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run_gsi_4densvar.sh
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run_gsi_4densvar.sh
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echo "Time starting at `date` "
VERBOSE=${VERBOSE:-"YES"}
if [[ "$VERBOSE" = "YES" ]]; then
set -x
fi
export OMP_NUM_THREADS=${OMP_NUM_THREADS:-1}
export OMP_STACKSIZE=${OMP_STACKSIZE:-256M}
export machine=${machine:='wcoss'}
# Set experiment name and analysis date
adate=${analdate:-2010081900}
adatem1=${analdatem1:-2010081900}
nens=${nanals:-80}
DONST=${DONST:-"NO"}
NST_GSI=${NST_GSI:-0}
NSTINFO=${NSTINFO:-0}
ZSEA1=${ZSEA1:-0}
ZSEA2=${ZSEA2:-0}
FAC_DTL=${FAC_DTL:-1}
FAC_TSL=${FAC_TSL:-1}
TZR_QC=${TZR_QC:-1}
HXONLY=${HXONLY:-"NO"}
HRLY_BKG=${HRLY_BKG:-"YES"}
NOSAT=${NOSAT:-"NO"}
skipcat=${skipcat:-"false"}
nprocs=${nprocs:-$PBS_NP}
# Set path/file for gsi executable
basedir=${HOMEGLOBAL}
gsipath=${gsipath:-${basedir}/gsi}
gsiexec=${gsiexec:-$gsipath/EXP-port/src/global_gsi}
charnanal=${charnanal:-'ensmean'}
# name just for diag files.
charnanal2=${charnanal2:-$charnanal}
# Given the analysis date, compute the date from which the
# first guess comes. Extract cycle and set prefix and suffix
# for guess and observation data files
gdate=`${incdate} $adate -${ANALINC}`
hha=`echo $adate | cut -c9-10`
hham1=`echo $analdatem1 | cut -c9-10`
hhg=`echo $gdate | cut -c9-10`
RUN=${RUN:-gfs}
prefix_obs=${RUN}.t${hha}z
prefix_obsm1=${RUN}.t${hham1}z
prefix_tbc=${RUN}.t${hhg}z
suffix=tm00.bufr_d
datges=${datapath2:-/lfs1/projects/fim/whitaker/gfsenkf_test/$adate}
datgesm1=${datapathm1:-/lfs1/projects/fim/whitaker/gfsenkf_test/$gdate}
adate0=`echo $adate | cut -c1-8`
echo "adate = $adate"
iy=`echo $adate | cut -c1-4`
im=`echo $adate | cut -c5-6`
id=`echo $adate | cut -c7-8`
ih=`echo $adate | cut -c9-10`
echo "iy,im,id,ih = $iy $im $id $ih"
date_fhour=`$python ${enkfscripts}/getidate.py ${datges}/bfg_${adate}_fhr03_${charnanal`
fdatei=`echo $date_fhour | cut -f1 -d " "`
fhr=`echo $date_fhour | cut -f2 -d " "`
fdatev=`${incdate} $fdatei $fhr`
echo "fdatei=$fdatei fhr=$fhr fdatev=$fdatev"
gdate0=`echo $gdate | cut -c1-8`
obs_datapath=${obs_datapath:-/lfs1/projects/fim/whitaker/bufr}
datobs=$obs_datapath/gdas.${iy}${im}${id}/${ih}
# Set runtime and save directories
tmpdir=${tmpdir:-$datges/gsitmp$$}
mkdir -p $tmpdir
savdir=${savdir:-$datges}
# Specify GSI fixed field and data directories.
export fixgsi=${fixgsi:-$gsipath/fix}
export fixcrtm=${fixcrtm:-$basedir/nwprod/CRTM_Coefficients}
export HOMEGLOBAL=${HOMEGLOBAL:-/lfs1/projects/fim/whitaker/gfsenkf}
export FIXGLOBAL=${FIXGLOBAL:-$HOMEGLOBAL/fix}
export EXECGLOBAL=${EXECGLOBAL:-$HOMEGLOBAL/bin}
# Set variables used in script
# CLEAN up $tmpdir when finished (YES=remove, NO=leave alone)
# ndate is a date manipulation utility
# ndate is a date manipulation utility
# ncp is cp replacement, currently keep as /bin/cp
ncp="/bin/cp -f"
nmv="/bin/mv -f"
nln="/bin/ln -fs"
# copy symlinks if needed.
if [[ "$lread_obs_save" = ".false." && "$HXONLY" = "YES" ]]; then
tmpdir_ensmean=${datges}/gsitmp_${charnanal2}
mkdir -p $tmpdir
for filein in ${tmpdir_ensmean}/obs_input*; do
file=`basename ${filein}`
ln -fs $filein ${tmpdir}/${file}
done
for filein in ${tmpdir_ensmean}/*bin; do
file=`basename ${filein}`
/bin/cp -a $filein ${tmpdir}/${file}
done
for filein in ${tmpdir_ensmean}/*bufr; do
file=`basename ${filein}`
/bin/cp -a $filein ${tmpdir}/${file}
done
for filein in ${tmpdir_ensmean}/*bufrears; do
file=`basename ${filein}`
/bin/cp -a $filein ${tmpdir}/${file}
done
for filein in ${tmpdir_ensmean}/*bufrears; do
file=`basename ${filein}`
/bin/cp -a $filein ${tmpdir}/${file}
done
/bin/cp -a ${tmpdir_ensmean}/tcvitals ${tmpdir}/tcvitals
/bin/cp -a ${tmpdir_ensmean}/satbias_in ${tmpdir}/satbias_in
/bin/cp -a ${tmpdir_ensmean}/satbias_angle ${tmpdir}/satbias_angle
fi
# go to $tmpdir
cd $tmpdir
echo "Time before global cycle `date` "
# Set the JCAP resolution which you want.
# All resolutions use LEVS=64
export JCAP_A=${JCAP_A:-$JCAP}
export LEVS=${LEVS:-64}
export JCAP_B=${JCAP_B:-$JCAP}
export lobsdiag_forenkf=${lobsdiag_forenkf:-".false."}
export NLAT=$((${LATA}+2))
JCAP_ENS=${JCAP_ENS:-$JCAP}
LATA_ENS=${LATA_ENS:-$LATA}
LONA_ENS=${LONA_ENS:-$LONA}
export NLAT_ENS=$((${LATA_ENS}+2))
SATANGO=${SATANGO:-$savdir/${RUN}.t${hha}z.satang}
BIASO=${BIASO:-$savdir/${RUN}.t${hha}z.abias}
BIASOAIR=${BIASOAIR:-$savdir/${RUN}.t${hha}z.abias_air}
BIASO_PC=${BIASO_PC:-$savdir/${RUN}.t${hha}z.abias_pc}
# Make gsi namelist
# CO2 namelist and file decisions
#ICO2=${ICO2:-0}
#if [ $ICO2 -gt 0 ] ; then
# # Copy co2 files to $tmpdir
# co2dir=${CO2DIR:-$fixgsi}
# yyyy=$(echo ${CDATE:-$adate}|cut -c1-4)
# rm ./global_co2_data.txt
# while [ $yyyy -ge 1957 ] ;do
# co2=$co2dir/global_co2historicaldata_$yyyy.txt
# #co2=$co2dir/global_co2.gcmscl_$yyyy.txt
# if [ -s $co2 ] ; then
# $ncp $co2 ./global_co2_data.txt
# break
# fi
# ((yyyy-=1))
# done
# if [ ! -s ./global_co2_data.txt ] ; then
# echo "\./global_co2_data.txt" not created
# exit 1
# fi
#fi
# CO2 namelist and file decisions
ICO2=${ICO2:-0}
if [ $ICO2 -gt 0 ] ; then
# Copy co2 files to $tmpdir
co2dir=${CO2DIR:-$fixgsi}
yyyy=$(echo ${CDATE:-$adate}|cut -c1-4)
rm ./global_co2_data.txt
co2=$co2dir/global_co2.gcmscl_$yyyy.txt
while [ ! -s $co2 ] ; do
((yyyy-=1))
co2=$co2dir/global_co2.gcmscl_$yyyy.txt
done
if [ -s $co2 ] ; then
$ncp $co2 ./global_co2_data.txt
fi
if [ ! -s ./global_co2_data.txt ] ; then
echo "\./global_co2_data.txt" not created
exit 1
fi
fi
#CH4 file decision
ICH4=${ICH4:-0}
if [ $ICH4 -gt 0 ] ; then
# # Copy ch4 files to $tmpdir
ch4dir=${CH4DIR:-$fixgsi}
yyyy=$(echo ${CDATE:-$adate}|cut -c1-4)
rm ./ch4globaldata.txt
ch4=$ch4dir/global_ch4_esrlctm_$yyyy.txt
while [ ! -s $ch4 ] ; do
((yyyy-=1))
ch4=$ch4dir/global_ch4_esrlctm_$yyyy.txt
done
if [ -s $ch4 ] ; then
$ncp $ch4 ./ch4globaldata.txt
fi
if [ ! -s ./ch4globaldata.txt ] ; then
echo "\./ch4globaldata.txt" not created
exit 1
fi
fi
IN2O=${IN2O:-0}
if [ $IN2O -gt 0 ] ; then
# # Copy n2o files to $tmpdir
n2odir=${N2ODIR:-$fixgsi}
yyyy=$(echo ${CDATE:-$adate}|cut -c1-4)
rm ./n2oglobaldata.txt
n2o=$n2odir/global_n2o_esrlctm_$yyyy.txt
while [ ! -s $n2o ] ; do
((yyyy-=1))
n2o=$n2odir/global_n2o_esrlctm_$yyyy.txt
done
if [ -s $n2o ] ; then
$ncp $n2o ./n2oglobaldata.txt
fi
if [ ! -s ./n2oglobaldata.txt ] ; then
echo "\./n2oglobaldata.txt" not created
exit 1
fi
fi
ICO=${ICO:-0}
if [ $ICO -gt 0 ] ; then
# # Copy CO files to $tmpdir
codir=${CODIR:-$fixgsi}
yyyy=$(echo ${CDATE:-$adate}|cut -c1-4)
rm ./coglobaldata.txt
co=$codir/global_co_esrlctm_$yyyy.txt
while [ ! -s $co ] ; do
((yyyy-=1))
co=$codir/global_co_esrlctm_$yyyy.txt
done
if [ -s $co ] ; then
$ncp $co ./coglobaldata.txt
fi
if [ ! -s ./coglobaldata.txt ] ; then
echo "\./coglobaldata.txt" not created
exit 1
fi
fi
if [ "${iau_delthrs}" != "-1" ]; then
lwrite4danl=.true.
else
lwrite4danl=.false.
fi
if [[ $beta1_inv > 0.999 ]]; then
lwrite4danl=.false.
fi
# if satwnd bufr file exists, use it.
if [[ -s $datobs/${prefix_obs}.satwnd.${suffix} ]]; then
use_prepb_satwnd=.false.
else
use_prepb_satwnd=.true.
fi
SETUP="reduce_diag=.true.,lwrite_peakwt=.true.,lread_obs_save=$lread_obs_save,lread_obs_skip=$lread_obs_skip,l4densvar=.true.,ens_nstarthr=3,iwrtinc=-1,nhr_assimilation=6,nhr_obsbin=$FHOUT,use_prepb_satwnd=$use_prepb_satwnd,lwrite4danl=$lwrite4danl,passive_bc=.true.,newpc4pred=.true.,adp_anglebc=.true.,angord=4,use_edges=.false.,diag_precon=.true.,step_start=1.e-3,emiss_bc=.true.,lobsdiag_forenkf=$lobsdiag_forenkf,lwrite_predterms=.true.,thin4d=.true."
if [[ "$HXONLY" = "YES" ]]; then
#SETUP="$SETUP,lobserver=.true.,l4dvar=.true." # can't use reduce_diag=T
SETUP="$SETUP,miter=0,niter=1"
fi
if [[ "$HXONLY" != "YES" ]]; then
if [[ $beta1_inv > 0.999 ]]; then # 3dvar or hybrid gain
STRONGOPTS="tlnmc_option=1,nstrong=1,nvmodes_keep=8,period_max=6.,period_width=1.5"
SETUP="$SETUP,miter=1,niter(1)=150,niter(2)=0"
else # envar
STRONGOPTS="tlnmc_option=3,nstrong=1,nvmodes_keep=8,period_max=6.,period_width=1.5,baldiag_full=.true.,baldiag_inc=.true.,"
# balance constraint on 3dvar part of envar increment
#STRONGOPTS="tlnmc_option=4,nstrong=1,nvmodes_keep=8,period_max=6.,period_width=1.5,baldiag_full=.true.,baldiag_inc=.true.,"
# no strong bal constraint
#STRONGOPTS="tlnmc_option=0,nstrong=0,nvmodes_keep=0,baldiag_full=.false.,baldiag_inc=.false.,"
SETUP="$SETUP,miter=2,niter(1)=50,niter(2)=150"
fi
else
STRONGOPTS="tlnmc_option=0,nstrong=0,nvmodes_keep=0,baldiag_full=.false.,baldiag_inc=.false.,"
fi
GRIDOPTS=""
BKGVERR=""
ANBKGERR=""
JCOPTS=""
# use tcv_mod, only: init_tcps_errvals,tcp_refps,tcp_width,tcp_ermin,tcp_ermax
OBSQC="tcp_width=60.0,tcp_ermin=2.0,tcp_ermax=12.0,aircraft_t_bc=$aircraft_bc,biaspredt=1000.0,upd_aircraft=$aircraft_bc,cleanup_tail=.true." # error variance goes from tcp_ermin (when O-F=0) to tcp_ermax (when O-F=tcp_width=50)
# GSI defaults
# tcp_width=50.0_r_kind
# tcp_ermin=0.75_r_kind
# tcp_ermax=5.0_r_kind
OBSINPUT=""
SUPERRAD=""
SINGLEOB=""
LAGDATA=""
RAPIDREFRESH_CLDSURF=""
CHEM=""
# l_hyb_ens: logical variable, if .true., then turn on hybrid ensemble option, default = .false.
# n_ens: ensemble size, default = 0
# beta1_inv: value between 0 and 1, relative weight given to static background B, default = 1.0
# s_ens_h: horizontal localization correlation length (units of km), default = 2828.0
# s_ens_v: vertical localization correlation length (grid units), default = 30.0
# generate_ens: if .true., generate ensemble perturbations internally as random samples of background B.
# (used primarily for testing/debugging)
# if .false., read external ensemble perturbations (not active yet)
# aniso_a_en: if .true., then allow anisotropic localization correlation (not active yet)
# uv_hyb_ens: if .true., then ensemble perturbation wind stored as u,v
# if .false., ensemble perturbation wind stored as psi,chi.
# (this is useful for regional application, where there is ambiguity in how to
# define psi,chi from u,v)
beta1_inv=${beta1_inv:-0.25}
s_ens_h=${s_ens_h:-400}
s_ens_v=${s_ens_v:-0.6}
if [ "$HXONLY" = "NO" ] && [[ $beta1_inv < 0.999 ]]; then
HYBRIDENSDATA="l_hyb_ens=.true.,n_ens=$nens,beta_s0=$beta1_inv,s_ens_h=$s_ens_h,s_ens_v=$s_ens_v,generate_ens=.false.,uv_hyb_ens=.true.,jcap_ens=$JCAP_ENS,nlat_ens=$NLAT_ENS,nlon_ens=$LONA_ENS,aniso_a_en=.false.,jcap_ens_test=$JCAP_ENS,readin_localization=$readin_localization,write_ens_sprd=.false.,oz_univ_static=.false.,q_hyb_ens=.false.,ens_fast_read=.true.,readin_beta=$readin_beta"
else
HYBRIDENSDATA=""
fi
NST=${NST:-""}
if [ $NST_GSI -gt 0 ]; then
NST="nstinfo=$NSTINFO,fac_dtl=$FAC_DTL,fac_tsl=$FAC_TSL,zsea1=$ZSEA1,zsea2=$ZSEA2,$NST"
fi
# Create global_gsi namelist
cat <<EOF > gsiparm.anl
&SETUP
niter_no_qc(1)=25,niter_no_qc(2)=0,
write_diag(1)=.true.,write_diag(2)=.false.,write_diag(3)=.true.,
netcdf_diag=.true.,binary_diag=.false.,
qoption=2,
factqmin=0.0,factqmax=0.0,deltim=$DELTIM,
tzr_qc=1,iguess=-1,
oneobtest=.false.,retrieval=.false.,l_foto=.false.,
use_pbl=.false.,use_compress=.true.,nsig_ext=12,gpstop=50.,
use_gfs_ncio=.true.,sfcnst_comb=.true.,cwoption=3,imp_physics=${imp_physics},
$SETUP
/
&GRIDOPTS
JCAP_B=$JCAP_B,JCAP=$JCAP_A,NLAT=$NLAT,NLON=$LONA,nsig=$LEVS,
regional=.false.,nlayers(63)=3,nlayers(64)=6,
$GRIDOPTS
/
&BKGERR
vs=0.7,
hzscl=1.7,0.8,0.5,
hswgt=0.45,0.3,0.25,
bw=0.0,norsp=4,
bkgv_flowdep=.false.,bkgv_rewgtfct=1.5,
bkgv_write=.false.,
cwcoveqqcov=.false.,
$BKGVERR
/
&ANBKGERR
anisotropic=.false.,
$ANBKGERR
/
&JCOPTS
ljcdfi=.false.,alphajc=0.0,ljcpdry=.false.,bamp_jcpdry=5.0e7,ljc4tlevs=.true.
$JCOPTS
/
&STRONGOPTS
$STRONGOPTS
/
&OBSQC
dfact=0.75,dfact1=3.0,noiqc=.true.,oberrflg=.false.,c_varqc=0.02,
use_poq7=.true.,qc_noirjaco3_pole=.true.,vqc=.true.,
$OBSQC
/
/
&OBS_INPUT
dmesh(1)=145.0,dmesh(2)=150.0,dmesh(3)=100.0,time_window_max=3.0,
$OBSINPUT
/
OBS_INPUT::
! dfile dtype dplat dsis dval dthin dsfcalc
prepbufr ps null ps 0.0 0 0
prepbufr t null t 0.0 0 0
prepbufr q null q 0.0 0 0
prepbufr pw null pw 0.0 0 0
prepbufr_profl t null t 0.0 0 0
prepbufr_profl q null q 0.0 0 0
prepbufr_profl uv null uv 0.0 0 0
satwndbufr uv null uv 0.0 0 0
prepbufr uv null uv 0.0 0 0
prepbufr spd null spd 0.0 0 0
prepbufr dw null dw 0.0 0 0
radarbufr rw null rw 0.0 0 0
nsstbufr sst nsst sst 0.0 0 0
gpsrobufr gps_bnd null gps 0.0 0 0
ssmirrbufr pcp_ssmi dmsp pcp_ssmi 0.0 -1 0
tmirrbufr pcp_tmi trmm pcp_tmi 0.0 -1 0
sbuvbufr sbuv2 n11 sbuv8_n11 0.0 0 0
sbuvbufr sbuv2 n14 sbuv8_n14 0.0 0 0
sbuvbufr sbuv2 n16 sbuv8_n16 0.0 0 0
sbuvbufr sbuv2 n17 sbuv8_n17 0.0 0 0
sbuvbufr sbuv2 n18 sbuv8_n18 0.0 0 0
sbuvbufr sbuv2 n19 sbuv8_n19 0.0 0 0
hirs2bufr hirs2 n11 hirs2_n11 0.0 1 1
hirs2bufr hirs2 n14 hirs2_n14 0.0 1 1
hirs3bufr hirs3 n15 hirs3_n15 0.0 1 1
hirs3bufr hirs3 n16 hirs3_n16 0.0 1 1
hirs3bufr hirs3 n17 hirs3_n17 0.0 1 1
hirs4bufr hirs4 metop-a hirs4_metop-a 0.0 1 1
gimgrbufr goes_img g11 imgr_g11 0.0 1 0
gimgrbufr goes_img g12 imgr_g12 0.0 1 0
airsbufr airs aqua airs281SUBSET_aqua 0.0 1 1
msubufr msu n11 msu_n11 0.0 1 1
msubufr msu n14 msu_n14 0.0 1 1
ssubufr ssu n14 ssu_n14 0.0 1 1
amsuabufr amsua n15 amsua_n15 0.0 1 1
amsuabufr amsua n16 amsua_n16 0.0 1 1
amsuabufr amsua n17 amsua_n17 0.0 1 1
amsuabufr amsua n18 amsua_n18 0.0 1 1
amsuabufr amsua metop-a amsua_metop-a 0.0 1 1
airsbufr amsua aqua amsua_aqua 0.0 1 1
amsubbufr amsub n15 amsub_n15 0.0 1 1
amsubbufr amsub n16 amsub_n16 0.0 1 1
amsubbufr amsub n17 amsub_n17 0.0 1 1
mhsbufr mhs n18 mhs_n18 0.0 1 1
mhsbufr mhs metop-a mhs_metop-a 0.0 1 1
ssmitbufr ssmi f14 ssmi_f14 0.0 1 0
ssmitbufr ssmi f15 ssmi_f15 0.0 1 0
amsrebufr amsre_low aqua amsre_aqua 0.0 1 0
amsrebufr amsre_mid aqua amsre_aqua 0.0 1 0
amsrebufr amsre_hig aqua amsre_aqua 0.0 1 0
ssmisbufr ssmis f16 ssmis_f16 0.0 1 0
gsnd1bufr sndr g08 sndr_g08 0.0 1 0
gsnd1bufr sndr g09 sndr_g09 0.0 1 0
gsnd1bufr sndr g10 sndr_g10 0.0 1 0
gsnd1bufr sndr g11 sndr_g11 0.0 1 0
gsnd1bufr sndr g12 sndr_g12 0.0 1 0
gsnd1bufr sndrd1 g12 sndrD1_g12 0.0 1 0
gsnd1bufr sndrd2 g12 sndrD2_g12 0.0 1 0
gsnd1bufr sndrd3 g12 sndrD3_g12 0.0 1 0
gsnd1bufr sndrd4 g12 sndrD4_g12 0.0 1 0
gsnd1bufr sndrd1 g11 sndrD1_g11 0.0 1 0
gsnd1bufr sndrd2 g11 sndrD2_g11 0.0 1 0
gsnd1bufr sndrd3 g11 sndrD3_g11 0.0 1 0
gsnd1bufr sndrd4 g11 sndrD4_g11 0.0 1 0
gsnd1bufr sndrd1 g13 sndrD1_g13 0.0 1 0
gsnd1bufr sndrd2 g13 sndrD2_g13 0.0 1 0
gsnd1bufr sndrd3 g13 sndrD3_g13 0.0 1 0
gsnd1bufr sndrd4 g13 sndrD4_g13 0.0 1 0
iasibufr iasi metop-a iasi616_metop-a 0.0 1 1
gomebufr gome metop-a gome_metop-a 0.0 2 0
omibufr omi aura omi_aura 0.0 2 0
hirs4bufr hirs4 n18 hirs4_n18 0.0 1 1
hirs4bufr hirs4 n19 hirs4_n19 0.0 1 1
amsuabufr amsua n19 amsua_n19 0.0 1 1
mhsbufr mhs n19 mhs_n19 0.0 1 1
tcvitl tcp null tcp 0.0 0 0
seviribufr seviri m08 seviri_m08 0.0 1 0
seviribufr seviri m09 seviri_m09 0.0 1 0
seviribufr seviri m10 seviri_m10 0.0 1 0
hirs4bufr hirs4 metop-b hirs4_metop-b 0.0 1 0
amsuabufr amsua metop-b amsua_metop-b 0.0 1 0
mhsbufr mhs metop-b mhs_metop-b 0.0 1 0
iasibufr iasi metop-b iasi616_metop-b 0.0 1 0
gomebufr gome metop-b gome_metop-b 0.0 2 0
atmsbufr atms npp atms_npp 0.0 1 0
crisbufr cris npp cris_npp 0.0 1 0
avhambufr avhrr n15 avhrr3_n15 0.0 1 0
avhambufr avhrr n17 avhrr3_n17 0.0 1 0
avhambufr avhrr metop-a avhrr3_metop-a 0.0 1 0
avhpmbufr avhrr n16 avhrr3_n16 0.0 1 0
avhpmbufr avhrr n18 avhrr3_n18 0.0 1 0
::
$OBSINPUT
/
&SUPEROB_RADAR
$SUPERRAD
/
&LAG_DATA
$LAGDATA
/
&HYBRID_ENSEMBLE
$HYBRIDENSDATA
/
&RAPIDREFRESH_CLDSURF
dfi_radar_latent_heat_time_period=30.0,
$RAPIDREFRESH_CLDSURF
/
&CHEM
$CHEM
/
&SINGLEOB_TEST
maginnov=0.1,magoberr=0.1,oneob_type='t',
oblat=45.,oblon=180.,obpres=1000.,obdattim=${CDATE},
obhourset=0.,
$SINGLEOB
/
&NST
nst_gsi=$NST_GSI,
$NST
/
EOF
# Set fixed files
# berror = forecast model background error statistics
# specoef = CRTM spectral coefficients
# trncoef = CRTM transmittance coefficients
# emiscoef = CRTM coefficients for IR sea surface emissivity model
# aerocoef = CRTM coefficients for aerosol effects
# cldcoef = CRTM coefficients for cloud effects
# satinfo = text file with information about assimilation of brightness temperatures
# satangl = angle dependent bias correction file (fixed in time)
# pcpinfo = text file with information about assimilation of prepcipitation rates
# ozinfo = text file with information about assimilation of ozone data
# errtable = text file with obs error for conventional data (optional)
# convinfo = text file with information about assimilation of conventional data
# bufrtable= text file ONLY needed for single obs test (oneobstest=.true.)
# bftab_sst= bufr table for sst ONLY needed for sst retrieval (retrieval=.true.)
berror=$fixgsi/Big_Endian/global_berror.l${LEVS}y${NLAT}.f77
# temporary fix until jeff moved this file into the master location
#if [ $JCAP -eq 1152 ]; then
# berror=/lfs1/projects/gfsenkf/fix/global_berror.l64y1154.f77
#fi
#emiscoef_IRwater=$fixcrtm/EmisCoeff/IR_Water/Big_Endian/Nalli.IRwater.EmisCoeff.bin
#emiscoef_IRice=$fixcrtm/EmisCoeff/IR_Ice/SEcategory/Big_Endian/NPOESS.IRice.EmisCoeff.bin
#emiscoef_IRland=$fixcrtm/EmisCoeff/IR_Land/SEcategory/Big_Endian/NPOESS.IRland.EmisCoeff.bin
#emiscoef_IRsnow=$fixcrtm/EmisCoeff/IR_Snow/SEcategory/Big_Endian/NPOESS.IRsnow.EmisCoeff.bin
#emiscoef_VISice=$fixcrtm/EmisCoeff/VIS_Ice/SEcategory/Big_Endian/NPOESS.VISice.EmisCoeff.bin
#emiscoef_VISland=$fixcrtm/EmisCoeff/VIS_Land/SEcategory/Big_Endian/NPOESS.VISland.EmisCoeff.bin
#emiscoef_VISsnow=$fixcrtm/EmisCoeff/VIS_Snow/SEcategory/Big_Endian/NPOESS.VISsnow.EmisCoeff.bin
#emiscoef_VISwater=$fixcrtm/EmisCoeff/VIS_Water/SEcategory/Big_Endian/NPOESS.VISwater.EmisCoeff.bin
#emiscoef_MWwater=$fixcrtm/EmisCoeff/MW_Water/Big_Endian/FASTEM6.MWwater.EmisCoeff.bin
emiscoef_IRwater=$fixcrtm/Nalli.IRwater.EmisCoeff.bin
emiscoef_IRice=$fixcrtm/NPOESS.IRice.EmisCoeff.bin
emiscoef_IRland=$fixcrtm/NPOESS.IRland.EmisCoeff.bin
emiscoef_IRsnow=$fixcrtm/NPOESS.IRsnow.EmisCoeff.bin
emiscoef_VISice=$fixcrtm/NPOESS.VISice.EmisCoeff.bin
emiscoef_VISland=$fixcrtm/NPOESS.VISland.EmisCoeff.bin
emiscoef_VISsnow=$fixcrtm/NPOESS.VISsnow.EmisCoeff.bin
emiscoef_VISwater=$fixcrtm/NPOESS.VISwater.EmisCoeff.bin
emiscoef_MWwater=$fixcrtm/FASTEM6.MWwater.EmisCoeff.bin
aercoef=$fixcrtm/AerosolCoeff.bin
cldcoef=$fixcrtm/CloudCoeff.bin
satinfo=${SATINFO:-$fixgsi/global_satinfo.txt}
atmsfilter=${ATMSFILTER:-$fixgsi/atms_beamwidth.txt}
scaninfo=$fixgsi/global_scaninfo.txt
satangl=$fixgsi/global_satangbias.txt
pcpinfo=$fixgsi/global_pcpinfo.txt
ozinfo=${OZINFO:-$fixgsi/global_ozinfo.txt}
convinfo=${CONVINFO:-$fixgsi/global_convinfo.txt}
errtable=$fixgsi/prepobs_errtable.global
anavinfo=${ANAVINFO:-$fixgsi/global_anavinfo.l64.txt}
radcloudinfo=${RADCLOUDINFO:-${fixgsi}/cloudy_radiance_info.txt}
# Only need this file for single obs test
bufrtable=$fixgsi/prepobs_prep.bufrtable
# Only need this file for sst retrieval
bftab_sst=$fixgsi/bufrtab.012
# Copy executable and fixed files to $tmpdir
if [[ "$lread_obs_skip" = ".false." ]]; then
$nln $gsiexec ./gsi.x
$ncp $anavinfo ./anavinfo
$ncp $radcloudinfo ./cloudy_radiance_info.txt
$nln $berror ./berror_stats
$ncp $emiscoef_IRwater ./Nalli.IRwater.EmisCoeff.bin
$ncp $emiscoef_IRice ./NPOESS.IRice.EmisCoeff.bin
$ncp $emiscoef_IRsnow ./NPOESS.IRsnow.EmisCoeff.bin
$ncp $emiscoef_IRland ./NPOESS.IRland.EmisCoeff.bin
$ncp $emiscoef_VISice ./NPOESS.VISice.EmisCoeff.bin
$ncp $emiscoef_VISland ./NPOESS.VISland.EmisCoeff.bin
$ncp $emiscoef_VISsnow ./NPOESS.VISsnow.EmisCoeff.bin
$ncp $emiscoef_VISwater ./NPOESS.VISwater.EmisCoeff.bin
$ncp $emiscoef_MWwater ./FASTEM6.MWwater.EmisCoeff.bin
$nln $aercoef ./AerosolCoeff.bin
$nln $cldcoef ./CloudCoeff.bin
$nln $satangl ./satbias_angle
$nln $satinfo ./satinfo
$nln $atmsfilter ./atms_beamwidth.txt
$nln $scaninfo ./scaninfo
$nln $pcpinfo ./pcpinfo
$nln $ozinfo ./ozinfo
$nln $convinfo ./convinfo
$nln $errtable ./errtable
$nln $bufrtable ./prepobs_prep.bufrtable
$nln $bftab_sst ./bftab_sstphr
GBIAS=${GBIAS:-$datgesm1/${prefix_tbc}.abias}
GBIAS_PC=${GBIAS_PC:-$datgesm1/${prefix_tbc}.abias_pc}
GBIASAIR=${GBIASAIR:-$datgesm1/${prefix_tbc}.abias_air}
GSATANG=${GSATANG:-$datgesm1/${prefix_tbc}.satang}
#coeffiles=`ls -1 ${fixcrtm}/SpcCoeff/Big_Endian/*.SpcCoeff.bin`
#for coeffile in $coeffiles; do
#for coeffile in ${fixcrtm}/SpcCoeff/Big_Endian/*.SpcCoeff.bin; do
for coeffile in ${fixcrtm}/*.SpcCoeff.bin; do
satsen=`basename $coeffile .SpcCoeff.bin`
count=`grep -c $satsen $satinfo`
if [[ $count -gt 0 ]]; then
spccoeff=${satsen}.SpcCoeff.bin
#if [[ -s $fixcrtm/SpcCoeff/Big_Endian/$spccoeff ]]; then
# #$nln $fixcrtm/SpcCoeff/Big_Endian/$spccoeff ./
if [[ -s $fixcrtm/$spccoeff ]]; then
$nln $fixcrtm/$spccoeff ./
fi
taucoeff=${satsen}.TauCoeff.bin
#if [[ -s $fixcrtm/TauCoeff/Big_Endian/$taucoeff ]]; then
#$nln $fixcrtm/TauCoeff/Big_Endian/$taucoeff ./
if [[ -s $fixcrtm/$taucoeff ]]; then
$nln $fixcrtm/$taucoeff ./
fi
fi
done
#ls -l *bin
# Copy observational data to $tmpdir
if [[ ! -s $datobs/${prefix_obs}.prepbufr ]]; then
echo "no prepbufr file!"
exit 1
fi
if [[ "$NOCONV" = "NO" ]]; then
$nln $datobs/${prefix_obs}.prepbufr ./prepbufr
if [[ -s $datobs/${prefix_obs}.nsstbufr ]]; then
$nln ${datobs}/${prefix_obs}.nsstbufr ./nsstbufr
fi
if [[ -s $datobs/${prefix_obs}.prepbufr.acft_profiles ]]; then
$nln $datobs/${prefix_obs}.prepbufr.acft_profiles ./prepbufr_profl
fi
if [[ -s $datobs/${prefix_obs}.syndata.tcvitals.tm00 ]]; then
$nln $datobs/${prefix_obs}.syndata.tcvitals.tm00 ./tcvitl
fi
if [[ -s $datobs/${prefix_obs}.gpsro.${suffix} ]]; then
$nln $datobs/${prefix_obs}.gpsro.${suffix} ./gpsrobufr
fi
if [[ -s $datobs/${prefix_obs}.satwnd.${suffix} ]]; then
$nln $datobs/${prefix_obs}.satwnd.${suffix} ./satwndbufr
fi
fi
if [[ "$NOSAT" = "NO" ]]; then
if [[ "$NOCONV" = "NO" ]]; then
if [[ -s $datobs/${prefix_obs}.osbuv8.${suffix} ]]; then
$nln $datobs/${prefix_obs}.osbuv8.${suffix} ./sbuvbufr
fi
fi
if [[ -s $datobs/${prefix_obs}.1bamua.${suffix} ]]; then
$nln $datobs/${prefix_obs}.1bamua.${suffix} ./amsuabufr
fi
if [[ -s $datobs/${prefix_obs}.1bmsu.${suffix} ]]; then
$nln $datobs/${prefix_obs}.1bmsu.${suffix} ./msubufr
fi
if [[ -s $datobs/${prefix_obs}.1bssu.${suffix} ]]; then
$nln $datobs/${prefix_obs}.1bssu.${suffix} ./ssubufr
fi
if [[ -s $datobs/${prefix_obs}.1bmhs.${suffix} ]]; then
$nln $datobs/${prefix_obs}.1bmhs.${suffix} ./mhsbufr
fi
if [[ -s $datobs/${prefix_obs}.esamua.${suffix} ]]; then
$nln $datobs/${prefix_obs}.esamua.${suffix} ./amsuabufrears
fi
if [[ -s $datobs/${prefix_obs}.atms.${suffix} ]]; then
$nln $datobs/${prefix_obs}.atms.${suffix} ./atmsbufr
fi
if [[ -s $datobs/${prefix_obs}.goesnd.${suffix} ]]; then
$nln $datobs/${prefix_obs}.goesnd.${suffix} ./gsnd1bufr
fi
if [[ -s $datobs/${prefix_obs}.goesnd.${suffix} ]]; then
$nln $datobs/${prefix_obs}.geoimr.${suffix} ./gimgrbufr
fi
if [[ -s $datobs/${prefix_obs}.1bamub.${suffix} ]]; then
$nln $datobs/${prefix_obs}.1bamub.${suffix} ./amsubbufr
fi
if [[ -s $datobs/${prefix_obs}.1bhrs2.${suffix} ]]; then
$nln $datobs/${prefix_obs}.1bhrs2.${suffix} ./hirs2bufr
fi
if [[ -s $datobs/${prefix_obs}.1bhrs3.${suffix} ]]; then
$nln $datobs/${prefix_obs}.1bhrs3.${suffix} ./hirs3bufr
fi
if [[ -s $datobs/${prefix_obs}.1bhrs4.${suffix} ]]; then
$nln $datobs/${prefix_obs}.1bhrs4.${suffix} ./hirs4bufr
fi
if [[ -s $datobs/${prefix_obs}.airsev.${suffix} ]]; then
$nln $datobs/${prefix_obs}.airsev.${suffix} ./airsbufr
fi
if [[ -s $datobs/${prefix_obs}.mtiasi.${suffix} ]]; then
$nln $datobs/${prefix_obs}.mtiasi.${suffix} ./iasibufr
fi
if [[ -s $datobs/${prefix_obs}.ssmit.${suffix} ]]; then
$nln $datobs/${prefix_obs}.ssmit.${suffix} ./ssmitbufr
fi
if [[ -s $datobs/${prefix_obs}.amsre.${suffix} ]]; then
$nln $datobs/${prefix_obs}.amsre.${suffix} ./amsrebufr
fi
if [[ -s $datobs/${prefix_obs}.ssmis.${suffix} ]]; then
$nln $datobs/${prefix_obs}.ssmis.${suffix} ./ssmisbufr
fi
if [[ -s $datobs/${prefix_obs}.ssmit.${suffix} ]]; then
$nln $datobs/${prefix_obs}.ssmit.${suffix} ./ssmitbufr
fi
if [[ -s $datobs/${prefix_obs}.eshrs3.${suffix} ]]; then
$nln $datobs/${prefix_obs}.eshrs3.${suffix} ./hirs3bufrears
fi
if [[ -s $datobs/${prefix_obs}.esamub.${suffix} ]]; then
$nln $datobs/${prefix_obs}.esamub.${suffix} ./amsubbufrears
fi
if [[ -s $datobs/${prefix_obs}.eshrs3.${suffix} ]]; then
$nln $datobs/${prefix_obs}.eshrs3.${suffix} ./hirs3bufrears
fi
if [[ -s $datobs/${prefix_obs}.gome.${suffix} ]]; then
$nln $datobs/${prefix_obs}.gome.${suffix} ./gomebufr
fi
if [[ -s $datobs/${prefix_obs}.omi.${suffix} ]]; then
$nln $datobs/${prefix_obs}.omi.${suffix} ./omibufr
fi
if [[ -s $datobs/${prefix_obs}.sevcsr.${suffix} ]]; then
$nln $datobs/${prefix_obs}.sevcsr.${suffix} ./seviribufr
fi
if [[ -s $datobs/${prefix_obs}.cris.${suffix} ]]; then
$nln $datobs/${prefix_obs}.cris.${suffix} ./crisbufr
fi
if [[ -s $datobs/${prefix_obs}.spssmi.${suffix} ]]; then
$nln $datobs/${prefix_obs}.spssmi.${suffix} ./ssmirrbufr
fi
if [[ -s $datobs/${prefix_obs}.sptrmm.${suffix} ]]; then
$nln $datobs/${prefix_obs}.sptrmm.${suffix} ./tmirrbufr
fi
if [[ -s $datobs/${prefix_obs}.avcsam.${suffix} ]]; then
$nln $datobs/${prefix_obs}.avcsam.${suffix} avhambufr
fi
if [[ -s $datobs/${prefix_obs}.avcspm.${suffix} ]]; then
$nln $datobs/${prefix_obs}.avcspm.${suffix} avhpmbufr
fi
fi # NOSAT
# link bias correction, atmospheric and surface files
$nln $GBIAS ./satbias_in
$nln $GBIAS_PC ./satbias_pc
$nln $GSATANG ./satbias_angle
$nln $GBIASAIR ./aircftbias_in
SFCG03=${SFCG03:-$datges/bfg_${adate}_fhr03_${charnanal}}
$nln $SFCG03 ./sfcf03
SFCG06=${SFCG06:-$datges/bfg_${adate}_fhr06_${charnanal}}
$nln $SFCG06 ./sfcf06
SFCG09=${SFCG09:-$datges/bfg_${adate}_fhr09_${charnanal}}
$nln $SFCG09 ./sfcf09
SIGG03=${SIGG03:-$datges/sfg_${adate}_fhr03_${charnanal}}
$nln $SIGG03 ./sigf03
SIGG06=${SIGG06:-$datges/sfg_${adate}_fhr06_${charnanal}}
$nln $SIGG06 ./sigf06
SIGG09=${SIGG09:-$datges/sfg_${adate}_fhr09_${charnanal}}
$nln $SIGG09 ./sigf09
if [[ "$HRLY_BKG" = "YES" ]]; then
SFCG04=${SFCG04:-$datges/bfg_${adate}_fhr04_${charnanal}}
$nln $SFCG04 ./sfcf04
SFCG05=${SFCG05:-$datges/bfg_${adate}_fhr05_${charnanal}}
$nln $SFCG05 ./sfcf05
SFCG07=${SFCG07:-$datges/bfg_${adate}_fhr07_${charnanal}}
$nln $SFCG07 ./sfcf07
SFCG08=${SFCG08:-$datges/bfg_${adate}_fhr08_${charnanal}}
$nln $SFCG08 ./sfcf08
SIGG04=${SIGG04:-$datges/sfg_${adate}_fhr04_${charnanal}}
$nln $SIGG04 ./sigf04
SIGG05=${SIGG05:-$datges/sfg_${adate}_fhr05_${charnanal}}
$nln $SIGG05 ./sigf05
SIGG07=${SIGG07:-$datges/sfg_${adate}_fhr07_${charnanal}}
$nln $SIGG07 ./sigf07
SIGG08=${SIGG08:-$datges/sfg_${adate}_fhr08_${charnanal}}
$nln $SIGG08 ./sigf08
fi
if [[ $beta1_inv < 0.999 ]]; then
ln -s $datges/ensmem*.pe* .
ln -s $datges/control*.pe* .
fh=3
while [ $fh -le 9 ] ;do
for ensfile in $datges/sfg_${adate}*fhr0${fh}*mem???; do
ensfilename=`basename $ensfile`
memnum=`echo $ensfilename | cut -f4 -d"_" | cut -c4-6`
$nln $ensfile ./sigf0${fh}_ens_mem${memnum}
done
((fh+=$FHOUT))
done
fi
fi
# make symlinks for diag files to initialize angle dependent bias correction for new channels.
satdiag="ssu_n14 hirs2_n14 msu_n14 sndr_g08 sndr_g09 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 sndrd1_g14 sndrd2_g14 sndrd3_g14 sndrd4_g14 sndrd1_g15 sndrd2_g15 sndrd3_g15 sndrd4_g15 hirs2_n14 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 imgr_g14 imgr_g15 gome_metop-a omi_aura mls_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 ssmis_las_f17 ssmis_uas_f17 ssmis_img_f17 ssmis_env_f17 ssmis_las_f18 ssmis_uas_f18 ssmis_img_f18 ssmis_env_f18 ssmis_las_f19 ssmis_uas_f19 ssmis_img_f19 ssmis_env_f19 ssmis_las_f20 ssmis_uas_f20 ssmis_img_f20 ssmis_env_f20 iasi_metop-a hirs4_n19 amsua_n19 mhs_n19 seviri_m08 seviri_m09 seviri_m10 cris_npp atms_npp hirs4_metop-b amsua_metop-b mhs_metop-b iasi_metop-b gome_metop-b avhrr_n18 avhrr_metop-a avhrr_n15 avhrr_n16 avhrr_n17"
alldiag="$satdiag pcp_ssmi_dmsp pcp_tmi_trmm conv_tcp conv_gps conv_t conv_q conv_uv conv_ps sbuv2_n11 sbuv2_n14 sbuv2_n16 sbuv2_n17 sbuv2_n18 sbuv2_n19"
string='ges'
for type in $satdiag; do
if [[ "$cold_start_bias" = "true" ]]; then
if [ -s $datges/diag_${type}_${string}.${adate}_${charnanal2}.nc4 ]; then
ln -fs $datges/diag_${type}_${string}.${adate}_${charnanal2}.nc4 diag_${type}.nc4
fi
else
if [ -s $datgesm1/diag_${type}_${string}.${adatem1}_${charnanal2}.nc4 ]; then
ln -fs $datgesm1/diag_${type}_${string}.${adatem1}_${charnanal2}.nc4 diag_${type}.nc4
fi
fi
done
# Run gsi.
#if [ -s ./satbias_in ] && [ -s ./satbias_angle ] && [ -s ./sfcf03 ] && [ -s ./sfcf06 ] && [ -s ./sfcf09 ] && [ -s ./sigf03 ] && [ -s ./sigf06 ] && [ -s ./sigf09 ] ; then
if [[ $NOSAT == "YES" || -s ./satbias_in ]] && [ -s ./sfcf03 ] && [ -s ./sfcf06 ] && [ -s ./sfcf09 ] && [ -s ./sigf03 ] && [ -s ./sigf06 ] && [ -s ./sigf09 ] ; then
cat gsiparm.anl
ulimit -s unlimited
pwd
ls -l
echo "Time before GSI `date` "
export PGM=$tmpdir/gsi.x
export FORT_BUFFERED=TRUE
sh ${scriptsdir}/runmpi
rc=$?
if [[ $rc -ne 0 ]];then
echo "GSI failed with exit code $rc"
exit $rc
fi
else
echo "some input files missing, exiting ..."
ls -l ./satbias_in
ls -l ./satbias_angle
ls -l ./sfcf03
ls -l ./sfcf06
ls -l ./sfcf09
ls -l ./sfcanl
ls -l ./sigf03
ls -l ./sigf06
ls -l ./sigf09
exit 1
fi
# Save output
mkdir -p $savdir
cat fort.2* > $savdir/gsistats.${adate}_${charnanal2}
#ls -l
if [[ "$HXONLY" = "NO" ]]; then
if [ -s ./siganl ] && [ -s ./satbias_out ]; then
if [ -s ./siga03 ]; then
$nmv siga03 $SIGANL03
fi
if [ -s ./siga04 ]; then
$nmv siga04 $SIGANL04
fi
if [ -s ./siga05 ]; then
$nmv siga05 $SIGANL05
fi
$nmv siganl $SIGANL06
if [ -s ./siga07 ]; then
$nmv siga07 $SIGANL07
fi
if [ -s ./siga08 ]; then
$nmv siga08 $SIGANL08
fi
if [ -s ./siga09 ]; then
$nmv siga09 $SIGANL09
fi
$nmv satbias_out $BIASO
$nmv satbias_pc.out $BIASO_PC
if [ -s aircftbias_out ]; then
$nmv aircftbias_out $BIASOAIR
fi
if [ $DONST = "YES" ]; then
$nmv dtfanl $DTFANL
fi
else
exit 1
fi
fi
# Loop over first and last outer loops to generate innovation
# diagnostic files for indicated observation types (groups)
#
# NOTE: Since we set miter=2 in GSI namelist SETUP, outer
# loop 03 will contain innovations with respect to
# the analysis. Creation of o-a innovation files
# is triggered by write_diag(3)=.true. The setting
# write_diag(1)=.true. turns on creation of o-g
# innovation files.
#
if [[ "$skipcat" = "false" ]]; then
echo "Time before diagnostic loop is `date` "
if [[ "$HXONLY" = "YES" ]]; then
loops="01"
else
loops="01 03"
fi
#corecount=0
## number of MPI tasks for each nc_diat_cat.x
## must be a divisor of total number of cores
#jobspernode=4
#export nprocs=`expr $corespernode \/ $jobspernode`
#export OMP_NUM_THREADS=1 # keep at 1
#if [ "$machine" == 'theia' ]; then
# HOSTFILE_FULL=$PBS_NODEFILE
#fi
#for loop in $loops; do
#
# case $loop in
# 01) string=ges;;
# 03) string=anl;;
# *) string=$loop;;
# esac
#
# # Collect diagnostic files for obs types (groups) below
# for type in $alldiag; do
# count=`ls pe*${type}_${loop}* | wc -l`
# if [[ $count -gt 0 ]]; then
# export PGM="${execdir}/nc_diag_cat.x -o ${savdir}/diag_${type}_${string}.${adate}_${charnanal2}.nc4 pe*${type}_${loop}*nc4"
# if [ "$machine" == 'theia' ]; then
# export HOSTFILE=hostfile_${corecount}
# /bin/rm -f $HOSTFILE
# n=1
# while [ $n -le $nprocs ]; do
# nn=$((n+$corecount))
# core=`head -$nn $HOSTFILE_FULL | tail -1`
# echo $core >> $HOSTFILE
# n=$((n+1))
# done
# echo "contents of hostfile_${corecount}..."
# cat $HOSTFILE
# fi
# corecount=$((corecount+$nprocs))
# sh ${scriptsdir}/runmpi 1> nc_diag_cat_${type}_${string}.out 2> nc_diag_cat_${type}_${string}.out &
# if [ $corecount -eq $cores ]; then
# echo "waiting... corecount=$corecount"
# wait
# corecount=0
# fi
# fi
# done
#
#done
# run each nc_diag_cat on a separate node, concurrently
nodecount=0
export nprocs=$corespernode
export mpitaskspernode=$nprocs
export OMP_NUM_THREADS=1
totnodes=$NODES
for loop in $loops; do
case $loop in
01) string=ges;;
03) string=anl;;
*) string=$loop;;
esac
# Collect diagnostic files for obs types (groups) below
for type in $alldiag; do
count=`ls pe*${type}_${loop}* | wc -l`
if [[ $count -gt 0 ]]; then
if [[ $count -eq 1 ]]; then
# just one file, no cat needed (just copy it)
file=`ls -1 pe*${type}_${loop}*`
/bin/cp -f $file ${savdir}/diag_${type}_${string}.${adate}_${charnanal2}.nc4
else
export PGM="${execdir}/nc_diag_cat.x -o ${savdir}/diag_${type}_${string}.${adate}_${charnanal2}.nc4 pe*${type}_${loop}*nc4"
ls -l pe*${type}_${loop}*nc4
nodecount=$((nodecount+1))
if [ ! -z $SLURM_JOB_ID ] && [ "$machine" == 'theia' ]; then
node=`head -$nodecount $NODEFILE | tail -1`
export HOSTFILE=hostfile_${nodecount}
/bin/rm -f $HOSTFILE
n=1
while [ $n -le $nprocs ]; do
echo $node >> $HOSTFILE
n=$((n+1))
done
echo "contents of hostfile_${nodecount}..."
cat $HOSTFILE
fi
sh ${scriptsdir}/runmpi 1> ${current_logdir}/nc_diag_cat_${type}_${string}_${charnanal2}.out 2> ${current_logdir}/nc_diag_cat_${type}_${string}_${charnanal2}.err &
#sh ${scriptsdir}/runmpi 1> nc_diag_cat_${type}_${string}.out &
if [ $nodecount -eq $totnodes ]; then
echo "waiting... nodecount=$nodecount"
wait
nodecount=0
fi
fi
fi
done