def get_memory_walltime(self, job_name, job_type='batch'):
"""
get memory, walltime and number of threads for the job from job_defaults.cfg
:param job_name: the job file name
:param job_type: 'batch' or 'script'
"""
config = putils.get_config_defaults(config_file='job_defaults.cfg')
if job_type == 'batch':
step_name = '_'
step_name = step_name.join(job_name.split('/')[-1].split('_')[2::])
else:
step_name = job_name
if self.memory in [None, 'None']:
if step_name in config:
self.default_memory = config[step_name]['memory']
else:
self.default_memory = config['DEFAULT']['memory']
else:
self.default_memory = self.memory
if self.wall_time in [None, 'None']:
if step_name in config:
self.default_wall_time = config[step_name]['walltime']
if config[step_name]['adjust'] == 'True':
if self.num_bursts is None:
self.num_bursts = putils.get_number_of_bursts(self)
else:
self.default_wall_time = config['DEFAULT']['walltime']
self.default_wall_time = putils.walltime_adjust(
self.num_bursts,
self.default_wall_time,
self.scheduler,
adjust=config[step_name]['adjust'])
else:
self.default_wall_time = self.wall_time
if step_name in config:
self.default_num_threads = config[step_name]['num_threads']
else:
self.default_num_threads = config['DEFAULT']['num_threads']
return
def main(iargs=None):
inps = putils.cmd_line_parse(iargs, script='execute_runfiles')
os.chdir(inps.work_dir)
config = putils.get_config_defaults(config_file='job_defaults.cfg')
job_file_name = 'execute_runfiles'
job_name = job_file_name
if inps.wall_time == 'None':
inps.wall_time = config[job_file_name]['walltime']
wait_seconds, new_wall_time = putils.add_pause_to_walltime(
inps.wall_time, inps.wait_time)
#########################################
# Submit job
#########################################
if inps.submit_flag:
js.submit_script(job_name, job_file_name, sys.argv[:], inps.work_dir,
new_wall_time)
sys.exit(0)
time.sleep(wait_seconds)
command_line = os.path.basename(sys.argv[0]) + ' ' + ' '.join(sys.argv[1:])
message_rsmas.log(inps.work_dir, command_line)
run_file_list = putils.read_run_list(inps.work_dir)
if inps.endrun == 0:
inps.endrun = len(run_file_list)
if not inps.startrun == 0:
inps.startrun = inps.startrun - 1
run_file_list = run_file_list[inps.startrun:inps.endrun]
if os.getenv('JOBSCHEDULER') == 'LSF' or os.getenv(
'JOBSCHEDULER') == 'PBS':
for item in run_file_list:
step_name = '_'
step_name = step_name.join(item.split('_')[3::])
try:
memorymax = config[step_name]['memory']
except:
memorymax = config['DEFAULT']['memory']
try:
if config[step_name]['adjust'] == 'True':
walltimelimit = putils.walltime_adjust(
inps, config[step_name]['walltime'])
else:
walltimelimit = config[step_name]['walltime']
except:
walltimelimit = config['DEFAULT']['walltime']
queuename = os.getenv('QUEUENAME')
putils.remove_last_job_running_products(run_file=item)
jobs = js.submit_batch_jobs(batch_file=item,
out_dir=os.path.join(
inps.work_dir, 'run_files'),
work_dir=inps.work_dir,
memory=memorymax,
walltime=walltimelimit,
queue=queuename)
putils.remove_zero_size_or_length_error_files(run_file=item)
putils.raise_exception_if_job_exited(run_file=item)
putils.concatenate_error_files(run_file=item,
work_dir=inps.work_dir)
putils.move_out_job_files_to_stdout(run_file=item)
else:
for item in run_file_list:
with open(item, 'r') as f:
command_lines = f.readlines()
for command_line in command_lines:
os.system(command_line)
return None
def main(iargs=None):
""" create orth and geo rectifying run jobs and submit them. """
inps = putils.cmd_line_parse(iargs)
inps.geom_masterDir = os.path.join(inps.work_dir, pathObj.geomlatlondir)
inps.master = os.path.join(inps.work_dir, pathObj.masterdir)
try:
inps.dem = glob.glob('{}/DEM/*.wgs84'.format(inps.work_dir))[0]
except:
print('DEM not exists!')
sys.exit(1)
if not os.path.exists(inps.geom_masterDir):
os.mkdir(inps.geom_masterDir)
config = putils.get_config_defaults(config_file='job_defaults.cfg')
job_file_name = 'export_ortho_geo'
job_name = job_file_name
if inps.wall_time == 'None':
inps.wall_time = config[job_file_name]['walltime']
wait_seconds, new_wall_time = putils.add_pause_to_walltime(inps.wall_time, inps.wait_time)
#########################################
# Submit job
#########################################
if inps.submit_flag:
js.submit_script(job_name, job_file_name, sys.argv[:], inps.work_dir, new_wall_time)
sys.exit(0)
time.sleep(wait_seconds)
if not iargs is None:
message_rsmas.log(inps.work_dir, os.path.basename(__file__) + ' ' + ' '.join(iargs[:]))
else:
message_rsmas.log(inps.work_dir, os.path.basename(__file__) + ' ' + ' '.join(sys.argv[1::]))
demZero = create_demZero(inps.dem, inps.geom_masterDir)
swathList = ut.getSwathList(inps.master)
create_georectified_lat_lon(swathList, inps.master, inps.geom_masterDir, demZero)
merge_burst_lat_lon(inps)
multilook_images(inps)
run_file_list = make_run_list_amplitude(inps)
for item in run_file_list:
step_name = 'amplitude_ortho_geo'
try:
memorymax = config[step_name]['memory']
except:
memorymax = config['DEFAULT']['memory']
try:
if config[step_name]['adjust'] == 'True':
walltimelimit = putils.walltime_adjust(config[step_name]['walltime'])
else:
walltimelimit = config[step_name]['walltime']
except:
walltimelimit = config['DEFAULT']['walltime']
queuename = os.getenv('QUEUENAME')
putils.remove_last_job_running_products(run_file=item)
jobs = js.submit_batch_jobs(batch_file=item,
out_dir=os.path.join(inps.work_dir, 'run_files'),
work_dir=inps.work_dir, memory=memorymax,
walltime=walltimelimit, queue=queuename)
putils.remove_zero_size_or_length_error_files(run_file=item)
putils.raise_exception_if_job_exited(run_file=item)
putils.concatenate_error_files(run_file=item, work_dir=inps.work_dir)
putils.move_out_job_files_to_stdout(run_file=item)
return
def main(iargs=None):
inps = putils.cmd_line_parse(iargs, script='execute_runfiles')
os.chdir(inps.work_dir)
config = putils.get_config_defaults(config_file='job_defaults.cfg')
job_file_name = 'execute_runfiles'
job_name = job_file_name
if inps.wall_time == 'None':
inps.wall_time = config[job_file_name]['walltime']
wait_seconds, new_wall_time = putils.add_pause_to_walltime(
inps.wall_time, inps.wait_time)
#########################################
# Submit job
#########################################
if inps.submit_flag:
js.submit_script(job_name, job_file_name, sys.argv[:], inps.work_dir,
new_wall_time)
sys.exit(0)
time.sleep(wait_seconds)
run_file_list = putils.read_run_list(inps.work_dir)
if inps.end_run == 0:
inps.end_run = len(run_file_list)
if not inps.start_run == 0:
inps.start_run = inps.start_run - 1
if not iargs is None:
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(iargs[:]))
else:
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(sys.argv[1::]))
run_file_list = run_file_list[inps.start_run:inps.end_run]
supported_schedulers = ['LSF', 'PBS', 'SLURM']
if os.getenv('JOBSCHEDULER') in supported_schedulers:
for item in run_file_list:
step_name = '_'
step_name = step_name.join(item.split('_')[3::])
try:
memorymax = config[step_name]['memory']
except:
memorymax = config['DEFAULT']['memory']
try:
if config[step_name]['adjust'] == 'True':
walltimelimit = putils.walltime_adjust(
inps, config[step_name]['walltime'])
else:
walltimelimit = config[step_name]['walltime']
except:
walltimelimit = config['DEFAULT']['walltime']
queuename = os.getenv('QUEUENAME')
putils.remove_last_job_running_products(run_file=item)
if os.getenv('JOBSCHEDULER') in ['SLURM', 'sge']:
js.submit_job_with_launcher(batch_file=item,
work_dir=os.path.join(
inps.work_dir, 'run_files'),
memory=memorymax,
walltime=walltimelimit,
queue=queuename)
else:
jobs = js.submit_batch_jobs(batch_file=item,
out_dir=os.path.join(
inps.work_dir, 'run_files'),
work_dir=inps.work_dir,
memory=memorymax,
walltime=walltimelimit,
queue=queuename)
putils.remove_zero_size_or_length_error_files(run_file=item)
putils.raise_exception_if_job_exited(run_file=item)
putils.concatenate_error_files(run_file=item,
work_dir=inps.work_dir)
putils.move_out_job_files_to_stdout(run_file=item)
date_str = datetime.datetime.strftime(datetime.datetime.now(),
'%Y%m%d:%H%M%S')
print(date_str + ' * Job {} completed'.format(item))
date_str = datetime.datetime.strftime(datetime.datetime.now(),
'%Y%m%d:%H%M%S')
print(date_str +
' * all jobs from {} to {} have been completed'.format(
os.path.basename(run_file_list[0]),
os.path.basename(run_file_list[-1])))
else:
for item in run_file_list:
with open(item, 'r') as f:
command_lines = f.readlines()
for command_line in command_lines:
os.system(command_line)
return None