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Merged
hu5970 merged 16 commits into from
May 13, 2021
Merged

Feature/rrfs dev1: add retrospective function and changes for running on WCOSS #104

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2723906
Cold start RRFS_dev1 3km CONUS hourly cycles from 09/21Z HRRR analysis.
hu5970 Apr 28, 2021
1a36dbd
Changes for running on RRFS cycles on WCOSS.
hu5970 Apr 29, 2021
7200c9a
scripts handle multiple time levels of radar data process and ref2tten
hu5970 Apr 29, 2021
6aa9445
Add groups and tasks for post process.
hu5970 May 1, 2021
21b86c8
Merge remote-tracking branch 'upstream/feature/RRFS_dev1' into featur…
hu5970 May 1, 2021
dcf3a06
Update configure files for RRFS dev1 CONUS, AK, and NA 13km for Sprin…
hu5970 May 2, 2021
6d540a0
Use early rap observation BUFR files for 00/12Z cycle.
hu5970 May 3, 2021
3a1140f
Bug fix to exregional_process_bufr.sh.
hu5970 May 3, 2021
fba687b
Finalize the configure files for RRFS dev1 CONUS, AK, and NA 13km.
hu5970 May 3, 2021
bae8e5d
Use Guoqing's method to generate the post process tasks so we can use…
hu5970 May 3, 2021
6edf08e
Merge remote-tracking branch 'upstream/feature/RRFS_dev1' into HEAD
hu5970 May 12, 2021
4f1ecbd
Add function to do retrospective test on WCOSS.
hu5970 May 12, 2021
cccc4dd
Merge remote-tracking branch 'upstream/feature/RRFS_dev1' into HEAD
hu5970 May 12, 2021
c33b68d
Code update for running on WCOSS with FV3GFS background.
hu5970 May 12, 2021
7ee8510
Bug fix to link the observation files on WCOSS.
hu5970 May 13, 2021
b2e252b
Clean the code for PR104.
hu5970 May 13, 2021
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2 changes: 2 additions & 0 deletions scripts/exregional_make_ics.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -403,6 +403,8 @@ case "${EXTRN_MDL_NAME_ICS}" in
fn_grib2="${EXTRN_MDL_FNS[0]}"
input_type="grib2"
convert_nst=False
fn_atm_nemsio="${EXTRN_MDL_FNS[0]}"
fn_sfc_nemsio="${EXTRN_MDL_FNS[1]}"
fi
vgtyp_from_climo=True
sotyp_from_climo=True
Expand Down
204 changes: 107 additions & 97 deletions scripts/exregional_run_analysis.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -78,64 +78,24 @@ case $MACHINE in
#
"WCOSS_C" | "WCOSS")
#

if [ "${USE_CCPP}" = "TRUE" ]; then

# Needed to change to the experiment directory because the module files
# for the CCPP-enabled version of FV3 have been copied to there.

cd_vrfy ${cycle_dir}

set +x
source ./module-setup.sh
module use $( pwd -P )
module load modules.fv3
module list
set -x

else

. /apps/lmod/lmod/init/sh
module purge
module use /scratch4/NCEPDEV/nems/noscrub/emc.nemspara/soft/modulefiles
module load intel/16.1.150 impi/5.1.1.109 netcdf/4.3.0
module list

fi

module load NCO/4.7.0
module list
ulimit -s unlimited
ulimit -a
APRUN="mpirun -l -np ${PE_MEMBER01}"
;;
#
"WCOSS_DELL_P3")
#
module load NCO/4.7.0
module list
ulimit -s unlimited
ulimit -a
APRUN="mpirun -l -np ${PE_MEMBER01}"
;;
#
"THEIA")
#

if [ "${USE_CCPP}" = "TRUE" ]; then

# Need to change to the experiment directory to correctly load necessary
# modules for CCPP-version of FV3LAM in lines below
cd_vrfy ${EXPTDIR}

set +x
source ./module-setup.sh
module use $( pwd -P )
module load modules.fv3
module load contrib wrap-mpi
module list
set -x

else

. /apps/lmod/lmod/init/sh
module purge
module use /scratch4/NCEPDEV/nems/noscrub/emc.nemspara/soft/modulefiles
module load intel/16.1.150 impi/5.1.1.109 netcdf/4.3.0
module load contrib wrap-mpi
module list

fi

ulimit -s unlimited
ulimit -a
np=${SLURM_NTASKS}
Expand All @@ -146,14 +106,12 @@ case $MACHINE in
ulimit -s unlimited
ulimit -a
APRUN="srun"
LD_LIBRARY_PATH="${UFS_WTHR_MDL_DIR}/FV3/ccpp/lib${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}"
;;
#
"JET")
ulimit -s unlimited
ulimit -a
APRUN="srun"
LD_LIBRARY_PATH="${UFS_WTHR_MDL_DIR}/FV3/ccpp/lib${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}"
NCKS=ncks
;;
#
Expand All @@ -175,10 +133,10 @@ esac
#
#-----------------------------------------------------------------------
#
START_DATE=`echo "${CDATE}" | sed 's/\([[:digit:]]\{2\}\)$/ \1/'`
START_DATE=$(echo "${CDATE}" | sed 's/\([[:digit:]]\{2\}\)$/ \1/')

YYYYMMDDHH=`date +%Y%m%d%H -d "${START_DATE}"`
JJJ=`date +%j -d "${START_DATE}"`
YYYYMMDDHH=$(date +%Y%m%d%H -d "${START_DATE}")
JJJ=$(date +%j -d "${START_DATE}")

YYYY=${YYYYMMDDHH:0:4}
MM=${YYYYMMDDHH:4:2}
Expand Down Expand Up @@ -216,43 +174,82 @@ print_info_msg "$VERBOSE" "background type is is $BKTYPE"
#
#-----------------------------------------------------------------------

stampcycle=`date -d "${START_DATE}" +%s`
stampcycle=$(date -d "${START_DATE}" +%s)
minHourDiff=100
loops="009" # or 009s for GFSv15
ens_type="nc" # or nemsio for GFSv15
foundens=false
for loop in $loops; do
for timelist in `ls ${ENKF_FCST}/*.gdas.t*z.atmf${loop}.mem080.${ens_type}`; do
availtimeyy=`basename ${timelist} | cut -c 1-2`
availtimeyyyy=20${availtimeyy}
availtimejjj=`basename ${timelist} | cut -c 3-5`
availtimemm=`date -d "${availtimeyyyy}0101 +$(( 10#${availtimejjj} - 1 )) days" +%m`
availtimedd=`date -d "${availtimeyyyy}0101 +$(( 10#${availtimejjj} - 1 )) days" +%d`
availtimehh=`basename ${timelist} | cut -c 6-7`
availtime=${availtimeyyyy}${availtimemm}${availtimedd}${availtimehh}
avail_time=`echo "${availtime}" | sed 's/\([[:digit:]]\{2\}\)$/ \1/'`
avail_time=`date -d "${avail_time}"`

stamp_avail=`date -d "${avail_time} ${loop} hours" +%s`

hourDiff=`echo "($stampcycle - $stamp_avail) / (60 * 60 )" | bc`;
if [[ ${stampcycle} -lt ${stamp_avail} ]]; then
hourDiff=`echo "($stamp_avail - $stampcycle) / (60 * 60 )" | bc`;
fi

if [[ ${hourDiff} -lt ${minHourDiff} ]]; then
minHourDiff=${hourDiff}
enkfcstname=${availtimeyy}${availtimejjj}${availtimehh}00.gdas.t${availtimehh}z.atmf${loop}
foundens=true
fi
cat "no ens found" >> filelist03

case $MACHINE in

"WCOSS_C" | "WCOSS" | "WCOSS_DELL_P3")

for loop in $loops; do
for timelist in $(ls ${ENKF_FCST}/enkfgdas.*/*/atmos/mem080/gdas*.atmf${loop}.${ens_type}); do
availtimeyyyymmdd=$(echo ${timelist} | cut -d'/' -f9 | cut -c 10-17)
availtimehh=$(echo ${timelist} | cut -d'/' -f10)
availtime=${availtimeyyyymmdd}${availtimehh}
avail_time=$(echo "${availtime}" | sed 's/\([[:digit:]]\{2\}\)$/ \1/')
avail_time=$(date -d "${avail_time}")

stamp_avail=$(date -d "${avail_time} ${loop} hours" +%s)

hourDiff=$(echo "($stampcycle - $stamp_avail) / (60 * 60 )" | bc);
if [[ ${stampcycle} -lt ${stamp_avail} ]]; then
hourDiff=$(echo "($stamp_avail - $stampcycle) / (60 * 60 )" | bc);
fi

if [[ ${hourDiff} -lt ${minHourDiff} ]]; then
minHourDiff=${hourDiff}
enkfcstname=gdas.t${availtimehh}z.atmf${loop}
eyyyymmdd=$(echo ${availtime} | cut -c1-8)
ehh=$(echo ${availtime} | cut -c9-10)
foundens=true
fi
done
done
done

if [ $foundens ]; then
ls ${ENKF_FCST}/${enkfcstname}.mem0??.${ens_type} >> filelist03
else
cat "no ens found" >> filelist03
fi
if [ ${foundens} ]
then
ls ${ENKF_FCST}/enkfgdas.${eyyyymmdd}/${ehh}/atmos/mem???/${enkfcstname}.nc > filelist03
fi

;;
"JET")

for loop in $loops; do
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@christinaholtNOAA christinaholtNOAA May 12, 2021

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Please use the $() syntax instead of backticks for clarity, ease of debugging, and supportability here and in the previous case statement.

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@hu5970 hu5970 May 13, 2021

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Yes, change all in this scripts.

for timelist in $(ls ${ENKF_FCST}/*.gdas.t*z.atmf${loop}.mem080.${ens_type}); do
availtimeyy=$(basename ${timelist} | cut -c 1-2)
availtimeyyyy=20${availtimeyy}
availtimejjj=$(basename ${timelist} | cut -c 3-5)
availtimemm=$(date -d "${availtimeyyyy}0101 +$(( 10#${availtimejjj} - 1 )) days" +%m)
availtimedd=$(date -d "${availtimeyyyy}0101 +$(( 10#${availtimejjj} - 1 )) days" +%d)
availtimehh=$(basename ${timelist} | cut -c 6-7)
availtime=${availtimeyyyy}${availtimemm}${availtimedd}${availtimehh}
avail_time=$(echo "${availtime}" | sed 's/\([[:digit:]]\{2\}\)$/ \1/')
avail_time=$(date -d "${avail_time}")

stamp_avail=$(date -d "${avail_time} ${loop} hours" +%s)

hourDiff=$(echo "($stampcycle - $stamp_avail) / (60 * 60 )" | bc);
if [[ ${stampcycle} -lt ${stamp_avail} ]]; then
hourDiff=$(echo "($stamp_avail - $stampcycle) / (60 * 60 )" | bc);
fi

if [[ ${hourDiff} -lt ${minHourDiff} ]]; then
minHourDiff=${hourDiff}
enkfcstname=${availtimeyy}${availtimejjj}${availtimehh}00.gdas.t${availtimehh}z.atmf${loop}
foundens=true
fi
done
done

if [ $foundens ]; then
ls ${ENKF_FCST}/${enkfcstname}.mem0??.${ens_type} >> filelist03
fi

esac

#
#-----------------------------------------------------------------------
Expand All @@ -268,15 +265,14 @@ ifhyb=.false.

# Determine if hybrid option is available
memname='atmf009'
nummem=`more filelist03 | wc -l`
nummem=$(more filelist03 | wc -l)
nummem=$((nummem - 3 ))
if [[ ${nummem} -eq 80 ]]; then
print_info_msg "$VERBOSE" "Do hybrid with ${memname}"
ifhyb=.true.
print_info_msg "$VERBOSE" " Cycle ${YYYYMMDDHH}: GSI hybrid uses ${memname} with n_ens=${nummem}"
fi


#
#-----------------------------------------------------------------------
#
Expand All @@ -293,7 +289,7 @@ cp_vrfy ${fixgriddir}/fv3_grid_spec fv3_grid_spec

if [ ${BKTYPE} -eq 1 ]; then # cold start uses background from INPUT
cp_vrfy ${bkpath}/gfs_data.tile7.halo0.nc gfs_data.tile7.halo0.nc_b
${NCKS} -A -v phis ${fixgriddir}/phis.nc gfs_data.tile7.halo0.nc_b
ncks -A -v phis ${fixgriddir}/phis.nc gfs_data.tile7.halo0.nc_b

cp_vrfy ${bkpath}/sfc_data.tile7.halo0.nc fv3_sfcdata
cp_vrfy gfs_data.tile7.halo0.nc_b fv3_dynvars
Expand Down Expand Up @@ -326,13 +322,27 @@ if [[ ${HH} -eq '00' || ${HH} -eq '12' ]]; then
obs_source=rap_e
fi

obs_files_source[0]=${OBSPATH}/${YYYYMMDDHH}.${obs_source}.t${HH}z.prepbufr.tm00
case $MACHINE in

"WCOSS_C" | "WCOSS" | "WCOSS_DELL_P3")
obsfileprefix=${obs_source}
obspath_tmp=${OBSPATH}/${obs_source}.${YYYYMMDD}

;;
"JET")
obsfileprefix=${YYYYMMDDHH}.${obs_source}
obspath_tmp=${OBSPATH}

esac


obs_files_source[0]=${obspath_tmp}/${obsfileprefix}.t${HH}z.prepbufr.tm00
obs_files_target[0]=prepbufr

obs_files_source[1]=${OBSPATH}/${YYYYMMDDHH}.${obs_source}.t${HH}z.satwnd.tm00.bufr_d
obs_files_source[1]=${obspath_tmp}/${obsfileprefix}.t${HH}z.satwnd.tm00.bufr_d
obs_files_target[1]=satwndbufr

obs_files_source[2]=${OBSPATH}/${YYYYMMDDHH}.${obs_source}.t${HH}z.nexrad.tm00.bufr_d
obs_files_source[2]=${obspath_tmp}/${obsfileprefix}.t${HH}z.nexrad.tm00.bufr_d
obs_files_target[2]=l2rwbufr

obs_number=${#obs_files_source[@]}
Expand Down Expand Up @@ -427,7 +437,7 @@ ln -s $cldcoef ./CloudCoeff.bin


# Copy CRTM coefficient files based on entries in satinfo file
for file in `awk '{if($1!~"!"){print $1}}' ./satinfo | sort | uniq` ;do
for file in $(awk '{if($1!~"!"){print $1}}' ./satinfo | sort | uniq) ;do
ln -s ${CRTMFIX}/${file}.SpcCoeff.bin ./
ln -s ${CRTMFIX}/${file}.TauCoeff.bin ./
done
Expand Down Expand Up @@ -558,9 +568,9 @@ esac
if [ $binary_diag = ".true." ]; then
listall="conv hirs2_n14 msu_n14 sndr_g08 sndr_g11 sndr_g11 sndr_g12 sndr_g13 sndr_g08_prep sndr_g11_prep sndr_g12_prep sndr_g13_prep sndrd1_g11 sndrd2_g11 sndrd3_g11 sndrd4_g11 sndrd1_g12 sndrd2_g12 sndrd3_g12 sndrd4_g12 sndrd1_g13 sndrd2_g13 sndrd3_g13 sndrd4_g13 hirs3_n15 hirs3_n16 hirs3_n17 amsua_n15 amsua_n16 amsua_n17 amsub_n15 amsub_n16 amsub_n17 hsb_aqua airs_aqua amsua_aqua imgr_g08 imgr_g11 imgr_g12 pcp_ssmi_dmsp pcp_tmi_trmm sbuv2_n16 sbuv2_n17 sbuv2_n18 omi_aura ssmi_f13 ssmi_f14 ssmi_f15 hirs4_n18 hirs4_metop-a amsua_n18 amsua_metop-a mhs_n18 mhs_metop-a amsre_low_aqua amsre_mid_aqua amsre_hig_aqua ssmis_las_f16 ssmis_uas_f16 ssmis_img_f16 ssmis_env_f16 iasi_metop-a"
for type in $listall; do
count=`ls pe*.${type}_${loop} | wc -l`
count=$(ls pe*.${type}_${loop} | wc -l)
if [[ $count -gt 0 ]]; then
`cat pe*.${type}_${loop} > diag_${type}_${string}.${YYYYMMDDHH}`
$(cat pe*.${type}_${loop} > diag_${type}_${string}.${YYYYMMDDHH})
fi
done
fi
Expand All @@ -582,7 +592,7 @@ if [ $netcdf_diag = ".true." ]; then
fi

for type in $listallnc; do
count=`ls pe*.${type}_${loop}.nc4 | wc -l`
count=$(ls pe*.${type}_${loop}.nc4 | wc -l)
if [[ $count -gt 0 ]]; then
./ncdiag_cat.x -o ncdiag_${type}_${string}.nc4.${YYYYMMDDHH} pe*.${type}_${loop}.nc4
fi
Expand Down
51 changes: 35 additions & 16 deletions ush/config.sh.RRFS_AK_dev1
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Expand Up @@ -28,6 +28,8 @@ PREEXISTING_DIR_METHOD="rename"
PREDEF_GRID_NAME=RRFS_AK_3km

DO_DACYCLE="true"
#DO_RETRO="true"
#LBCS_ICS_ONLY="true"
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@christinaholtNOAA christinaholtNOAA May 12, 2021

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Please remove commented configurations.

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@hu5970 hu5970 May 13, 2021

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We will use the retro functions a a lot soon. This is not just a comment. This is a place hold for retro because ti is much easier and safe to uncomment those options for retrospective runs.


QUILTING="TRUE"
CCPP_PHYS_SUITE="FV3_HRRR"
Expand All @@ -39,18 +41,39 @@ LBC_SPEC_INTVL_HRS="1"
EXTRN_MDL_LBCS_OFFSET_HRS="0"
EXTRN_MDL_LBCS_SEARCH_OFFSET_HRS="0"

#CYCLEDAY="1-4"
DATE_FIRST_CYCL="20210401"
DATE_LAST_CYCL="20211231"
CYCL_HRS=( "00" "12" )
CYCLEMONTH="5-7"
INITIAL_CYCLEDEF="00 09,21 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
BOUNDARY_CYCLEDEF="00 00-02,04-08,10-14,16-20,22,23 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
BOUNDARY_LONG_CYCLEDEF="00 03,09,15,21 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
PREP_COLDSTART_CYCLEDEF="00 09,21 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
PREP_WARMSTART_CYCLEDEF="00 00-08,10-20,22,23 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
ANALYSIS_CYCLEDEF="00 00-23 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
FORECAST_CYCLEDEF="00 00-23 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
POSTPROC_CYCLEDEF="00 00-23 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
POSTPROC_LONG_CYCLEDEF="00 00-23/03 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
ARCHIVE_CYCLEDEF="00 07 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
#CYCLEDAY="1-4"

if [[ $DO_RETRO == "true" ]] ; then
if [[ $LBCS_ICS_ONLY == "true" ]]; then
PREEXISTING_DIR_METHOD="rename"
INITIAL_CYCLEDEF="00 09,21 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
BOUNDARY_CYCLEDEF="00 00-02,04-08,10-14,16-20,22,23 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
BOUNDARY_LONG_CYCLEDEF="00 03,09,15,21 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
else
PREEXISTING_DIR_METHOD="overwrite"
PREP_COLDSTART_CYCLEDEF="00 09,21 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
PREP_WARMSTART_CYCLEDEF="00 00-08,10-20,22,23 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
ANALYSIS_CYCLEDEF="00 00-23 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
FORECAST_CYCLEDEF="00 00-23 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
POSTPROC_CYCLEDEF="00 00-23 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
POSTPROC_LONG_CYCLEDEF="00 00-23/03 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
fi
else
INITIAL_CYCLEDEF="00 09,21 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
BOUNDARY_CYCLEDEF="00 00-02,04-08,10-14,16-20,22,23 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
BOUNDARY_LONG_CYCLEDEF="00 03,09,15,21 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
PREP_COLDSTART_CYCLEDEF="00 09,21 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
PREP_WARMSTART_CYCLEDEF="00 00-08,10-20,22,23 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
ANALYSIS_CYCLEDEF="00 00-23 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
FORECAST_CYCLEDEF="00 00-23 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
POSTPROC_CYCLEDEF="00 00-23 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
POSTPROC_LONG_CYCLEDEF="00 00-23/03 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
ARCHIVE_CYCLEDEF="00 07 ${CYCLEDAY} ${CYCLEMONTH} 2021 *"
fi

FCST_LEN_HRS="18"
POSTPROC_LEN_HRS="3"
Expand All @@ -74,11 +97,7 @@ if [[ -n $RESERVATION ]] ; then
fi

WTIME_RUN_FCST="03:00:00"
DT_ATMOS=20

DATE_FIRST_CYCL="20210401"
DATE_LAST_CYCL="20211231"
CYCL_HRS=( "00" "12" )
DT_ATMOS=30
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@christinaholtNOAA christinaholtNOAA May 12, 2021

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Was this an intended change for RRFS_dev1 in real time?

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@hu5970 hu5970 May 13, 2021

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Yes, that is the number in real-time runs now.


EXTRN_MDL_NAME_ICS="RAP"
EXTRN_MDL_NAME_LBCS="RAP"
Expand Down
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