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Merged
merged 18 commits into from
Oct 25, 2022
Merged

Feature/updates for gdas app #1091

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1a1004f
Various updates to restore ability to cycle GDASApp (see #1067)
RussTreadon-NOAA Oct 17, 2022
d71af26
Merge branch 'develop' into feature/updates_for_GDASApp
RussTreadon-NOAA Oct 19, 2022
bee4d87
Add missing argument, atmges_fv3, to INCPY (#1067)
RussTreadon-NOAA Oct 19, 2022
bb0cf88
Merge branch 'develop' into feature/updates_for_GDASApp
RussTreadon-NOAA Oct 20, 2022
ab6dec0
Update hash for UFS-based DA checkout, correct typo in load_ufsda_mod…
RussTreadon-NOAA Oct 20, 2022
8b155de
add FV3_GFS_v16_no_nsst to CCPP_SUITES for UFS-based DA (#1067)
RussTreadon-NOAA Oct 20, 2022
5a97bda
Use identity B for fv3jedi_var, set OMP_NUM_THREADS in fv3jedi analys…
RussTreadon-NOAA Oct 20, 2022
670602b
Revert R2D2_BC_DUMP in config.atmensanal back to original default (#1…
RussTreadon-NOAA Oct 21, 2022
b7127fd
Merge branch 'develop' into feature/updates_for_GDASApp (#1067)
RussTreadon-NOAA Oct 22, 2022
f2672be
Merge branch 'develop' into feature/updates_for_GDASApp (#1067)
RussTreadon-NOAA Oct 24, 2022
8764a0d
Merge branch 'develop' into feature/updates_for_GDASApp (#1067)
RussTreadon-NOAA Oct 24, 2022
a3d60d4
Update GDASApp hash, address linter warnings for load_ufsda_module.sh…
RussTreadon-NOAA Oct 24, 2022
1997c26
address linter errors in ufsda analysis run scripts (#1067)
RussTreadon-NOAA Oct 24, 2022
508bf32
Merge branch 'develop' into feature/updates_for_GDASApp (#1067)
RussTreadon-NOAA Oct 24, 2022
f82fab4
refactor correction to linter errors in ufsda analysis run scripts (#…
RussTreadon-NOAA Oct 24, 2022
ed2a98c
Update GDASAapp hash in checkout.sh (#1067)
RussTreadon-NOAA Oct 25, 2022
3c452dd
Update gsi-enkf and GDASApps hashes in Externals.cfg (#1067)
RussTreadon-NOAA Oct 25, 2022
5b576f0
Merge branch 'develop' into feature/updates_for_GDASApp
RussTreadon-NOAA Oct 25, 2022
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4 changes: 2 additions & 2 deletions Externals.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ protocol = git
required = True

[GSI-EnKF]
hash = 67f5ab4
hash = 48d8676
local_path = sorc/gsi_enkf.fd
repo_url = https://github.com/NOAA-EMC/GSI.git
protocol = git
Expand All @@ -50,7 +50,7 @@ protocol = git
required = False

[GDASApp]
hash = 5952c9d
hash = 843d3a9
local_path = sorc/gdas.cd
repo_url = https://github.com/NOAA-EMC/GDASApp.git
protocol = git
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11 changes: 2 additions & 9 deletions jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_POST
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Expand Up @@ -79,20 +79,13 @@ mkdir -p $COMOUT
export COMIN_GES="$ROTDIR/$GDUMP.$gPDY/$gcyc/$COMPONENT"
export COMIN_GES_ENS="$ROTDIR/enkf$GDUMP.$gPDY/$gcyc/$COMPONENT"

# NOTE BELOW IS A HACK FOR TESTING
# PLEASE FIX THIS LATER
# ASK @aerorahul
# HOW TO HANDLE DIFFERENT COMPILERS/ETC. FOR MODEL VS DA
# PROD_UTIL, ETC. DO NOT EXIST FOR JEDI MODULE VERSIONS
module purge
module use $HOMEgfs/sorc/gdas.cd/modulefiles
module load GDAS/orion
# Add UFSDA to PYTHONPATH
export PYTHONPATH=$HOMEgfs/sorc/gdas.cd/ush/:$PYTHONPATH

###############################################################
# Run relevant script

EXSCRIPT=${GDASPOSTPY:-$HOMEgfs/sorc/gdas.cd/scripts/exgdas_global_atmos_analysis_post.py}
EXSCRIPT=${GDASPOSTPY:-$HOMEgfs/scripts/exgdas_global_atmos_analysis_post.py}
$EXSCRIPT
status=$?
[[ $status -ne 0 ]] && exit $status
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12 changes: 2 additions & 10 deletions jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_PREP
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Expand Up @@ -79,20 +79,12 @@ mkdir -p $COMOUT
export COMIN_GES="$ROTDIR/$GDUMP.$gPDY/$gcyc/$COMPONENT"
export COMIN_GES_ENS="$ROTDIR/enkf$GDUMP.$gPDY/$gcyc/$COMPONENT"

# NOTE BELOW IS A HACK FOR TESTING
# PLEASE FIX THIS LATER
# ASK @aerorahul
# HOW TO HANDLE DIFFERENT COMPILERS/ETC. FOR MODEL VS DA
# PROD_UTIL, ETC. DO NOT EXIST FOR JEDI MODULE VERSIONS
module purge
module use $HOMEgfs/sorc/gdas.cd/modulefiles
module load GDAS/orion
# Add UFSDA to PYTHONPATH
export PYTHONPATH=$HOMEgfs/sorc/gdas.cd/ush/:$PYTHONPATH

###############################################################
# Run relevant script

EXSCRIPT=${GDASPREPPY:-$HOMEgfs/sorc/gdas.cd/scripts/exgdas_global_atmos_analysis_prep.py}
EXSCRIPT=${GDASPREPPY:-$HOMEgfs/scripts/exgdas_global_atmos_analysis_prep.py}
$EXSCRIPT
status=$?
[[ $status -ne 0 ]] && exit $status
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11 changes: 2 additions & 9 deletions jobs/JGDAS_GLOBAL_ATMOS_ANALYSIS_RUN
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Expand Up @@ -79,20 +79,13 @@ mkdir -p $COMOUT
export COMIN_GES="$ROTDIR/$GDUMP.$gPDY/$gcyc/$COMPONENT"
export COMIN_GES_ENS="$ROTDIR/enkf$GDUMP.$gPDY/$gcyc/$COMPONENT"

# NOTE BELOW IS A HACK FOR TESTING
# PLEASE FIX THIS LATER
# ASK @aerorahul
# HOW TO HANDLE DIFFERENT COMPILERS/ETC. FOR MODEL VS DA
# PROD_UTIL, ETC. DO NOT EXIST FOR JEDI MODULE VERSIONS
module purge
module use $HOMEgfs/sorc/gdas.cd/modulefiles
module load GDAS/orion
# Add UFSDA to PYTHONPATH
export PYTHONPATH=$HOMEgfs/sorc/gdas.cd/ush/:$PYTHONPATH

###############################################################
# Run relevant script

EXSCRIPT=${GDASRUNSH:-$HOMEgfs/sorc/gdas.cd/scripts/exgdas_global_atmos_analysis_run.sh}
EXSCRIPT=${GDASRUNSH:-$HOMEgfs/scripts/exgdas_global_atmos_analysis_run.sh}
$EXSCRIPT
status=$?
[[ $status -ne 0 ]] && exit $status
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11 changes: 2 additions & 9 deletions jobs/JGDAS_GLOBAL_ATMOS_ENSANAL_POST
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Expand Up @@ -82,20 +82,13 @@ export COMIN="$ROTDIR/$CDUMP.$PDY/$cyc/$COMPONENT"
export COMIN_GES="$ROTDIR/$GDUMP.$gPDY/$gcyc/$COMPONENT"
export COMIN_GES_ENS="$ROTDIR/enkf$GDUMP.$gPDY/$gcyc/$COMPONENT"

# NOTE BELOW IS A HACK FOR TESTING
# PLEASE FIX THIS LATER
# ASK @aerorahul
# HOW TO HANDLE DIFFERENT COMPILERS/ETC. FOR MODEL VS DA
# PROD_UTIL, ETC. DO NOT EXIST FOR JEDI MODULE VERSIONS
module purge
module use $HOMEgfs/sorc/gdas.cd/modulefiles
module load GDAS/orion
# Add UFSDA to PYTHONPATH
export PYTHONPATH=$HOMEgfs/sorc/gdas.cd/ush/:$PYTHONPATH

###############################################################
# Run relevant script

EXSCRIPT=${GDASPOSTPY:-$HOMEgfs/sorc/gdas.cd/scripts/exgdas_global_atmos_ensanal_post.py}
EXSCRIPT=${GDASPOSTPY:-$HOMEgfs/scripts/exgdas_global_atmos_ensanal_post.py}
$EXSCRIPT
status=$?
[[ $status -ne 0 ]] && exit $status
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11 changes: 2 additions & 9 deletions jobs/JGDAS_GLOBAL_ATMOS_ENSANAL_PREP
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Expand Up @@ -82,20 +82,13 @@ export COMIN="$ROTDIR/$CDUMP.$PDY/$cyc/$COMPONENT"
export COMIN_GES="$ROTDIR/$GDUMP.$gPDY/$gcyc/$COMPONENT"
export COMIN_GES_ENS="$ROTDIR/enkf$GDUMP.$gPDY/$gcyc/$COMPONENT"

# NOTE BELOW IS A HACK FOR TESTING
# PLEASE FIX THIS LATER
# ASK @aerorahul
# HOW TO HANDLE DIFFERENT COMPILERS/ETC. FOR MODEL VS DA
# PROD_UTIL, ETC. DO NOT EXIST FOR JEDI MODULE VERSIONS
module purge
module use $HOMEgfs/sorc/gdas.cd/modulefiles
module load GDAS/orion
# Add UFSDA to PYTHONPATH
export PYTHONPATH=$HOMEgfs/sorc/gdas.cd/ush/:$PYTHONPATH

###############################################################
# Run relevant script

EXSCRIPT=${GDASPREPPY:-$HOMEgfs/sorc/gdas.cd/scripts/exgdas_global_atmos_analysis_prep.py}
EXSCRIPT=${GDASPREPPY:-$HOMEgfs/scripts/exgdas_global_atmos_analysis_prep.py}
$EXSCRIPT
status=$?
[[ $status -ne 0 ]] && exit $status
Expand Down
11 changes: 2 additions & 9 deletions jobs/JGDAS_GLOBAL_ATMOS_ENSANAL_RUN
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Original file line number Diff line number Diff line change
Expand Up @@ -82,20 +82,13 @@ export COMIN="$ROTDIR/$CDUMP.$PDY/$cyc/$COMPONENT"
export COMIN_GES="$ROTDIR/$GDUMP.$gPDY/$gcyc/$COMPONENT"
export COMIN_GES_ENS="$ROTDIR/enkf$GDUMP.$gPDY/$gcyc/$COMPONENT"

# NOTE BELOW IS A HACK FOR TESTING
# PLEASE FIX THIS LATER
# ASK @aerorahul
# HOW TO HANDLE DIFFERENT COMPILERS/ETC. FOR MODEL VS DA
# PROD_UTIL, ETC. DO NOT EXIST FOR JEDI MODULE VERSIONS
module purge
module use $HOMEgfs/sorc/gdas.cd/modulefiles
module load GDAS/orion
# Add UFSDA to PYTHONPATH
export PYTHONPATH=$HOMEgfs/sorc/gdas.cd/ush/:$PYTHONPATH

###############################################################
# Run relevant script

EXSCRIPT=${GDASRUNSH:-$HOMEgfs/sorc/gdas.cd/scripts/exgdas_global_atmos_ensanal_run.sh}
EXSCRIPT=${GDASRUNSH:-$HOMEgfs/scripts/exgdas_global_atmos_ensanal_run.sh}
$EXSCRIPT
status=$?
[[ $status -ne 0 ]] && exit $status
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6 changes: 4 additions & 2 deletions jobs/rocoto/atmanalpost.sh
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@@ -1,10 +1,12 @@
#! /usr/bin/env bash

export STRICT="NO"
source "$HOMEgfs/ush/preamble.sh"
export STRICT="YES"

###############################################################
# Source FV3GFS workflow modules
. $HOMEgfs/ush/load_fv3gfs_modules.sh
# Source UFSDA workflow modules
. $HOMEgfs/ush/load_ufsda_modules.sh
status=$?
[[ $status -ne 0 ]] && exit $status

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6 changes: 4 additions & 2 deletions jobs/rocoto/atmanalprep.sh
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@@ -1,10 +1,12 @@
#! /usr/bin/env bash

export STRICT="NO"
source "$HOMEgfs/ush/preamble.sh"
export STRICT="YES"

###############################################################
# Source FV3GFS workflow modules
. $HOMEgfs/ush/load_fv3gfs_modules.sh
# Source UFSDA workflow modules
. $HOMEgfs/ush/load_ufsda_modules.sh
status=$?
[[ $status -ne 0 ]] && exit $status

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6 changes: 4 additions & 2 deletions jobs/rocoto/atmanalrun.sh
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@@ -1,10 +1,12 @@
#! /usr/bin/env bash

export STRICT="NO"
source "$HOMEgfs/ush/preamble.sh"
export STRICT="YES"

###############################################################
# Source FV3GFS workflow modules
. $HOMEgfs/ush/load_fv3gfs_modules.sh
# Source UFSDA workflow modules
. $HOMEgfs/ush/load_ufsda_modules.sh
status=$?
[[ $status -ne 0 ]] && exit $status

Expand Down
6 changes: 4 additions & 2 deletions jobs/rocoto/atmensanalpost.sh
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@@ -1,10 +1,12 @@
#! /usr/bin/env bash

export STRICT="NO"
source "$HOMEgfs/ush/preamble.sh"
export STRICT="YES"

###############################################################
# Source FV3GFS workflow modules
. $HOMEgfs/ush/load_fv3gfs_modules.sh
# Source UFSDA workflow modules
. $HOMEgfs/ush/load_ufsda_modules.sh
status=$?
[[ $status -ne 0 ]] && exit $status

Expand Down
6 changes: 4 additions & 2 deletions jobs/rocoto/atmensanalprep.sh
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@@ -1,10 +1,12 @@
#! /usr/bin/env bash

export STRICT="NO"
source "$HOMEgfs/ush/preamble.sh"
export STRICT="YES"

###############################################################
# Source FV3GFS workflow modules
. $HOMEgfs/ush/load_fv3gfs_modules.sh
# Source UFSDA workflow modules
. $HOMEgfs/ush/load_ufsda_modules.sh
status=$?
[[ $status -ne 0 ]] && exit $status

Expand Down
6 changes: 4 additions & 2 deletions jobs/rocoto/atmensanalrun.sh
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@@ -1,10 +1,12 @@
#! /usr/bin/env bash

export STRICT="NO"
source "$HOMEgfs/ush/preamble.sh"
export STRICT="YES"

###############################################################
# Source FV3GFS workflow modules
. $HOMEgfs/ush/load_fv3gfs_modules.sh
# Source UFSDA workflow modules
. $HOMEgfs/ush/load_ufsda_modules.sh
status=$?
[[ $status -ne 0 ]] && exit $status

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2 changes: 1 addition & 1 deletion parm/config/config.atmanal
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Expand Up @@ -8,7 +8,7 @@ echo "BEGIN: config.atmanal"
export OBS_YAML_DIR=$HOMEgfs/sorc/gdas.cd/parm/atm/obs/config/
export OBS_LIST=$HOMEgfs/sorc/gdas.cd/parm/atm/obs/lists/gdas_prototype.yaml
export ATMVARYAML=$HOMEgfs/sorc/gdas.cd/parm/atm/variational/3dvar_dripcg.yaml
export BERROR_YAML=$HOMEgfs/sorc/gdas.cd/parm/atm/berror/hybvar_bump.yaml
export BERROR_YAML=$HOMEgfs/sorc/gdas.cd/parm/atm/berror/staticb_identity.yaml
export FV3JEDI_FIX=$HOMEgfs/fix/gdas
export R2D2_OBS_DB='ufsda_test'
export R2D2_OBS_DUMP='oper_gdas'
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3 changes: 1 addition & 2 deletions parm/config/config.atmensanal
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Expand Up @@ -14,8 +14,7 @@ export R2D2_OBS_DB='ufsda_test'
export R2D2_OBS_DUMP='oper_gdas'
export R2D2_OBS_SRC='ncdiag'
export R2D2_BC_SRC='gsi'
##export R2D2_BC_DUMP='oper_gdas'
export R2D2_BC_DUMP='prgdasens'
export R2D2_BC_DUMP='oper_gdas'
export R2D2_ARCH_DB='local'
export INTERP_METHOD='barycentric'

Expand Down
8 changes: 5 additions & 3 deletions scripts/exgdas_global_atmos_analysis_run.sh
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Expand Up @@ -131,17 +131,19 @@ $NLN $JEDIVAREXE $DATA/fv3jedi_var.x

################################################################################
# run executable
export OMP_NUM_THREADS=$NTHREADS_ATMANAL
export pgm=$JEDIVAREXE
. prep_step
$APRUN_ATMANAL $DATA/fv3jedi_var.x $DATA/fv3jedi_var.yaml 1>&1 2>&2
export err=$?; err_chk

################################################################################
# translate FV3-JEDI increment to FV3 readable format
atmges_fv3=$COMIN_GES/${GPREFIX}atmf006.ensres.nc
atminc_jedi=$DATA/anl/atminc.${PDY}_${cyc}0000z.nc4
atminc_fv3=$COMOUT/${CDUMP}.${cycle}.atminc.nc
if [ -s $atminc_jedi ]; then
$INCPY $atminc_jedi $atminc_fv3
$INCPY $atmges_fv3 $atminc_jedi $atminc_fv3
export err=$?
else
echo "***WARNING*** missing $atminc_jedi ABORT"
Expand All @@ -164,11 +166,11 @@ cp -rf $DATA/bc $COMOUT/
# Deterministic abias used in enkf cycle
alist="abias abias_air abias_int abias_pc"
for abias in $alist; do
cp $COMIN_GES/${GPREFIX}${abias} $COMOUT/${APREFIX}${abias}
cp "${COMIN_GES}/${GPREFIX}${abias}" "${COMOUT}/${APREFIX}${abias}"
done

################################################################################

exit $err
exit ${err}

################################################################################
12 changes: 7 additions & 5 deletions scripts/exgdas_global_atmos_ensanal_run.sh
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Expand Up @@ -126,7 +126,8 @@ $NLN $JEDIENSEXE $DATA/fv3jedi_ens.x

################################################################################
# run executable
export pgm=$JEDIVAREXE
export OMP_NUM_THREADS=$NTHREADS_ATMENSANAL
export pgm=$JEDIENSEXE
. prep_step
$APRUN_ATMENSANAL $DATA/fv3jedi_ens.x $DATA/fv3jedi_ens.yaml 1>&1 2>&2
export err=$?; err_chk
Expand All @@ -135,11 +136,12 @@ export err=$?; err_chk
# translate FV3-JEDI increment to FV3 readable format
for imem in $(seq 1 $NMEM_ENKF); do
memchar="mem"$(printf %03i $imem)
atmges_fv3=$COMIN_GES_ENS/$memchar/${GPREFIX}atmf006.nc
atminc_jedi=$DATA/anl/$memchar/atminc.${PDY}_${cyc}0000z.nc4
atminc_fv3=$COMOUT_ENS/$memchar/${CDUMP}.${cycle}.atminc.nc
mkdir -p $COMOUT_ENS/$memchar
if [ -s $atminc_jedi ]; then
$INCPY $atminc_jedi $atminc_fv3
$INCPY $atmges_fv3 $atminc_jedi $atminc_fv3
export err=$?
else
echo "***WARNING*** missing $atminc_jedi ABORT"
Expand All @@ -154,12 +156,12 @@ echo "$CDUMP $CDATE atminc done at $(date)" > $COMOUT_ENS/${CDUMP}.${cycle}.logi

################################################################################
# Copy diags and YAML to $COMOUT
cp -r $DATA/fv3jedi_ens.yaml $COMOUT_ENS/${CDUMP}.${cycle}.fv3jedi_ens.yaml
cp -rf $DATA/diags $COMOUT_ENS/
cp -r ${DATA}/fv3jedi_ens.yaml ${COMOUT_ENS}/${CDUMP}.${cycle}.fv3jedi_ens.yaml
cp -rf "${DATA}/diags" "${COMOUT_ENS}/"


################################################################################

exit $err
exit ${err}

################################################################################
2 changes: 1 addition & 1 deletion sorc/build_ufs.sh
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Expand Up @@ -5,7 +5,7 @@ cwd=$(pwd)

# Default settings
APP="S2SWA"
CCPP_SUITES="FV3_GFS_v16,FV3_GFS_v16_ugwpv1,FV3_GFS_v17_p8,FV3_GFS_v16_coupled_nsstNoahmpUGWPv1,FV3_GFS_v17_coupled_p8"
CCPP_SUITES="FV3_GFS_v16,FV3_GFS_v16_no_nsst,FV3_GFS_v16_ugwpv1,FV3_GFS_v17_p8,FV3_GFS_v16_coupled_nsstNoahmpUGWPv1,FV3_GFS_v17_coupled_p8"

export RT_COMPILER="intel"
source $cwd/ufs_model.fd/tests/detect_machine.sh
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4 changes: 2 additions & 2 deletions sorc/checkout.sh
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Expand Up @@ -157,11 +157,11 @@ checkout "ufs_utils.fd" "https://github.com/ufs-community/UFS_UTILS.git"
checkout "verif-global.fd" "https://github.com/NOAA-EMC/EMC_verif-global.git" "c267780" ; errs=$((errs + $?))

if [[ ${checkout_gsi} == "YES" ]]; then
checkout "gsi_enkf.fd" "https://github.com/NOAA-EMC/GSI.git" "67f5ab4"; errs=$((errs + $?))
checkout "gsi_enkf.fd" "https://github.com/NOAA-EMC/GSI.git" "48d8676"; errs=$((errs + $?))
fi

if [[ ${checkout_gdas} == "YES" ]]; then
checkout "gdas.cd" "https://github.com/NOAA-EMC/GDASApp.git" "5952c9d"; errs=$((errs + $?))
checkout "gdas.cd" "https://github.com/NOAA-EMC/GDASApp.git" "843d3a9"; errs=$((errs + $?))
fi

if [[ ${checkout_gsi} == "YES" || ${checkout_gdas} == "YES" ]]; then
Expand Down
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