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working version of refactoring
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@TeaganKing
TeaganKing committed Feb 13, 2024
1 parent c030c23 commit 2744f79
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Showing 5 changed files with 270 additions and 181 deletions.
1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -111,6 +111,7 @@ unit_test_build
/tools/site_and_regional/????.ad/
/tools/site_and_regional/????.postad/
/tools/site_and_regional/????.transient/
/tools/site_and_regional/archive/

# build output
*.o
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4 changes: 2 additions & 2 deletions cime_config/buildnml
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Expand Up @@ -144,8 +144,8 @@ def buildnml(case, caseroot, compname):
or clm_usrdat_name is "NEON.PRISM"
):
logger.warning(
"WARNING: Do you have approriprate initial conditions for this simulation?"
+ " Check that the finidat file used in the lnd_in namelist is apprporiately spunup for your case"
"WARNING: Do you have appropriate initial conditions for this simulation?"
+ " Check that the finidat file used in the lnd_in namelist is appropriately spunup for your case"
)

if comp_atm != "datm":
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198 changes: 20 additions & 178 deletions python/ctsm/site_and_regional/neon_site.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,10 @@
_CTSM_PYTHON = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..", "python"))
sys.path.insert(1, _CTSM_PYTHON)

# -- import local classes for this script
# pylint: disable=wrong-import-position
from ctsm.site_and_regional.tower_site import TowerSite

# pylint: disable=wrong-import-position, import-error, unused-import, wrong-import-order
from ctsm import add_cime_to_path
from ctsm.path_utils import path_to_ctsm_root
Expand All @@ -27,126 +31,23 @@


# pylint: disable=too-many-instance-attributes
class NeonSite:
class NeonSite(TowerSite):
"""
A class for encapsulating neon sites.
"""

def __init__(self, name, start_year, end_year, start_month, end_month, finidat):
self.name = name
self.start_year = int(start_year)
self.end_year = int(end_year)
self.start_month = int(start_month)
self.end_month = int(end_month)
self.cesmroot = path_to_ctsm_root()
self.finidat = finidat
super().__init__(name, start_year, end_year, start_month, end_month, finidat)

def build_base_case(
self, cesmroot, output_root, res, compset, overwrite=False, setup_only=False
):
"""
Function for building a base_case to clone.
To spend less time on building ctsm for the neon cases,
all the other cases are cloned from this case
Args:
self:
The NeonSite object
base_root (str):
root of the base_case CIME
res (str):
base_case resolution or gridname
compset (str):
base case compset
overwrite (bool) :
Flag to overwrite the case if exists
"""
print("---- building a base case -------")
# pylint: disable=attribute-defined-outside-init
self.base_case_root = output_root
# pylint: enable=attribute-defined-outside-init
user_mods_dirs = [os.path.join(cesmroot, "cime_config", "usermods_dirs", "NEON", self.name)]
if not output_root:
output_root = os.getcwd()
case_path = os.path.join(output_root, self.name)

logger.info("base_case_name : %s", self.name)
logger.info("user_mods_dir : %s", user_mods_dirs[0])

if overwrite and os.path.isdir(case_path):
print("Removing the existing case at: {}".format(case_path))
shutil.rmtree(case_path)

with Case(case_path, read_only=False) as case:
if not os.path.isdir(case_path):
print("---- creating a base case -------")
case_path = super().build_base_case(cesmroot, output_root, res, compset)

case.create(
case_path,
cesmroot,
compset,
res,
run_unsupported=True,
answer="r",
output_root=output_root,
user_mods_dirs=user_mods_dirs,
driver="nuopc",
)

print("---- base case created ------")

# --change any config for base_case:
# case.set_value("RUN_TYPE","startup")
print("---- base case setup ------")
case.case_setup()
else:
# For existing case check that the compset name is correct
existingcompname = case.get_value("COMPSET")
match = re.search("^HIST", existingcompname, flags=re.IGNORECASE)
if re.search("^HIST", compset, flags=re.IGNORECASE) is None:
expect(
match is None,
"""Existing base case is a historical type and should not be
--rerun with the --overwrite option""",
)
else:
expect(
match is not None,
"""Existing base case should be a historical type and is not
--rerun with the --overwrite option""",
)
# reset the case
case.case_setup(reset=True)
case_path = case.get_value("CASEROOT")

if setup_only:
return case_path

print("---- base case build ------")
print("--- This may take a while and you may see WARNING messages ---")
# always walk through the build process to make sure it's up to date.
initial_time = time.time()
build.case_build(case_path, case=case)
end_time = time.time()
total = end_time - initial_time
print("Time required to building the base case: {} s.".format(total))
# update case_path to be the full path to the base case
return case_path

# pylint: disable=no-self-use
def get_batch_query(self, case):
"""
Function for querying the batch queue query command for a case, depending on the
user's batch system.
Args:
case:
case object
"""

if case.get_value("BATCH_SYSTEM") == "none":
return "none"
return case.get_value("batch_query")
return super().get_batch_query(case)

# pylint: disable=too-many-statements
def run_case(
Expand Down Expand Up @@ -190,7 +91,7 @@ def run_case(
"""
user_mods_dirs = [
os.path.join(self.cesmroot, "cime_config", "usermods_dirs", "NEON", self.name)
]
] #TODO: bring into neon_site
expect(
os.path.isdir(base_case_root),
"Error base case does not exist in {}".format(base_case_root),
Expand Down Expand Up @@ -272,9 +173,9 @@ def run_case(
case.set_value("STOP_OPTION", "ndays")
case.set_value("REST_OPTION", "end")
case.set_value("CONTINUE_RUN", False)
case.set_value("NEONVERSION", version)
case.set_value("NEONVERSION", version) #TODO: put in neon_site
if prism:
case.set_value("CLM_USRDAT_NAME", "NEON.PRISM")
case.set_value("CLM_USRDAT_NAME", "NEON.PRISM") #TODO: put in neon_site

if run_type == "ad":
case.set_value("CLM_FORCE_COLDSTART", "on")
Expand Down Expand Up @@ -321,74 +222,15 @@ def run_case(
print(f"Use {batch_query} to check its run status")

def set_ref_case(self, case):
"""
Set an existing case as the reference case, eg for use with spinup.
"""
rundir = case.get_value("RUNDIR")
case_root = case.get_value("CASEROOT")
if case_root.endswith(".postad"):
ref_case_root = case_root.replace(".postad", ".ad")
root = ".ad"
else:
ref_case_root = case_root.replace(".transient", ".postad")
root = ".postad"
if not os.path.isdir(ref_case_root):
logger.warning(
"ERROR: spinup must be completed first, could not find directory %s", ref_case_root
)
return False

with Case(ref_case_root) as refcase:
refrundir = refcase.get_value("RUNDIR")
case.set_value("RUN_REFDIR", refrundir)
case.set_value("RUN_REFCASE", os.path.basename(ref_case_root))
refdate = None
for reffile in glob.iglob(refrundir + "/{}{}.clm2.r.*.nc".format(self.name, root)):
m_searched = re.search(r"(\d\d\d\d-\d\d-\d\d)-\d\d\d\d\d.nc", reffile)
if m_searched:
refdate = m_searched.group(1)
symlink_force(reffile, os.path.join(rundir, os.path.basename(reffile)))
logger.info("Found refdate of %s", refdate)
if not refdate:
logger.warning("Could not find refcase for %s", case_root)
return False

for rpfile in glob.iglob(refrundir + "/rpointer*"):
safe_copy(rpfile, rundir)
if not os.path.isdir(os.path.join(rundir, "inputdata")) and os.path.isdir(
os.path.join(refrundir, "inputdata")
):
symlink_force(os.path.join(refrundir, "inputdata"), os.path.join(rundir, "inputdata"))

case.set_value("RUN_REFDATE", refdate)
if case_root.endswith(".postad"):
case.set_value("RUN_STARTDATE", refdate)
# NOTE: if start options are set, RUN_STARTDATE should be modified here
return True
super().set_ref_case(case)
return True ### Check if super returns false, if this will still return True?

def modify_user_nl(self, case_root, run_type, rundir):
"""
Modify user namelist. If transient, include finidat in user_nl;
Otherwise, adjust user_nl to include different mfilt, nhtfrq, and variables in hist_fincl1.
"""
user_nl_fname = os.path.join(case_root, "user_nl_clm")
user_nl_lines = None
if run_type == "transient":
if self.finidat:
user_nl_lines = [
"finidat = '{}/inputdata/lnd/ctsm/initdata/{}'".format(rundir, self.finidat)
]
else:
user_nl_lines = [
"hist_fincl2 = ''",
"hist_mfilt = 20",
"hist_nhtfrq = -8760",
"hist_empty_htapes = .true.",
"""hist_fincl1 = 'TOTECOSYSC', 'TOTECOSYSN', 'TOTSOMC', 'TOTSOMN', 'TOTVEGC',
'TOTVEGN', 'TLAI', 'GPP', 'CPOOL', 'NPP', 'TWS', 'H2OSNO'""",
]
# TODO: include neon-specific user namelist lines, using this as just an example currently
site_lines = [
"""hist_fincl1 = 'TOTECOSYSC', 'TOTECOSYSN', 'TOTSOMC', 'TOTSOMN', 'TOTVEGC',
'TOTVEGN', 'TLAI', 'GPP', 'CPOOL', 'NPP', 'TWS', 'H2OSNO',"""
]
super().modify_user_nl(case_root, run_type, rundir, site_lines)


if user_nl_lines:
with open(user_nl_fname, "a") as nl_file:
for line in user_nl_lines:
nl_file.write("{}\n".format(line))
2 changes: 1 addition & 1 deletion python/ctsm/site_and_regional/run_neon.py
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Original file line number Diff line number Diff line change
Expand Up @@ -176,7 +176,7 @@ def main(description):
# Get the list of supported neon sites from usermods
valid_neon_sites = glob.glob(
os.path.join(cesmroot, "cime_config", "usermods_dirs", "NEON", "[!d]*")
)
) # TODO: This is currently including FATES and a secondary list of all sites...
valid_neon_sites = sorted([v.split("/")[-1] for v in valid_neon_sites])

(
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