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Merge branch 'develop' into release/MAPL-v3
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# Conflicts:
#	components.yaml
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@mathomp4
mathomp4 committed Feb 21, 2024
2 parents a4bbdbc + 20c9649 commit 0d0a8db
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1 change: 1 addition & 0 deletions components.yaml
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Expand Up @@ -37,6 +37,7 @@ GEOS_Util:
local: ./src/Shared/@GMAO_Shared/@GEOS_Util
remote: ../GEOS_Util.git
branch: release/MAPL-v3
sparse: ./config/GEOS_Util.sparse
develop: main

MAPL:
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3 changes: 3 additions & 0 deletions config/GEOS_Util.sparse
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@@ -0,0 +1,3 @@
/CMakeLists.txt
/pre/remap_restart
/pre/CMakeLists.txt
2 changes: 1 addition & 1 deletion src/Applications/LDAS_App/CMakeLists.txt
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Expand Up @@ -21,7 +21,7 @@ ecbuild_add_executable (

set (scripts
process_hist.csh
process_rst.py
remap_config_ldas.py
ens_forcing/average_ensemble_forcing.py
ens_forcing/ensemble_forc.py
ens_forcing/regrid_forc.csh
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86 changes: 41 additions & 45 deletions src/Applications/LDAS_App/ldas_setup
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ from collections import OrderedDict
from dateutil.relativedelta import relativedelta
from remap_utils import *
from remap_catchANDcn import *
from process_rst import *
from remap_config_ldas import *

"""
This script is intended to be run from any installed directory with GEOSldas.x and ldas_setup
Expand Down Expand Up @@ -122,6 +122,10 @@ class LDASsetup:
self.in_rstfile = None
self.in_tilefile = 'None' # default string
self.ens_id_width = 6 # _eXXXX
self.bcs_land = ''
self.bcs_geom = ''
self.bcs_landshared = ''

# ------
# Read exe input file which is required to set up the dir
# ------
Expand Down Expand Up @@ -251,17 +255,18 @@ class LDASsetup:
_d = _d+ _difftime

# make sure path is path
if self.rqdExeInp['BCS_PATH'][-1] != '/':
self.rqdExeInp['BCS_PATH'] = self.rqdExeInp['BCS_PATH']+'/'
self.rqdExeInp['BCS_PATH'] = self.rqdExeInp['BCS_PATH']+self.rqdExeInp['BCS_RESOLUTION']+'/'
self.bcs_land = self.rqdExeInp['BCS_PATH']+ '/land/' + self.rqdExeInp['BCS_RESOLUTION']+'/'
self.bcs_geom = self.rqdExeInp['BCS_PATH']+ '/geometry/' + self.rqdExeInp['BCS_RESOLUTION']+'/'
self.bcs_landshared = self.rqdExeInp['BCS_PATH']+ '/land/shared/'

if self.rqdExeInp['MET_PATH'][-1] != '/':
self.rqdExeInp['MET_PATH'] = self.rqdExeInp['MET_PATH']+'/'
if self.rqdExeInp['RESTART_PATH'][-1] != '/':
self.rqdExeInp['RESTART_PATH'] = self.rqdExeInp['RESTART_PATH']+'/'

# make sure catchment and vegdyn restart files ( at least one for each) exist
if 'CATCH_DEF_FILE' not in self.rqdExeInp:
self.rqdExeInp['CATCH_DEF_FILE']=self.rqdExeInp['BCS_PATH']+'clsm/catchment.def'
self.rqdExeInp['CATCH_DEF_FILE']= self.bcs_land + 'clsm/catchment.def'
assert os.path.isfile(self.rqdExeInp['CATCH_DEF_FILE']),"[%s] file does not exist " % self.rqdExeInp['CATCH_DEF_FILE']

self.rqdExeInp['RST_FROM_GLOBAL'] = 1
Expand All @@ -280,21 +285,21 @@ class LDASsetup:

self.rqdExeInp['LNFM_FILE'] = ''
if int(self.rqdExeInp['RST_FROM_GLOBAL']) == 1 :
self.rqdExeInp['TILING_FILE'] =glob.glob(self.rqdExeInp['BCS_PATH']+'*.til')[0]
self.rqdExeInp['GRN_FILE']= glob.glob(self.rqdExeInp['BCS_PATH']+'green_clim_*.data')[0]
self.rqdExeInp['LAI_FILE']= glob.glob(self.rqdExeInp['BCS_PATH']+'lai_clim_*.data')[0]
tmp_ = glob.glob(self.rqdExeInp['BCS_PATH']+'lnfm_clim_*.data')
self.rqdExeInp['TILING_FILE'] =glob.glob(self.bcs_geom + '*.til')[0]
self.rqdExeInp['GRN_FILE']= glob.glob(self.bcs_land + 'green_clim_*.data')[0]
self.rqdExeInp['LAI_FILE']= glob.glob(self.bcs_land + 'lai_clim_*.data')[0]
tmp_ = glob.glob(self.bcs_land + 'lnfm_clim_*.data')
if (len(tmp_) ==1) :
self.rqdExeInp['LNFM_FILE'] = tmp_[0]
self.rqdExeInp['NDVI_FILE']= glob.glob(self.rqdExeInp['BCS_PATH']+'ndvi_clim_*.data')[0]
self.rqdExeInp['NIRDF_FILE']= glob.glob(self.rqdExeInp['BCS_PATH']+'nirdf_*.dat')[0]
self.rqdExeInp['VISDF_FILE']= glob.glob(self.rqdExeInp['BCS_PATH']+'visdf_*.dat')[0]
self.rqdExeInp['NDVI_FILE'] = glob.glob(self.bcs_land + 'ndvi_clim_*.data')[0]
self.rqdExeInp['NIRDF_FILE']= glob.glob(self.bcs_land + 'nirdf_*.dat')[0]
self.rqdExeInp['VISDF_FILE']= glob.glob(self.bcs_land + 'visdf_*.dat')[0]
else :
inpdir=self.rqdExeInp['RESTART_PATH']+self.rqdExeInp['RESTART_ID']+'/input/'
self.rqdExeInp['TILING_FILE'] =os.path.realpath(glob.glob(inpdir+'*tile.data')[0])
self.rqdExeInp['GRN_FILE']= os.path.realpath(glob.glob(inpdir+'green*data')[0])
self.rqdExeInp['LAI_FILE']= os.path.realpath(glob.glob(inpdir+'lai*data')[0])
tmp_ = glob.glob(self.rqdExeInp['BCS_PATH']+'lnfm_clim_*.data')
tmp_ = glob.glob(self.bcs_land + 'lnfm_clim_*.data')
if (len(tmp_) == 1) :
self.rqdExeInp['LNFM_FILE'] = tmp_[0]
self.rqdExeInp['NDVI_FILE']= os.path.realpath(glob.glob(inpdir+'ndvi*data')[0])
Expand All @@ -318,16 +323,16 @@ class LDASsetup:

if os.path.isfile(ldas_domain) :
_numd = int(linecache.getline(ldas_domain, 1).strip())
self.rqdExeInp['TILING_FILE'] =glob.glob(self.rqdExeInp['BCS_PATH']+'*.til')[0]
self.rqdExeInp['GRN_FILE']= glob.glob(self.rqdExeInp['BCS_PATH']+'green_clim_*.data')[0]
self.rqdExeInp['LAI_FILE']= glob.glob(self.rqdExeInp['BCS_PATH']+'lai_clim_*.data')[0]
tmp_ = glob.glob(self.rqdExeInp['BCS_PATH']+'lnfm_clim_*.data')
self.rqdExeInp['TILING_FILE'] =glob.glob(self.bcs_geom + '*.til')[0]
self.rqdExeInp['GRN_FILE']= glob.glob(self.bcs_land + 'green_clim_*.data')[0]
self.rqdExeInp['LAI_FILE']= glob.glob(self.bcs_land + 'lai_clim_*.data')[0]
tmp_ = glob.glob(self.bcs_land + 'lnfm_clim_*.data')
if (len(tmp_) == 1) :
self.rqdExeInp['LNFM_FILE'] = tmp_[0]
self.rqdExeInp['LNFM_FILE']= glob.glob(self.rqdExeInp['BCS_PATH']+'lnfm_clim_*.data')[0]
self.rqdExeInp['NDVI_FILE']= glob.glob(self.rqdExeInp['BCS_PATH']+'ndvi_clim_*.data')[0]
self.rqdExeInp['NIRDF_FILE']= glob.glob(self.rqdExeInp['BCS_PATH']+'nirdf_*.dat')[0]
self.rqdExeInp['VISDF_FILE']= glob.glob(self.rqdExeInp['BCS_PATH']+'visdf_*.dat')[0]
self.rqdExeInp['LNFM_FILE'] = glob.glob(self.bcs_land + 'lnfm_clim_*.data')[0]
self.rqdExeInp['NDVI_FILE'] = glob.glob(self.bcs_land + 'ndvi_clim_*.data')[0]
self.rqdExeInp['NIRDF_FILE']= glob.glob(self.bcs_land + 'nirdf_*.dat')[0]
self.rqdExeInp['VISDF_FILE']= glob.glob(self.bcs_land + 'visdf_*.dat')[0]

if 'GRIDNAME' not in self.rqdExeInp :
tmptile =self.rqdExeInp['TILING_FILE']
Expand Down Expand Up @@ -800,7 +805,7 @@ class LDASsetup:
os.symlink(bc,myBC)

if ("catchcn" in self.catch):
os.symlink(self.rqdExeInp['BCS_PATH']+'../land/shared/CO2_MonthlyMean_DiurnalCycle.nc4', \
os.symlink(self.bcs_landshared + 'CO2_MonthlyMean_DiurnalCycle.nc4', \
self.inpdir+'/CO2_MonthlyMean_DiurnalCycle.nc4')

# create and link restart
Expand All @@ -819,7 +824,7 @@ class LDASsetup:
self.rqdExeInp['RESTART_ID'] + \
'/output/'+self.rqdExeInp['RESTART_DOMAIN']+'/rc_out/'

# pass into process_rst
# pass into remap_config_ldas
sponsorid = self.rqdRmInp['account']
exp_id = self.rqdExeInp['EXP_ID']
exp_dir = self.exphome
Expand All @@ -843,17 +848,19 @@ class LDASsetup:
os.symlink(_seeds, myRstDir+ '/landassim_obspertrseed'+ _ensid +'_rst')
self.has_landassim_seed = True
mk_outdir = self.exphome+'/'+exp_id+'/mk_restarts/'
cmd= ' '.join(['./process_rst.csh', sponsorid, exp_id, mk_outdir,
out_bcdir, out_tilefile, self.catch, RESTART_str, YYYYMMDDHH,
self.in_rstfile, self.in_tilefile, dzsf, wemin_in, wemin_out])

if (RESTART_str != '1'):
bcs_path = self.rqdExeInp['BCS_PATH']
while bcs_path[-1] == '/' : bcs_path = bcs_path[0:-1]
bc_base = os.path.dirname(bcs_path)
bc_version = os.path.basename(bcs_path)

remap_tpl = os.path.dirname(os.path.realpath(__file__)) + '/remap_params.tpl'
config = yaml_to_config(remap_tpl)

config['slurm']['account'] = self.rqdRmInp['account']
config['slurm']['qos'] = 'debug'
config['slurm']['qos'] = 'cas'
config['slurm']['constraint'] = 'cas|sky'

config['input']['surface']['catch_tilefile'] = self.in_tilefile
config['input']['shared']['expid'] = self.rqdExeInp['RESTART_ID']
Expand All @@ -865,7 +872,10 @@ class LDASsetup:
config['output']['shared']['out_dir'] = mk_outdir
config['output']['surface']['catch_remap'] = True
config['output']['surface']['catch_tilefile'] = self.rqdExeInp['TILING_FILE']
config['output']['shared']['bcs_dir'] = self.rqdExeInp['BCS_PATH']
config['output']['shared']['bc_base'] = bc_base
config['output']['shared']['bc_version'] = bc_version
config['output']['surface']['EASE_grid'] = self.rqdExeInp['BCS_RESOLUTION']

config['output']['shared']['expid'] = self.rqdExeInp['EXP_ID']
config['output']['surface']['surflay'] = dzsf
config['output']['surface']['wemin'] = wemin_out
Expand All @@ -875,20 +885,6 @@ class LDASsetup:
catch_obj = catchANDcn(config_obj = config)
catch_obj.remap()

#print "cmd: " + cmd
#os.system(cmd)

#done_rst=self.exphome+'/'+exp_id+'/mk_restarts/done_rst_file'
#print "Please hold on for a while until the restart file is created ....."
#_animation = "|/-\\"
#_idx = 0
#while not os.path.isfile(done_rst):
# sys.stdout.write('\r'+_animation[_idx % len(_animation)])
# sys.stdout.flush()
# _idx += 1
# time.sleep(1.)


#for ens in self.ensdirs :
catchRstFile0 = ''
vegdynRstFile0 = ''
Expand All @@ -907,16 +903,16 @@ class LDASsetup:
if self.rqdExeInp['RESTART'].isdigit() :

if int(self.rqdExeInp['RESTART']) == 0 or int(self.rqdExeInp['RESTART']) == 2 :
vegdynRstFile = glob.glob(self.rqdExeInp['BCS_PATH']+'vegdyn_*.dat')[0]
vegdynRstFile = glob.glob(self.bcs_land + 'vegdyn_*.dat')[0]
catchRstFile = glob.glob(self.exphome+'/'+exp_id+'/mk_restarts/*'+self.catch+'_internal_rst.'+YYYYMMDD+'*')[0]
else : # RESTART == 1
catchRstFile = rstpath+ensdir +'/'+ y4m2+'/'+self.rqdExeInp['RESTART_ID']+'.'+self.catch+'_internal_rst.'+y4m2d2_h2m2
vegdynRstFile= rstpath+ensdir +'/'+self.rqdExeInp['RESTART_ID']+ '.vegdyn_internal_rst'
if not os.path.isfile(vegdynRstFile): # no vegdyn restart from LDASsa
if not os.path.isfile(vegdynRstFile0):
vegdynRstFile = glob.glob(self.rqdExeInp['BCS_PATH']+'vegdyn_*.dat')[0]
vegdynRstFile = glob.glob(self.bcs_land + 'vegdyn_*.dat')[0]
else :
vegdynRstFile = glob.glob(self.rqdExeInp['BCS_PATH']+'vegdyn_*.dat')[0]
vegdynRstFile = glob.glob(self.bcs_land + 'vegdyn_*.dat')[0]
catchRstFile = glob.glob(self.exphome+'/'+exp_id+'/mk_restarts/*'+self.catch+'_internal_rst.'+YYYYMMDD+'*')[0]

# catchment restart file
Expand Down
20 changes: 16 additions & 4 deletions src/Applications/LDAS_App/process_rst.py → ...pplications/LDAS_App/remap_config_ldas.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,8 +16,12 @@ def remap_config_ldas(config, RESTART_str, RESTART_PATH, RESTART_ID):
config['input']['shared'] = merra2_expid(config['input']['shared'])
config['input']['shared']['rst_dir'] = out_dir+ '/merra2_tmp_'+ yyyymmddhh
config['input']['surface']['wemin'] = 26
config['input']['shared']['bcs_dir'] = '/discover/nobackup/projects/gmao/bcs_shared/legacy_bcs/Ganymed-4_0/Ganymed-4_0_MERRA-2/CF0180x6C_DE1440xPE0720/'

config['input']['shared']['bc_base'] = '/discover/nobackup/projects/gmao/bcs_shared/fvInput/ExtData/esm/tiles'
config['input']['shared']['bc_version'] = 'GM4'
config['input']['shared']['agrid'] = 'C180'
config['input']['shared']['ogrid'] = '1440x720'
config['input']['shared']['omodel'] = 'data'

if RESTART_str == "G" :
# WY note: it is a bad idea to overload restart_path and restart_id
config['input']['surface']['catch_tilefile'] = os.path.realpath(RESTART_ID+'scratch/tile.data')
Expand All @@ -39,15 +43,23 @@ def remap_config_ldas(config, RESTART_str, RESTART_PATH, RESTART_ID):
print( " Please select RESTART: M and use MERRA-2, instead.")
sys.exit(1)

config['input']['shared']['bcs_dir'] = '/discover/nobackup/projects/gmao/bcs_shared/legacy_bcs/Icarus/Icarus_Ostia/CF0720x6C_CF0720x6C/'
config['input']['shared']['bc_base'] = '/discover/nobackup/projects/gmao/bcs_shared/fvInput/ExtData/esm/tiles'
config['input']['shared']['bc_version'] = 'ICA'
config['input']['shared']['agrid'] = 'C720'
config['input']['shared']['ogrid'] = 'C720'

config['input']['surface']['wemin'] = 26
config['input']['shared']['rst_dir'] = out_dir+'/InData'+ '/'
suffix = '_21z.tar'

if ((date_16 <= expdate) and (expdate < date_17)):
fpver = 'GEOS-5.16/GEOSadas-5_16/'
fplab = 'f516_fp'
config['input']['shared']['bcs_dir'] = '/discover/nobackup/projects/gmao/bcs_shared/legacy_bcs/Ganymed-4_0/Ganymed-4_0_Ostia/CF0720x6C_DE2880xPE1440/'
config['input']['shared']['bc_base'] = '/discover/nobackup/projects/gmao/bcs_shared/fvInput/ExtData/esm/tiles'
config['input']['shared']['bc_version'] = 'GM4'
config['input']['shared']['agrid'] = 'C720'
config['input']['shared']['ogrid'] = '2880x1440'

suffix = '_21z.bin'

if ((date_17 <= expdate) and (expdate < date_21)):
Expand Down

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