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):
inps = putils.cmd_line_parse(iargs, script='execute_runfiles')
if not iargs is None:
input_arguments = iargs
else:
input_arguments = sys.argv[1::]
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(input_arguments))
os.chdir(inps.work_dir)
time.sleep(putils.pause_seconds(inps.wait_time))
if inps.prefix == 'stripmap':
inps.num_bursts = 1
inps.out_dir = os.path.join(inps.work_dir, 'run_files')
job_obj = JOB_SUBMIT(inps)
#########################################
# Submit job
#########################################
if inps.submit_flag:
job_name = 'execute_runfiles'
job_file_name = job_name
if '--submit' in input_arguments:
input_arguments.remove('--submit')
command = [os.path.abspath(__file__)] + input_arguments
job_obj.submit_script(job_name, job_file_name, command)
sys.exit(0)
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 inps.step:
inps.start_run = inps.step - 1
inps.end_run = inps.step
run_file_list = run_file_list[inps.start_run:inps.end_run]
for item in run_file_list:
putils.remove_last_job_running_products(run_file=item)
job_status = job_obj.submit_batch_jobs(batch_file=item)
if job_status:
putils.remove_zero_size_or_length_error_files(run_file=item)
putils.rerun_job_if_exit_code_140(run_file=item, inps_dict=inps)
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])))
return None
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:
# FA 26 Dec commented out as it seemed wrong
#if config[step_name]['adjust'] == 'True':
# walltimelimit = putils.walltime_adjust(inps, config[step_name]['walltime'])
#else:
# walltimelimit = config[step_name]['walltime']
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.rerun_job_if_exit_code_140(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
def main(iargs=None):
inps = putils.cmd_line_parse(iargs, script='execute_runfiles')
os.chdir(inps.work_dir)
time.sleep(putils.pause_seconds(inps.wait_time))
#########################################
# Submit job
#########################################
if inps.submit_flag:
job_name = 'execute_runfiles'
job_file_name = job_name
js.submit_script(job_name, job_file_name, sys.argv[:], inps.work_dir)
sys.exit(0)
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]
for item in run_file_list:
putils.remove_last_job_running_products(run_file=item)
job_status = js.submit_batch_jobs(batch_file=item,
out_dir=os.path.join(
inps.work_dir, 'run_files'),
work_dir=inps.work_dir)
if job_status:
putils.remove_zero_size_or_length_error_files(run_file=item)
putils.rerun_job_if_exit_code_140(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])))
return None