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Merged
hu5970 merged 3 commits into from
May 14, 2021
Merged

Feature/rrfs dev2: add configure files #106

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fe83181
Feature/rrfs dev1: add retrospective function and changes for running…
May 13, 2021
99cb1c7
Copy addtional grid from UPP run directory to comout space. (#105)
May 14, 2021
00521b1
Add 3-km CONUS and AK configure files for dev2
hu5970 May 14, 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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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
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
6 changes: 5 additions & 1 deletion scripts/exregional_run_post.sh
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Expand Up @@ -345,8 +345,12 @@ if [ ${#ADDNL_OUTPUT_GRIDS[@]} -gt 0 ]; then
# Remove temporary files
rm -f ${subdir}/${fhr}/tmp_${grid}.grib2

# Save to com directory
mkdir -p ${comout}/${grid}_grid
cp_vrfy ${bg_remap} ${comout}/${grid}_grid/${NET}.t${cyc}z.bg${leveltype}f${fhr}.${tmmark}.grib2

# Link output for transfer from Jet to web
ln -fs ${bg_remap} ${subdir}/BG${leveltype^^}_${basetime}${post_fhr}00
ln_vrfy -fs --relative ${comout}/${grid}_grid/${NET}.t${cyc}z.bg${leveltype}f${fhr}.${tmmark}.grib2 ${comout}/${grid}_grid/BG${leveltype^^}_${basetime}${post_fhr}00
done
done
fi
Expand Down
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