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Call err_chk in forecast scripts for fatal errors #3515

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Merged
aerorahul merged 52 commits into from
Apr 4, 2025
Merged

Call err_chk in forecast scripts for fatal errors #3515

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23d3206
Replace status with err in all J-Jobs
DavidHuber-NOAA Mar 25, 2025
6a48b24
Replace exit with true to match other J-jobs
DavidHuber-NOAA Mar 25, 2025
c2e5d04
Replace rc with err in run_mpmd
DavidHuber-NOAA Mar 25, 2025
662fce8
Remove erroneous -
DavidHuber-NOAA Mar 25, 2025
1fb3263
Replace logic with if block
DavidHuber-NOAA Mar 25, 2025
d703df7
Call err_chk instead of checking for non-zero err manually
DavidHuber-NOAA Mar 25, 2025
18e443c
Update jobs/JGLOBAL_FORECAST
DavidHuber-NOAA Mar 26, 2025
5d4ea02
Add err_exit function
DavidHuber-NOAA Mar 26, 2025
c014b5f
Replace [] with [[]]
DavidHuber-NOAA Mar 26, 2025
029977d
More double quotes
DavidHuber-NOAA Mar 26, 2025
d174fd2
Merge develop; resolve conflicts in jobs
DavidHuber-NOAA Mar 27, 2025
6b0bfca
Update version number in comment
DavidHuber-NOAA Mar 27, 2025
db8d876
Merge remote-tracking branch 'emc/develop' into feature/err_fcst
DavidHuber-NOAA Mar 28, 2025
37ee01f
Use err_chk for fatal forecast errors, including common scripts
DavidHuber-NOAA Mar 28, 2025
3d4fa5c
Update ush/jjob_header.sh
DavidHuber-NOAA Mar 28, 2025
a2db90d
Merge remote-tracking branch 'emc/develop' into feature/err_fcst
DavidHuber-NOAA Mar 31, 2025
40961ae
Use cpreq instead of checking status
DavidHuber-NOAA Mar 31, 2025
a48c7a0
EE2-ify error messages in jjob_header.sh
DavidHuber-NOAA Mar 31, 2025
e70dd49
Move preamble into jjob_header
DavidHuber-NOAA Apr 1, 2025
d90df49
Fix variable name
DavidHuber-NOAA Apr 1, 2025
7a896a6
Do not fail on external command errors/undefined variables
DavidHuber-NOAA Apr 1, 2025
d4cd4b0
Remove preamble from forecast script
DavidHuber-NOAA Apr 1, 2025
22c2826
Remove preamble from J-Jobs (in jjob_header now)
DavidHuber-NOAA Apr 1, 2025
0eddc1c
Remove preamble from ex-scripts (now in jjob_header)
DavidHuber-NOAA Apr 1, 2025
2352a79
Merge branch 'develop' into feature/err_fcst
DavidHuber-NOAA Apr 1, 2025
7a784e8
Replace preamble with set -x in rocoto scripts
DavidHuber-NOAA Apr 1, 2025
adf4ea8
Add preamble back in for bash_utils python_ver function
DavidHuber-NOAA Apr 1, 2025
3bb788f
Merge branch 'feature/err_fcst' of github.com:davidhuber-noaa/global-…
DavidHuber-NOAA Apr 1, 2025
ae52121
Add braces for SC2250 warnings
DavidHuber-NOAA Apr 1, 2025
adf093f
More shellcheck stuff
DavidHuber-NOAA Apr 1, 2025
80217c5
Assign status to variable
DavidHuber-NOAA Apr 1, 2025
2f51318
Remove preamble from ush scripts
DavidHuber-NOAA Apr 1, 2025
e07e948
Fix error check
DavidHuber-NOAA Apr 1, 2025
f07dda7
Assign error to variable
DavidHuber-NOAA Apr 1, 2025
47e013a
Disable verif-global's -e shebang
DavidHuber-NOAA Apr 2, 2025
fb1b3ed
Disable errexit in prep job
DavidHuber-NOAA Apr 2, 2025
6a89a8f
Get the calling script name in jjob_header
DavidHuber-NOAA Apr 2, 2025
d6c17f3
Restore set -x when loading modules
DavidHuber-NOAA Apr 2, 2025
e76871b
Improve logging, export preamble functions
DavidHuber-NOAA Apr 2, 2025
e9a04b2
Allow sat count to be 0 without raising an error
DavidHuber-NOAA Apr 2, 2025
da21409
Double quote verif-global script variable
DavidHuber-NOAA Apr 2, 2025
6a7568e
Reinstate fatal error message in forecast_predet.sh
DavidHuber-NOAA Apr 2, 2025
da5a86c
Delete extra blank lines from ex scripts
DavidHuber-NOAA Apr 2, 2025
056b406
Remove extra blank lines from ush scripts
DavidHuber-NOAA Apr 2, 2025
313cce1
Merge branch 'develop' into feature/err_fcst
DavidHuber-NOAA Apr 2, 2025
3dfeae7
Add ':' to TODOs
DavidHuber-NOAA Apr 2, 2025
2071d0d
Un-export SHELLOPTS for metp jobs; needed for WCOSS2
DavidHuber-NOAA Apr 3, 2025
a701a0d
Merge branch 'develop' into feature/err_fcst
DavidHuber-NOAA Apr 3, 2025
0a82e36
Merge develop, resolve conflicts in wavegempak.sh, forecast_predet, r…
DavidHuber-NOAA Apr 3, 2025
7cbb005
Merge branch 'feature/err_fcst' of github.com:davidhuber-noaa/global-…
DavidHuber-NOAA Apr 3, 2025
0e2a625
Merge remote-tracking branch 'emc/develop' into feature/err_fcst
DavidHuber-NOAA Apr 3, 2025
6c6e878
Merge branch 'develop' into feature/err_fcst
DavidHuber-NOAA Apr 4, 2025
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1 change: 0 additions & 1 deletion jobs/JGDAS_AERO_ANALYSIS_GENERATE_BMATRIX
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "aeroanlgenb" -c "base aeroanl aeroanlgenb"

##############################################
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1 change: 0 additions & 1 deletion jobs/JGDAS_ATMOS_ANALYSIS_DIAG
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "anal" -c "base anal analdiag"


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1 change: 0 additions & 1 deletion jobs/JGDAS_ATMOS_CHGRES_FORENKF
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "anal" -c "base anal echgres"


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1 change: 0 additions & 1 deletion jobs/JGDAS_ATMOS_GEMPAK
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "gempak" -c "base gempak"

############################################
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1 change: 0 additions & 1 deletion jobs/JGDAS_ATMOS_GEMPAK_META_NCDC
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# GDAS GEMPAK META NCDC PRODUCT GENERATION
############################################

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "gempak_meta" -c "base gempak"

# Now set up GEMPAK/NTRANS environment
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1 change: 0 additions & 1 deletion jobs/JGDAS_ATMOS_VERFOZN
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#############################################################
# Set up environment for GDAS Ozone Monitor job
#############################################################
source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "verfozn" -c "base verfozn"

#############################################
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1 change: 0 additions & 1 deletion jobs/JGDAS_ATMOS_VERFRAD
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#############################################################
# Set up environment for GDAS Radiance Monitor job
#############################################################
source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "verfrad" -c "base verfrad"

#############################################
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1 change: 0 additions & 1 deletion jobs/JGDAS_ENKF_DIAG
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "eobs" -c "base anal eobs analdiag ediag"


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1 change: 0 additions & 1 deletion jobs/JGDAS_ENKF_ECEN
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "ecen" -c "base ecen"


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1 change: 0 additions & 1 deletion jobs/JGDAS_ENKF_ECEN_FV3JEDI
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# Ignore possible spelling error (nothing is misspelled)
# shellcheck disable=SC2153

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "ecen_fv3jedi" -c "base ecen_fv3jedi"

##############################################
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1 change: 0 additions & 1 deletion jobs/JGDAS_ENKF_POST
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "epos" -c "base epos"


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1 change: 0 additions & 1 deletion jobs/JGDAS_ENKF_SELECT_OBS
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "eobs" -c "base anal eobs"


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1 change: 0 additions & 1 deletion jobs/JGDAS_ENKF_SFC
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "esfc" -c "base esfc"


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1 change: 0 additions & 1 deletion jobs/JGDAS_ENKF_UPDATE
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "eupd" -c "base anal eupd"


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1 change: 0 additions & 1 deletion jobs/JGDAS_FIT2OBS
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "fit2obs" -c "base fit2obs"


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1 change: 0 additions & 1 deletion jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_ECEN
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#!/bin/bash
source "${HOMEgfs}/ush/preamble.sh"

export DATAjob="${DATAROOT}/${RUN}marineanalysis.${PDY:-}${cyc}"
export DATA="${DATAjob}/${jobid}"
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1 change: 0 additions & 1 deletion jobs/JGFS_ATMOS_AWIPS_20KM_1P0DEG
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "awips" -c "base awips"

export OMP_NUM_THREADS=${OMP_NUM_THREADS:-1}
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7 changes: 5 additions & 2 deletions jobs/JGFS_ATMOS_CYCLONE_GENESIS
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "genesis" -c "base genesis"

##############################################
Expand Down Expand Up @@ -49,9 +48,13 @@ export JYYYY=${PDY:0:4}
# Run relevant script
##############################################

${SCRIPTens_tracker}/exgfs_tc_genesis.sh
# Do not fail on errors or unassigned variables in external code
set +eu
${SCRIPTens_tracker}/exgfs_tc_genesis.sh && true
export err=$?; err_chk

set_strict

##############################################
# Final processing
##############################################
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1 change: 0 additions & 1 deletion jobs/JGFS_ATMOS_CYCLONE_TRACKER
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "tracker" -c "base tracker"

export COMPONENT="atmos"
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1 change: 0 additions & 1 deletion jobs/JGFS_ATMOS_FBWIND
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############################################
# GFS FBWIND PRODUCT GENERATION
############################################
source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "fbwind" -c "base fbwind"

###################################
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1 change: 0 additions & 1 deletion jobs/JGFS_ATMOS_FSU_GENESIS
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "genesis_fsu" -c "base genesis_fsu"

# Hack to temporary skip this as the tracker has not been build
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1 change: 0 additions & 1 deletion jobs/JGFS_ATMOS_GEMPAK
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "gempak" -c "base gempak"

############################################
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1 change: 0 additions & 1 deletion jobs/JGFS_ATMOS_GEMPAK_META
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############################################
# GFS GEMPAK META PRODUCT GENERATION
############################################
source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "gempak_meta" -c "base gempak"


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1 change: 0 additions & 1 deletion jobs/JGFS_ATMOS_GEMPAK_NCDC_UPAPGIF
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############################################
# GFS GEMPAK NCDC PRODUCT GENERATION
############################################
source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "gempak_gif" -c "base gempak"

export MP_PULSE=0
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1 change: 0 additions & 1 deletion jobs/JGFS_ATMOS_GEMPAK_PGRB2_SPEC
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "gempak_spec" -c "base gempak"

############################################
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1 change: 0 additions & 1 deletion jobs/JGFS_ATMOS_PGRB2_SPEC_NPOESS
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############################################
# GFS PGRB2_SPECIAL_POST PRODUCT GENERATION
############################################
source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "npoess" -c "base npoess"

export OMP_NUM_THREADS=${OMP_NUM_THREADS:-1}
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1 change: 0 additions & 1 deletion jobs/JGFS_ATMOS_POSTSND
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "postsnd" -c "base postsnd"


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7 changes: 5 additions & 2 deletions jobs/JGFS_ATMOS_VERIFICATION
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "metp" -c "base metp"

###############################################################
Expand Down Expand Up @@ -28,7 +27,11 @@ done

# TODO: If none of these are on, why are we running this job?
if [[ "${RUN_GRID2GRID_STEP1}" == "YES" || "${RUN_GRID2OBS_STEP1}" == "YES" || "${RUN_PRECIP_STEP1}" == "YES" ]]; then
${VERIF_GLOBALSH}
# Override the -e in VERIF_GLOBALSH's shebang and un-export SHELLOPTS
# TODO: clean up the verif-global script so it does not raise false-positive errors
set +eu
export -n SHELLOPTS
bash -x "${VERIF_GLOBALSH}"
Comment thread
DavidHuber-NOAA marked this conversation as resolved.
err=$?
if [[ ${err} -ne 0 ]];
then exit "${err}"
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1 change: 0 additions & 1 deletion jobs/JGLOBAL_AERO_ANALYSIS_FINALIZE
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
export WIPE_DATA="NO"
export DATA=${DATA:-${DATAROOT}/${RUN}aeroanl_${cyc}}
source "${HOMEgfs}/ush/jjob_header.sh" -e "aeroanlfinal" -c "base aeroanl aeroanlfinal"
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1 change: 0 additions & 1 deletion jobs/JGLOBAL_AERO_ANALYSIS_INITIALIZE
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
export DATA=${DATA:-${DATAROOT}/${RUN}aeroanl_${cyc}}
source "${HOMEgfs}/ush/jjob_header.sh" -e "aeroanlinit" -c "base aeroanl aeroanlinit"

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1 change: 0 additions & 1 deletion jobs/JGLOBAL_AERO_ANALYSIS_VARIATIONAL
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
export WIPE_DATA="NO"
export DATA=${DATA:-${DATAROOT}/${RUN}aeroanl_${cyc}}
source "${HOMEgfs}/ush/jjob_header.sh" -e "aeroanlvar" -c "base aeroanl aeroanlvar"
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8 changes: 3 additions & 5 deletions jobs/JGLOBAL_ARCHIVE_TARS
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "arch_tars" -c "base arch_tars wave"
source "${USHgfs}/wave_domain_grid.sh"

Expand Down Expand Up @@ -74,11 +73,10 @@ fi
# Run archive script
###############################################################

set +eu
${GLOBALARCHIVESH:-${SCRgfs}/exglobal_archive_tars.py}
err=$?
if [[ ${err} -ne 0 ]]; then
exit "${err}"
fi
export err=$?; err_chk "FATAL ERROR: failed to archive the COM structure"
set_strict

##############################################
# End JOB SPECIFIC work
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1 change: 0 additions & 1 deletion jobs/JGLOBAL_ARCHIVE_VRFY
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "arch_vrfy" -c "base arch_vrfy wave"


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1 change: 0 additions & 1 deletion jobs/JGLOBAL_ATMENS_ANALYSIS_FINALIZE
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
export WIPE_DATA="NO"
export DATA=${DATA:-${DATAROOT}/${RUN}atmensanl_${cyc}}
source "${HOMEgfs}/ush/jjob_header.sh" -e "atmensanlfinal" -c "base atmensanl atmensanlfinal"
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1 change: 0 additions & 1 deletion jobs/JGLOBAL_ATMENS_ANALYSIS_FV3_INCREMENT
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
export WIPE_DATA="NO"
export DATA=${DATA:-${DATAROOT}/${RUN}atmensanl_${cyc}}
source "${HOMEgfs}/ush/jjob_header.sh" -e "atmensanlfv3inc" -c "base atmensanl atmensanlfv3inc"
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1 change: 0 additions & 1 deletion jobs/JGLOBAL_ATMENS_ANALYSIS_INITIALIZE
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
export DATA=${DATA:-${DATAROOT}/${RUN}atmensanl_${cyc}}
source "${HOMEgfs}/ush/jjob_header.sh" -e "atmensanlinit" -c "base atmensanl atmensanlinit"

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1 change: 0 additions & 1 deletion jobs/JGLOBAL_ATMENS_ANALYSIS_LETKF
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
export WIPE_DATA="NO"
export DATA=${DATA:-${DATAROOT}/${RUN}atmensanl_${cyc}}
source "${HOMEgfs}/ush/jjob_header.sh" -e "atmensanlletkf" -c "base atmensanl atmensanlletkf"
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1 change: 0 additions & 1 deletion jobs/JGLOBAL_ATMENS_ANALYSIS_OBS
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
export WIPE_DATA="NO"
export DATA=${DATA:-${DATAROOT}/${RUN}atmensanl_${cyc}}
source "${HOMEgfs}/ush/jjob_header.sh" -e "atmensanlobs" -c "base atmensanl atmensanlobs"
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1 change: 0 additions & 1 deletion jobs/JGLOBAL_ATMENS_ANALYSIS_SOL
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
export WIPE_DATA="NO"
export DATA=${DATA:-${DATAROOT}/${RUN}atmensanl_${cyc}}
source "${HOMEgfs}/ush/jjob_header.sh" -e "atmensanlsol" -c "base atmensanl atmensanlsol"
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1 change: 0 additions & 1 deletion jobs/JGLOBAL_ATMOS_ANALYSIS
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "anal" -c "base anal"


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1 change: 0 additions & 1 deletion jobs/JGLOBAL_ATMOS_ANALYSIS_CALC
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "analcalc" -c "base anal analcalc"


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1 change: 0 additions & 1 deletion jobs/JGLOBAL_ATMOS_ANALYSIS_CALC_FV3JEDI
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Expand Up @@ -4,7 +4,6 @@
# shellcheck disable=SC2153
# shellcheck disable=SC2312

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "analcalc_fv3jedi" -c "base analcalc_fv3jedi"

##############################################
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1 change: 0 additions & 1 deletion jobs/JGLOBAL_ATMOS_EMCSFC_SFC_PREP
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "sfc_prep" -c "base"

export SENDDBN=${SENDDBN:-NO}
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1 change: 0 additions & 1 deletion jobs/JGLOBAL_ATMOS_ENSSTAT
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# Caculate the mean, spread, and other probabilistic fields.
#

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "atmos_ensstat" -c "base atmos_ensstat"


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1 change: 0 additions & 1 deletion jobs/JGLOBAL_ATMOS_POST_MANAGER
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# TODO (#1227) This job is not used in the rocoto suite

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "post" -c "base post"


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1 change: 0 additions & 1 deletion jobs/JGLOBAL_ATMOS_PRODUCTS
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "atmos_products" -c "base atmos_products"


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1 change: 0 additions & 1 deletion jobs/JGLOBAL_ATMOS_SFCANL
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "sfcanl" -c "base sfcanl"


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1 change: 0 additions & 1 deletion jobs/JGLOBAL_ATMOS_TROPCY_QC_RELOC
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "prep" -c "base prep"


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1 change: 0 additions & 1 deletion jobs/JGLOBAL_ATMOS_UPP
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#! /usr/bin/env bash

source "${HOMEgfs}/ush/preamble.sh"
source "${HOMEgfs}/ush/jjob_header.sh" -e "upp" -c "base upp"

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