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workflows.py 12.69 KiB
#!/usr/bin/python3
"""
These functions mostly call python scripts via the shell,
e.g. assimilate() calls dartwrf/assim_synth_obs.py through the shell.
This would not be necessary, but some users might want to use queueing systems (e.g. SLURM) which must call scripts.
"""
import os, sys, shutil, glob, warnings
import datetime as dt
import importlib
from dartwrf.utils import script_to_str
from config.cfg import exp
def dict_to_py(d, outfile):
with open(outfile, 'w') as f:
txt = '# this file is autogenerated \nobs_kind_nrs = {'
for k,v in d.items():
txt += '"'+k+'": '+str(v)+', \n'
txt += '}'
f.write(txt)
class WorkFlows(object):
def __init__(self, exp_config='cfg.py', server_config='server.py'):
"""Set up the experiment folder in `archivedir`.
Args:
exp (str): Path to exp config file
config (str): Path to the cluster config file
"""
# in WorkFlows, we load the config from the git cloned folder
# in all other dartwrf scripts, load the config from cluster.scripts_rundir
# exp = __import__('config/'+exp_config)
self.cluster = importlib.import_module('config.'+server_config.strip('.py')).cluster
# Set paths and backup scripts
self.cluster.log_dir = self.cluster.archivedir+'/logs/'
print('logging to', self.cluster.log_dir)
if self.cluster.use_slurm:
self.cluster.slurm_scripts_dir = self.cluster.archivedir+'/slurm-scripts/'
print('scripts, which are submitted to SLURM:', self.cluster.slurm_scripts_dir)
# copy obs kind def to config, we will read a table from there
# file needs to exist within package so sphinx can read it
def obskind_read():
"""Read dictionary of observation types + ID numbers ("kind")
from DART f90 script
"""
definitionfile = self.cluster.dart_srcdir+'/../../../assimilation_code/modules/observations/obs_kind_mod.f90'
with open(definitionfile, 'r') as f:
kind_def_f = f.readlines()
obskind_nrs = {}
for i, line in enumerate(kind_def_f):
if 'Integer definitions for DART OBS TYPES' in line:
# data starts below this line
i_start = i
break
for line in kind_def_f[i_start+1:]:
if 'MAX_DEFINED_TYPES_OF_OBS' in line:
# end of data
break
if '::' in line:
# a line looks like this
# integer, parameter, public :: MSG_4_SEVIRI_TB = 261
data = line.split('::')[-1].split('=')
kind_str = data[0].strip()
kind_nr = int(data[1].strip())
obskind_nrs[kind_str] = kind_nr
return obskind_nrs
dict_to_py(obskind_read(), self.cluster.scriptsdir+'/../config/obskind.py')
# Copy scripts to self.cluster.archivedir folder
os.makedirs(self.cluster.archivedir, exist_ok=True)
try:
shutil.copytree(self.cluster.scriptsdir, self.cluster.scripts_rundir)
print('scripts have been copied to', self.cluster.archivedir)
except FileExistsError as e:
warnings.warn(str(e))
except:
raise
# later, we can load the exp cfg with `from config.cfg import exp`
shutil.copy('config/'+exp_config, self.cluster.scripts_rundir+'/config/cfg.py')
# later, we can load the cluster cfg with `from config.cluster import cluster`
shutil.copy('config/'+server_config, self.cluster.scripts_rundir+'/config/cluster.py') # whatever server, the config name is always the same!
# probably not needed
# shutil.copy('config/'+server_config, 'config/cluster.py') # whatever server, the config name is always the same!
def prepare_WRFrundir(self, init_time):
"""Create WRF/run directories and wrfinput files
"""
cmd = self.cluster.python+' '+self.cluster.scripts_rundir+'/prepare_wrfrundir.py '+init_time.strftime('%Y-%m-%d_%H:%M')
print(cmd)
os.system(cmd)
def run_ideal(self, depends_on=None):
"""Run ideal for every ensemble member"""
cmd = """# run ideal.exe in parallel, then add geodata
export SLURM_STEP_GRES=none
for ((n=1; n<="""+str(exp.n_ens)+"""; n++))
do
rundir="""+self.cluster.wrf_rundir_base+'/'+exp.expname+"""/$n
echo $rundir
cd $rundir
mpirun -np 1 ./ideal.exe &
done
wait
for ((n=1; n<="""+str(exp.n_ens)+"""; n++))
do
rundir="""+self.cluster.wrf_rundir_base+'/'+exp.expname+"""/$n
mv $rundir/rsl.out.0000 $rundir/rsl.out.input
done
"""
id = self.cluster.run_job(cmd, "ideal", cfg_update={"ntasks": str(exp.n_ens),
"time": "10", "mem": "100G"}, depends_on=[depends_on])
return id
def wrfinput_insert_wbubble(self, perturb=True, depends_on=None):
"""Given that directories with wrfinput files exist,
update these wrfinput files with warm bubbles
"""
pstr = ' '
if perturb:
pstr = ' perturb'
cmd = self.cluster.python+' '+self.cluster.scripts_rundir+'/create_wbubble_wrfinput.py'+pstr
id = self.cluster.run_job(cmd, "ins_wbubble", cfg_update={"time": "5"}, depends_on=[depends_on])
return id
def run_ENS(self, begin, end, depends_on=None, first_minute=True,
input_is_restart=True, restart_path=False, output_restart_interval=720):
"""Run forecast for 1 minute, save output.
Then run whole timespan with 5 minutes interval.
if input_is_restart: # start WRF in restart mode
"""
restart_flag = '.false.' if not input_is_restart else '.true.'
# if False: # doesnt work with restarts at the moment# first_minute:
# # first minute forecast (needed for validating an assimilation)
# hist_interval = 1
# radt = 1 # calc CFRAC also in first minute
# begin_plus1 = begin+dt.timedelta(minutes=1)
# s = self.cluster.run_job("preWRF1", cfg_update=dict(time="2"))
# args = [self.cluster.python, self.cluster.scripts_rundir+'/prepare_namelist.py',
# begin.strftime('%Y-%m-%d_%H:%M'),
# begin_plus1.strftime('%Y-%m-%d_%H:%M'),
# str(hist_interval),
# '--radt='+str(radt),
# '--restart='+restart_flag,]
# id = s.run(' '.join(args), depends_on=[id])
# s = self.cluster.run_job("runWRF1", cfg_update={"nodes": "1", "array": "1-"+str(exp.n_nodes),
# "time": "2", "mem-per-cpu": "2G"})
# cmd = script_to_str(self.cluster.run_WRF).replace('<expname>', exp.expname)
# id = s.run(cmd, depends_on=[id])
# # apply forward operator (DART filter without assimilation)
# s = self.cluster.run_job("fwOP-1m", cfg_update=dict(time="10", ntasks=48))
# id = s.run(self.cluster.python+' '+self.cluster.scripts_rundir+'/apply_obs_op_dart.py '
# + begin.strftime('%Y-%m-%d_%H:%M')+' '
# + begin_plus1.strftime('%Y-%m-%d_%H:%M'),
# depends_on=[id])
# whole forecast timespan
hist_interval = 5
radt = 5
args = [self.cluster.python,
self.cluster.scripts_rundir+'/prepare_namelist.py',
begin.strftime('%Y-%m-%d_%H:%M'),
end.strftime('%Y-%m-%d_%H:%M'),
str(hist_interval),
'--radt='+str(radt),
'--restart='+restart_flag,]
if output_restart_interval:
args.append('--restart_interval='+str(int(float(output_restart_interval))))
id = self.cluster.run_job(' '.join(args), "preWRF", cfg_update=dict(time="2"), depends_on=[depends_on])
cmd = script_to_str(self.cluster.run_WRF).replace('<exp.expname>', exp.expname
).replace('<cluster.wrf_rundir_base>', self.cluster.wrf_rundir_base)
time_in_simulation_hours = (end-begin).total_seconds()/3600
runtime_wallclock_mins_expected = int(8+time_in_simulation_hours*9.5) # usually below 9 min/hour
id = self.cluster.run_job(cmd, "WRF", cfg_update={"array": "1-"+str(self.cluster.size_jobarray), "ntasks": "10", "nodes": "1",
"time": str(runtime_wallclock_mins_expected), "mem": "140G"}, depends_on=[id])
return id
def assimilate(self, assim_time, prior_init_time, prior_valid_time, prior_path_exp,
depends_on=None):
"""Creates observations from a nature run and assimilates them.
Args:
assim_time (dt.datetime): timestamp of prior wrfout files
prior_init_time (dt.datetime): timestamp to find the directory where the prior wrfout files are
prior_path_exp (str): use this directory to get prior state (i.e. self.cluster.archivedir)
"""
if not os.path.exists(prior_path_exp):
raise IOError('prior_path_exp does not exist: '+prior_path_exp)
cmd = (self.cluster.python+' '+self.cluster.scripts_rundir+'/assim_synth_obs.py '
+assim_time.strftime('%Y-%m-%d_%H:%M ')
+prior_init_time.strftime('%Y-%m-%d_%H:%M ')
+prior_valid_time.strftime('%Y-%m-%d_%H:%M ')
+prior_path_exp)
id = self.cluster.run_job(cmd, "Assim", cfg_update={"ntasks": "12", "time": "60",
"mem": "200G", "ntasks-per-node": "12", "ntasks-per-core": "2"}, depends_on=[depends_on])
return id
def prepare_IC_from_prior(self, prior_path_exp, prior_init_time, prior_valid_time, new_start_time=None, depends_on=None):
if new_start_time != None:
tnew = new_start_time.strftime(' %Y-%m-%d_%H:%M')
else:
tnew = ''
cmd = (self.cluster.python+' '+self.cluster.scripts_rundir+'/prep_IC_prior.py '
+prior_path_exp
+prior_init_time.strftime(' %Y-%m-%d_%H:%M')
+prior_valid_time.strftime(' %Y-%m-%d_%H:%M')
+tnew)
id = self.cluster.run_job(cmd, "IC-prior", cfg_update=dict(time="8"), depends_on=[depends_on])
return id
def update_IC_from_DA(self, assim_time, depends_on=None):
cmd = self.cluster.python+' '+self.cluster.scripts_rundir+'/update_IC.py '+assim_time.strftime('%Y-%m-%d_%H:%M')
id = self.cluster.run_job(cmd, "IC-update", cfg_update=dict(time="8"), depends_on=[depends_on])
return id
def create_satimages(self, init_time, depends_on=None):
cmd = self.cluster.python_verif+' ~/RTTOV-WRF/run_init.py '+self.cluster.archivedir+init_time.strftime('/%Y-%m-%d_%H:%M/')
id = self.cluster.run_job(cmd, "RTTOV", cfg_update={"ntasks": "12", "time": "80", "mem": "200G"}, depends_on=[depends_on])
return id
def gen_obsseq(self, depends_on=None):
cmd = self.cluster.python+' '+self.cluster.scripts_rundir+'/obsseq_to_netcdf.py'
id = self.cluster.run_job("obsseq_netcdf", cfg_update={"time": "10", "mail-type": "FAIL,END"},
depends_on=[depends_on])
return id
def verify_sat(self, depends_on=None):
cmd = self.cluster.python_verif+' /jetfs/home/lkugler/osse_analysis/plot_from_raw/analyze_fc.py '+exp.expname+' has_node sat verif1d FSS BS'
self.cluster.run_job(cmd, "verif-SAT-"+exp.expname,
cfg_update={"time": "60", "mail-type": "FAIL,END", "ntasks": "20",
"ntasks-per-node": "20", "ntasks-per-core": "1", "mem": "100G",}, depends_on=[depends_on])
def verify_wrf(self, depends_on=None):
cmd = self.cluster.python_verif+' /jetfs/home/lkugler/osse_analysis/plot_from_raw/analyze_fc.py '+exp.expname+' has_node wrf verif1d verif3d FSS BS'
self.cluster.run_job(cmd, "verif-WRF-"+exp.expname,
cfg_update={"time": "120", "mail-type": "FAIL,END", "ntasks": "20",
"ntasks-per-node": "20", "ntasks-per-core": "1", "mem": "250G"}, depends_on=[depends_on])
def verify_fast(self, depends_on=None):
cmd = self.cluster.python_verif+' /jetfs/home/lkugler/osse_analysis/plot_fast/plot_single_exp.py '+exp.expname
self.cluster.run_job(cmd, "verif-fast-"+exp.expname,
cfg_update={"time": "10", "mail-type": "FAIL", "ntasks": "1",
"ntasks-per-node": "1", "ntasks-per-core": "1"}, depends_on=[depends_on])