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Merge pull request #145 from AndrewEichmann-NOAA/EXP-efso_fv3_PR_scripts
GitHub Issue #118. EFSOI additions to scripts directory for issue.
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#!/bin/ksh | ||
################################################################################ | ||
#### UNIX Script Documentation Block | ||
# . . | ||
# Script name: exgdas_efsoi.sh | ||
# Script description: Runs efsoi to make observation sensitivities | ||
# | ||
# Author: Liaofan Lin/Andrew Eichmann Date: 2020-12-03 | ||
# | ||
# Abstract: This script runs the efsoi executable | ||
# | ||
# $Id$ | ||
# | ||
# Attributes: | ||
# Language: POSIX shell | ||
# Machine: Hera | ||
# | ||
################################################################################ | ||
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# Set environment. | ||
VERBOSE=${VERBOSE:-"YES"} | ||
if [ $VERBOSE = "YES" ] ; then | ||
echo $(date) EXECUTING $0 $* >&2 | ||
set -x | ||
fi | ||
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# Directories. | ||
pwd=$(pwd) | ||
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# Utilities | ||
NCP=${NCP:-"/bin/cp -p"} | ||
NLN=${NLN:-"/bin/ln -sf"} | ||
ERRSCRIPT=${ERRSCRIPT:-'eval [[ $err = 0 ]]'} | ||
NEMSIOGET=${NEMSIOGET:-$NWPROD/utils/exec/nemsio_get} | ||
NCLEN=${NCLEN:-$HOMEgfs/ush/getncdimlen} | ||
USE_CFP=${USE_CFP:-"NO"} | ||
CFP_MP=${CFP_MP:-"NO"} | ||
nm="" | ||
if [ $CFP_MP = "YES" ]; then | ||
nm=0 | ||
fi | ||
APRUNCFP=${APRUNCFP:-""} | ||
APRUN_ENKF=${APRUN_ENKF:-${APRUN:-""}} | ||
NTHREADS_ENKF=${NTHREADS_ENKF:-${NTHREADS:-1}} | ||
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# Executables | ||
EFSOIEXEC=${EFSOIEXEC:-$HOMEgfs/exec/efsoi.x} | ||
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# Cycling and forecast hour specific parameters | ||
CDATE=${CDATE:-"2001010100"} | ||
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# Filenames. | ||
GPREFIX=${GPREFIX:-""} | ||
GSUFFIX=${GSUFFIX:-$SUFFIX} | ||
APREFIX=${APREFIX:-""} | ||
ASUFFIX=${ASUFFIX:-$SUFFIX} | ||
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SMOOTH_ENKF=${SMOOTH_ENKF:-"YES"} | ||
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GBIASe=${GBIASe:-${APREFIX}abias_int.ensmean} | ||
CNVSTAT=${CNVSTAT:-${APREFIX}cnvstat} # AFE not needed? | ||
OZNSTAT=${OZNSTAT:-${APREFIX}oznstat} # AFE not needed? | ||
RADSTAT=${RADSTAT:-${APREFIX}radstat} # AFE not needed? | ||
#ENKFSTAT=${ENKFSTAT:-${APREFIX}enkfstat} | ||
EFSOISTAT=${EFSOISTAT:-${APREFIX}efsoistat} | ||
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#AFE for EFSOI | ||
#VERFANL=${VERFANL:-${APREFIX}atmanl.nemsio} | ||
VERFANL=${VERFANL:-${APREFIX}atmanl.ensres.nc} | ||
FCSTLONG=${GPREFIX}atmf030.ensmean.nc | ||
FCSTSHORT=${APREFIX}atmf024.ensmean.nc | ||
FCST6HRS=${PPREFIX}atmf006.ensmean.nc | ||
OSENSEIN=osense_${CDATE}_init.dat | ||
OSENSEOUT=osense_${CDATE}_final.dat | ||
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# this needs to be set manually because params in enkf will default to fhr03 | ||
fgfileprefixes=sfg_${CDATE}_fhr06_ | ||
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#analysise Namelst parameters | ||
USE_CORRELATED_OBERRS=${USE_CORRELATED_OBERRS:-"NO"} | ||
NMEM_ENKF=${NMEM_ENKF:-80} | ||
NAM_ENKF=${NAM_ENKF:-""} | ||
SATOBS_ENKF=${SATOBS_ENKF:-""} | ||
OZOBS_ENKF=${OZOBS_ENKF:-""} | ||
use_correlated_oberrs=${use_correlated_oberrs:-".false."} | ||
if [ $USE_CORRELATED_OBERRS == "YES" ]; then | ||
use_correlated_oberrs=".true." | ||
fi | ||
imp_physics=${imp_physics:-"99"} | ||
#lupp=${lupp:-".true."} | ||
lupp=${lupp:-".false."} # AFE to match old EFSOI | ||
corrlength=${corrlength:-1250} | ||
lnsigcutoff=${lnsigcutoff:-2.5} | ||
analpertwt=${analpertwt:-0.85} | ||
#readin_localization_enkf=${readin_localization_enkf:-".true."} | ||
readin_localization_enkf=${readin_localization_enkf:-".false."} # AFE | ||
reducedgrid=${reducedgrid:-".true."} | ||
letkf_flag=${letkf_flag:-".false."} | ||
getkf=${getkf:-".false."} | ||
denkf=${denkf:-".false."} | ||
nobsl_max=${nobsl_max:-10000} | ||
lobsdiag_forenkf=${lobsdiag_forenkf:-".false."} | ||
write_spread_diag=${write_spread_diag:-".false."} | ||
cnvw_option=${cnvw_option:-".false."} | ||
netcdf_diag=${netcdf_diag:-".true."} | ||
modelspace_vloc=${modelspace_vloc:-".false."} # if true, 'vlocal_eig.dat' is needed | ||
IAUFHRS_ENKF=${IAUFHRS_ENKF:-6} | ||
DO_CALC_INCREMENT=${DO_CALC_INCREMENT:-"NO"} | ||
INCREMENTS_TO_ZERO=${INCREMENTS_TO_ZERO:-"'NONE'"} | ||
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################################################################################ | ||
#ATMGES_ENSMEAN=$COMIN_GES_ENS/${GPREFIX}atmf006.ensmean${GSUFFIX} | ||
ATMGES_ENSMEAN=$COMIN_ANL/$VERFANL | ||
if [ $SUFFIX = ".nc" ]; then | ||
LONB_ENKF=${LONB_ENKF:-$($NCLEN $ATMGES_ENSMEAN grid_xt)} # get LONB_ENKF | ||
LATB_ENKF=${LATB_ENKF:-$($NCLEN $ATMGES_ENSMEAN grid_yt)} # get LATB_ENFK | ||
LEVS_ENKF=${LEVS_ENKF:-$($NCLEN $ATMGES_ENSMEAN pfull)} # get LEVS_ENFK | ||
use_gfs_ncio=".true." | ||
use_gfs_nemsio=".false." | ||
paranc=${paranc:-".true."} | ||
if [ $DO_CALC_INCREMENT = "YES" ]; then | ||
write_fv3_incr=".false." | ||
else | ||
write_fv3_incr=".true." | ||
WRITE_INCR_ZERO="incvars_to_zero= $INCREMENTS_TO_ZERO," | ||
fi | ||
else | ||
LEVS_ENKF=${LEVS_ENKF:-$($NEMSIOGET $ATMGES_ENSMEAN dimz | awk '{print $2}')} | ||
LATB_ENKF=${LATB_ENKF:-$($NEMSIOGET $ATMGES_ENSMEAN dimy | awk '{print $2}')} | ||
LONB_ENKF=${LONB_ENKF:-$($NEMSIOGET $ATMGES_ENSMEAN dimx | awk '{print $2}')} | ||
use_gfs_ncio=".false." | ||
use_gfs_nemsio=".true." | ||
paranc=${paranc:-".false."} | ||
fi | ||
LATA_ENKF=${LATA_ENKF:-$LATB_ENKF} | ||
LONA_ENKF=${LONA_ENKF:-$LONB_ENKF} | ||
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SATANGL=${SATANGL:-${FIXgsi}/global_satangbias.txt} | ||
SATINFO=${SATINFO:-${FIXgsi}/global_satinfo.txt} | ||
CONVINFO=${CONVINFO:-${FIXgsi}/global_convinfo.txt} | ||
OZINFO=${OZINFO:-${FIXgsi}/global_ozinfo.txt} | ||
SCANINFO=${SCANINFO:-${FIXgsi}/global_scaninfo.txt} | ||
HYBENSINFO=${HYBENSINFO:-${FIXgsi}/global_hybens_info.l${LEVS_ENKF}.txt} | ||
ANAVINFO=${ANAVINFO:-${FIXgsi}/global_anavinfo.l${LEVS_ENKF}.txt} | ||
VLOCALEIG=${VLOCALEIG:-${FIXgsi}/vlocal_eig_l${LEVS_ENKF}.dat} | ||
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ENKF_SUFFIX="s" | ||
[[ $SMOOTH_ENKF = "NO" ]] && ENKF_SUFFIX="" | ||
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################################################################################ | ||
# Preprocessing | ||
mkdata=NO | ||
if [ ! -d $DATA ]; then | ||
mkdata=YES | ||
mkdir -p $DATA | ||
fi | ||
cd $DATA || exit 99 | ||
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################################################################################ | ||
# Fixed files | ||
$NLN $SATANGL satbias_angle | ||
$NLN $SATINFO satinfo | ||
$NLN $SCANINFO scaninfo | ||
$NLN $CONVINFO convinfo | ||
$NLN $OZINFO ozinfo | ||
$NLN $HYBENSINFO hybens_info | ||
$NLN $ANAVINFO anavinfo | ||
$NLN $VLOCALEIG vlocal_eig.dat | ||
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# Bias correction coefficients based on the ensemble mean | ||
$NLN $COMOUT_ANL_ENSFSOI/$GBIASe satbias_in | ||
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################################################################################ | ||
# Ensemble guess, observational data and analyses/increments | ||
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nfhrs=`echo $IAUFHRS_ENKF | sed 's/,/ /g'` | ||
for imem in $(seq 1 $NMEM_ENKF); do | ||
memchar="mem"$(printf %03i $imem) | ||
mkdir ${memchar} | ||
$NLN $COMOUT_ANL_ENSFSOI/$memchar/${APREFIX}atmf024.nc ${memchar} | ||
done | ||
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$NLN $COMIN_GES_ENS/${GPREFIX}atmf006.ensmean${GSUFFIX} sfg_${CDATE}_fhr06_ensmean | ||
$NLN $COMIN_GES_ENS/${GPREFIX}atmf006.ensmean${GSUFFIX} sfg_${CDATE}_fhr03_ensmean | ||
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# verifying analysis | ||
$NLN ${COMIN_ANL}/${VERFANL} . | ||
# the above way is the proper one, but this bit of subterfuge | ||
# is necessary because ensmean is hard coded into GSI - needs | ||
# to changed | ||
$NLN ${COMIN_ANL}/${VERFANL} ${APREFIX}atmanl.ensmean.nc | ||
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# forecasts | ||
$NLN $COMIN_GES_ENS/$FCSTLONG . | ||
$NLN $COMOUT_ANL_ENSFSOI/$FCSTSHORT . | ||
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# inital osense file | ||
# efsoi.x will read then clobber this | ||
$NCP $COMOUT_ANL_ENSFSOI/$OSENSEIN osense_${CDATE}.dat | ||
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if [ $USE_CFP = "YES" ]; then | ||
chmod 755 $DATA/mp_untar.sh | ||
ncmd=$(cat $DATA/mp_untar.sh | wc -l) | ||
if [ $ncmd -gt 0 ]; then | ||
ncmd_max=$((ncmd < npe_node_max ? ncmd : npe_node_max)) | ||
APRUNCFP=$(eval echo $APRUNCFP) | ||
$APRUNCFP $DATA/mp_untar.sh | ||
export ERR=$? | ||
export err=$ERR | ||
$ERRSCRIPT || exit 3 | ||
fi | ||
fi | ||
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################################################################################ | ||
# Create global_enkf namelist | ||
# AFE changed from original: | ||
# gdatehr, datehr, andataname added | ||
# analpertwt and lnsigcutoff changed upstream | ||
# numiter from 0 to 1 | ||
# fso_cycling=.true., | ||
# efsoi_flag=.true., | ||
# wmoist=1.0,adrate=0.75 | ||
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cat > enkf.nml << EOFnml | ||
&nam_enkf | ||
datestring="$CDATE",datapath="$DATA/", | ||
gdatehr=$gcyc, | ||
datehr=$cyc, | ||
fgfileprefixes=$fgfileprefixes | ||
andataname="$VERFANL", | ||
analpertwtnh=${analpertwt},analpertwtsh=${analpertwt},analpertwttr=${analpertwt}, | ||
covinflatemax=1.e2,covinflatemin=1,pseudo_rh=.true.,iassim_order=0, | ||
corrlengthnh=${corrlength},corrlengthsh=${corrlength},corrlengthtr=${corrlength}, | ||
lnsigcutoffnh=${lnsigcutoff},lnsigcutoffsh=${lnsigcutoff},lnsigcutofftr=${lnsigcutoff}, | ||
lnsigcutoffpsnh=${lnsigcutoff},lnsigcutoffpssh=${lnsigcutoff},lnsigcutoffpstr=${lnsigcutoff}, | ||
lnsigcutoffsatnh=${lnsigcutoff},lnsigcutoffsatsh=${lnsigcutoff},lnsigcutoffsattr=${lnsigcutoff}, | ||
obtimelnh=1.e30,obtimelsh=1.e30,obtimeltr=1.e30, | ||
saterrfact=1.0,numiter=1, | ||
sprd_tol=1.e30,paoverpb_thresh=0.98, | ||
nlons=$LONA_ENKF,nlats=$LATA_ENKF,nlevs=$LEVS_ENKF,nanals=$NMEM_ENKF, | ||
deterministic=.true.,sortinc=.true.,lupd_satbiasc=.false., | ||
reducedgrid=${reducedgrid},readin_localization=${readin_localization_enkf}., | ||
use_gfs_nemsio=${use_gfs_nemsio},use_gfs_ncio=${use_gfs_ncio},imp_physics=$imp_physics,lupp=$lupp, | ||
univaroz=.false.,adp_anglebc=.true.,angord=4,use_edges=.false.,emiss_bc=.true., | ||
letkf_flag=${letkf_flag},nobsl_max=${nobsl_max},denkf=${denkf},getkf=${getkf}., | ||
nhr_anal=${IAUFHRS_ENKF},nhr_state=${IAUFHRS_ENKF},use_qsatensmean=.true., | ||
lobsdiag_forenkf=$lobsdiag_forenkf, | ||
write_spread_diag=$write_spread_diag, | ||
modelspace_vloc=$modelspace_vloc, | ||
use_correlated_oberrs=${use_correlated_oberrs}, | ||
netcdf_diag=$netcdf_diag,cnvw_option=$cnvw_option, | ||
paranc=$paranc,write_fv3_incr=$write_fv3_incr, | ||
efsoi_cycling=.true., | ||
efsoi_flag=.true., | ||
wmoist=1.0,adrate=0.75 | ||
$WRITE_INCR_ZERO | ||
$NAM_ENKF | ||
/ | ||
&satobs_enkf | ||
sattypes_rad(1) = 'amsua_n15', dsis(1) = 'amsua_n15', | ||
sattypes_rad(2) = 'amsua_n18', dsis(2) = 'amsua_n18', | ||
sattypes_rad(3) = 'amsua_n19', dsis(3) = 'amsua_n19', | ||
sattypes_rad(4) = 'amsub_n16', dsis(4) = 'amsub_n16', | ||
sattypes_rad(5) = 'amsub_n17', dsis(5) = 'amsub_n17', | ||
sattypes_rad(6) = 'amsua_aqua', dsis(6) = 'amsua_aqua', | ||
sattypes_rad(7) = 'amsua_metop-a', dsis(7) = 'amsua_metop-a', | ||
sattypes_rad(8) = 'airs_aqua', dsis(8) = 'airs_aqua', | ||
sattypes_rad(9) = 'hirs3_n17', dsis(9) = 'hirs3_n17', | ||
sattypes_rad(10)= 'hirs4_n19', dsis(10)= 'hirs4_n19', | ||
sattypes_rad(11)= 'hirs4_metop-a', dsis(11)= 'hirs4_metop-a', | ||
sattypes_rad(12)= 'mhs_n18', dsis(12)= 'mhs_n18', | ||
sattypes_rad(13)= 'mhs_n19', dsis(13)= 'mhs_n19', | ||
sattypes_rad(14)= 'mhs_metop-a', dsis(14)= 'mhs_metop-a', | ||
sattypes_rad(15)= 'goes_img_g11', dsis(15)= 'imgr_g11', | ||
sattypes_rad(16)= 'goes_img_g12', dsis(16)= 'imgr_g12', | ||
sattypes_rad(17)= 'goes_img_g13', dsis(17)= 'imgr_g13', | ||
sattypes_rad(18)= 'goes_img_g14', dsis(18)= 'imgr_g14', | ||
sattypes_rad(19)= 'goes_img_g15', dsis(19)= 'imgr_g15', | ||
sattypes_rad(20)= 'avhrr_n18', dsis(20)= 'avhrr3_n18', | ||
sattypes_rad(21)= 'avhrr_metop-a', dsis(21)= 'avhrr3_metop-a', | ||
sattypes_rad(22)= 'avhrr_n19', dsis(22)= 'avhrr3_n19', | ||
sattypes_rad(23)= 'amsre_aqua', dsis(23)= 'amsre_aqua', | ||
sattypes_rad(24)= 'ssmis_f16', dsis(24)= 'ssmis_f16', | ||
sattypes_rad(25)= 'ssmis_f17', dsis(25)= 'ssmis_f17', | ||
sattypes_rad(26)= 'ssmis_f18', dsis(26)= 'ssmis_f18', | ||
sattypes_rad(27)= 'ssmis_f19', dsis(27)= 'ssmis_f19', | ||
sattypes_rad(28)= 'ssmis_f20', dsis(28)= 'ssmis_f20', | ||
sattypes_rad(29)= 'sndrd1_g11', dsis(29)= 'sndrD1_g11', | ||
sattypes_rad(30)= 'sndrd2_g11', dsis(30)= 'sndrD2_g11', | ||
sattypes_rad(31)= 'sndrd3_g11', dsis(31)= 'sndrD3_g11', | ||
sattypes_rad(32)= 'sndrd4_g11', dsis(32)= 'sndrD4_g11', | ||
sattypes_rad(33)= 'sndrd1_g12', dsis(33)= 'sndrD1_g12', | ||
sattypes_rad(34)= 'sndrd2_g12', dsis(34)= 'sndrD2_g12', | ||
sattypes_rad(35)= 'sndrd3_g12', dsis(35)= 'sndrD3_g12', | ||
sattypes_rad(36)= 'sndrd4_g12', dsis(36)= 'sndrD4_g12', | ||
sattypes_rad(37)= 'sndrd1_g13', dsis(37)= 'sndrD1_g13', | ||
sattypes_rad(38)= 'sndrd2_g13', dsis(38)= 'sndrD2_g13', | ||
sattypes_rad(39)= 'sndrd3_g13', dsis(39)= 'sndrD3_g13', | ||
sattypes_rad(40)= 'sndrd4_g13', dsis(40)= 'sndrD4_g13', | ||
sattypes_rad(41)= 'sndrd1_g14', dsis(41)= 'sndrD1_g14', | ||
sattypes_rad(42)= 'sndrd2_g14', dsis(42)= 'sndrD2_g14', | ||
sattypes_rad(43)= 'sndrd3_g14', dsis(43)= 'sndrD3_g14', | ||
sattypes_rad(44)= 'sndrd4_g14', dsis(44)= 'sndrD4_g14', | ||
sattypes_rad(45)= 'sndrd1_g15', dsis(45)= 'sndrD1_g15', | ||
sattypes_rad(46)= 'sndrd2_g15', dsis(46)= 'sndrD2_g15', | ||
sattypes_rad(47)= 'sndrd3_g15', dsis(47)= 'sndrD3_g15', | ||
sattypes_rad(48)= 'sndrd4_g15', dsis(48)= 'sndrD4_g15', | ||
sattypes_rad(49)= 'iasi_metop-a', dsis(49)= 'iasi_metop-a', | ||
sattypes_rad(50)= 'seviri_m08', dsis(50)= 'seviri_m08', | ||
sattypes_rad(51)= 'seviri_m09', dsis(51)= 'seviri_m09', | ||
sattypes_rad(52)= 'seviri_m10', dsis(52)= 'seviri_m10', | ||
sattypes_rad(53)= 'seviri_m11', dsis(53)= 'seviri_m11', | ||
sattypes_rad(54)= 'amsua_metop-b', dsis(54)= 'amsua_metop-b', | ||
sattypes_rad(55)= 'hirs4_metop-b', dsis(55)= 'hirs4_metop-b', | ||
sattypes_rad(56)= 'mhs_metop-b', dsis(56)= 'mhs_metop-b', | ||
sattypes_rad(57)= 'iasi_metop-b', dsis(57)= 'iasi_metop-b', | ||
sattypes_rad(58)= 'avhrr_metop-b', dsis(58)= 'avhrr3_metop-b', | ||
sattypes_rad(59)= 'atms_npp', dsis(59)= 'atms_npp', | ||
sattypes_rad(60)= 'atms_n20', dsis(60)= 'atms_n20', | ||
sattypes_rad(61)= 'cris_npp', dsis(61)= 'cris_npp', | ||
sattypes_rad(62)= 'cris-fsr_npp', dsis(62)= 'cris-fsr_npp', | ||
sattypes_rad(63)= 'cris-fsr_n20', dsis(63)= 'cris-fsr_n20', | ||
sattypes_rad(64)= 'gmi_gpm', dsis(64)= 'gmi_gpm', | ||
sattypes_rad(65)= 'saphir_meghat', dsis(65)= 'saphir_meghat', | ||
sattypes_rad(66)= 'amsua_metop-c', dsis(66)= 'amsua_metop-c', | ||
sattypes_rad(67)= 'mhs_metop-c', dsis(67)= 'mhs_metop-c', | ||
sattypes_rad(68)= 'ahi_himawari8', dsis(68)= 'ahi_himawari8', | ||
sattypes_rad(69)= 'abi_g16', dsis(69)= 'abi_g16', | ||
sattypes_rad(70)= 'abi_g17', dsis(70)= 'abi_g17', | ||
$SATOBS_ENKF | ||
/ | ||
&ozobs_enkf | ||
sattypes_oz(1) = 'sbuv2_n16', | ||
sattypes_oz(2) = 'sbuv2_n17', | ||
sattypes_oz(3) = 'sbuv2_n18', | ||
sattypes_oz(4) = 'sbuv2_n19', | ||
sattypes_oz(5) = 'omi_aura', | ||
sattypes_oz(6) = 'gome_metop-a', | ||
sattypes_oz(7) = 'gome_metop-b', | ||
sattypes_oz(8) = 'mls30_aura', | ||
sattypes_oz(9) = 'ompsnp_npp', | ||
sattypes_oz(10) = 'ompstc8_npp', | ||
$OZOBS_ENKF | ||
/ | ||
EOFnml | ||
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################################################################################ | ||
# Run enkf update | ||
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export OMP_NUM_THREADS=$NTHREADS_ENKF | ||
#export pgm=$ENKFEXEC AFE | ||
export pgm=$EFSOIEXEC | ||
. prep_step | ||
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#$NCP $ENKFEXEC $DATA AFE | ||
#$APRUN_ENKF ${DATA}/$(basename $ENKFEXEC) 1>stdout 2>stderr AFE | ||
$NCP $EFSOIEXEC $DATA | ||
$APRUN_ENKF ${DATA}/$(basename $EFSOIEXEC) 1>stdout 2>stderr | ||
rc=$? | ||
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export ERR=$rc | ||
export err=$ERR | ||
$ERRSCRIPT || exit 2 | ||
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# Cat runtime output files. | ||
cat stdout stderr > $COMOUT_ANL_ENSFSOI/$EFSOISTAT | ||
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$NCP osense_${CDATE}.dat $COMOUT_ANL_ENSFSOI/$OSENSEOUT | ||
$NCP osense_${CDATE}.dat $OSENSE_SAVE_DIR/$OSENSEOUT | ||
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################################################################################ | ||
# Postprocessing | ||
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cd $pwd | ||
[[ $mkdata = "YES" ]] && rm -rf $DATA | ||
set +x | ||
if [ $VERBOSE = "YES" ]; then | ||
echo $(date) EXITING $0 with return code $err >&2 | ||
fi | ||
exit $err |
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