}"
if ! wait_for_file "${filename}" "${sleep_interval}" "${max_tries}"; then
echo "Waiting for the file ${filename} for $((sleep_interval * (max_tries - 1))) seconds..."
err_exit "FATAL ERROR: logf${fhr} not found after waiting $((sleep_interval * (max_tries - 1))) secs"
fi
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echo "${runscript} \"${fhr}\" \"${fhr_p}\" \"${FINT}\" \"${F00FLAG}\" \"${DATA}/${fhr}\"" >> "${DATA}/poescript_bufr"
done

chmod +x "${DATA}/poescript_bufr"
startmsg
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$APRUN "${DATA}/poescript_bufr"
export err=$?; err_chk

cd ${DATA}
Fixed Show fixed Hide fixed

# Initialize fortnum
fortnum=20

# Loop through each element in the array
for fhr in "${hour_list[@]}"; do
# Increment fortnum
fortnum=$((fortnum + 1))
${NLN} "${DATA}/${fhr}/fort.${fortnum}" "fort.${fortnum}"
done

export MAKEBUFR=YES
export fhr=${ENDHOUR}
export FINT=${NINT1}
## 1-hourly output before $NEND1, 3-hourly output after
if [[ $((10#${fhr})) -gt $((10#${NEND1})) ]]; then
export FINT=${NINT3}
fi
if [ ${fhr} -eq 000 ]; then
Fixed Show fixed Hide fixed
export F00FLAG="YES"
else
export F00FLAG="NO"
fi
${runscript} "${fhr}" "${fhr_p}" "${FINT}" "${F00FLAG}" "${DATA}"

##############################################################
# Tar and gzip the individual bufr files and send them to /com
##############################################################
Expand All @@ -105,7 +179,7 @@
# add appropriate WMO Headers.
########################################
rm -rf poe_col
for (( m = 1; m <= NUM_SND_COLLECTIVES ; m++ )); do
for (( m = 1; m <= $((10#$NUM_SND_COLLECTIVES)); m++ )); do
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echo "sh ${USHgfs}/gfs_sndp.sh ${m} " >> poe_col
done

Expand All @@ -123,4 +197,5 @@
sh "${USHgfs}/gfs_bfr2gpk.sh"



############## END OF SCRIPT #######################
63 changes: 40 additions & 23 deletions ush/gfs_bufr.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -18,8 +18,17 @@
# 2018-05-30 Guang Ping Lou: Make sure all files are available.
# 2019-10-10 Guang Ping Lou: Read in NetCDF files
# 2024-03-03 Bo Cui: Add options to use different bufr table for different resolution NetCDF files
# 2024-08-08 Bo Cui: Update to handle one forecast at a time
# echo "History: February 2003 - First implementation of this utility script"
#
fhr=$1
fhr_p=$2
FINT=$3
F00FLAG=$4
workdir=$5

cd ${workdir}
Fixed Show fixed Hide fixed
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source "${USHgfs}/preamble.sh"

if [[ "${F00FLAG}" == "YES" ]]; then
Expand All @@ -45,30 +54,37 @@
&NAMMET
levs=${LEVS},makebufr=${bufrflag},
dird="${COM_ATMOS_BUFR}/bufr",
nstart=${FSTART},nend=${FEND},nint=${FINT},
nstart=${fhr},nend=${fhr},nint=${FINT},
nend1=${NEND1},nint1=${NINT1},nint3=${NINT3},
nsfc=80,f00=${f00flag},fformat=${fformat},np1=0
nsfc=80,f00=${f00flag},fformat=${fformat},np1=0,
fnsig="sigf${fhr}",
fngrib="flxf${fhr}",
fngrib2="flxf${fhr_p}"
/
EOF

sleep_interval=10
max_tries=1000
for (( hr = 10#${FSTART}; hr <= 10#${FEND}; hr = hr + 10#${FINT} )); do
hh2=$(printf %02i "${hr}")
hh3=$(printf %03i "${hr}")

#---------------------------------------------------------
# Make sure all files are available:
filename="${COM_ATMOS_HISTORY}/${RUN}.${cycle}.atm.logf${hh3}.${logfm}"
if ! wait_for_file "${filename}" "${sleep_interval}" "${max_tries}"; then
echo "FATAL ERROR: COULD NOT LOCATE logf${hh3} file"
exit 2
fi

#------------------------------------------------------------------
${NLN} "${COM_ATMOS_HISTORY}/${RUN}.${cycle}.atmf${hh3}.${atmfm}" "sigf${hh2}"
${NLN} "${COM_ATMOS_HISTORY}/${RUN}.${cycle}.sfcf${hh3}.${atmfm}" "flxf${hh2}"
done

#---------------------------------------------------------
# Make sure all files are available:

filename="${COM_ATMOS_HISTORY}/${RUN}.${cycle}.atm.logf${fhr}.${logfm}"
if ! wait_for_file "${filename}" "${sleep_interval}" "${max_tries}"; then
echo "FATAL ERROR: COULD NOT LOCATE logf${fhr} file"
exit 2
fi

filename="${COM_ATMOS_HISTORY}/${RUN}.${cycle}.atm.logf${fhr_p}.${logfm}"
if ! wait_for_file "${filename}" "${sleep_interval}" "${max_tries}"; then
echo "FATAL ERROR: COULD NOT LOCATE logf${fhr_p} file"
exit 2
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fi

#------------------------------------------------------------------
${NLN} "${COM_ATMOS_HISTORY}/${RUN}.${cycle}.atmf${fhr}.${atmfm}" "sigf${fhr}"
${NLN} "${COM_ATMOS_HISTORY}/${RUN}.${cycle}.sfcf${fhr}.${atmfm}" "flxf${fhr}"
${NLN} "${COM_ATMOS_HISTORY}/${RUN}.${cycle}.sfcf${fhr_p}.${atmfm}" "flxf${fhr_p}"

# define input BUFR table file.
${NLN} "${PARMgfs}/product/bufr_gfs_${CLASS}.tbl" fort.1
Expand All @@ -82,18 +98,19 @@
${NLN} "${PARMgfs}/product/bufr_ij9km.txt" fort.7
;;
*)
echo "WARNING: No bufr table for this resolution, using the one for C768"
${NLN} "${PARMgfs}/product/bufr_ij13km.txt" fort.7
echo "FATAL ERROR: Unrecognized bufr_ij*km.txt For CASE ${CASE}, ABORT!"
exit 1
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;;
esac

${APRUN_POSTSND} "${EXECgfs}/${pgm}" < gfsparm > "out_gfs_bufr_${FEND}"
"${EXECgfs}/${pgm}" < gfsparm > "out_gfs_bufr_${fhr}"

export err=$?

if [[ "${err}" -ne 0 ]]; then
echo "GFS postsnd job error, Please check files "
echo "${COM_ATMOS_HISTORY}/${RUN}.${cycle}.atmf${hh2}.${atmfm}"
echo "${COM_ATMOS_HISTORY}/${RUN}.${cycle}.sfcf${hh2}.${atmfm}"
echo "${COM_ATMOS_HISTORY}/${RUN}.${cycle}.atmf${fhr}.${atmfm}"
echo "${COM_ATMOS_HISTORY}/${RUN}.${cycle}.sfcf${fhr}.${atmfm}"
err_chk
fi

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