def updatebc_run(self, domain):
# set domain specific workdir
wrfda_workdir = os.path.join(self.wrfda_workdir, "d0" + str(domain))
# run da_update_bc.exe
j_id = None
if len(self.config['options_slurm']['slurm_updatebc.exe']):
if j_id:
mid = "--dependency=afterok:%d" % j_id
updatebc_command = [
'sbatch', mid,
self.config['options_slurm']['slurm_updatebc.exe']
]
else:
updatebc_command = [
'sbatch',
self.config['options_slurm']['slurm_updatebc.exe']
]
try:
res = subprocess.check_output(updatebc_command,
cwd=wrfda_workdir,
stderr=utils.devnull())
j_id = int(res.split()[-1]) # slurm job-id
except subprocess.CalledProcessError:
#logger.error('Updatebc failed %s:' % updatebc_command)
raise # re-raise exception
utils.waitJobToFinish(j_id)
else:
# run locally
subprocess.check_call(os.path.join(wrfda_workdir,
'da_update_bc.exe'),
cwd=wrfda_workdir,
stdout=utils.devnull(),
stderr=utils.devnull())
def _run_metgrid(self, j_id=None):
'''
run metgrid.exe (locally or using slurm script defined in config.json)
'''
if len(self.config['options_slurm']['slurm_metgrid.exe']):
if j_id:
mid = "--dependency=afterok:%d" %j_id
metgrid_command = ['sbatch', mid, self.config['options_slurm']['slurm_metgrid.exe']]
else:
metgrid_command = ['sbatch', self.config['options_slurm']['slurm_metgrid.exe']]
utils.check_file_exists(metgrid_command[-1])
utils.silentremove(os.path.join(self.wps_workdir, 'metgrid', 'metgrid.exe'))
os.symlink(os.path.join(self.config['filesystem']['wps_dir'],'metgrid','metgrid.exe'),
os.path.join(self.wps_workdir, 'metgrid', 'metgrid.exe'))
try:
res = subprocess.check_output(metgrid_command, cwd=self.wps_workdir,
stderr=utils.devnull())
j_id = int(res.split()[-1]) # slurm job-id
except subprocess.CalledProcessError:
#logger.error('Metgrid failed %s:' %metgrid_command)
raise # re-raise exception
return j_id # return slurm job-id
else:
metgrid_command = os.path.join(self.config['filesystem']['wps_dir'],
'metgrid', 'metgrid.exe')
utils.check_file_exists(metgrid_command)
try:
subprocess.check_call(metgrid_command, cwd=self.wps_workdir,
stdout=utils.devnull(), stderr=utils.devnull())
except subprocess.CalledProcessError:
#logger.error('Metgrid failed %s:' %metgrid_command)
raise # re-raise exception
def run_wrf(self):
'''
run wrf
'''
j_id = None
if len(self.config['options_slurm']['slurm_wrf.exe']):
# run using slurm
if j_id:
mid = "--dependency=afterok:%d" %j_id
wrf_command = ['sbatch', mid, self.config['options_slurm']['slurm_wrf.exe']]
else:
wrf_command = ['sbatch', self.config['options_slurm']['slurm_wrf.exe']]
utils.check_file_exists(wrf_command[-1])
try:
res = subprocess.check_output(wrf_command, cwd=self.wrf_run_dir,
stderr=utils.devnull())
j_id = int(res.split()[-1]) # slurm job-id
except subprocess.CalledProcessError:
#logger.error('WRF failed %s:' %wrf_command)
raise # re-raise exception
utils.waitJobToFinish(j_id)
else:
# run locally
subprocess.check_call(os.path.join(self.wrf_run_dir, 'wrf.exe'), cwd=self.wrf_run_dir,
stdout=utils.devnull(), stderr=utils.devnull())
def _run_unipost_step(self, wrfout, current_time, thours):
'''
Input variables for the function are:
- full path to a wrfout file (regular wrfout naming)
- time to run unipost for in format YYYY-MM-DD_HH
- thours: TODO add description
The following functionality is provided by the function:
- validate input parameters
- write itag file
- run unipost.exe command
- rename output
- archive output
- cleanup output
'''
# see if current_time is in wrfout AND validate time format
utils.validate_time_wrfout(wrfout, current_time)
# extract domain information from wrfout filename
domain = int(wrfout[-22:-20])
# write itag file
self._write_itag(wrfout, current_time)
# run unipost.exe
subprocess.check_call(os.path.join(
self.config['filesystem']['upp_dir'], 'bin', 'unipost.exe'),
cwd=self.post_dir,
stdout=utils.devnull(),
stderr=utils.devnull())
# rename and archive output
self._archive_output(current_time, thours, domain)
# cleanup output files
self._cleanup_output_files()
def _run_geogrid(self, j_id=None):
'''
run geogrid.exe (locally or using slurm script defined in config.json)
'''
# get number of domains from wps namelist
wps_nml = f90nml.read(self.config['options_wps']['namelist.wps'])
ndoms = wps_nml['share']['max_dom']
# check if geo_em files already exist for all domains
try:
for dom in range(1, ndoms + 1):
fname = "geo_em.d{}.nc".format(str(dom).zfill(2))
ncfile = Dataset(os.path.join(self.wps_workdir, fname))
ncfile.close()
except IOError:
# create geo_em nc files
if len(self.config['options_slurm']['slurm_geogrid.exe']):
# run using slurm
if j_id:
mid = "--dependency=afterok:%d" % j_id
geogrid_command = [
'sbatch', mid,
self.config['options_slurm']['slurm_geogrid.exe']
]
else:
geogrid_command = [
'sbatch',
self.config['options_slurm']['slurm_geogrid.exe']
]
utils.check_file_exists(geogrid_command[1])
utils.silentremove(
os.path.join(self.wps_workdir, 'geogrid', 'geogrid.exe'))
os.symlink(
os.path.join(self.config['filesystem']['wps_dir'],
'geogrid', 'geogrid.exe'),
os.path.join(self.wps_workdir, 'geogrid', 'geogrid.exe'))
try:
res = subprocess.check_output(geogrid_command,
cwd=self.wps_workdir,
stderr=utils.devnull())
j_id = int(res.split()[-1]) # slurm job-id
except subprocess.CalledProcessError:
#logger.error('Metgrid failed %s:' %geogrid_command)
raise # re-raise exception
utils.waitJobToFinish(j_id)
else:
geogrid_command = os.path.join(
self.config['filesystem']['wps_dir'], 'geogrid',
'geogrid.exe')
utils.check_file_exists(geogrid_command)
try:
subprocess.check_call(geogrid_command,
cwd=self.wps_workdir,
stdout=utils.devnull(),
stderr=utils.devnull())
except subprocess.CalledProcessError:
#logger.error('Geogrid failed %s:' %geogrid_command)
raise # re-raise exception
def _run_ungrib(self, j_id=None):
'''
run ungrib.exe (locally or using slurm script defined in config.json)
'''
if len(self.config['options_slurm']['slurm_ungrib.exe']):
# run using slurm
if j_id:
mid = "--dependency=afterok:%d" % j_id
ungrib_command = [
'sbatch', mid,
self.config['options_slurm']['slurm_ungrib.exe']
]
else:
ungrib_command = [
'sbatch', self.config['options_slurm']['slurm_ungrib.exe']
]
utils.check_file_exists(ungrib_command[-1])
utils.silentremove(
os.path.join(self.wps_workdir, 'ungrib', 'ungrib.exe'))
if not os.path.isdir(os.path.join(self.wps_workdir, 'ungrib')):
utils._create_directory(
os.path.join(self.wps_workdir, 'ungrib'))
os.symlink(
os.path.join(self.config['filesystem']['wps_dir'], 'ungrib',
'ungrib.exe'),
os.path.join(self.wps_workdir, 'ungrib', 'ungrib.exe'))
try:
res = subprocess.check_output(ungrib_command,
cwd=self.wps_workdir,
stderr=utils.devnull())
j_id = int(res.split()[-1]) # slurm job-id
except subprocess.CalledProcessError:
#logger.error('Ungrib failed %s:' %ungrib_command)
raise # re-raise exception
utils.waitJobToFinish(j_id)
else:
ungrib_command = os.path.join(self.config['filesystem']['wps_dir'],
'ungrib', 'ungrib.exe')
utils.check_file_exists(ungrib_command)
try:
subprocess.check_call(ungrib_command,
cwd=self.wps_workdir,
stdout=utils.devnull(),
stderr=utils.devnull())
except subprocess.CalledProcessError:
#logger.error('Ungrib failed %s:' %ungrib_command)
raise # re-raise exception
def run_wrf(self, j_id=None):
'''
run wrf.exe
'''
# check if slurm_wrf.exe is defined
if len(self.config['options_slurm']['slurm_wrf.exe']):
if j_id:
mid = "--dependency=afterok:%d" % j_id
wrf_command = [
'sbatch', mid,
self.config['options_slurm']['slurm_wrf.exe']
]
else:
wrf_command = [
'sbatch', self.config['options_slurm']['slurm_wrf.exe']
]
utils.check_file_exists(wrf_command[-1])
utils.silentremove(os.path.join(self.wrf_rundir, 'wrf.exe'))
os.symlink(
os.path.join(self.config['filesystem']['wrf_dir'], 'main',
'wrf.exe'),
os.path.join(self.wrf_rundir, 'wrf.exe'))
try:
res = subprocess.check_output(wrf_command,
cwd=self.wrf_rundir,
stderr=utils.devnull())
j_id = int(res.split()[-1]) # slurm job-id
except subprocess.CalledProcessError:
logger.error('Wrf failed %s:' % wrf_command)
raise # re-raise exception
utils.waitJobToFinish(j_id)
else: # run locally
wrf_command = os.path.join(self.config['filesystem']['wrf_dir'],
'main', 'wrf.exe')
utils.check_file_exists(wrf_command)
try:
subprocess.check_call(wrf_command,
cwd=self.wrf_rundir,
stdout=utils.devnull(),
stderr=utils.devnull())
except subprocess.CalledProcessError:
logger.error('wrf.exe failed %s:' % wrf_command)
raise # re-raise exception
def wrfvar_run(self, domain):
'''
run da_wrfvar.exe
'''
# set domain specific workdir
wrfda_workdir = os.path.join(self.wrfda_workdir, "d0" + str(domain))
logfile = os.path.join(wrfda_workdir, 'log.wrfda_d' + str(domain))
j_id = None
if len(self.config['options_slurm']['slurm_wrfvar.exe']):
if j_id:
mid = "--dependency=afterok:%d" % j_id
wrfvar_command = [
'sbatch', mid,
self.config['options_slurm']['slurm_wrfvar.exe']
]
else:
wrfvar_command = [
'sbatch', self.config['options_slurm']['slurm_wrfvar.exe']
]
utils.check_file_exists(wrfvar_command[-1])
try:
res = subprocess.check_output(wrfvar_command,
cwd=wrfda_workdir,
stderr=utils.devnull())
j_id = int(res.split()[-1]) # slurm job-id
except subprocess.CalledProcessError:
logger.error('Wrfvar failed %s:' % wrfvar_command)
raise # re-raise exception
while True:
time.sleep(1)
if not utils.testjob(j_id):
break
else:
# run locally
subprocess.check_call(
[os.path.join(wrfda_workdir, 'da_wrfvar.exe'), '>&!', logfile],
cwd=wrfda_workdir,
stdout=utils.devnull(),
stderr=utils.devnull())
def obsproc_run(self):
'''
run obsproc.exe
'''
obslist = list(set(self.obs.values()))
obsproc_dir = obslist[0][0]
# TODO: check if output is file is created and no errors have occurred
j_id = None
if len(self.config['options_slurm']['slurm_obsproc.exe']):
# run using slurm
if j_id:
mid = "--dependency=afterok:%d" % j_id
obsproc_command = [
'sbatch', mid,
self.config['options_slurm']['slurm_obsproc.exe']
]
else:
obsproc_command = [
'sbatch', self.config['options_slurm']['slurm_obsproc.exe']
]
utils.check_file_exists(obsproc_command[-1])
try:
res = subprocess.check_output(obsproc_command,
cwd=obsproc_dir,
stderr=utils.devnull())
j_id = int(res.split()[-1]) # slurm job-id
except subprocess.CalledProcessError:
#logger.error('Obsproc failed %s:' % obsproc_command)
raise # re-raise exception
utils.waitJobToFinish(j_id)
else:
# run locally
subprocess.check_call(os.path.join(obsproc_dir, 'obsproc.exe'),
cwd=obsproc_dir,
stdout=utils.devnull(),
stderr=utils.devnull())
return None
