def test_amgr_setup_mqs():
amgr = Amgr(hostname=hostname, port=port)
assert amgr._setup_mqs() == True
assert len(amgr._pending_queue) == 1
assert len(amgr._completed_queue) == 1
mq_connection = pika.BlockingConnection(pika.ConnectionParameters(host=amgr._mq_hostname, port=amgr._port))
mq_channel = mq_connection.channel()
qs = [
'%s-tmgr-to-sync' % amgr._sid,
'%s-cb-to-sync' % amgr._sid,
'%s-enq-to-sync' % amgr._sid,
'%s-deq-to-sync' % amgr._sid,
'%s-sync-to-tmgr' % amgr._sid,
'%s-sync-to-cb' % amgr._sid,
'%s-sync-to-enq' % amgr._sid,
'%s-sync-to-deq' % amgr._sid
]
for q in qs:
mq_channel.queue_delete(queue=q)
with open('.%s.txt' % amgr._sid, 'r') as fp:
lines = fp.readlines()
for i in range(len(lines)):
lines[i] = lines[i].strip()
assert set(qs) < set(lines)
def test_stage_post_exec():
global p1
p1.name = 'p1'
s = Stage()
s.name = 's1'
for t in range(NUM_TASKS):
s.add_tasks(create_single_task())
s.post_exec = condition
p1.add_stages(s)
res_dict = {
'resource': 'local.localhost',
'walltime': 30,
'cpus': 1,
}
os.environ['RADICAL_PILOT_DBURL'] = MLAB
appman = AppManager(rts='radical.pilot', hostname=hostname, port=port)
appman.resource_desc = res_dict
appman.workflow = [p1]
appman.run()
def test_sid_in_mqs():
appman = Amgr(hostname=hostname, port=port)
appman._setup_mqs()
sid = appman._sid
qs = [
'%s-tmgr-to-sync' % sid,
'%s-cb-to-sync' % sid,
'%s-enq-to-sync' % sid,
'%s-deq-to-sync' % sid,
'%s-sync-to-tmgr' % sid,
'%s-sync-to-cb' % sid,
'%s-sync-to-enq' % sid,
'%s-sync-to-deq' % sid
]
mq_connection = pika.BlockingConnection(
pika.ConnectionParameters(host=hostname, port=port))
mq_channel = mq_connection.channel()
def callback():
print True
for q in qs:
try:
mq_channel.basic_consume(callback, queue=q, no_ack=True)
except Exception as ex:
raise EnTKError(ex)
def test_amgr_read_config():
amgr = Amgr(hostname=host, port=port)
assert amgr._reattempts == 3
assert amgr._rmq_cleanup
assert amgr._autoterminate
assert not amgr._write_workflow
assert not amgr._resubmit_failed
assert amgr._rts == 'radical.pilot'
assert amgr._num_pending_qs == 1
assert amgr._num_completed_qs == 1
assert amgr._rts_config == {"sandbox_cleanup": False,
"db_cleanup" : False}
d = {"hostname" : "radical.two",
"port" : 25672,
"username" : user,
"password" : passwd,
"reattempts" : 5,
"resubmit_failed": True,
"autoterminate" : False,
"write_workflow" : True,
"rts" : "mock",
"rts_config" : {"sandbox_cleanup": True,
"db_cleanup" : True},
"pending_qs" : 2,
"completed_qs" : 3,
"rmq_cleanup" : False}
ru.write_json(d, './config.json')
amgr._read_config(config_path='./',
hostname=None,
port=None,
username=None,
password=None,
reattempts=None,
resubmit_failed=None,
autoterminate=None,
write_workflow=None,
rts=None,
rmq_cleanup=None,
rts_config=None)
assert amgr._hostname == d['hostname']
assert amgr._port == d['port']
assert amgr._reattempts == d['reattempts']
assert amgr._resubmit_failed == d['resubmit_failed']
assert amgr._autoterminate == d['autoterminate']
assert amgr._write_workflow == d['write_workflow']
assert amgr._rts == d['rts']
assert amgr._rts_config == d['rts_config']
assert amgr._num_pending_qs == d['pending_qs']
assert amgr._num_completed_qs == d['completed_qs']
assert amgr._rmq_cleanup == d['rmq_cleanup']
os.remove('./config.json')
def test_wfp_check_processor():
p = Pipeline()
s = Stage()
t = Task()
t.executable = '/bin/date'
s.add_tasks(t)
p.add_stages(s)
amgr = Amgr(hostname=hostname, port=port)
amgr._setup_mqs()
wfp = WFprocessor(sid=amgr._sid,
workflow=[p],
pending_queue=amgr._pending_queue,
completed_queue=amgr._completed_queue,
rmq_conn_params=amgr._rmq_conn_params,
resubmit_failed=False)
wfp.start_processor()
assert wfp.check_processor()
wfp.terminate_processor()
assert not wfp.check_processor()
def test_amgr_cleanup_mqs():
amgr = Amgr(hostname=hostname, port=port)
sid = amgr._sid
amgr._setup_mqs()
amgr._cleanup_mqs()
mq_connection = pika.BlockingConnection(
pika.ConnectionParameters(host=hostname, port=port))
qs = [
'%s-tmgr-to-sync' % sid,
'%s-cb-to-sync' % sid,
'%s-enq-to-sync' % sid,
'%s-deq-to-sync' % sid,
'%s-sync-to-tmgr' % sid,
'%s-sync-to-cb' % sid,
'%s-sync-to-enq' % sid,
'%s-sync-to-deq' % sid,
'%s-pendingq-1' % sid,
'%s-completedq-1' % sid
]
for q in qs:
with pytest.raises(pika.exceptions.ChannelClosed):
mq_channel = mq_connection.channel()
mq_channel.queue_purge(q)
def __init__(self, resource='local', comm_server=None):
"""The workhorse of high throughput binding affinity calculations.
Manages arbitrary number of protocols on any resource (including supercomputers).
Parameters
----------
resource: str
The name of the resource where the protocols will be run. This is usually then name of the supercomputer
or 'local' if the job will be executed locally. (the default is to try to run locally).
comm_server: tuple(str, int)
The communication server used by the execution system. Specify a hostname and port number as a tuple. If
None, then the dedicated server might be used from the resource description if present.
"""
self.resource = yaml.load(resource_stream(__name__, 'resources.yaml'))[resource]
if comm_server is None:
comm_server = self.resource.get('dedicated_rabbitmq_server')
self._protocols = list()
self._app_manager = AppManager(*comm_server)
# Profiler for Runner
self._uid = ru.generate_id('radical.htbac.workflow_runner')
self._logger = ru.get_logger('radical.htbac.workflow_runner')
self._prof = ru.Profiler(name=self._uid)
self._prof.prof('create workflow_runner obj', uid=self._uid)
self._root_directories = list()
def run(self, strong_scaled=1, autoterminate=True, queue='high', walltime=1440):
pipelines = set()
input_data = list()
for protocol in self._protocols:
gen_pipeline = protocol.generate_pipeline()
pipelines.add(gen_pipeline)
input_data.extend(protocol.input_data)
self.ids[protocol.id()] = gen_pipeline
# protocol.id is the uuid, gen_pipeline.uid is the pipeline
self.total_replicas += protocol.replicas
self._cores = self._cores * self.total_replicas
print 'Running on', self._cores, 'cores.'
res_dict = {'resource': 'ncsa.bw_aprun',
'walltime': walltime,
'cores': int(self._cores*strong_scaled),
'project': 'bamm',
'queue': queue,
'access_schema': 'gsissh'}
# Create Resource Manager object with the above resource description
resource_manager = ResourceManager(res_dict)
resource_manager.shared_data = input_data
# Create Application Manager
self.app_manager = AppManager(hostname=self._hostname, port=self._port, autoterminate=autoterminate)
self.app_manager.resource_manager = resource_manager
self.app_manager.assign_workflow(pipelines)
self._prof.prof('execution_run')
print 'Running...'
self.app_manager.run() # this method is blocking until all pipelines show state = completed
def test_issue_271():
# Create Application Manager
appman = AppManager(hostname=hostname, port=port)
# Create a dictionary describe four mandatory keys:
# resource, walltime, and cpus
# resource is 'local.localhost' to execute locally
res_dict = {
'resource': 'local.localhost',
'walltime': 10,
'cpus': 1
}
# Assign resource request description to the Application Manager
appman.resource_desc = res_dict
# Assign the workflow as a set or list of Pipelines to the Application Manager
# Note: The list order is not guaranteed to be preserved
p = generate_pipeline()
appman.workflow = set([p])
# Run the Application Manager
appman.run()
# assert
for t in p.stages[0].tasks:
assert t.state == states.FAILED
def test_sid_in_mqs():
# FIXME: what is tested / asserted here?
appman = Amgr(hostname=host, port=port)
sid = appman._sid
appman._setup_mqs()
qs = ['%s-tmgr-to-sync' % sid,
'%s-cb-to-sync' % sid,
'%s-sync-to-tmgr' % sid,
'%s-sync-to-cb' % sid]
mq_connection = pika.BlockingConnection(pika.ConnectionParameters(
host=host, port=port))
mq_channel = mq_connection.channel()
def callback():
pass
for q in qs:
try:
mq_channel.basic_consume(callback, queue=q, no_ack=True)
except Exception as ex:
raise EnTKError(ex)
def test_issue_199():
# Create a dictionary describe four mandatory keys:
# resource, walltime, cpus and project
# resource is 'local.localhost' to execute locally
res_dict = {
'resource': 'local.localhost',
'walltime': 10,
'cpus': 1
}
os.environ['RADICAL_PILOT_DBURL'] = MLAB
# Create Application Manager
appman = AppManager(hostname=hostname, port=port)
# Assign resource manager to the Application Manager
appman.resource_desc = res_dict
p = generate_pipeline()
# Assign the workflow as a set of Pipelines to the Application Manager
appman.workflow = [p]
# Run the Application Manager
appman.run()
def test_amgr_setup_mqs():
amgr = Amgr(hostname=hostname, port=port)
assert amgr._setup_mqs() == True
assert len(amgr._pending_queue) == 1
assert len(amgr._completed_queue) == 1
mq_connection = pika.BlockingConnection(pika.ConnectionParameters(host=amgr._mq_hostname, port=amgr._port))
mq_channel = mq_connection.channel()
qs = [
'%s-tmgr-to-sync' % amgr._sid,
'%s-cb-to-sync' % amgr._sid,
'%s-enq-to-sync' % amgr._sid,
'%s-deq-to-sync' % amgr._sid,
'%s-sync-to-tmgr' % amgr._sid,
'%s-sync-to-cb' % amgr._sid,
'%s-sync-to-enq' % amgr._sid,
'%s-sync-to-deq' % amgr._sid
]
for q in qs:
mq_channel.queue_delete(queue=q)
with open('.%s.txt' % amgr._sid, 'r') as fp:
lines = fp.readlines()
for ind, val in enumerate(lines):
lines[ind] = val.strip()
assert set(qs) < set(lines)
def test_amgr_cleanup_mqs():
amgr = Amgr(hostname=hostname, port=port)
sid = amgr._sid
amgr._setup_mqs()
amgr._cleanup_mqs()
mq_connection = pika.BlockingConnection(
pika.ConnectionParameters(host=hostname, port=port))
qs = ['%s-tmgr-to-sync' % sid,
'%s-cb-to-sync' % sid,
'%s-enq-to-sync' % sid,
'%s-deq-to-sync' % sid,
'%s-sync-to-tmgr' % sid,
'%s-sync-to-cb' % sid,
'%s-sync-to-enq' % sid,
'%s-sync-to-deq' % sid,
'%s-pendingq-1' % sid,
'%s-completedq-1' % sid]
for q in qs:
with pytest.raises(pika.exceptions.ChannelClosed):
mq_channel = mq_connection.channel()
mq_channel.queue_purge(q)
def test_amgr_setup_mqs():
amgr = Amgr(hostname=hostname, port=port)
amgr._setup_mqs()
assert len(amgr._pending_queue) == 1
assert len(amgr._completed_queue) == 1
mq_connection = pika.BlockingConnection(pika.ConnectionParameters(
host=amgr._hostname, port=amgr._port))
mq_channel = mq_connection.channel()
qs = ['%s-tmgr-to-sync' % amgr._sid,
'%s-cb-to-sync' % amgr._sid,
'%s-sync-to-tmgr' % amgr._sid,
'%s-sync-to-cb' % amgr._sid,
'%s-pendingq-1' % amgr._sid,
'%s-completedq-1' % amgr._sid]
for q in qs:
mq_channel.queue_delete(queue=q)
with open('.%s.txt' % amgr._sid, 'r') as fp:
lines = fp.readlines()
for ind, val in enumerate(lines):
lines[ind] = val.strip()
assert set(qs) == set(lines)
def test_sid_in_mqs():
appman = Amgr(hostname=hostname, port=port)
appman._setup_mqs()
sid = appman._sid
qs = [
'%s-tmgr-to-sync' % sid,
'%s-cb-to-sync' % sid,
'%s-enq-to-sync' % sid,
'%s-deq-to-sync' % sid,
'%s-sync-to-tmgr' % sid,
'%s-sync-to-cb' % sid,
'%s-sync-to-enq' % sid,
'%s-sync-to-deq' % sid
]
mq_connection = pika.BlockingConnection(
pika.ConnectionParameters(
host=hostname,
port=port)
)
mq_channel = mq_connection.channel()
def callback():
print True
for q in qs:
try:
mq_channel.basic_consume(callback, queue=q, no_ack=True)
except Exception as ex:
raise EnTKError(ex)
def test_wfp_start_processor():
p = Pipeline()
s = Stage()
t = Task()
t.executable = ['/bin/date']
s.add_tasks(t)
p.add_stages(s)
amgr = Amgr(hostname=hostname, port=port)
amgr._setup_mqs()
wfp = WFprocessor(sid=amgr._sid,
workflow=[p],
pending_queue=amgr._pending_queue,
completed_queue=amgr._completed_queue,
mq_hostname=amgr._mq_hostname,
port=amgr._port,
resubmit_failed=False)
assert wfp.start_processor()
assert not wfp._enqueue_thread
assert not wfp._dequeue_thread
assert not wfp._enqueue_thread_terminate.is_set()
assert not wfp._dequeue_thread_terminate.is_set()
assert not wfp._wfp_terminate.is_set()
assert wfp._wfp_process.is_alive()
wfp._wfp_terminate.set()
wfp._wfp_process.join()
def test_wfp_check_processor():
p = Pipeline()
s = Stage()
t = Task()
t.executable = ['/bin/date']
s.add_tasks(t)
p.add_stages(s)
amgr = Amgr(hostname=hostname, port=port)
amgr._setup_mqs()
wfp = WFprocessor(sid=amgr._sid,
workflow=[p],
pending_queue=amgr._pending_queue,
completed_queue=amgr._completed_queue,
mq_hostname=amgr._mq_hostname,
port=amgr._port,
resubmit_failed=False)
wfp.start_processor()
assert wfp.check_processor()
wfp.terminate_processor()
assert not wfp.check_processor()
def test_issue_26():
def create_pipeline():
p = Pipeline()
s = Stage()
t1 = Task()
t1.name = 'simulation'
t1.executable = ['/bin/echo']
t1.arguments = ['hello']
t1.copy_input_data = []
t1.copy_output_data = []
s.add_tasks(t1)
p.add_stages(s)
return p
res_dict = {
'resource': 'local.localhost',
'walltime': 10,
'cpus': 1,
'project': ''
}
os.environ['RADICAL_PILOT_DBURL'] = MLAB
appman = AppManager(hostname=hostname, port=port, autoterminate=False)
appman.resource_desc = res_dict
p1 = create_pipeline()
appman.workflow = [p1]
appman.run()
print p1.uid, p1.stages[0].uid
p2 = create_pipeline()
appman.workflow = [p2]
appman.run()
print p2.uid, p2.stages[0].uid
appman.resource_terminate()
lhs = int(p1.stages[0].uid.split('.')[-1]) + 1
rhs = int(p2.stages[0].uid.split('.')[-1])
assert lhs == rhs
for t in p1.stages[0].tasks:
for tt in p2.stages[0].tasks:
lhs = int(t.uid.split('.')[-1]) + 1
rhs = int(tt.uid.split('.')[-1])
assert lhs == rhs
def test_state_order():
"""
**Purpose**: Test if the Pipeline, Stage and Task are assigned their states in the correct order
"""
def create_single_task():
t1 = Task()
t1.name = 'simulation'
t1.executable = ['/bin/date']
t1.copy_input_data = []
t1.copy_output_data = []
return t1
p1 = Pipeline()
p1.name = 'p1'
s = Stage()
s.name = 's1'
s.tasks = create_single_task()
s.add_tasks(create_single_task())
p1.add_stages(s)
res_dict = {
'resource': 'local.localhost',
'walltime': 5,
'cpus': 1,
'project': ''
}
os.environ['RADICAL_PILOT_DBURL'] = MLAB
os.environ['RP_ENABLE_OLD_DEFINES'] = 'True'
appman = Amgr(hostname=hostname, port=port)
appman.resource_desc = res_dict
appman.workflow = [p1]
appman.run()
p_state_hist = p1.state_history
assert p_state_hist == ['DESCRIBED', 'SCHEDULING', 'DONE']
s_state_hist = p1.stages[0].state_history
assert s_state_hist == ['DESCRIBED', 'SCHEDULING', 'SCHEDULED', 'DONE']
tasks = p1.stages[0].tasks
for t in tasks:
t_state_hist = t.state_history
assert t_state_hist == ['DESCRIBED', 'SCHEDULING', 'SCHEDULED', 'SUBMITTING', 'SUBMITTED',
'EXECUTED', 'DEQUEUEING', 'DEQUEUED', 'DONE']
def test_wfp_dequeue():
p = Pipeline()
s = Stage()
t = Task()
t.executable = '/bin/date'
s.add_tasks(t)
p.add_stages(s)
amgr = Amgr(hostname=hostname, port=port)
amgr._setup_mqs()
wfp = WFprocessor(sid=amgr._sid,
workflow=[p],
pending_queue=amgr._pending_queue,
completed_queue=amgr._completed_queue,
mq_hostname=amgr._hostname,
port=amgr._port,
resubmit_failed=False)
wfp.initialize_workflow()
assert p.state == states.INITIAL
assert p.stages[0].state == states.INITIAL
for t in p.stages[0].tasks:
assert t.state == states.INITIAL
p.state == states.SCHEDULED
p.stages[0].state == states.SCHEDULING
for t in p.stages[0].tasks:
t.state = states.COMPLETED
task_as_dict = json.dumps(t.to_dict())
mq_connection = pika.BlockingConnection(
pika.ConnectionParameters(host=amgr._hostname, port=amgr._port))
mq_channel = mq_connection.channel()
mq_channel.basic_publish(exchange='',
routing_key='%s' % amgr._completed_queue[0],
body=task_as_dict)
wfp.start_processor()
th = mt.Thread(target=func_for_dequeue_test, name='temp-proc', args=(p, ))
th.start()
th.join()
wfp.terminate_processor()
assert p.state == states.DONE
assert p.stages[0].state == states.DONE
for t in p.stages[0].tasks:
assert t.state == states.DONE
def test_assign_workload_exception():
appman = AppManager()
data_type = [1, 'a', True, [1], set([1])]
for data in data_type:
with pytest.raises(TypeError):
appman.assign_workflow(data)
def test_state_order():
"""
**Purpose**: Test if the Pipeline, Stage and Task are assigned their states in the correct order
"""
def create_single_task():
t1 = Task()
t1.name = 'simulation'
t1.executable = ['/bin/date']
t1.copy_input_data = []
t1.copy_output_data = []
return t1
p1 = Pipeline()
p1.name = 'p1'
s = Stage()
s.name = 's1'
s.tasks = create_single_task()
s.add_tasks(create_single_task())
p1.add_stages(s)
res_dict = {
'resource': 'local.localhost',
'walltime': 5,
'cpus': 1,
'project': ''
}
os.environ['RADICAL_PILOT_DBURL'] = MLAB
os.environ['RP_ENABLE_OLD_DEFINES'] = 'True'
appman = Amgr(hostname=hostname, port=port)
appman.resource_desc = res_dict
appman.workflow = [p1]
appman.run()
p_state_hist = p1.state_history
assert p_state_hist == ['DESCRIBED', 'SCHEDULING', 'DONE']
s_state_hist = p1.stages[0].state_history
assert s_state_hist == ['DESCRIBED', 'SCHEDULING', 'SCHEDULED', 'DONE']
tasks = p1.stages[0].tasks
for t in tasks:
t_state_hist = t.state_history
assert t_state_hist == ['DESCRIBED', 'SCHEDULING', 'SCHEDULED', 'SUBMITTING', 'SUBMITTED',
'EXECUTED', 'DEQUEUEING', 'DEQUEUED', 'DONE']
def test_wfp_workflow_incomplete():
p = Pipeline()
s = Stage()
t = Task()
t.executable = ['/bin/date']
s.add_tasks(t)
p.add_stages(s)
amgr = Amgr(hostname=hostname, port=port)
amgr._setup_mqs()
wfp = WFprocessor(sid=amgr._sid,
workflow=[p],
pending_queue=amgr._pending_queue,
completed_queue=amgr._completed_queue,
mq_hostname=amgr._mq_hostname,
port=amgr._port,
resubmit_failed=False)
wfp._initialize_workflow()
assert wfp.workflow_incomplete()
amgr.workflow = [p]
profiler = ru.Profiler(name='radical.entk.temp')
p.stages[0].state == states.SCHEDULING
p.state == states.SCHEDULED
for t in p.stages[0].tasks:
t.state = states.COMPLETED
import json
import pika
task_as_dict = json.dumps(t.to_dict())
mq_connection = pika.BlockingConnection(
pika.ConnectionParameters(host=amgr._mq_hostname, port=amgr._port))
mq_channel = mq_connection.channel()
mq_channel.basic_publish(exchange='',
routing_key='%s-completedq-1' % amgr._sid,
body=task_as_dict)
amgr._terminate_sync = Event()
sync_thread = Thread(target=amgr._synchronizer, name='synchronizer-thread')
sync_thread.start()
proc = Process(target=func_for_dequeue_test,
name='temp-proc',
args=(wfp, ))
proc.start()
proc.join()
amgr._terminate_sync.set()
sync_thread.join()
assert not wfp.workflow_incomplete()
def test_amgr_synchronizer():
logger = ru.get_logger('radical.entk.temp_logger')
profiler = ru.Profiler(name='radical.entk.temp')
amgr = Amgr(hostname=hostname, port=port)
mq_connection = pika.BlockingConnection(pika.ConnectionParameters(host=hostname, port=port))
mq_channel = mq_connection.channel()
amgr._setup_mqs()
p = Pipeline()
s = Stage()
# Create and add 100 tasks to the stage
for cnt in range(100):
t = Task()
t.executable = ['some-executable-%s' % cnt]
s.add_tasks(t)
p.add_stages(s)
p._assign_uid(amgr._sid)
p._validate()
amgr.workflow = [p]
for t in p.stages[0].tasks:
assert t.state == states.INITIAL
assert p.stages[0].state == states.INITIAL
assert p.state == states.INITIAL
# Start the synchronizer method in a thread
amgr._terminate_sync = Event()
sync_thread = Thread(target=amgr._synchronizer, name='synchronizer-thread')
sync_thread.start()
# Start the synchronizer method in a thread
proc = Process(target=func_for_synchronizer_test, name='temp-proc',
args=(amgr._sid, p, logger, profiler))
proc.start()
proc.join()
for t in p.stages[0].tasks:
assert t.state == states.SCHEDULING
assert p.stages[0].state == states.SCHEDULING
assert p.state == states.SCHEDULING
amgr._terminate_sync.set()
sync_thread.join()
def test_wfp_workflow_incomplete():
p = Pipeline()
s = Stage()
t = Task()
t.executable = ['/bin/date']
s.add_tasks(t)
p.add_stages(s)
amgr = Amgr(hostname=hostname, port=port)
amgr._setup_mqs()
wfp = WFprocessor(sid=amgr._sid,
workflow=[p],
pending_queue=amgr._pending_queue,
completed_queue=amgr._completed_queue,
mq_hostname=amgr._mq_hostname,
port=amgr._port,
resubmit_failed=False)
wfp._initialize_workflow()
assert wfp.workflow_incomplete()
amgr.workflow = [p]
profiler = ru.Profiler(name='radical.entk.temp')
p.stages[0].state == states.SCHEDULING
p.state == states.SCHEDULED
for t in p.stages[0].tasks:
t.state = states.COMPLETED
import json
import pika
task_as_dict = json.dumps(t.to_dict())
mq_connection = pika.BlockingConnection(pika.ConnectionParameters(host=amgr._mq_hostname, port=amgr._port))
mq_channel = mq_connection.channel()
mq_channel.basic_publish(exchange='',
routing_key='%s-completedq-1' % amgr._sid,
body=task_as_dict)
amgr._terminate_sync = Event()
sync_thread = Thread(target=amgr._synchronizer, name='synchronizer-thread')
sync_thread.start()
proc = Process(target=func_for_dequeue_test, name='temp-proc', args=(wfp,))
proc.start()
proc.join()
amgr._terminate_sync.set()
sync_thread.join()
assert not wfp.workflow_incomplete()
def test_amgr_read_config():
amgr = Amgr()
assert amgr._mq_hostname == 'localhost'
assert amgr._port == 5672
assert amgr._reattempts == 3
assert amgr._resubmit_failed == False
assert amgr._autoterminate == True
assert amgr._write_workflow == False
assert amgr._rts == 'radical.pilot'
assert amgr._num_pending_qs == 1
assert amgr._num_completed_qs == 1
assert amgr._rmq_cleanup == True
assert amgr._rts_config == { "sandbox_cleanup": False, "db_cleanup": False}
d = {"hostname": "radical.two",
"port": 25672,
"reattempts": 5,
"resubmit_failed": True,
"autoterminate": False,
"write_workflow": True,
"rts": "mock",
"rts_config": { "sandbox_cleanup": True, "db_cleanup": True},
"pending_qs": 2,
"completed_qs": 3,
"rmq_cleanup": False}
ru.write_json(d, './config.json')
amgr._read_config(config_path='./',
hostname=None,
port=None,
reattempts=None,
resubmit_failed=None,
autoterminate=None,
write_workflow=None,
rts=None,
rmq_cleanup=None,
rts_config=None)
assert amgr._mq_hostname == d['hostname']
assert amgr._port == d['port']
assert amgr._reattempts == d['reattempts']
assert amgr._resubmit_failed == d['resubmit_failed']
assert amgr._autoterminate == d['autoterminate']
assert amgr._write_workflow == d['write_workflow']
assert amgr._rts == d['rts']
assert amgr._rts_config == d['rts_config']
assert amgr._num_pending_qs == d['pending_qs']
assert amgr._num_completed_qs == d['completed_qs']
assert amgr._rmq_cleanup == d['rmq_cleanup']
os.remove('./config.json')
def test_amgr_read_config(self, mocked_init, mocked_PlainCredentials,
mocked_ConnectionParameters, d):
amgr = Amgr(hostname='host',
port='port',
username='******',
password='******')
d["rts"] = "mock"
d["rts_config"] = {"sandbox_cleanup": True, "db_cleanup": True}
ru.write_json(d, './config.json')
amgr._read_config(config_path='./',
hostname=None,
port=None,
username=None,
password=None,
reattempts=None,
resubmit_failed=None,
autoterminate=None,
write_workflow=None,
rts=None,
rmq_cleanup=None,
rts_config=None)
self.assertEqual(amgr._hostname, d['hostname'])
self.assertEqual(amgr._port, d['port'])
self.assertEqual(amgr._reattempts, d['reattempts'])
self.assertEqual(amgr._resubmit_failed, d['resubmit_failed'])
self.assertEqual(amgr._autoterminate, d['autoterminate'])
self.assertEqual(amgr._write_workflow, d['write_workflow'])
self.assertEqual(amgr._rts, d['rts'])
self.assertEqual(amgr._rts_config, d['rts_config'])
self.assertEqual(amgr._num_pending_qs, d['pending_qs'])
self.assertEqual(amgr._num_completed_qs, d['completed_qs'])
self.assertEqual(amgr._rmq_cleanup, d['rmq_cleanup'])
d['rts'] = 'another'
ru.write_json(d, './config.json')
print(d)
with self.assertRaises(ValueError):
amgr._read_config(config_path='./',
hostname=None,
port=None,
username=None,
password=None,
reattempts=None,
resubmit_failed=None,
autoterminate=None,
write_workflow=None,
rts=None,
rmq_cleanup=None,
rts_config=None)
def test_issue_236():
'''
Create folder temp to transfer as input to task:
.
./temp
./temp/dir1
./temp/dir1/file2.txt
./temp/file1.txt
'''
os.makedirs('%s/temp' %cur_dir)
os.makedirs('%s/temp/dir1' %cur_dir)
os.system('echo "Hello world" > %s/temp/file1.txt' %cur_dir)
os.system('echo "Hello world" > %s/temp/dir1/file2.txt' %cur_dir)
# Create a dictionary describe four mandatory keys:
# resource, walltime, cpus and project
# resource is 'local.localhost' to execute locally
res_dict = {
'resource': 'local.localhost',
'walltime': 10,
'cpus': 1
}
os.environ['RADICAL_PILOT_DBURL'] = MLAB
# Create Application Manager
appman = AppManager(hostname=hostname, port=port)
# Assign resource manager to the Application Manager
appman.resource_desc = res_dict
p = generate_pipeline()
# Assign the workflow as a set of Pipelines to the Application Manager
appman.workflow = [p]
# Run the Application Manager
appman.run()
# Assert folder movement
assert len(glob('/tmp/temp*')) >=1
assert len(glob('/tmp/temp/dir*')) ==1
assert len(glob('/tmp/temp/*.txt')) ==1
assert len(glob('/tmp/temp/dir1/*.txt')) ==1
# Cleanup
shutil.rmtree('%s/temp' %cur_dir)
shutil.rmtree('/tmp/temp')
def test_amgr_assign_shared_data():
amgr = Amgr(rts='radical.pilot', hostname=host, port=port)
res_dict = {'resource': 'xsede.supermic',
'walltime': 30,
'cpus' : 20,
'project' : 'TG-MCB090174'}
amgr.resource_desc = res_dict
amgr.shared_data = ['file1.txt','file2.txt']
assert amgr._rmgr.shared_data == ['file1.txt','file2.txt']
def test_amgr_run():
amgr = Amgr(hostname=host, port=port)
with pytest.raises(MissingError):
amgr.run()
p1 = Pipeline()
p2 = Pipeline()
p3 = Pipeline()
with pytest.raises(MissingError):
amgr.workflow = [p1, p2, p3]
def test_amgr_synchronizer():
logger = ru.Logger('radical.entk.temp_logger')
profiler = ru.Profiler(name='radical.entk.temp')
amgr = Amgr(hostname=hostname, port=port)
amgr._setup_mqs()
p = Pipeline()
s = Stage()
# Create and add 100 tasks to the stage
for cnt in range(100):
t = Task()
t.executable = ['some-executable-%s' % cnt]
s.add_tasks(t)
p.add_stages(s)
p._assign_uid(amgr._sid)
p._validate()
amgr.workflow = [p]
for t in p.stages[0].tasks:
assert t.state == states.INITIAL
assert p.stages[0].state == states.INITIAL
assert p.state == states.INITIAL
# Start the synchronizer method in a thread
amgr._terminate_sync = Event()
sync_thread = Thread(target=amgr._synchronizer, name='synchronizer-thread')
sync_thread.start()
# Start the synchronizer method in a thread
proc = Process(target=func_for_synchronizer_test, name='temp-proc',
args=(amgr._sid, p, logger, profiler))
proc.start()
proc.join()
for t in p.stages[0].tasks:
assert t.state == states.SCHEDULING
assert p.stages[0].state == states.SCHEDULING
assert p.state == states.SCHEDULING
amgr._terminate_sync.set()
sync_thread.join()
def test_amgr_resource_terminate():
res_dict = {
'resource': 'xsede.supermic',
'walltime': 30,
'cpus': 20,
'project': 'TG-MCB090174'
}
from radical.entk.execman.rp import TaskManager
amgr = Amgr(rts='radical.pilot', hostname=hostname, port=port)
amgr.resource_desc = res_dict
amgr._setup_mqs()
amgr._rmq_cleanup = True
amgr._task_manager = TaskManager(sid='test',
pending_queue=list(),
completed_queue=list(),
mq_hostname=amgr._mq_hostname,
rmgr=amgr._resource_manager,
port=amgr._port
)
amgr.resource_terminate()
def test_amgr_terminate():
res_dict = {
'resource': 'xsede.supermic',
'walltime': 30,
'cpus': 20,
'project': 'TG-MCB090174'
}
from radical.entk.execman.rp import TaskManager
amgr = Amgr(rts='radical.pilot', hostname=hostname, port=port)
amgr.resource_desc = res_dict
amgr._setup_mqs()
amgr._rmq_cleanup = True
amgr._task_manager = TaskManager(sid='test',
pending_queue=list(),
completed_queue=list(),
mq_hostname=amgr._mq_hostname,
rmgr=amgr._resource_manager,
port=amgr._port
)
amgr.terminate()
def test_issue_255():
def create_pipeline():
p = Pipeline()
s = Stage()
t1 = Task()
t1.name = 'simulation'
t1.executable = ['sleep']
t1.arguments = ['10']
s.add_tasks(t1)
p.add_stages(s)
return p
res_dict = {
'resource': 'local.localhost',
'walltime': 5,
'cpus': 1,
'project': ''
}
os.environ['RADICAL_PILOT_DBURL'] = MLAB
appman = AppManager(hostname=hostname, port=port, autoterminate=False)
appman.resource_desc = res_dict
p1 = create_pipeline()
appman.workflow = [p1]
appman.run()
# p1 = create_pipeline()
# appman.workflow = [p1]
# appman.run()
# appman.resource_terminate()
tmgr = appman._task_manager
tmgr.terminate_manager()
# tmgr.terminate_heartbeat()
tmgr.start_manager()
def test_wfp_enqueue():
p = Pipeline()
s = Stage()
t = Task()
t.executable = ['/bin/date']
s.add_tasks(t)
p.add_stages(s)
amgr = Amgr(hostname=hostname, port=port)
amgr._setup_mqs()
wfp = WFprocessor(sid=amgr._sid,
workflow=[p],
pending_queue=amgr._pending_queue,
completed_queue=amgr._completed_queue,
mq_hostname=amgr._mq_hostname,
port=amgr._port,
resubmit_failed=False)
wfp._initialize_workflow()
amgr.workflow = [p]
profiler = ru.Profiler(name='radical.entk.temp')
for t in p.stages[0].tasks:
assert t.state == states.INITIAL
assert p.stages[0].state == states.INITIAL
assert p.state == states.INITIAL
amgr._terminate_sync = Event()
sync_thread = Thread(target=amgr._synchronizer, name='synchronizer-thread')
sync_thread.start()
proc = Process(target=func_for_enqueue_test,
name='temp-proc',
args=(wfp, ))
proc.start()
proc.join()
amgr._terminate_sync.set()
sync_thread.join()
for t in p.stages[0].tasks:
assert t.state == states.SCHEDULED
assert p.stages[0].state == states.SCHEDULED
assert p.state == states.SCHEDULING
def test_write_workflow():
try:
wf = list()
wf.append(generate_pipeline(1))
wf.append(generate_pipeline(2))
amgr = AppManager(hostname=hostname, port=port)
amgr.workflow = wf
amgr._wfp = WFprocessor(sid=amgr._sid,
workflow=amgr._workflow,
pending_queue=amgr._pending_queue,
completed_queue=amgr._completed_queue,
mq_hostname=amgr._mq_hostname,
port=amgr._port,
resubmit_failed=amgr._resubmit_failed)
amgr._wfp._initialize_workflow()
wf = amgr._wfp.workflow
write_workflow(wf, 'test')
data = ru.read_json('test/entk_workflow.json')
assert len(data) == len(wf) + 1
stack = data.pop(0)
assert stack.keys() == ['stack']
assert stack['stack'].keys() == ['sys','radical']
assert stack['stack']['sys'].keys() == ["python","pythonpath","virtualenv"]
assert stack['stack']['radical'].keys() == ['saga', 'radical.pilot', 'radical.utils', 'radical.entk']
p_cnt = 0
for p in data:
assert p['uid'] == wf[p_cnt].uid
assert p['name'] == wf[p_cnt].name
assert p['state_history'] == wf[p_cnt].state_history
s_cnt = 0
for s in p['stages']:
assert s['uid'] == wf[p_cnt].stages[s_cnt].uid
assert s['name'] == wf[p_cnt].stages[s_cnt].name
assert s['state_history'] == wf[p_cnt].stages[s_cnt].state_history
for t in wf[p_cnt].stages[s_cnt].tasks:
assert t.to_dict() in s['tasks']
s_cnt += 1
p_cnt += 1
except Exception as ex:
shutil.rmtree('test')
raise
def test_amgr_assign_workflow():
amgr = Amgr()
with pytest.raises(TypeError):
amgr.workflow = [1, 2, 3]
with pytest.raises(TypeError):
amgr.workflow = set([1, 2, 3])
p1 = Pipeline()
p2 = Pipeline()
p3 = Pipeline()
amgr._workflow = [p1, p2, p3]
amgr._workflow = set([p1, p2, p3])
def test_amgr_assign_workflow():
amgr = Amgr()
with pytest.raises(TypeError):
amgr.workflow = [1, 2, 3]
with pytest.raises(TypeError):
amgr.workflow = set([1, 2, 3])
p1 = Pipeline()
p2 = Pipeline()
p3 = Pipeline()
amgr._workflow = [p1, p2, p3]
amgr._workflow = set([p1, p2, p3])
def test_wfp_enqueue():
p = Pipeline()
s = Stage()
t = Task()
t.executable = ['/bin/date']
s.add_tasks(t)
p.add_stages(s)
amgr = Amgr(hostname=hostname, port=port)
amgr._setup_mqs()
wfp = WFprocessor(sid=amgr._sid,
workflow=[p],
pending_queue=amgr._pending_queue,
completed_queue=amgr._completed_queue,
mq_hostname=amgr._mq_hostname,
port=amgr._port,
resubmit_failed=False)
wfp._initialize_workflow()
amgr.workflow = [p]
profiler = ru.Profiler(name='radical.entk.temp')
for t in p.stages[0].tasks:
assert t.state == states.INITIAL
assert p.stages[0].state == states.INITIAL
assert p.state == states.INITIAL
amgr._terminate_sync = Event()
sync_thread = Thread(target=amgr._synchronizer, name='synchronizer-thread')
sync_thread.start()
proc = Process(target=func_for_enqueue_test, name='temp-proc', args=(wfp,))
proc.start()
proc.join()
amgr._terminate_sync.set()
sync_thread.join()
for t in p.stages[0].tasks:
assert t.state == states.SCHEDULED
assert p.stages[0].state == states.SCHEDULED
assert p.state == states.SCHEDULING
def test_amgr_assign_workflow():
amgr = Amgr(hostname=host, port=port, username=username,
password=password)
with pytest.raises(TypeError):
amgr.workflow = [1, 2, 3]
with pytest.raises(TypeError):
amgr.workflow = set([1, 2, 3])
p1 = Pipeline()
p2 = Pipeline()
p3 = Pipeline()
amgr._workflow = [p1, p2, p3]
amgr._workflow = set([p1, p2, p3])
def test_wfp_enqueue():
p = Pipeline()
s = Stage()
t = Task()
t.executable = '/bin/date'
s.add_tasks(t)
p.add_stages(s)
amgr = Amgr(hostname=hostname, port=port, username=username,
password=password)
amgr._setup_mqs()
wfp = WFprocessor(sid=amgr._sid,
workflow=[p],
pending_queue=amgr._pending_queue,
completed_queue=amgr._completed_queue,
rmq_conn_params=amgr._rmq_conn_params,
resubmit_failed=False)
assert p.uid is not None
assert p.stages[0].uid is not None
for t in p.stages[0].tasks:
assert t.uid is not None
assert p.state == states.INITIAL
assert p.stages[0].state == states.INITIAL
for t in p.stages[0].tasks:
assert t.state == states.INITIAL
wfp.start_processor()
th = mt.Thread(target=func_for_enqueue_test, name='temp-proc', args=(p,))
th.start()
th.join()
wfp.terminate_processor()
assert p.state == states.SCHEDULING
assert p.stages[0].state == states.SCHEDULED
for t in p.stages[0].tasks:
assert t.state == states.SCHEDULED
def test_write_session_description():
amgr = AppManager(hostname=hostname, port=port)
amgr.resource_desc = {'resource' : 'xsede.stampede',
'walltime' : 59,
'cpus' : 128,
'gpus' : 64,
'project' : 'xyz',
'queue' : 'high'}
workflow = [generate_pipeline(1), generate_pipeline(2)]
amgr.workflow = workflow
amgr._wfp = WFprocessor(sid=amgr.sid,
workflow=amgr._workflow,
pending_queue=amgr._pending_queue,
completed_queue=amgr._completed_queue,
resubmit_failed=amgr._resubmit_failed,
rmq_conn_params=amgr._rmq_conn_params)
amgr._workflow = amgr._wfp.workflow
amgr._task_manager = TaskManager(sid=amgr._sid,
pending_queue=amgr._pending_queue,
completed_queue=amgr._completed_queue,
rmgr=amgr._rmgr,
rmq_conn_params=amgr._rmq_conn_params
)
write_session_description(amgr)
desc = ru.read_json('%s/radical.entk.%s.json' % (amgr._sid, amgr._sid))
src = '%s/sample_data' % pwd
assert desc == ru.read_json('%s/expected_desc_write_session.json' % src)
def test_shared_data():
for f in glob('%s/file*.txt' % cur_dir):
os.remove(f)
os.system('echo "Hello" > %s/file1.txt' % cur_dir)
os.system('echo "World" > %s/file2.txt' % cur_dir)
# Create a dictionary describe four mandatory keys:
# resource, walltime, cpus and project
# resource is 'local.localhost' to execute locally
res_dict = {'resource': 'local.localhost', 'walltime': 1, 'cpus': 1}
# Create Application Manager
appman = AppManager(hostname=hostname, port=port)
# Assign resource manager to the Application Manager
appman.resource_desc = res_dict
appman.shared_data = ['%s/file1.txt' % cur_dir, '%s/file2.txt' % cur_dir]
p = generate_pipeline()
# Assign the workflow as a set of Pipelines to the Application Manager
appman.workflow = [p]
# Run the Application Manager
appman.run()
with open('%s/output.txt' % cur_dir, 'r') as fp:
assert [d.strip() for d in fp.readlines()] == ['Hello', 'World']
os.remove('%s/file1.txt' % cur_dir)
os.remove('%s/file2.txt' % cur_dir)
os.remove('%s/output.txt' % cur_dir)
def test_amgr_resource_description_assignment():
res_dict = {'resource': 'xsede.supermic',
'walltime': 30,
'cpus' : 1000,
'project' : 'TG-MCB090174'}
amgr = Amgr(rts='radical.pilot')
amgr.resource_desc = res_dict
from radical.entk.execman.rp import ResourceManager as RM_RP
assert isinstance(amgr._rmgr, RM_RP)
amgr = Amgr(rts='mock')
amgr.resource_desc = res_dict
from radical.entk.execman.mock import ResourceManager as RM_MOCK
assert isinstance(amgr._rmgr, RM_MOCK)
def test_wfp_workflow_incomplete():
p = Pipeline()
s = Stage()
t = Task()
t.executable = '/bin/date'
s.add_tasks(t)
p.add_stages(s)
amgr = Amgr(hostname=hostname, port=port, username=username,
password=password)
amgr._setup_mqs()
wfp = WFprocessor(sid=amgr._sid,
workflow=[p],
pending_queue=amgr._pending_queue,
completed_queue=amgr._completed_queue,
rmq_conn_params=amgr._rmq_conn_params,
resubmit_failed=False)
for t in p.stages[0].tasks:
t.state = states.COMPLETED
task_as_dict = json.dumps(t.to_dict())
credentials = pika.PlainCredentials(amgr._username, amgr._password)
mq_connection = pika.BlockingConnection(pika.ConnectionParameters(
host=amgr._hostname, port=amgr._port,
credentials=credentials))
mq_channel = mq_connection.channel()
mq_channel.basic_publish(exchange = '',
routing_key = '%s' % amgr._completed_queue[0],
body = task_as_dict)
wfp.start_processor()
th = mt.Thread(target=func_for_dequeue_test, name='temp-proc', args=(p,))
th.start()
th.join()
wfp.terminate_processor()
assert not wfp.workflow_incomplete()
def test_integration_local():
"""
**Purpose**: Run an EnTK application on localhost
"""
def create_single_task():
t1 = Task()
t1.name = 'simulation'
t1.executable = ['/bin/echo']
t1.arguments = ['hello']
t1.copy_input_data = []
t1.copy_output_data = []
return t1
p1 = Pipeline()
p1.name = 'p1'
s = Stage()
s.name = 's1'
s.tasks = create_single_task()
s.add_tasks(create_single_task())
p1.add_stages(s)
res_dict = {
'resource': 'local.localhost',
'walltime': 5,
'cpus': 1,
'project': ''
}
os.environ['RADICAL_PILOT_DBURL'] = MLAB
appman = AppManager(hostname=hostname, port=port)
appman.resource_desc = res_dict
appman.workflow = [p1]
appman.run()
def test_amgr_assign_shared_data(s, i, b, se):
amgr = Amgr(rts='radical.pilot', hostname=hostname, port=port)
res_dict = {
'resource': 'xsede.supermic',
'walltime': 30,
'cpus': 20,
'project': 'TG-MCB090174'
}
amgr.resource_desc = res_dict
data = [s, i, b, se]
for d in data:
with pytest.raises(TypeError):
amgr.shared_data = d
amgr.shared_data = ['file1.txt', 'file2.txt']
assert amgr._resource_manager.shared_data == ['file1.txt', 'file2.txt']
def test_amgr_resource_description_assignment():
res_dict = {
'resource': 'xsede.supermic',
'walltime': 30,
'cpus': 1000,
'project': 'TG-MCB090174'
}
amgr = Amgr(rts='radical.pilot')
amgr.resource_desc = res_dict
from radical.entk.execman.rp import ResourceManager
assert isinstance(amgr._resource_manager, ResourceManager)
amgr = Amgr(rts='mock')
amgr.resource_desc = res_dict
from radical.entk.execman.mock import ResourceManager
assert isinstance(amgr._resource_manager, ResourceManager)
def test_amgr_setup_mqs():
amgr = Amgr(hostname=host, port=port)
amgr._setup_mqs()
assert len(amgr._pending_queue) == 1
assert len(amgr._completed_queue) == 1
mq_connection = pika.BlockingConnection(pika.ConnectionParameters(
host=amgr._hostname, port=amgr._port))
mq_channel = mq_connection.channel()
qs = ['%s-tmgr-to-sync' % amgr._sid,
'%s-cb-to-sync' % amgr._sid,
'%s-sync-to-tmgr' % amgr._sid,
'%s-sync-to-cb' % amgr._sid,
'%s-pendingq-1' % amgr._sid,
'%s-completedq-1' % amgr._sid]
for q in qs:
mq_channel.queue_delete(queue=q)
def test_amgr_assign_shared_data(s,i,b,se):
amgr = Amgr(rts='radical.pilot', hostname=hostname, port=port)
res_dict = {
'resource': 'xsede.supermic',
'walltime': 30,
'cpus': 20,
'project': 'TG-MCB090174'
}
amgr.resource_desc = res_dict
data = [s, i, b, se]
for d in data:
with pytest.raises(TypeError):
amgr.shared_data = d
amgr.shared_data = ['file1.txt','file2.txt']
assert amgr._resource_manager.shared_data == ['file1.txt','file2.txt']
def test_diff_rmq():
def create_pipeline():
p = Pipeline()
s = Stage()
t1 = Task()
t1.name = 'simulation'
t1.executable = ['/bin/echo']
t1.arguments = ['hello']
t1.copy_input_data = []
t1.copy_output_data = []
s.add_tasks(t1)
p.add_stages(s)
return p
res_dict = {
'resource': 'local.localhost',
'walltime': 5,
'cpus': 1,
}
os.environ['RADICAL_PILOT_DBURL'] = MLAB
appman = AppManager(hostname=hostname, port=port)
appman.resource_desc = res_dict
p1 = create_pipeline()
print p1.uid, p1.stages[0].uid
appman.workflow = [p1]
appman.run()
def test_amgr_run_mock():
p = Pipeline()
s = Stage()
t = Task()
t.name = 'simulation'
t.executable = ['/bin/date']
s.tasks = t
p.add_stages(s)
res_dict = {
'resource': 'local.localhost',
'walltime': 5,
'cpus': 1,
'project': ''
}
appman = Amgr(hostname=hostname, port=port, rts="mock")
appman.resource_desc = res_dict
appman.workflow = [p]
appman.run()
def test_amgr_run():
amgr = Amgr()
with pytest.raises(MissingError):
amgr.run()
p1 = Pipeline()
p2 = Pipeline()
p3 = Pipeline()
amgr._workflow = [p1, p2, p3]
with pytest.raises(MissingError):
amgr.run()
def test_shared_data():
for f in glob('%s/file*.txt' %cur_dir):
os.remove(f)
os.system('echo "Hello" > %s/file1.txt' %cur_dir)
os.system('echo "World" > %s/file2.txt' %cur_dir)
# Create a dictionary describe four mandatory keys:
# resource, walltime, cpus and project
# resource is 'local.localhost' to execute locally
res_dict = {
'resource': 'local.localhost',
'walltime': 1,
'cpus': 1
}
os.environ['RADICAL_PILOT_DBURL'] = MLAB
# Create Application Manager
appman = AppManager(hostname=hostname, port=port)
# Assign resource manager to the Application Manager
appman.resource_desc = res_dict
appman.shared_data = ['%s/file1.txt' %cur_dir, '%s/file2.txt' %cur_dir]
p = generate_pipeline()
# Assign the workflow as a set of Pipelines to the Application Manager
appman.workflow = [p]
# Run the Application Manager
appman.run()
with open('%s/output.txt' %cur_dir, 'r') as fp:
assert [d.strip() for d in fp.readlines()] == ['Hello', 'World']
os.remove('%s/file1.txt' %cur_dir)
os.remove('%s/file2.txt' %cur_dir)
os.remove('%s/output.txt' %cur_dir)
}
# Add Stage to the Pipeline
p.add_stages(s1)
return p
if __name__ == '__main__':
# Create a dictionary describe four mandatory keys:
# resource, walltime, cores and project
# resource is 'local.localhost' to execute locally
res_dict = {
'resource': 'local.localhost',
'walltime': 15,
'cpus': 2,
}
# Create Application Manager
appman = AppManager()
appman.resource_desc = res_dict
p = generate_pipeline()
# Assign the workflow as a set of Pipelines to the Application Manager
appman.workflow = [p]
# Run the Application Manager
appman.run()
t3.copy_input_data = ['$Pipeline_%s_Stage_%s_Task_%s/ccount.txt' % (p.name, s2.name, s2_task_uids[cnt])]
# Download the output of the current task to the current location
t3.download_output_data = ['chksum.txt > chksum_%s.txt' % cnt]
# Add the Task to the Stage
s3.add_tasks(t3)
# Add Stage to the Pipeline
p.add_stages(s3)
return p
if __name__ == '__main__':
# Create Application Manager
appman = AppManager(hostname=hostname, port=port)
# Create a dictionary describe four mandatory keys:
# resource, walltime, and cpus
# resource is 'local.localhost' to execute locally
res_dict = {
# 'resource': 'ncsa.bw_aprun',
# 'walltime': 10,
# 'cpus': 32,
#'project': 'bamm',
#'queue': 'high'
'resource': 'local.localhost',
'walltime': 10,
'cpus':2
}
print p.stages
print p.stages[1].tasks
# Create a dictionary describe four mandatory keys:
# resource, walltime, cores and project
# resource is 'local.localhost' to execute locally
res_dict = {
'resource': 'xsede.supermic',
'walltime': 240,
'cores': 96,
'access_schema': 'gsissh',
'queue': 'workq',
'project': 'TG-MCB090174',
}
# Create Resource Manager object with the above resource description
rman = ResourceManager(res_dict)
# Create Application Manager
appman = AppManager()
# Assign resource manager to the Application Manager
appman.resource_manager = rman
# Assign the workflow as a set of Pipelines to the Application Manager
appman.assign_workflow(set([p]))
# Run the Application Manager
## appman.run()
s = Stage()
# Create a Task object
t = Task()
t.name = 'my-first-task' # Assign a name to the task (optional, do not use ',' or '_')
t.executable = '/bin/echo' # Assign executable to the task
t.arguments = ['Hello World'] # Assign arguments for the task executable
# Add Task to the Stage
s.add_tasks(t)
# Add Stage to the Pipeline
p.add_stages(s)
# Create Application Manager
appman = AppManager(hostname=hostname, port=port)
# Create a dictionary describe four mandatory keys:
# resource, walltime, and cpus
# resource is 'local.localhost' to execute locally
res_dict = {
'resource': 'local.localhost',
'walltime': 10,
'cpus': 1
}
# Assign resource request description to the Application Manager
appman.resource_desc = res_dict
# Assign the workflow as a set or list of Pipelines to the Application Manager
# Add Stage to the Pipeline
p.add_stages(s3)
return p
if __name__ == '__main__':
pipelines = []
for cnt in range(10):
pipelines.append(generate_pipeline())
# Create Application Manager
appman = AppManager(hostname=hostname, port=port)
# Create a dictionary describe four mandatory keys:
# resource, walltime, and cpus
# resource is 'local.localhost' to execute locally
res_dict = {
'resource': 'local.localhost',
'walltime': 10,
'cpus': 1
}
# Assign resource request description to the Application Manager
appman.resource_desc = res_dict
# Assign the workflow as a set or list of Pipelines to the Application Manager
# Create a dictionary describe four mandatory keys:
# resource, walltime, cpus and project
# resource is 'local.localhost' to execute locally
res_dict = {
'resource': 'local.localhost',
'walltime': 1,
'cpus': 1
}
os.environ['RADICAL_PILOT_DBURL'] = 'mongodb://*****:*****@ds227821.mlab.com:27821/entk_0_7_0_release'
# Create Application Manager
appman = AppManager(hostname=hostname, port=port)
# Assign resource manager to the Application Manager
appman.resource_desc = res_dict
appman.shared_data = ['%s/file1.txt' %cur_dir, '%s/file2.txt' %cur_dir]
p = generate_pipeline()
# Assign the workflow as a set of Pipelines to the Application Manager
appman.workflow = [p]
# Run the Application Manager
appman.run()
for x in range(10):
with open('%s/output_%s.txt' %(cur_dir,x+1), 'r') as fp: