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additional default settings and command line args for land-atm DAS #94

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Merged
gmao-rreichle merged 35 commits into from
May 27, 2025
Merged

additional default settings and command line args for land-atm DAS #94

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888cca4
add setting defaults and more commdline options for ladas
saraqzhang Apr 25, 2025
07cde3d
additional edit for integrated configuration of land-atm DAS (ldas_se…
gmao-rreichle May 2, 2025
5bdce17
update input strings for agcm_res
saraqzhang May 2, 2025
29f77d8
add land BCs version input for ladas
saraqzhang May 5, 2025
a1a2533
cleanup of command line args for land-atm DAS config (ldas_setup)
gmao-rreichle May 6, 2025
2443b5a
updated CHANGELOG.md
gmao-rreichle May 6, 2025
7742280
changed handling of N_ens for coupled land-atm DAS setup (ldas_setup)
gmao-rreichle May 6, 2025
8a7c7fc
add README on construction of exeinp.txt for LADAS
saraqzhang May 6, 2025
01f0f63
minor cleanup as suggested by Weiyuan (ldas_setup)
gmao-rreichle May 7, 2025
f07f2e4
additional cleanup as suggested by Weiyuan for integrated land-atm DA…
gmao-rreichle May 7, 2025
0ec5846
change handling of BCS_PATH in setup of coupled land-atm DAS (ldas_se…
gmao-rreichle May 7, 2025
ab9c3c3
exclude AGCM defaults of GEOS_SurfaceGridComp.rc from sample exeinp f…
gmao-rreichle May 7, 2025
ea03973
further changes in setting exeinp & batinp variables
saraqzhang May 13, 2025
11dca45
minor cleanup to improve readability (ldas_setup)
gmao-rreichle May 13, 2025
7f115d9
additional changes and cleanup for integrated land-atm DAS config (ld…
gmao-rreichle May 13, 2025
ef43e7e
additional commandline inputs for ladas
saraqzhang May 15, 2025
7a023c9
minor edit insert adas_cyc input in JOB_SGMT
saraqzhang May 16, 2025
21e3584
Merge branch 'develop' into feature/saraqzhang/setupfunc4ladas
weiyuan-jiang May 19, 2025
86056e5
fixed errors in most recent merge (conflict resolution); white-space …
gmao-rreichle May 19, 2025
14f5186
remove README.exeinp.txt.forladas (no longer needed)
gmao-rreichle May 19, 2025
ae2717e
edits of previous commit (ldas_setup):
gmao-rreichle May 20, 2025
8dbd52a
edits on varwindow, walltime and nml path default
saraqzhang May 20, 2025
d36c72c
for coupled land-atm DAS, ensure consistency between LANDASSIM_DT and…
gmao-rreichle May 20, 2025
29a2b3c
clean up processing of defaults from GEOS_SurfaceGridComp.rc (ldas_se…
gmao-rreichle May 20, 2025
1352dbb
fixed indent error introduced in last commit (ldas_setup)
gmao-rreichle May 20, 2025
a3c4312
fixed py bugs from previous commit (ldas_setup)
gmao-rreichle May 21, 2025
5278ce0
skip writing extra lines with #agcm=> or #ldas=>
saraqzhang May 21, 2025
054ba56
no exeinp for adas coupling
weiyuan-jiang May 22, 2025
8a8c1d6
remove unnecessary message
weiyuan-jiang May 22, 2025
df1b1f3
minor changes for ladas_cpl case
saraqzhang May 22, 2025
4a1802e
additional changes and cleanup for coupled land-atm DAS (ldas_setup):
gmao-rreichle May 22, 2025
08a8078
fixed syntax error from previous commit (ldas_setup)
gmao-rreichle May 22, 2025
c3ca2d5
fix path to rc template files (ldas_setup)
gmao-rreichle May 22, 2025
0f220cb
cleaned up logic of processing defaults from GEOS_SurfaceGridComp.rc …
gmao-rreichle May 22, 2025
3d9121e
Merge branch 'develop' into feature/saraqzhang/setupfunc4ladas (manua…
gmao-rreichle May 22, 2025
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204 changes: 136 additions & 68 deletions GEOSldas_App/ldas_setup
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Original file line number Diff line number Diff line change
Expand Up @@ -70,59 +70,62 @@ class LDASsetup:
# sample sub-command
# by construction, we can have
# either: {'exeinp': False, 'batinp': 'lasgh'} <-- 'lasgh'???
# or: {'exeinp': True, 'batinp': None}
# or: {'exeinp': True, 'batinp': None }
if cmdLineArgs['exeinp']:
_printExeInputKeys(rqdExeInpKeys)
elif cmdLineArgs['batinp'] :
_printRmInputKeys(rqdRmInpKeys, optSlurmInpKeys)
else:
raise Exception('not recognized option')
raise Exception('unrecognized option')
sys.exit(0)

# ------
# ./ldsetup.py setup ...
# ------
# Instance variables
self.exeinpfile = cmdLineArgs['exeinpfile']
self.batinpfile = cmdLineArgs['batinpfile']
exphome_ = cmdLineArgs['exphome'].rstrip('/')
assert os.path.isdir(exphome_) # exphome should exist
self.exphome = os.path.abspath(exphome_)
self.nymdb = cmdLineArgs['nymdb']
self.nhmsb = cmdLineArgs['nhmsb']
self.verbose = cmdLineArgs['verbose']
self.runmodel = cmdLineArgs['runmodel']
self.exeinpfile = cmdLineArgs['exeinpfile']
self.batinpfile = cmdLineArgs['batinpfile']
exphome_ = cmdLineArgs['exphome'].rstrip('/')
assert os.path.isdir(exphome_) # exphome should exist
self.exphome = os.path.abspath(exphome_)
self.nymdb = cmdLineArgs['nymdb']
self.nhmsb = cmdLineArgs['nhmsb']
self.agcm_res = cmdLineArgs['agcm_res']
self.ladas_cpl = cmdLineArgs['ladas_cpl']
self.rstdir = cmdLineArgs['rstdir']
self.verbose = cmdLineArgs['verbose']
self.runmodel = cmdLineArgs['runmodel']
if self.runmodel :
print('\n The option "--runmodel" is out of date, not necessary anymore. \n')
self.daysperjob = cmdLineArgs['daysperjob']
self.monthsperjob = cmdLineArgs['monthsperjob']
self.rqdExeInp = OrderedDict()
self.rqdRmInp = OrderedDict()
self.optRmInp = OrderedDict()
self.rundir = None
self.blddir = None
self.blddirLn = None
self.outdir = None
self.out_path = None
self.inpdir = None
self.exefyl = None
self.islocal = False
self.catch = ''
self.has_mwrtm = False
self.has_vegopacity = False
self.assim = False
self.daysperjob = cmdLineArgs['daysperjob']
self.monthsperjob = cmdLineArgs['monthsperjob']
self.rqdExeInp = OrderedDict()
self.rqdRmInp = OrderedDict()
self.optRmInp = OrderedDict()
self.rundir = None
self.blddir = None
self.blddirLn = None
self.outdir = None
self.out_path = None
self.inpdir = None
self.exefyl = None
self.islocal = False
self.catch = ''
self.has_mwrtm = False
self.has_vegopacity = False
self.assim = False
self.has_landassim_seed = False
self.has_geos_pert = False
self.nSegments = 1
self.perturb = 0
self.first_ens_id = 0
self.ladas_coupling = 0
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 = ''
self.has_geos_pert = False
self.nSegments = 1
self.perturb = 0
self.first_ens_id = 0
self.ladas_coupling = 0
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 @@ -152,32 +155,79 @@ class LDASsetup:
if cmdLineArgs['nymdb'] != 'None' and cmdLineArgs['nhmsb'] != 'None' :
self.date = f"{self.nymdb} {self.nhmsb}"
self.rqdExeInp[ 'BEG_DATE' ] = self.date
if cmdLineArgs['ladas_cpl'] != 'None' :
self.lacase = self.ladas_cpl
self.rqdExeInp['LADAS_COUPLING'] = self.lacase
if cmdLineArgs['agcm_res'] != 'None' :
res_string = self.agcm_res
if len(res_string) == 4 :
adres = res_string.replace("C", "0")
if len(res_string) == 3 :
adres = res_string.replace("C", "00")
self.adasdomain = adres
if cmdLineArgs['rstdir'] != 'None' :
rstdir_ = cmdLineArgs['rstdir'].rstrip('/') # remove trailing '/'
assert os.path.isdir(rstdir_) # ldas exp for rs should exist
self.rstdir = os.path.abspath(rstdir_)

# print rqd exe inputs
if self.verbose:
print ('\nInputs from execfile:\n')
_printdict(self.rqdExeInp)

# nens is an integer and =1 for model run
self.nens = int(self.rqdExeInp['NUM_LDAS_ENSEMBLE']) # fail if Nens's val is not int
self.nens = int(self.rqdExeInp['NUM_LDAS_ENSEMBLE']) # fail if Nens's val is not int
assert self.nens>0, 'NUM_LDAS_ENSEMBLE [%d] <= 0' % self.nens
_mydir = self.exphome + '/' + self.rqdExeInp['EXP_ID']
assert not os.path.isdir(_mydir), 'Dir [%s] already exists!' % _mydir
_mydir = None
self.ladas_coupling = int(self.rqdExeInp.get('LADAS_COUPLING',0))
self.adas_expdir =''
self.first_ens_id = int(self.rqdExeInp.get('FIRST_ENS_ID',0))

### check if ldas is coupled to adas; if so, set input parameters accordingly
self.ladas_coupling = int(self.rqdExeInp.get('LADAS_COUPLING',0))
self.adas_expdir = ''
if self.ladas_coupling > 0 :
self.adas_expdir = os.path.dirname(self.exphome)
self.rqdExeInp[ 'ADAS_EXPDIR'] = self.adas_expdir
self.adas_expid = os.path.basename(self.adas_expdir)
self.rqdExeInp[ 'MET_TAG' ] = self.adas_expid + '__bkg'
self.adas_expdir = os.path.dirname(self.exphome)
self.rqdExeInp['ADAS_EXPDIR'] = self.adas_expdir
self.adas_expid = os.path.basename(self.adas_expdir)
self.rqdExeInp['MET_TAG'] = self.adas_expid + '__bkg'
if self.ladas_coupling == 1 :
self.rqdExeInp[ 'EXP_ID' ] = self.adas_expid + '_LDAS'
if self.ladas_coupling == 2 :
self.rqdExeInp[ 'EXP_ID' ] = self.adas_expid + '_LDAS4ens'
self.rqdExeInp[ 'MET_PATH' ] = self.adas_expdir +'/atmens/mem'

self.first_ens_id = int(self.rqdExeInp.get('FIRST_ENS_ID',0))
# ldas coupled with determistic component of adas
self.rqdExeInp['EXP_ID'] = self.adas_expid + '_LDAS'
self.rqdExeInp['MET_PATH'] = self.adas_expdir + '/recycle/holdpredout'
self.rqdExeInp['ENSEMBLE_FORCING'] = 'NO'
self.nens = 24
elif self.ladas_coupling == 2 :
# ldas coupled with ensemble component of adas
self.rqdExeInp['EXP_ID'] = self.adas_expid + '_LDAS4ens'
self.rqdExeInp['MET_PATH'] = self.adas_expdir + '/atmens/mem'
self.rqdExeInp['ENSEMBLE_FORCING'] = 'YES'
self.nens = 32
else :
exit("Error. Unknown value of ladas_coupling.\n")
self.rqdExeInp['NUM_LDAS_ENSEMBLE'] = self.nens
self.first_ens_id = 1
self.rqdExeInp['FIRST_ENS_ID'] = self.first_ens_id
self.rqdExeInp['EXP_DOMAIN'] = 'CF'+ self.adasdomain +'x6C_GLOBAL'
self.rqdExeInp['BCS_RESOLUTION'] = 'CF'+ self.adasdomain +'x6C_CF' + self.adasdomain +'x6C'
self.rqdExeInp['RESTART_DOMAIN'] = 'CF'+ self.adasdomain +'x6C_GLOBAL'
self.rsdir = os.path.dirname(self.rstdir)
self.rqdExeInp[ 'RESTART_PATH' ] = self.rsdir
self.rqdExeInp[ 'RESTART_ID' ] = os.path.basename(self.rstdir)
# the following are not in default rqdExeInp list
self.met_hinterp = int(self.rqdExeInp.get('MET_HINTERP',0))
self.rqdExeInp['MET_HINTERP'] = 0
self.landassim_dt = str(self.rqdExeInp.get('LANDASSIM_DT', "10800"))
self.rqdExeInp['LANDASSIM_DT'] = "10800"
self.landassim_t0 = str(self.rqdExeInp.get('LANDASSIM_T0', "013000"))
self.rqdExeInp['LANDASSIM_T0'] = "013000"
jobsgmtdef = "00000000 060000"
self.jobsgmt = str(self.rqdExeInp.get('JOB_SGMT', jobsgmtdef ))
self.rqdExeInp['JOB_SGMT'] = jobsgmtdef
self.num_sgmt = int(self.rqdExeInp.get('NUM_SGMT', 1))
self.rqdExeInp['NUM_SGMT'] = 1
###

self.perturb = int(self.rqdExeInp.get('PERTURBATIONS',0))
if self.nens > 1:
self.perturb = 1
Expand Down Expand Up @@ -234,12 +284,6 @@ class LDASsetup:

if 'NUM_SGMT' not in self.rqdExeInp:
self.rqdExeInp['NUM_SGMT'] = 1
# hard set NUM_SGMT and NUM_SGMT
if (self.ladas_coupling > 0) :
if int(self.rqdExeInp['NUM_SGMT']) != 1 :
sys.exit("'NUM_SGMT' should be set to 1 with LADAS_COUPLING")
if self.rqdExeInp['JOB_SGMT'] != "00000000 060000" :
sys.exit("'JOB_SGMT' should be set to 00000000 060000 with LADAS_COUPLING")

_years = int(self.rqdExeInp['JOB_SGMT'][0:4])
_months = int(self.rqdExeInp['JOB_SGMT'][4:6])
Expand Down Expand Up @@ -671,7 +715,7 @@ class LDASsetup:
status = True
return status

# create link, BCs , restarts
# create links to BCs, restarts, met forcing, ...
def createLnRstBc(self) :
# link bld dir
status = False
Expand Down Expand Up @@ -1061,6 +1105,9 @@ class LDASsetup:
special_nml=[]
if 'NML_INPUT_PATH' in self.rqdExeInp :
special_nml = glob.glob(self.rqdExeInp['NML_INPUT_PATH']+'/LDASsa_SPECIAL_inputs_*.nml')
if self.ladas_coupling > 0:
special_nml = glob.glob(self.rqdExeInp['NML_INPUT_PATH']+'/'+ self.rqdExeInp['EXP_DOMAIN'] + '/LDASsa_SPECIAL_inputs_*.nml')

for nmlfile in special_nml:
shortfile=nmlfile.split('/')[-1]
shutil.copy2(nmlfile, self.rundir+'/'+shortfile)
Expand Down Expand Up @@ -1560,12 +1607,13 @@ def _printExeInputKeys(rqdExeInpKeys):
print ('# Coupling of LDAS to ADAS ("LADAS"): #')
print ('# #')
print ('# 0 -- LDAS not coupled with ADAS (default) #')
print ('# 1 -- LDAS coupled with central member of ADAS #')
print ('# 1 -- LDAS coupled with central (det) member of ADAS #')
print ('# 2 -- LDAS coupled with ens component of ADAS #')
print ('# #')
print ('# Requirements for LADAS_COUPLING > 0: #')
print ('# Requirements for LADAS_COUPLING > 0 are as follows, #')
print ('# with most requirements hardwired into ldas_setup: #')
print ('# #')
print ('# (0) Specify ADAS_EXPDIR = [full_path]/[ADAS_EXPID] #')
print ('# (0) ADAS_EXPDIR = [full_path]/[ADAS_EXPID] #')
print ('# #')
print ('# (1) BEG_DATE must be consistent with first cycle date #')
print ('# and time of ADAS experiment (time is typically #')
Expand All @@ -1591,7 +1639,8 @@ def _printExeInputKeys(rqdExeInpKeys):
print ('# (7) HISTORY: #')
print ('# - instantaneous "catch_progn_incr" must be in #')
print ('# HISTORY collection #')
print ('# - time step must match that of LDAS analysis #')
print ('# - time step must be consistent with that of #')
print ('# LDAS analysis #')
print ('# - for LADAS_COUPLING=2, HISTORY must include #')
print ('# "catch_progn_incr[ENS_INDEX]" #')
print ('# #')
Expand Down Expand Up @@ -1697,7 +1746,7 @@ def parseCmdLine():
)
group.add_argument(
'--batinp',
help='print sample input file for SLURM ',
help='print sample input file for the resource manager (SLURM)',
action='store_true',
)
# subparser: setup command
Expand All @@ -1706,7 +1755,7 @@ def parseCmdLine():
help='setup LDAS experiment',
description="The 'setup' sub-command is used to setup a GEOSldas " \
"experiment. The positional argument 'exphome' is used to create " \
"work_path (exphome+/output) and run_path (exphome+/run)."
"work_path (=exphome+/output) and run_path (=exphome+/run)."
)
p_setup.add_argument(
'-v',
Expand All @@ -1723,21 +1772,40 @@ def parseCmdLine():
'batinpfile',
help='input file with arguments for SLURM',
)

# the following command line arguments, if present, take precedence over what
# is specified in the exeinp and batinp files
p_setup.add_argument(
'--account',
help='replace computing/sponsor account in batinp file',
help='overwrites computing/sponsor account from batinp file',
type=str, default='None'
)
p_setup.add_argument(
'--nymdb',
help='replaces BEG_DATE date in exeinp file ',
help='overwrites date in BEG_DATE from exeinp file',
type=str, default='None'
)
p_setup.add_argument(
'--nhmsb',
help='replaces BEG_DATE time in exeinp file ',
help='overwrites time in BEG_DATE from exeinp file',
type=str, default='None'
)
p_setup.add_argument(
'--ladas_cpl',
help='specifies LDAS/ADAS coupling mode: (1) ADAS deterministic member or (2) ADAS ensemble',
type=str, default='None'
)
p_setup.add_argument(
'--agcm_res',
help='specifies AGCM resolution of coupled ADAS component',
type=str, default='None'
)
p_setup.add_argument(
'--rstdir',
help='specifies LDAS restart dir (exp path/exp id)',
type=str, default='None'
)

p_setup.add_argument(
'--runmodel',
help='Obsolete.',
Expand Down
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