From f3be948bea7405608236e4d4b961e344767c2487 Mon Sep 17 00:00:00 2001 From: Ricardo Todling Date: Fri, 4 Sep 2026 11:45:32 -0400 Subject: [PATCH] Forgot to upd geopotential var names in some yaml files --- .../GEOSdas_App/jedi/etc/convertana_geos.yaml | 4 ++-- .../GEOSdas_App/jedi/etc/diffstates_geos.yaml | 10 ++++++++-- src/Applications/GEOSdas_App/jedi/jedi_run.csh | 14 +++++++++++++- src/Applications/GEOSdas_App/jedi/jedi_set.csh | 4 ++-- .../GEOSdas_App/jedi/jedi_upd4geos.csh | 12 ++++++++++-- 5 files changed, 35 insertions(+), 9 deletions(-) diff --git a/src/Applications/GEOSdas_App/jedi/etc/convertana_geos.yaml b/src/Applications/GEOSdas_App/jedi/etc/convertana_geos.yaml index 29a96b20..f4aae8cc 100644 --- a/src/Applications/GEOSdas_App/jedi/etc/convertana_geos.yaml +++ b/src/Applications/GEOSdas_App/jedi/etc/convertana_geos.yaml @@ -33,7 +33,7 @@ states: - rain_water - snow_water - mole_fraction_of_ozone_in_air - - geopotential_height_times_gravity_at_surface + - geopotential_at_surface - initial_mass_fraction_of_large_scale_cloud_condensate - initial_mass_fraction_of_convective_cloud_condensate - convective_cloud_area_fraction @@ -72,7 +72,7 @@ states: rain_water: qr snow_water: qs mole_fraction_of_ozone_in_air: o3ppmv - geopotential_height_times_gravity_at_surface: phis + geopotential_at_surface: phis initial_mass_fraction_of_large_scale_cloud_condensate: qls initial_mass_fraction_of_convective_cloud_condensate: qcn convective_cloud_area_fraction: cfcn diff --git a/src/Applications/GEOSdas_App/jedi/etc/diffstates_geos.yaml b/src/Applications/GEOSdas_App/jedi/etc/diffstates_geos.yaml index 568a8985..d7007131 100644 --- a/src/Applications/GEOSdas_App/jedi/etc/diffstates_geos.yaml +++ b/src/Applications/GEOSdas_App/jedi/etc/diffstates_geos.yaml @@ -35,9 +35,12 @@ state1: - rain_water - snow_water - mole_fraction_of_ozone_in_air - - geopotential_height_times_gravity_at_surface + - geopotential_at_surface - air_pressure_levels - air_pressure_at_surface + - fraction_of_ocean + - fraction_of_lake + - fraction_of_ice - skin_temperature_at_surface field io names: &field_io_names eastward_wind: ua @@ -49,9 +52,12 @@ state1: rain_water: qr snow_water: qs mole_fraction_of_ozone_in_air: o3ppmv - geopotential_height_times_gravity_at_surface: phis + geopotential_at_surface: phis air_pressure_levels: pe air_pressure_at_surface: ps + fraction_of_ocean: frocean + fraction_of_lake: frlake + fraction_of_ice: frseaice skin_temperature_at_surface: ts state2: datetime: $ISO_STATES_DATE diff --git a/src/Applications/GEOSdas_App/jedi/jedi_run.csh b/src/Applications/GEOSdas_App/jedi/jedi_run.csh index f1d10af1..89600d1c 100755 --- a/src/Applications/GEOSdas_App/jedi/jedi_run.csh +++ b/src/Applications/GEOSdas_App/jedi/jedi_run.csh @@ -73,6 +73,7 @@ set mmb = `echo $nymdb | cut -c5-6` set ddb = `echo $nymdb | cut -c7-8` set hhb = `echo $nhmsb | cut -c1-2` set yyyymmddhh = ${nymdb}${hhb} +setenv BYYYYYMMDDTHH0000Z ${nymdb}T${hhb}0000Z set anadate = `tick $nymdb $nhmsb $JEDI_VAROFFSET` set nymda = $anadate[1] @@ -209,6 +210,11 @@ if ( ! -e $FVWORK/.DONE_jedi_run_ana.csh.$yyyymmddhh) then endif endif endif + set ichk = `grep NaN $FVWORK/$JEDIVARLOG | wc` + if ( $ichk[1] > 0 ) then + echo " ${MYNAME}: NaNs found in JEDI, failed in VAR, aborting ..." + exit (1) + endif set lstinc = `ls *inc*nc4` if ( ! $status ) /bin/mv *inc*nc4 ./inc # somehow datapath setting in yaml is not effective at inc part endif @@ -346,7 +352,13 @@ cd - # ------------- touch $JEDIETC/VBC.BOOTSTRAP.DONE cd $JEDIWRK/vbc -tar cvf $FVWORK/$EXPID.jedi_vbc.${nymdb}_${hhb}z.tar *satbias*nc4 *aircraft*csv +/bin/cp $JEDIWRK/obs/*tlapse.txt . +foreach fn (`ls *tlapse.txt`) + set pfx = `echo $fn | cut -d. -f1` + /bin/mv $fn $pfx.$BYYYYYMMDDTHH0000Z.tlapse.txt # time tag as current as + # if JEDI output these +end +tar cvf $FVWORK/$EXPID.jedi_vbc.${nymdb}_${hhb}z.tar *satbias*nc4 *aircraft*csv *.txt cd - # If here, likely successful diff --git a/src/Applications/GEOSdas_App/jedi/jedi_set.csh b/src/Applications/GEOSdas_App/jedi/jedi_set.csh index 5a4ed910..b1aebac6 100755 --- a/src/Applications/GEOSdas_App/jedi/jedi_set.csh +++ b/src/Applications/GEOSdas_App/jedi/jedi_set.csh @@ -183,8 +183,8 @@ end # If so, retrieve IODA files from existig ru # In adjoint case, IODA files are from same exp if ( $JEDI_RUN_ANASA || $JEDI_RUN_ADANA || $JEDI_OBS_OPT == 1 ) then - setenv NYMDB $nymdb # initial date of current cycle - setenv NHMSB $nhmsb # initial time of current cycle + setenv NYMD $nymdb # initial date of current cycle + setenv NHMS $nhmsb # initial time of current cycle setenv ACQWORK $FVWORK vED -env $FVHOME/run/jedi/jedi_acquire_ioda.j -o jedi_acquire_ioda.j if ( $BATCH_SUBCMD == "sbatch" ) then diff --git a/src/Applications/GEOSdas_App/jedi/jedi_upd4geos.csh b/src/Applications/GEOSdas_App/jedi/jedi_upd4geos.csh index dc8f49b6..e31a8207 100755 --- a/src/Applications/GEOSdas_App/jedi/jedi_upd4geos.csh +++ b/src/Applications/GEOSdas_App/jedi/jedi_upd4geos.csh @@ -42,7 +42,15 @@ if ( -d $JEDIWORK/iau ) then cd $FVWORK # set cost = `grep "cost type" $JEDIWORK/Config/geosvar.yaml | cut -d: -f2 | cut -d- -f1` # if ( $cost == "3D" ) then - foreach fn ( `ls $JEDIWORK/iau/*.agcm_import_rst.*nc4` ) + set alliau = `ls $JEDIWORK/iau/*.agcm_import_rst.*nc4` + if ($status) then + echo " ${MYNAME}: JEDI IAU increments not found, no overwrite taken place. " + if ( $JEDI_IAU_OVERWRITE ) then + echo " ${MYNAME}: Aborting(1) ..." + exit (1) + endif + endif + foreach fn ( $alliau ) set bname = `basename $fn` set noexpid = `echo $bname | cut -d. -f2-` echo /bin/ln -sf $fn $noexpid @@ -66,7 +74,7 @@ if ( -d $JEDIWORK/iau ) then else echo " ${MYNAME}: JEDI IAU increments not found, no overwrite taken place. " if ( $JEDI_IAU_OVERWRITE ) then - echo " ${MYNAME}: Aborting ..." + echo " ${MYNAME}: Aborting(2) ..." exit (1) endif endif