def archive(self):
super(UnifiedModel, self).archive()
# Delete all the stdout log files except the root PE
# Sorts to ensure root PE is first entry
files = sorted(glob.glob(
os.path.join(self.work_path, 'atm.fort6.pe*')),
key=lambda name: int(name.rpartition('.')[-1][2:]))
if len(files) > 1:
for f_path in files[1:]:
os.remove(f_path)
mkdir_p(self.restart_path)
# Need to figure out the end date of the model.
nml_path = os.path.join(self.work_path, 'namelists')
nml = f90nml.read(nml_path)
resubmit_inc = nml['NLSTCALL']['RUN_RESUBMIT_INC']
runtime = um_time_to_time(resubmit_inc)
# runtime = datetime.timedelta(seconds=runtime)
basis_time = nml['NLSTCALL']['MODEL_BASIS_TIME']
init_date = um_date_to_date(basis_time)
end_date = cal.date_plus_seconds(init_date,
runtime,
cal.GREGORIAN)
# Save model time to restart next run
with open(os.path.join(self.restart_path,
self.restart_calendar_file), 'w') as restart_file:
restart_file.write(yaml.dump({'end_date': end_date},
default_flow_style=False))
end_date = date_to_um_dump_date(end_date)
restart_dump = os.path.join(self.work_path,
'aiihca.da{0}'.format(end_date))
f_dst = os.path.join(self.restart_path, self.restart)
if os.path.exists(restart_dump):
shutil.copy(restart_dump, f_dst)
else:
print('payu: error: Model has not produced a restart dump file:\n'
'{} does not exist.\n'
'Check DUMPFREQim in namelists'.format(restart_dump))
def archive(self):
super(UnifiedModel, self).archive()
# Delete all the stdout log files except the root PE
# Sorts to ensure root PE is first entry
files = sorted(glob.glob(os.path.join(self.work_path,
'atm.fort6.pe*')),
key=lambda name: int(name.rpartition('.')[-1][2:]))
if len(files) > 1:
for f_path in files[1:]:
os.remove(f_path)
mkdir_p(self.restart_path)
# Need to figure out the end date of the model.
nml_path = os.path.join(self.work_path, 'namelists')
nml = f90nml.read(nml_path)
resubmit_inc = nml['NLSTCALL']['RUN_RESUBMIT_INC']
runtime = um_time_to_time(resubmit_inc)
# runtime = datetime.timedelta(seconds=runtime)
basis_time = nml['NLSTCALL']['MODEL_BASIS_TIME']
init_date = um_date_to_date(basis_time)
end_date = cal.date_plus_seconds(init_date, runtime, cal.GREGORIAN)
# Save model time to restart next run
with open(os.path.join(self.restart_path, self.restart_calendar_file),
'w') as restart_file:
restart_file.write(
yaml.dump({'end_date': end_date}, default_flow_style=False))
end_date = date_to_um_dump_date(end_date)
restart_dump = os.path.join(self.work_path,
'aiihca.da{0}'.format(end_date))
f_dst = os.path.join(self.restart_path, self.restart)
if os.path.exists(restart_dump):
shutil.copy(restart_dump, f_dst)
else:
print('payu: error: Model has not produced a restart dump file:\n'
'{} does not exist.\n'
'Check DUMPFREQim in namelists'.format(restart_dump))
def setup(self):
super(Cice, self).setup()
setup_nml = self.ice_in['setup_nml']
init_date = datetime.date(year=setup_nml['year_init'], month=1, day=1)
if setup_nml['days_per_year'] == 365:
caltype = cal.NOLEAP
else:
caltype = cal.GREGORIAN
if self.prior_restart_path:
# Generate ice.restart_file
# TODO: better check of restart filename
iced_restart_file = None
iced_restart_files = [
f for f in self.get_prior_restart_files()
if f.startswith('iced.')
]
if len(iced_restart_files) > 0:
iced_restart_file = sorted(iced_restart_files)[-1]
if iced_restart_file is None:
print('payu: error: No restart file available.')
sys.exit(errno.ENOENT)
res_ptr_path = os.path.join(self.work_init_path,
'ice.restart_file')
if os.path.islink(res_ptr_path):
# If we've linked in a previous pointer it should be deleted
os.remove(res_ptr_path)
with open(res_ptr_path, 'w') as res_ptr:
res_dir = self.get_ptr_restart_dir()
print(os.path.join(res_dir, iced_restart_file), file=res_ptr)
# Update input namelist
setup_nml['runtype'] = 'continue'
setup_nml['restart'] = True
prior_nml_path = os.path.join(self.prior_restart_path,
self.ice_nml_fname)
# With later versions this file exists in the prior restart path,
# but this was not always the case, so check, and if not there use
# prior output path
if not os.path.exists(prior_nml_path) and self.prior_output_path:
prior_nml_path = os.path.join(self.prior_output_path,
self.ice_nml_fname)
# If we cannot find a prior namelist, then we cannot determine
# the start time and must abort the run.
if not os.path.exists(prior_nml_path):
print('payu: error: Cannot find prior namelist {nml}'.format(
nml=self.ice_nml_fname))
sys.exit(errno.ENOENT)
prior_setup_nml = f90nml.read(prior_nml_path)['setup_nml']
# The total time in seconds since the beginning of the experiment
total_runtime = prior_setup_nml['istep0'] + prior_setup_nml['npt']
total_runtime = total_runtime * prior_setup_nml['dt']
run_start_date = cal.date_plus_seconds(init_date, total_runtime,
caltype)
else:
# Locate and link any restart files (if required)
if not setup_nml['ice_ic'] in ('none', 'default'):
self.link_restart(setup_nml['ice_ic'])
if setup_nml['restart']:
self.link_restart(setup_nml['pointer_file'])
# Initialise runtime
total_runtime = 0
run_start_date = init_date
# Set runtime for this run.
if self.expt.runtime:
run_runtime = cal.runtime_from_date(
run_start_date, self.expt.runtime['years'],
self.expt.runtime['months'], self.expt.runtime['days'],
self.expt.runtime.get('seconds', 0), caltype)
else:
run_runtime = setup_nml['npt'] * setup_nml['dt']
# Now write out new run start date and total runtime.
setup_nml['npt'] = run_runtime / setup_nml['dt']
assert (total_runtime % setup_nml['dt'] == 0)
setup_nml['istep0'] = int(total_runtime / setup_nml['dt'])
# Force creation of a dump (restart) file at end of run
setup_nml['dump_last'] = True
nml_path = os.path.join(self.work_path, self.ice_nml_fname)
self.ice_in.write(nml_path, force=True)
def setup(self):
super(Cice, self).setup()
# Change perms of restart files, these get overwritten so much be
# writable.
for fname in ['o2i.nc', 'i2o.nc', 'u_star.nc', 'grid.nc', 'kmt.nc',
'monthly_sstsss.nc', 'mice.nc']:
path = os.path.join(self.work_input_path, fname)
if os.path.exists(path):
perm = (stat.S_IRUSR | stat.S_IRGRP | stat.S_IROTH
| stat.S_IWUSR)
os.chmod(path, perm)
setup_nml = self.ice_in['setup_nml']
init_date = datetime.date(year=setup_nml['year_init'], month=1, day=1)
if setup_nml['days_per_year'] == 365:
caltype = cal.NOLEAP
else:
caltype = cal.GREGORIAN
if self.prior_restart_path and not self.expt.repeat_run:
# Generate ice.restart_file
# TODO: better check of restart filename
iced_restart_file = None
for f in self.get_prior_restart_files():
if 'iced.' in f:
iced_restart_file = f
if iced_restart_file is None:
print('payu: error: No restart file available.')
sys.exit(errno.ENOENT)
res_ptr_path = os.path.join(self.work_init_path,
'ice.restart_file')
with open(res_ptr_path, 'w') as res_ptr:
res_dir = self.get_ptr_restart_dir()
print(os.path.join(res_dir, iced_restart_file), file=res_ptr)
# Update input namelist
setup_nml['runtype'] = 'continue'
setup_nml['restart'] = True
prior_nml_path = os.path.join(self.prior_restart_path,
self.ice_nml_fname)
# With later versions this file exists in the prior restart path,
# but this was not always the case, so check, and if not there use
# prior output path
if not os.path.exists(prior_nml_path):
prior_nml_path = os.path.join(self.prior_output_path,
self.ice_nml_fname)
prior_setup_nml = f90nml.read(prior_nml_path)['setup_nml']
# The total time in seconds since the beginning of the experiment
total_runtime = prior_setup_nml['istep0'] + prior_setup_nml['npt']
total_runtime = total_runtime * prior_setup_nml['dt']
run_start_date = cal.date_plus_seconds(init_date, total_runtime,
caltype)
else:
# Locate and link any restart files (if required)
if not setup_nml['ice_ic'] in ('none', 'default'):
self.link_restart(setup_nml['ice_ic'])
if setup_nml['restart']:
self.link_restart(setup_nml['pointer_file'])
# Initialise runtime
total_runtime = 0
run_start_date = init_date
# Set runtime for this run.
if self.expt.runtime:
run_runtime = cal.runtime_from_date(
run_start_date,
self.expt.runtime['years'],
self.expt.runtime['months'],
self.expt.runtime['days'],
self.expt.runtime.get('seconds', 0),
caltype
)
else:
run_runtime = setup_nml['npt']*setup_nml['dt']
# Now write out new run start date and total runtime.
setup_nml['npt'] = run_runtime / setup_nml['dt']
assert(total_runtime % setup_nml['dt'] == 0)
setup_nml['istep0'] = int(total_runtime / setup_nml['dt'])
# Force creation of a dump (restart) file at end of run
setup_nml['dump_last'] = True
nml_path = os.path.join(self.work_path, self.ice_nml_fname)
self.ice_in.write(nml_path, force=True)
def setup(self):
super(Cice, self).setup()
setup_nml = self.ice_in['setup_nml']
init_date = datetime.date(year=setup_nml['year_init'], month=1, day=1)
if setup_nml['days_per_year'] == 365:
caltype = cal.NOLEAP
else:
caltype = cal.GREGORIAN
if self.prior_restart_path:
# Generate ice.restart_file
# TODO: better check of restart filename
iced_restart_file = None
iced_restart_files = [f for f in self.get_prior_restart_files()
if f.startswith('iced.')]
if len(iced_restart_files) > 0:
iced_restart_file = sorted(iced_restart_files)[-1]
if iced_restart_file is None:
print('payu: error: No restart file available.')
sys.exit(errno.ENOENT)
res_ptr_path = os.path.join(self.work_init_path,
'ice.restart_file')
if os.path.islink(res_ptr_path):
# If we've linked in a previous pointer it should be deleted
os.remove(res_ptr_path)
with open(res_ptr_path, 'w') as res_ptr:
res_dir = self.get_ptr_restart_dir()
print(os.path.join(res_dir, iced_restart_file), file=res_ptr)
# Update input namelist
setup_nml['runtype'] = 'continue'
setup_nml['restart'] = True
prior_nml_path = os.path.join(self.prior_restart_path,
self.ice_nml_fname)
# With later versions this file exists in the prior restart path,
# but this was not always the case, so check, and if not there use
# prior output path
if not os.path.exists(prior_nml_path) and self.prior_output_path:
prior_nml_path = os.path.join(self.prior_output_path,
self.ice_nml_fname)
# If we cannot find a prior namelist, then we cannot determine
# the start time and must abort the run.
if not os.path.exists(prior_nml_path):
print('payu: error: Cannot find prior namelist {nml}'.format(
nml=self.ice_nml_fname))
sys.exit(errno.ENOENT)
prior_setup_nml = f90nml.read(prior_nml_path)['setup_nml']
# The total time in seconds since the beginning of the experiment
total_runtime = prior_setup_nml['istep0'] + prior_setup_nml['npt']
total_runtime = total_runtime * prior_setup_nml['dt']
run_start_date = cal.date_plus_seconds(init_date, total_runtime,
caltype)
else:
# Locate and link any restart files (if required)
if not setup_nml['ice_ic'] in ('none', 'default'):
self.link_restart(setup_nml['ice_ic'])
if setup_nml['restart']:
self.link_restart(setup_nml['pointer_file'])
# Initialise runtime
total_runtime = 0
run_start_date = init_date
# Set runtime for this run.
if self.expt.runtime:
run_runtime = cal.runtime_from_date(
run_start_date,
self.expt.runtime['years'],
self.expt.runtime['months'],
self.expt.runtime['days'],
self.expt.runtime.get('seconds', 0),
caltype
)
else:
run_runtime = setup_nml['npt']*setup_nml['dt']
# Now write out new run start date and total runtime.
setup_nml['npt'] = run_runtime / setup_nml['dt']
assert(total_runtime % setup_nml['dt'] == 0)
setup_nml['istep0'] = int(total_runtime / setup_nml['dt'])
# Force creation of a dump (restart) file at end of run
setup_nml['dump_last'] = True
nml_path = os.path.join(self.work_path, self.ice_nml_fname)
self.ice_in.write(nml_path, force=True)
def setup(self):
if not self.top_level_model:
return
cpl_keys = {'cice': ('input_ice.nml', 'coupling', 'runtime0'),
'matm': ('input_atm.nml', 'coupling', 'truntime0')}
# Keep track of this in order to set the oasis runtime.
run_runtime = 0
for model in self.expt.models:
if model.model_type == 'cice' or model.model_type == 'cice5':
# Horrible hack to make a link to o2i.nc in the
# work/ice/RESTART directory
f_name = 'o2i.nc'
f_src = os.path.join(model.work_path, f_name)
f_dst = os.path.join(model.work_restart_path, f_name)
if os.path.isfile(f_src):
make_symlink(f_src, f_dst)
if model.model_type == 'cice5':
# Stage the supplemental input files
if model.prior_restart_path:
for f_name in model.access_restarts:
f_src = os.path.join(model.prior_restart_path, f_name)
f_dst = os.path.join(model.work_input_path, f_name)
if os.path.isfile(f_src):
make_symlink(f_src, f_dst)
if model.model_type in ('cice', 'matm'):
# Update the supplemental OASIS namelists
cpl_fname, cpl_group, runtime0_key = cpl_keys[model.model_type]
cpl_fpath = os.path.join(model.work_path, cpl_fname)
cpl_nml = f90nml.read(cpl_fpath)
# Which calendar are we using, noleap or Gregorian.
caltype = cpl_nml[cpl_group]['caltype']
init_date = cal.int_to_date(cpl_nml[cpl_group]['init_date'])
# Get time info about the beginning of this run. We're
# interested in:
# 1. start date of run
# 2. total runtime of all previous runs.
if model.prior_restart_path and not self.expt.repeat_run:
prior_cpl_fpath = os.path.join(model.prior_restart_path,
cpl_fname)
# With later versions this file exists in the prior restart
# path, but this was not always the case, so check, and if
# not there use prior output path
if not os.path.exists(prior_cpl_fpath):
print('payu: warning: {0} missing from prior restart '
'path; checking prior output.'.format(cpl_fname),
file=sys.stderr)
if not os.path.isdir(model.prior_output_path):
print('payu: error: No prior output path; '
'aborting run.')
sys.exit(errno.ENOENT)
prior_cpl_fpath = os.path.join(model.prior_output_path,
cpl_fname)
try:
prior_cpl_nml = f90nml.read(prior_cpl_fpath)
except IOError as exc:
if exc.errno == errno.ENOENT:
print('payu: error: {0} does not exist; aborting.'
''.format(prior_cpl_fpath), file=sys.stderr)
sys.exit(exc.errno)
else:
raise
cpl_nml_grp = prior_cpl_nml[cpl_group]
# The total time in seconds since the beginning of
# the experiment.
total_runtime = int(cpl_nml_grp[runtime0_key] +
cpl_nml_grp['runtime'])
run_start_date = cal.date_plus_seconds(init_date,
total_runtime,
caltype)
else:
total_runtime = 0
run_start_date = init_date
# Get new runtime for this run. We get this from either the
# 'runtime' part of the payu config, or from the namelist
if self.expt.runtime:
run_runtime = cal.runtime_from_date(
run_start_date,
self.expt.runtime['years'],
self.expt.runtime['months'],
self.expt.runtime['days'],
self.expt.runtime.get('seconds', 0),
caltype)
else:
run_runtime = cpl_nml[cpl_group]['runtime']
# Now write out new run start date and total runtime.
cpl_nml[cpl_group]['inidate'] = cal.date_to_int(run_start_date)
cpl_nml[cpl_group][runtime0_key] = total_runtime
cpl_nml[cpl_group]['runtime'] = int(run_runtime)
if model.model_type == 'cice':
if self.expt.counter and not self.expt.repeat_run:
cpl_nml[cpl_group]['jobnum'] = 1 + self.expt.counter
else:
cpl_nml[cpl_group]['jobnum'] = 1
nml_work_path = os.path.join(model.work_path, cpl_fname)
f90nml.write(cpl_nml, nml_work_path + '~')
shutil.move(nml_work_path + '~', nml_work_path)
# Now change the oasis runtime. This needs to be done after the others.
for model in self.expt.models:
if model.model_type == 'oasis':
namcouple = os.path.join(model.work_path, 'namcouple')
s = ''
with open(namcouple, 'r+') as f:
s = f.read()
m = re.search(r"^[ \t]*\$RUNTIME.*?^[ \t]*(\d+)", s,
re.MULTILINE | re.DOTALL)
assert(m is not None)
s = s[:m.start(1)] + str(run_runtime) + s[m.end(1):]
with open(namcouple, 'w') as f:
f.write(s)
def setup(self):
super(Cice, self).setup()
setup_nml = self.ice_in['setup_nml']
init_date = datetime.date(year=setup_nml['year_init'], month=1, day=1)
if setup_nml['days_per_year'] == 365:
caltype = cal.NOLEAP
else:
caltype = cal.GREGORIAN
if self.prior_output_path and not self.expt.repeat_run:
# Generate ice.restart_file
# TODO: Check the filenames more aggressively
try:
prior_restart_file = self.get_prior_restart_files()[0]
except IndexError:
print('payu: error: No restart file available.')
sys.exit(errno.ENOENT)
res_ptr_path = os.path.join(self.work_init_path,
'ice.restart_file')
with open(res_ptr_path, 'w') as res_ptr:
res_dir = self.get_ptr_restart_dir()
print(os.path.join(res_dir, prior_restart_file), file=res_ptr)
# Update input namelist
setup_nml['runtype'] = 'continue'
setup_nml['restart'] = True
prior_nml_path = os.path.join(self.prior_output_path,
self.ice_nml_fname)
prior_setup_nml = f90nml.read(prior_nml_path)['setup_nml']
# The total time in seconds since the beginning of the experiment
total_runtime = prior_setup_nml['istep0'] + prior_setup_nml['npt']
total_runtime = total_runtime * prior_setup_nml['dt']
run_start_date = cal.date_plus_seconds(init_date, total_runtime,
caltype)
else:
# Locate and link any restart files (if required)
if not setup_nml['ice_ic'] in ('none', 'default'):
self.link_restart(setup_nml['ice_ic'])
if setup_nml['restart']:
self.link_restart(setup_nml['pointer_file'])
# Initialise runtime
total_runtime = 0
run_start_date = init_date
# Set runtime for this run.
if self.expt.runtime:
run_runtime = cal.runtime_from_date(
run_start_date, self.expt.runtime['years'],
self.expt.runtime['months'], self.expt.runtime['days'],
self.expt.runtime.get('seconds', 0), caltype)
else:
run_runtime = setup_nml['npt'] * setup_nml['dt']
# Now write out new run start date and total runtime.
setup_nml['npt'] = run_runtime / setup_nml['dt']
assert (total_runtime % setup_nml['dt'] == 0)
setup_nml['istep0'] = int(total_runtime / setup_nml['dt'])
# Force creation of a dump (restart) file at end of run
setup_nml['dump_last'] = True
nml_path = os.path.join(self.work_path, self.ice_nml_fname)
self.ice_in.write(nml_path, force=True)
def setup(self):
cpl_keys = {'cice': ('input_ice.nml', 'coupling_nml', 'runtime0'),
'matm': ('input_atm.nml', 'coupling', 'truntime0')}
# Keep track of this in order to set the oasis runtime.
run_runtime = 0
for model in self.expt.models:
if model.model_type == 'cice':
# Stage the supplemental input files
if model.prior_restart_path:
for f_name in model.access_restarts:
f_src = os.path.join(model.prior_restart_path, f_name)
f_dst = os.path.join(model.work_input_path, f_name)
if os.path.isfile(f_src):
make_symlink(f_src, f_dst)
if model.model_type in ('cice', 'matm'):
# Update the supplemental OASIS namelists
cpl_fname, cpl_group, runtime0_key = cpl_keys[model.model_type]
cpl_fpath = os.path.join(model.work_path, cpl_fname)
cpl_nml = f90nml.read(cpl_fpath)
# Which calendar are we using, noleap or Gregorian.
caltype = cpl_nml[cpl_group]['caltype']
init_date = cal.int_to_date(cpl_nml[cpl_group]['init_date'])
# Get time info about the beginning of this run. We're
# interested in:
# 1. start date of run
# 2. total runtime of all previous runs.
if model.prior_output_path and not self.expt.repeat_run:
prior_cpl_fpath = os.path.join(model.prior_output_path,
cpl_fname)
prior_cpl_nml = f90nml.read(prior_cpl_fpath)
cpl_nml_grp = prior_cpl_nml[cpl_group]
# The total time in seconds since the beginning of
# the experiment.
total_runtime = int(cpl_nml_grp[runtime0_key] +
cpl_nml_grp['runtime'])
run_start_date = cal.date_plus_seconds(init_date,
total_runtime,
caltype)
else:
total_runtime = 0
run_start_date = init_date
# Get new runtime for this run. We get this from either the
# 'runtime' part of the payu config, or from the namelist
if self.expt.runtime:
run_runtime = cal.runtime_from_date(
run_start_date,
self.expt.runtime['years'],
self.expt.runtime['months'],
self.expt.runtime['days'],
self.expt.runtime.get('seconds', 0),
caltype)
else:
run_runtime = cpl_nml[cpl_group]['runtime']
# Now write out new run start date and total runtime.
cpl_nml[cpl_group]['inidate'] = cal.date_to_int(run_start_date)
cpl_nml[cpl_group][runtime0_key] = total_runtime
cpl_nml[cpl_group]['runtime'] = int(run_runtime)
if model.model_type == 'cice':
if self.expt.counter and not self.expt.repeat_run:
cpl_nml[cpl_group]['jobnum'] = 1 + self.expt.counter
else:
cpl_nml[cpl_group]['jobnum'] = 1
nml_work_path = os.path.join(model.work_path, cpl_fname)
f90nml.write(cpl_nml, nml_work_path + '~')
shutil.move(nml_work_path + '~', nml_work_path)
# Now change the oasis runtime. This needs to be done after the others.
for model in self.expt.models:
if model.model_type == 'oasis':
namcouple = os.path.join(model.work_path, 'namcouple')
s = ''
with open(namcouple, 'r+') as f:
s = f.read()
m = re.search(r"^[ \t]*\$RUNTIME.*?^[ \t]*(\d+)", s,
re.MULTILINE | re.DOTALL)
assert(m is not None)
s = s[:m.start(1)] + str(run_runtime) + s[m.end(1):]
with open(namcouple, 'w') as f:
f.write(s)
def setup(self):
super(Cice, self).setup()
setup_nml = self.ice_in['setup_nml']
init_date = datetime.date(year=setup_nml['year_init'], month=1, day=1)
if setup_nml['days_per_year'] == 365:
caltype = cal.NOLEAP
else:
caltype = cal.GREGORIAN
if self.prior_output_path and not self.expt.repeat_run:
# Generate ice.restart_file
# TODO: Check the filenames more aggressively
try:
prior_restart_file = self.get_prior_restart_files()[0]
except IndexError:
print('payu: error: No restart file available.')
sys.exit(errno.ENOENT)
res_ptr_path = os.path.join(self.work_init_path,
'ice.restart_file')
with open(res_ptr_path, 'w') as res_ptr:
res_dir = self.get_ptr_restart_dir()
print(os.path.join(res_dir, prior_restart_file), file=res_ptr)
# Update input namelist
setup_nml['runtype'] = 'continue'
setup_nml['restart'] = True
prior_nml_path = os.path.join(self.prior_output_path,
self.ice_nml_fname)
prior_setup_nml = f90nml.read(prior_nml_path)['setup_nml']
# The total time in seconds since the beginning of the experiment
total_runtime = prior_setup_nml['istep0'] + prior_setup_nml['npt']
total_runtime = total_runtime * prior_setup_nml['dt']
run_start_date = cal.date_plus_seconds(init_date, total_runtime,
caltype)
else:
# Locate and link any restart files (if required)
if not setup_nml['ice_ic'] in ('none', 'default'):
self.link_restart(setup_nml['ice_ic'])
if setup_nml['restart']:
self.link_restart(setup_nml['pointer_file'])
# Initialise runtime
total_runtime = 0
run_start_date = init_date
# Set runtime for this run.
if self.expt.runtime:
run_runtime = cal.runtime_from_date(
run_start_date,
self.expt.runtime['years'],
self.expt.runtime['months'],
self.expt.runtime['days'],
self.expt.runtime.get('seconds', 0),
caltype)
else:
run_runtime = setup_nml['npt']*setup_nml['dt']
# Now write out new run start date and total runtime.
setup_nml['npt'] = run_runtime / setup_nml['dt']
assert(total_runtime % setup_nml['dt'] == 0)
setup_nml['istep0'] = int(total_runtime / setup_nml['dt'])
# Force creation of a dump (restart) file at end of run
setup_nml['dump_last'] = True
nml_path = os.path.join(self.work_path, self.ice_nml_fname)
self.ice_in.write(nml_path, force=True)
def setup(self):
cpl_keys = {
'cice': ('input_ice.nml', 'coupling_nml', 'runtime0'),
'matm': ('input_atm.nml', 'coupling', 'truntime0')
}
# Keep track of this in order to set the oasis runtime.
run_runtime = 0
for model in self.expt.models:
if model.model_type == 'cice':
# Stage the supplemental input files
if model.prior_restart_path:
for f_name in model.access_restarts:
f_src = os.path.join(model.prior_restart_path, f_name)
f_dst = os.path.join(model.work_input_path, f_name)
if os.path.isfile(f_src):
make_symlink(f_src, f_dst)
if model.model_type in ('cice', 'matm'):
# Update the supplemental OASIS namelists
cpl_fname, cpl_group, runtime0_key = cpl_keys[model.model_type]
cpl_fpath = os.path.join(model.work_path, cpl_fname)
cpl_nml = f90nml.read(cpl_fpath)
# Which calendar are we using, noleap or Gregorian.
caltype = cpl_nml[cpl_group]['caltype']
init_date = cal.int_to_date(cpl_nml[cpl_group]['init_date'])
# Get time info about the beginning of this run. We're
# interested in:
# 1. start date of run
# 2. total runtime of all previous runs.
if model.prior_output_path and not self.expt.repeat_run:
prior_cpl_fpath = os.path.join(model.prior_output_path,
cpl_fname)
prior_cpl_nml = f90nml.read(prior_cpl_fpath)
cpl_nml_grp = prior_cpl_nml[cpl_group]
# The total time in seconds since the beginning of
# the experiment.
total_runtime = int(cpl_nml_grp[runtime0_key] +
cpl_nml_grp['runtime'])
run_start_date = cal.date_plus_seconds(
init_date, total_runtime, caltype)
else:
total_runtime = 0
run_start_date = init_date
# Get new runtime for this run. We get this from either the
# 'runtime' part of the payu config, or from the namelist
if self.expt.runtime:
run_runtime = cal.runtime_from_date(
run_start_date, self.expt.runtime['years'],
self.expt.runtime['months'], self.expt.runtime['days'],
self.expt.runtime.get('seconds', 0), caltype)
else:
run_runtime = cpl_nml[cpl_group]['runtime']
# Now write out new run start date and total runtime.
cpl_nml[cpl_group]['inidate'] = cal.date_to_int(run_start_date)
cpl_nml[cpl_group][runtime0_key] = total_runtime
cpl_nml[cpl_group]['runtime'] = int(run_runtime)
if model.model_type == 'cice':
if self.expt.counter and not self.expt.repeat_run:
cpl_nml[cpl_group]['jobnum'] = 1 + self.expt.counter
else:
cpl_nml[cpl_group]['jobnum'] = 1
nml_work_path = os.path.join(model.work_path, cpl_fname)
f90nml.write(cpl_nml, nml_work_path + '~')
shutil.move(nml_work_path + '~', nml_work_path)
# Now change the oasis runtime. This needs to be done after the others.
for model in self.expt.models:
if model.model_type == 'oasis':
namcouple = os.path.join(model.work_path, 'namcouple')
s = ''
with open(namcouple, 'r+') as f:
s = f.read()
m = re.search(r"^[ \t]*\$RUNTIME.*?^[ \t]*(\d+)", s,
re.MULTILINE | re.DOTALL)
assert (m is not None)
s = s[:m.start(1)] + str(run_runtime) + s[m.end(1):]
with open(namcouple, 'w') as f:
f.write(s)
def setup(self):
super(UnifiedModel, self).setup()
# Set up environment variables needed to run UM.
# Look for a python file in the config directory.
um_env = imp.load_source('um_env',
os.path.join(self.control_path, 'um_env.py'))
um_vars = um_env.vars
# Stage the UM restart file.
if self.prior_restart_path and not self.expt.repeat_run:
f_src = os.path.join(self.prior_restart_path, self.restart)
f_dst = os.path.join(self.work_input_path, self.restart)
if os.path.isfile(f_src):
make_symlink(f_src, f_dst)
# every run is an NRUN with an updated ASTART file
um_vars['ASTART'] = self.restart
um_vars['TYPE'] = 'NRUN'
# Set paths in environment variables.
for k in um_vars.keys():
um_vars[k] = um_vars[k].format(input_path=self.input_paths[0],
work_path=self.work_path)
os.environ.update(um_vars)
# The above needs to be done in parexe also.
# FIXME: a better way to do this or remove.
parexe = os.path.join(self.work_path, 'parexe')
for line in fileinput.input(parexe, inplace=True):
line = line.format(input_path=self.input_paths[0],
work_path=self.work_path)
print(line, end='')
work_nml_path = os.path.join(self.work_path, 'namelists')
work_nml = f90nml.read(work_nml_path)
# Modify namelists for a continuation run.
if self.prior_output_path and not self.expt.repeat_run:
prior_nml_path = os.path.join(self.prior_output_path, 'namelists')
prior_nml = f90nml.read(prior_nml_path)
basis_time = prior_nml['NLSTCALL']['MODEL_BASIS_TIME']
init_date = um_date_to_date(basis_time)
resubmit_inc = prior_nml['NLSTCALL']['RUN_RESUBMIT_INC']
runtime = um_time_to_time(resubmit_inc)
run_start_date = cal.date_plus_seconds(init_date, runtime,
cal.GREGORIAN)
# Write out and save new calendar information.
run_start_date_um = date_to_um_date(run_start_date)
work_nml['NLSTCALL']['MODEL_BASIS_TIME'] = run_start_date_um
work_nml['NLSTCALL']['ANCIL_REFTIME'] = run_start_date_um
# Tell CABLE that this is a continuation run.
cable_nml_path = os.path.join(self.work_path, 'cable.nml')
cable_nml = f90nml.read(cable_nml_path)
cable_nml['cable']['cable_user']['CABLE_RUNTIME_COUPLED'] = False
cable_nml.write(cable_nml_path, force=True)
else:
run_start_date = work_nml['NLSTCALL']['MODEL_BASIS_TIME']
run_start_date = um_date_to_date(run_start_date)
# Set the runtime for this run.
if self.expt.runtime:
run_runtime = cal.runtime_from_date(
run_start_date, self.expt.runtime['years'],
self.expt.runtime['months'], self.expt.runtime['days'],
self.expt.runtime.get('seconds', 0), cal.GREGORIAN)
run_runtime = time_to_um_time(run_runtime)
work_nml['NLSTCALL']['RUN_RESUBMIT_INC'] = run_runtime
work_nml['NLSTCALL']['RUN_TARGET_END'] = run_runtime
work_nml['STSHCOMP']['RUN_TARGET_END'] = run_runtime
work_nml.write(work_nml_path, force=True)
def setup(self):
super(UnifiedModel, self).setup()
# Stage the UM restart file.
if self.prior_restart_path and not self.expt.repeat_run:
f_src = os.path.join(self.prior_restart_path, self.restart)
f_dst = os.path.join(self.work_input_path, self.restart)
if os.path.isfile(f_src):
make_symlink(f_src, f_dst)
# Set up environment variables needed to run UM.
# Look for a python file in the config directory.
um_env = imp.load_source("um_env", os.path.join(self.control_path, "um_env.py"))
um_vars = um_env.vars
assert len(self.input_paths) == 1
# Set paths in environment variables.
for k in um_vars.keys():
um_vars[k] = um_vars[k].format(input_path=self.input_paths[0], work_path=self.work_path)
os.environ.update(um_vars)
# The above needs to be done in parexe also.
# FIXME: a better way to do this or remove.
parexe = os.path.join(self.work_path, "parexe")
for line in fileinput.input(parexe, inplace=True):
line = line.format(input_path=self.input_paths[0], work_path=self.work_path)
print(line, end="")
work_nml_path = os.path.join(self.work_path, "namelists")
work_nml = f90nml.read(work_nml_path)
# Modify namelists for a continuation run.
if self.prior_output_path and not self.expt.repeat_run:
prior_nml_path = os.path.join(self.prior_output_path, "namelists")
prior_nml = f90nml.read(prior_nml_path)
basis_time = prior_nml["NLSTCALL"]["MODEL_BASIS_TIME"]
init_date = um_date_to_date(basis_time)
resubmit_inc = prior_nml["NLSTCALL"]["RUN_RESUBMIT_INC"]
runtime = um_time_to_time(resubmit_inc)
run_start_date = cal.date_plus_seconds(init_date, runtime, cal.GREGORIAN)
# Write out and save new calendar information.
run_start_date_um = date_to_um_date(run_start_date)
work_nml["NLSTCALL"]["MODEL_BASIS_TIME"] = run_start_date_um
work_nml["NLSTCALL"]["ANCIL_REFTIME"] = run_start_date_um
# Tell CABLE that this is a continuation run.
cable_nml_path = os.path.join(self.work_path, "cable.nml")
cable_nml = f90nml.read(cable_nml_path)
cable_nml["cable"]["cable_user"]["CABLE_RUNTIME_COUPLED"] = False
cable_nml.write(cable_nml_path, force=True)
else:
run_start_date = work_nml["NLSTCALL"]["MODEL_BASIS_TIME"]
run_start_date = um_date_to_date(run_start_date)
# Set the runtime for this run.
if self.expt.runtime:
run_runtime = cal.runtime_from_date(
run_start_date,
self.expt.runtime["years"],
self.expt.runtime["months"],
self.expt.runtime["days"],
self.expt.runtime.get("seconds", 0),
cal.GREGORIAN,
)
run_runtime = time_to_um_time(run_runtime)
work_nml["NLSTCALL"]["RUN_RESUBMIT_INC"] = run_runtime
work_nml["NLSTCALL"]["RUN_TARGET_END"] = run_runtime
work_nml["STSHCOMP"]["RUN_TARGET_END"] = run_runtime
work_nml.write(work_nml_path, force=True)
def setup(self):
super(UnifiedModel, self).setup()
# Set up environment variables needed to run UM.
# Look for a python file in the config directory.
um_env = imp.load_source('um_env',
os.path.join(self.control_path, 'um_env.py'))
um_vars = um_env.vars
# Stage the UM restart file.
if self.prior_restart_path and not self.expt.repeat_run:
f_src = os.path.join(self.prior_restart_path, self.restart)
f_dst = os.path.join(self.work_input_path, self.restart)
if os.path.isfile(f_src):
make_symlink(f_src, f_dst)
# every run is an NRUN with an updated ASTART file
um_vars['ASTART'] = self.restart
um_vars['TYPE'] = 'NRUN'
# Set paths in environment variables.
for k in um_vars.keys():
um_vars[k] = um_vars[k].format(input_path=self.input_paths[0],
work_path=self.work_path)
os.environ.update(um_vars)
# The above needs to be done in parexe also.
# FIXME: a better way to do this or remove.
parexe = os.path.join(self.work_path, 'parexe')
for line in fileinput.input(parexe, inplace=True):
line = line.format(input_path=self.input_paths[0],
work_path=self.work_path)
print(line, end='')
work_nml_path = os.path.join(self.work_path, 'namelists')
work_nml = f90nml.read(work_nml_path)
# Modify namelists for a continuation run.
if self.prior_output_path and not self.expt.repeat_run:
prior_nml_path = os.path.join(self.prior_output_path, 'namelists')
prior_nml = f90nml.read(prior_nml_path)
basis_time = prior_nml['NLSTCALL']['MODEL_BASIS_TIME']
init_date = um_date_to_date(basis_time)
resubmit_inc = prior_nml['NLSTCALL']['RUN_RESUBMIT_INC']
runtime = um_time_to_time(resubmit_inc)
run_start_date = cal.date_plus_seconds(init_date,
runtime,
cal.GREGORIAN)
# Write out and save new calendar information.
run_start_date_um = date_to_um_date(run_start_date)
work_nml['NLSTCALL']['MODEL_BASIS_TIME'] = run_start_date_um
work_nml['NLSTCALL']['ANCIL_REFTIME'] = run_start_date_um
# Tell CABLE that this is a continuation run.
cable_nml_path = os.path.join(self.work_path, 'cable.nml')
cable_nml = f90nml.read(cable_nml_path)
cable_nml['cable']['cable_user']['CABLE_RUNTIME_COUPLED'] = False
cable_nml.write(cable_nml_path, force=True)
else:
run_start_date = work_nml['NLSTCALL']['MODEL_BASIS_TIME']
run_start_date = um_date_to_date(run_start_date)
# Set the runtime for this run.
if self.expt.runtime:
run_runtime = cal.runtime_from_date(
run_start_date,
self.expt.runtime['years'],
self.expt.runtime['months'],
self.expt.runtime['days'],
self.expt.runtime.get('seconds', 0),
cal.GREGORIAN)
run_runtime = time_to_um_time(run_runtime)
work_nml['NLSTCALL']['RUN_RESUBMIT_INC'] = run_runtime
work_nml['NLSTCALL']['RUN_TARGET_END'] = run_runtime
work_nml['STSHCOMP']['RUN_TARGET_END'] = run_runtime
work_nml.write(work_nml_path, force=True)
