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Update an offline marine vrfy tool (#1447)
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# Description

Update some features for avoiding fails of task and make the script easy
to use

# Companion PRs

N/A

# Issues

Resolves #1384
Partially Resolves #1398

# Automated CI tests to run in Global Workflow
<!-- Which Global Workflow CI tests are required to adequately test this
PR? -->
- [ ] atm_jjob <!-- JEDI atm single cycle DA !-->
- [ ] C96C48_ufs_hybatmDA <!-- JEDI atm cycled DA !-->
- [ ] C96C48_hybatmaerosnowDA  <!-- JEDI aero/snow cycled DA !-->
- [ ] C48mx500_3DVarAOWCDA <!-- JEDI low-res marine 3DVar cycled DA !-->
- [ ] C48mx500_hybAOWCDA <!-- JEDI marine hybrid envar cycled DA !-->
- [ ] C96C48_hybatmDA <!-- GSI atm cycled DA !-->

---------

Co-authored-by: Guillaume Vernieres <[email protected]>
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@apchoiCMD @guillaumevernieres
apchoiCMD and guillaumevernieres authored Jan 27, 2025
1 parent a3cb645 commit 708d75f
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2 changes: 1 addition & 1 deletion ush/soca/soca_vrfy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ def plotConfig(grid_file=[],
'ave_ssh': 'meter',
'Temp': 'deg C',
'Salt': 'psu',
'aice_h': 'meter',
'aice_h': 'unitless',
'hi_h': 'meter',
'hs_h': 'meter',
'u': 'm/s',
Expand Down
107 changes: 67 additions & 40 deletions utils/soca/fig_gallery/exgdas_global_marine_analysis_vrfy_manual.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,5 @@
#!/usr/bin/env python3

import os
import numpy as np
import gen_eva_obs_yaml
Expand All @@ -11,11 +13,19 @@
com_ice_history = os.getenv('COM_ICE_HISTORY_PREV')
com_ocean_history = os.getenv('COM_OCEAN_HISTORY_PREV')
cyc = os.getenv('cyc')
bcyc = os.getenv('bcyc')
gcyc = os.getenv('gcyc')
RUN = os.getenv('RUN')

bcyc = str((int(cyc) - 3) % 24).zfill(2)
gcyc = str((int(cyc) - 6) % 24).zfill(2)
grid_file = os.path.join(comout, f'{RUN}.t'+bcyc+'z.ocngrid.nc')
# Construct the first potential grid_file path
vrfy_grid_file = os.path.join(comout, f'{RUN}.t'+bcyc+'z.ocngrid.nc')

# Check if the file exists, then decide on grid_file
if os.path.exists(vrfy_grid_file):
grid_file = vrfy_grid_file
else:
grid_file = '/scratch1/NCEPDEV/da/common/validation/vrfy/gdas.t21z.ocngrid.nc'

layer_file = os.path.join(comout, f'{RUN}.t'+cyc+'z.ocninc.nc')

# for eva
Expand All @@ -26,7 +36,8 @@
run_ensemble_analysis = os.getenv('RUN_ENSENBLE_ANALYSIS', 'OFF').upper() == 'ON'
run_bkgerr_analysis = os.getenv('RUN_BACKGROUND_ERROR_ANALYSIS', 'OFF').upper() == 'ON'
run_bkg_analysis = os.getenv('RUN_BACKGROUND_ANALYSIS', 'OFF').upper() == 'ON'
run_increment_analysis = os.getenv('RUN_INCREMENT_ANLYSIS', 'OFF').upper() == 'ON'
run_increment_analysis = os.getenv('RUN_INCREMENT_ANALYSIS', 'OFF').upper() == 'ON'
run_eva_analysis = os.getenv('RUN_EVA_ANALYSIS', 'OFF').upper() == 'ON'

# Initialize an empty list for the main config
configs = [plotConfig(grid_file=grid_file,
Expand Down Expand Up @@ -76,23 +87,32 @@

if run_bkgerr_analysis:
config_bkgerr = [plotConfig(grid_file=grid_file,
data_file=os.path.join(comout, os.path.pardir, os.path.pardir,
'bmatrix', 'ice', f'{RUN}.t'+cyc+'z.ice.bkgerr_stddev.nc'),
variables_horiz={'aice_h': [0.0, 0.5],
'hi_h': [0.0, 2.0],
'hs_h': [0.0, 0.2]},
colormap='jet',
projs=['North', 'South', 'Global'],
comout=os.path.join(comout, 'vrfy', 'bkgerr')), # sea ice baigerr stddev
plotConfig(grid_file=grid_file,
layer_file=layer_file,
data_file=os.path.join(comout, os.path.pardir, os.path.pardir,
'bmatrix', 'ocean', f'{RUN}.t'+cyc+'z.ocean.bkgerr_stddev.nc'),
'bmatrix', 'ocean', f'{RUN}.t'+cyc+'z.ocean.bkgerr_stddev.nc'),
lats=np.arange(-60, 60, 10),
lons=np.arange(-280, 80, 30),
variables_zonal={'Temp': [0, 2],
'Salt': [0, 0.2],
'u': [0, 0.2],
'v': [0, 0.2]},
'u': [0, 0.5],
'v': [0, 0.5]},
variables_meridional={'Temp': [0, 2],
'Salt': [0, 0.2],
'u': [0, 0.2],
'v': [0, 0.2]},
'u': [0, 0.5],
'v': [0, 0.5]},
variables_horiz={'Temp': [0, 2],
'Salt': [0, 0.2],
'u': [0, 0.2],
'v': [0, 0.2],
'u': [0, 0.5],
'v': [0, 0.5],
'ave_ssh': [0, 0.1]},
colormap='jet',
comout=os.path.join(comout, 'vrfy', 'bkgerr'))] # ocn bkgerr stddev
Expand All @@ -113,12 +133,18 @@
lats=np.arange(-60, 60, 10),
lons=np.arange(-280, 80, 30),
variables_zonal={'Temp': [-1.8, 34.0],
'Salt': [32, 40]},
'Salt': [32, 40],
'u': [-1.0, 1.0],
'v': [-1.0, 1.0]},
variables_meridional={'Temp': [-1.8, 34.0],
'Salt': [32, 40]},
'Salt': [32, 40],
'u': [-1.0, 1.0],
'v': [-1.0, 1.0]},
variables_horiz={'ave_ssh': [-1.8, 1.3],
'Temp': [-1.8, 34.0],
'Salt': [32, 40]},
'Salt': [32, 40],
'u': [-1.0, 1.0],
'v': [-1.0, 1.0]},
colormap='nipy_spectral',
comout=os.path.join(comout, 'vrfy', 'bkg'))]
configs.extend(config_bkg)
Expand Down Expand Up @@ -185,32 +211,33 @@ def plot_marine_vrfy(config):
#######################################
# eva plots
#######################################

evadir = os.path.join(HOMEgfs, 'sorc', f'{RUN}.cd', 'ush', 'eva')
marinetemplate = os.path.join(evadir, 'marine_gdas_plots.yaml')
varyaml = os.path.join(comout, 'yaml', 'var_original.yaml')

# it would be better to refrence the dirs explicitly with the comout path
# but eva doesn't allow for specifying output directories
os.chdir(os.path.join(comout, 'vrfy'))
if not os.path.exists('preevayamls'):
os.makedirs('preevayamls')
if not os.path.exists('evayamls'):
os.makedirs('evayamls')

gen_eva_obs_yaml.gen_eva_obs_yaml(varyaml, marinetemplate, 'preevayamls')

files = os.listdir('preevayamls')
for file in files:
infile = os.path.join('preevayamls', file)
marine_eva_post.marine_eva_post(infile, 'evayamls', diagdir)

files = os.listdir('evayamls')
for file in files:
infile = os.path.join('evayamls', file)
print('running eva on', infile)
subprocess.run(['eva', infile], check=True)

if run_eva_analysis:
evadir = os.path.join(HOMEgfs, 'sorc', f'{RUN}.cd', 'ush', 'eva')
marinetemplate = os.path.join(evadir, 'marine_gdas_plots.yaml')
varyaml = os.path.join(comout, 'yaml', 'var.yaml')

# it would be better to refrence the dirs explicitly with the comout path
# but eva doesn't allow for specifying output directories
os.chdir(os.path.join(comout, 'vrfy'))
if not os.path.exists('preevayamls'):
os.makedirs('preevayamls')
if not os.path.exists('evayamls'):
os.makedirs('evayamls')

gen_eva_obs_yaml.gen_eva_obs_yaml(varyaml, marinetemplate, 'preevayamls')

files = os.listdir('preevayamls')
for file in files:
infile = os.path.join('preevayamls', file)
marine_eva_post.marine_eva_post(infile, 'evayamls', diagdir)

files = os.listdir('evayamls')
for file in files:
infile = os.path.join('evayamls', file)
print('running eva on', infile)
subprocess.run(['eva', infile], check=True)
else:
print("RUN_EVA_PLOT is set to OFF. Skipping EVA plot generation.")
#######################################
# calculate diag statistics
#######################################
Expand Down
40 changes: 32 additions & 8 deletions utils/soca/fig_gallery/run_marine_analysis_vrfy_manual.job
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Original file line number Diff line number Diff line change
Expand Up @@ -11,10 +11,18 @@
#SBATCH --mem=24GB # Request 24GB of memory
#SBATCH --time=00:30:00 # Set the walltime limit to 30 minutes

# Define HOMEgfs
export HOMEgfs="/scratch1/NCEPDEV/da/Mindo.Choi/workflow_11122024/global-workflow/"
# Define Your HOMEgfs
export HOMEgfs="/scratch1/NCEPDEV/da/Mindo.Choi/wk_01152025/global-workflow/"

# Define Base_Direcrory (to the achieves for v2)
base_dir="/scratch1/NCEPDEV/global/John.Steffen/hpss_arch/marine_test_112024_v2"

# Define Target Date and cycle
tdate="20210701"
cyc="00"

# Load EVA module
module purge
module use ${HOMEgfs}sorc/gdas.cd/modulefiles
module load EVA/hera

Expand All @@ -28,18 +36,34 @@ $PYTHONPATH"
export RUN_ENSENBLE_ANALYSIS=OFF # Check if ensemble run is ON
export RUN_BACKGROUND_ERROR_ANALYSIS=ON
export RUN_BACKGROUND_ANALYSIS=ON
export RUN_INCREMENT_ANLYSIS=ON
export RUN_INCREMENT_ANALYSIS=ON
export RUN_EVA_ANALYSIS=ON

# Define and export the environment variables
export cyc="00"
# Calculate bcyc and gcyc
bcyc=$(printf "%02d" $(( (10#$cyc - 3 + 24) % 24 )))
gcyc=$(printf "%02d" $(( (10#$cyc - 6 + 24) % 24 )))

# Determine PDY_PREV if cyc is "00"
if [ "$cyc" == "00" ]; then
PDY_PREV=$(date -d "$tdate -1 day" +%Y%m%d)
else
PDY_PREV="$tdate"
fi

# Export the necessary environment variables
export cyc="$cyc"
export bcyc="$bcyc"
export gcyc="$gcyc"
export PDY="$tdate"
export PDY_PREV="$PDY_PREV"
export RUN="gdas"
export PSLOT="gdas_test"
export PDY="20210827"

# Define and export environment variables with paths
export COM_OCEAN_ANALYSIS="/scratch1/NCEPDEV/da/Mindo.Choi/sandbox/marine_vrfy/gdas.20210827/00/analysis/ocean"
export COM_ICE_HISTORY_PREV="/scratch1/NCEPDEV/da/Mindo.Choi/sandbox/marine_vrfy/gdas.20210826/18/model/ice/history"
export COM_OCEAN_HISTORY_PREV="/scratch1/NCEPDEV/da/Mindo.Choi/sandbox/marine_vrfy/gdas.20210826/18/model/ocean/history"
export COM_OCEAN_ANALYSIS="${base_dir}/${tdate}${cyc}/${RUN}.${tdate}/${cyc}/analysis/ocean"
export COM_ICE_HISTORY_PREV="${base_dir}/${PDY_PREV}${gcyc}/${RUN}.${PDY_PREV}/${gcyc}/model/ice/history"
export COM_OCEAN_HISTORY_PREV="${base_dir}/${PDY_PREV}${gcyc}/${RUN}.${PDY_PREV}/${gcyc}/model/ocean/history"

# Excute Marine Verify Analysis
python3 ${HOMEgfs}sorc/gdas.cd/utils/soca/fig_gallery/exgdas_global_marine_analysis_vrfy_manual.py

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