def distribute(self):
"""
Submit the step to the scheduler parallelizing the iterable inputs
"""
self.status = JOB_STATUS.QUEUED
#initialize the scheduler
if self.local_step:
self.scheduler = get_scheduler("SCHED_LOCAL")
else:
self.scheduler = scheduler
if Step.__cfg_is_changed(self.cfg):
Step.__write_cfg_file(self.cfg)
Step.__remove_pickle(self.cfg)
elif self.is_pickled():
self.load_pickle()
if self.status == JOB_STATUS.SUCCEEDED:
self.log.info(
'Skipping step %s: configuration has not been changed' %
self.name)
return len(self.jobs)
iterables = self.get_iterables()
if iterables:
# Step needs to be distributed
for iterable in iterables:
# If this is a file, convert it to list from file contents
iterable_input = self.cfg.get(iterable, [])
if not hasattr(iterable_input, '__iter__') \
and os.path.exists(iterable_input):
with open(iterable_input) as f:
self.cfg[iterable] = f.read().splitlines()
for index in range(0, len(self.cfg[iterables[0]])):
#copy the config file
job_cfg = copy.deepcopy(self.cfg)
#copy the iterable specific to the job
for iterable in iterables:
if iterable in self.cfg and self.cfg[
iterable]: # permit a null file
job_cfg[iterable] = self.cfg[iterable][index]
job_cfg['meta']['pipeline'] = self.cfg['meta']['pipeline']
job_cfg['meta']['step'] = self.cfg['meta']['step']
for key, value in self.cfg['meta']['job'].iteritems():
job_cfg['meta']['job'][key] = value[index]
self.submit_job(job_cfg)
else:
job_cfg = copy.deepcopy(self.cfg)
self.submit_job(job_cfg)
return len(self.jobs)
def distribute(self):
"""
Submit the step to the scheduler parallelizing the iterable inputs
"""
self.status = JOB_STATUS.QUEUED
#initialize the scheduler
if self.local_step:
self.scheduler = get_scheduler("SCHED_LOCAL")
else:
self.scheduler = scheduler
if Step.__cfg_is_changed(self.cfg):
Step.__write_cfg_file(self.cfg)
Step.__remove_pickle(self.cfg)
elif self.is_pickled():
self.load_pickle()
if self.status == JOB_STATUS.SUCCEEDED:
self.log.info('Skipping step %s: configuration has not been changed' % self.name)
return len(self.jobs)
iterables = self.get_iterables()
if iterables:
# Step needs to be distributed
for iterable in iterables:
# If this is a file, convert it to list from file contents
iterable_input = self.cfg.get(iterable,[])
if not hasattr(iterable_input, '__iter__') \
and os.path.exists(iterable_input):
with open(iterable_input) as f:
self.cfg[iterable] = f.read().splitlines()
for index in range(0, len(self.cfg[iterables[0]])):
#copy the config file
job_cfg = copy.deepcopy(self.cfg)
#copy the iterable specific to the job
for iterable in iterables:
if iterable in self.cfg and self.cfg[iterable]: # permit a null file
job_cfg[iterable] = self.cfg[iterable][index]
job_cfg['meta']['pipeline'] = self.cfg['meta']['pipeline']
job_cfg['meta']['step'] = self.cfg['meta']['step']
for key, value in self.cfg['meta']['job'].iteritems():
job_cfg['meta']['job'][key] = value[index]
self.submit_job(job_cfg)
else:
job_cfg = copy.deepcopy(self.cfg)
self.submit_job(job_cfg)
return len(self.jobs)
def __init__(self):
self.bootstrap = STARTUP_CYCLE
self.status = JOB_STATUS.QUEUED
self.meta = {'pipeline': {}, 'step': {}, 'job': {}}
self.requirements = {'memory': '1', 'cpus': '1'}
self.output_dir = '.'
self.jobs = OrderedDict()
self.cmd_count = 0
logger.set_stdout_level(logger.DEBUG)
self.log = logger.get_log()
# parse specs and create keys
self.spec["name"] = self.__module__.replace('nespipe.steps.',
'').split('.')[-1]
self.name = self.spec["name"]
self.__version__ = self.spec['version']
self.local_step = self.spec.get('local', False)
global scheduler
if self.local_step:
self.scheduler = get_scheduler("SCHED_LOCAL")
else:
self.scheduler = scheduler
for k, v in self.spec["args"].iteritems():
for param in v:
if param.get('name', None):
setattr(self, param['name'], param.get('value', []))
ut.dict_update(
self.requirements,
self.spec.get('requirements', {
'memory': '1',
'cpus': '1'
}))
for k, v in self.requirements.iteritems():
setattr(self, k, int(v))
#set the jvm memory
if 'memory' in self.requirements:
self.jvm_memory = int(int(self.requirements['memory']) * 0.9)
if not self.jvm_memory:
self.jvm_memory = 1
def __init__(self):
self.bootstrap = STARTUP_CYCLE
self.status = JOB_STATUS.QUEUED
self.meta = { 'pipeline':{}, 'step':{}, 'job':{}}
self.requirements = {'memory' : '1', 'cpus' : '1'}
self.output_dir = '.'
self.jobs = OrderedDict()
self.cmd_count = 0
logger.set_stdout_level(logger.DEBUG)
self.log = logger.get_log()
# parse specs and create keys
self.spec["name"] = self.__module__.replace('nespipe.steps.','').split('.')[-1]
self.name = self.spec["name"]
self.__version__ = self.spec['version']
self.local_step = self.spec.get('local', False)
global scheduler
if self.local_step:
self.scheduler = get_scheduler("SCHED_LOCAL")
else:
self.scheduler = scheduler
for k, v in self.spec["args"].iteritems():
for param in v:
if param.get('name', None):
setattr(self, param['name'], param.get('value', []))
ut.dict_update(self.requirements, self.spec.get('requirements', {'memory' : '1', 'cpus' : '1'}))
for k, v in self.requirements.iteritems():
setattr(self, k, int(v))
#set the jvm memory
if 'memory' in self.requirements:
self.jvm_memory = int(int(self.requirements['memory']) * 0.9)
if not self.jvm_memory:
self.jvm_memory = 1
def set_scheduler(schedname):
global scheduler
scheduler = get_scheduler(schedname)
from nespipe.core.constants import *
from nespipe.core.schedulers import get_scheduler
from nespipe.core.constants import *
NOT_DB_ATTR = [
'cfg', 'reqs', 'jvm_memory', 'memory', 'cpus', 'jobs', 'sys_path',
'step_class', 'cmd_count'
'name', 'local_step', '__version__', 'scheduler', 'log'
]
STEP_PICKLE = '.status.pickle'
ITERABLE_TYPE = 'input_key_iterable'
STARTUP_CYCLE = 50
scheduler = get_scheduler()
def set_scheduler(schedname):
global scheduler
scheduler = get_scheduler(schedname)
class Step(object):
"""
Base class for any step
Members:
- status: current status of the step
- parameters: dictionary containing the definition of the parameters
N.B. The actual values are stored as members
def set_scheduler(schedname):
global scheduler
scheduler = get_scheduler(schedname)
from nespipe.core.constants import *
NOT_DB_ATTR = ['cfg', 'reqs', 'jvm_memory', 'memory', 'cpus',
'jobs', 'sys_path', 'step_class', 'cmd_count'
'name', 'local_step', '__version__', 'scheduler', 'log']
STEP_PICKLE = '.status.pickle'
ITERABLE_TYPE = 'input_key_iterable'
STARTUP_CYCLE = 50
scheduler = get_scheduler()
def set_scheduler(schedname):
global scheduler
scheduler = get_scheduler(schedname)
class Step(object):
"""
Base class for any step
Members:
- status: current status of the step
- parameters: dictionary containing the definition of the parameters
N.B. The actual values are stored as members
- meta: dictionary containing the metadata information