def _parallel_run_many(self, generator, execution: MLClientCtx,
runobj: RunObject) -> RunList:
results = RunList()
tasks = generator.generate(runobj)
handler = runobj.spec.handler
self._force_handler(handler)
set_paths(self.spec.pythonpath)
_, handler = self._get_handler(handler)
client, function_name = self._get_dask_client(generator.options)
parallel_runs = generator.options.parallel_runs or 4
queued_runs = 0
num_errors = 0
def process_result(future):
nonlocal num_errors
resp, sout, serr = future.result()
runobj = RunObject.from_dict(resp)
try:
log_std(self._db_conn, runobj, sout, serr, skip=self.is_child)
resp = self._update_run_state(resp)
except RunError as err:
resp = self._update_run_state(resp, err=str(err))
num_errors += 1
results.append(resp)
if num_errors > generator.max_errors:
logger.error("max errors reached, stopping iterations!")
return True
run_results = resp["status"].get("results", {})
stop = generator.eval_stop_condition(run_results)
if stop:
logger.info(
f"reached early stop condition ({generator.options.stop_condition}), stopping iterations!"
)
return stop
completed_iter = as_completed([])
for task in tasks:
resp = client.submit(remote_handler_wrapper, task.to_json(),
handler, self.spec.workdir)
completed_iter.add(resp)
queued_runs += 1
if queued_runs >= parallel_runs:
future = next(completed_iter)
early_stop = process_result(future)
queued_runs -= 1
if early_stop:
break
for future in completed_iter:
process_result(future)
client.close()
if function_name and generator.options.teardown_dask:
logger.info("tearing down the dask cluster..")
mlrun.get_run_db().delete_runtime_object("dask",
function_name,
force=True)
return results
def execute_list_of_clustering_tasks_chunked(clustering_tasks,
tests_per_batch=None):
if tests_per_batch is None:
tests_per_batch = len(clustering_tasks)
with Client(address=SCHEDULER_HOSTNAME) as client:
nb_of_chunks = math.ceil(len(clustering_tasks) / tests_per_batch)
for chunk in tqdm(chunks(clustering_tasks, tests_per_batch),
desc="chunks",
total=nb_of_chunks):
dataset_dict = scatter_datasets(client)
# tasks_ready_to_execute = fill_dataset_in_clustering_tasks(chunk, dataset_dict)
futures = []
for task in chunk:
futures.append(
client.submit(ClusteringTask.run,
task,
dataset_dict[task.dataset_name],
pure=False))
# futures = client.map(lambda x: ClusteringTask.run(x), tasks_ready_to_execute, pure = False)
for _ in tqdm(distributed.as_completed(futures,
with_results=True,
raise_errors=False),
total=len(futures),
desc="tasks in chunk",
leave=False):
pass
def get_minmax(varname, varpath, client):
futures = list()
numfiles = 0
for root, _, files in os.walk(varpath):
if not files:
continue
numfiles = len(files)
pbar = tqdm(files, desc="{}".format(varname))
for i, f in enumerate(sorted(files)):
inpath = os.path.join(root, f)
futures.append(client.submit(run_minmax, inpath, varname, i))
mins = []
mins2d = [[] for x in range(numfiles)]
maxs = []
maxs2d = [[] for x in range(numfiles)]
for future, minmax in as_completed(futures, with_results=True):
pbar.update(1)
mins2d[minmax[2]] = minmax[0]
maxs2d[minmax[2]] = minmax[1]
pbar.close()
for l in mins2d:
for i in l:
mins.append(i)
for l in maxs2d:
for i in l:
maxs.append(i)
return mins, maxs
def main():
args = parse_args()
cluster = LocalCluster(
n_workers=int(args.processes),
threads_per_worker=1,
interface='lo')
client = Client(address=cluster.scheduler_address)
contents = os.listdir(args.input)
futures = []
with open(args.hashfile, 'r') as hashfile:
for line in hashfile.readline():
name, expected_hash = line.split('|')
_, name = os.path.split(name)
if name not in contents:
continue()
futures.append(
client.submit(
checkhash,
os.path.join(args.input, name),
expected_hash))
for future in as_completed(futures):
path, match = future.results()
print(path, match)
def sample_problems(self,
n_min_objects=1,
n_max_objects=12,
n_configs=100,
workspace=((0.25, -0.25), (0.75, 0.25)),
radius=0.0375,
timeout=2.0,
n_max_iter=50):
"""
n_min_objects, n_max_objects: interval of number of objects to consider for the problems
n_configs: number of configurations for each number of objects
workspace: workspace in which to sample objects
radius: radius for collision checks
timeout: time limit that defines when a configuration should be discarded
because more objects cannot be added
n_max_iter: Number of times we allow timeout to be reached
"""
workspace = np.asarray(workspace).tolist()
self.infos = dict(workspace=workspace, radius=radius)
def sample_state(n_objects):
sampler = StateSampler(workspace=workspace, radius=radius)
n_iter = 0
success = False
while not success:
if n_iter > n_max_iter:
raise SamplerError('Too many objects for this workspace.')
try:
state = sampler(n_objects, max_time=timeout)
success = True
except SamplerError:
success = False
n_iter += 1
return state
def sample_src_tgt(n_objects, seed):
np.random.seed(seed)
src = sample_state(n_objects)
tgt = sample_state(n_objects)
return src, tgt, n_objects
eval_df = defaultdict(list)
futures = []
for n in np.arange(n_min_objects, n_max_objects + 1):
for _ in range(n_configs):
fut = self.client.submit(sample_src_tgt, n,
np.random.randint(2**32 - 1))
futures.append(fut)
print("Sampling configurations ...")
for fut in tqdm(as_completed(futures), total=len(futures)):
src, tgt, n_objects = fut.result()
eval_df['src'].append(src)
eval_df['tgt'].append(tgt)
eval_df['n_objects'].append(n_objects)
self.eval_df = pd.DataFrame(eval_df)
self.eval_df = self.eval_df.sort_values('n_objects').reset_index(
drop=True)
def run(self):
""" Execute the algorithm. """
self.start_computing_time = time.time()
population_to_evaluate = self.create_initial_solutions()
task_pool = as_completed(self.evaluate(population_to_evaluate))
self.init_progress()
auxiliar_population = []
for future in task_pool:
# The initial population is not full
if len(auxiliar_population) < self.population_size:
received_solution = future.result()
auxiliar_population.append(received_solution)
new_task = self.client.submit(self.problem.evaluate,
self.problem.create_solution())
task_pool.add(new_task)
# Perform an algorithm step to create a new solution to be evaluated
else:
offspring_population = []
if not self.stopping_condition_is_met():
offspring_population.append(future.result())
# Replacement
join_population = auxiliar_population + offspring_population
auxiliar_population = RankingAndCrowdingDistanceSelection(
self.population_size).execute(join_population)
# Selection
mating_population = []
for _ in range(2):
solution = self.selection_operator.execute(
population_to_evaluate)
mating_population.append(solution)
# Reproduction and evaluation
new_task = self.client.submit(reproduction,
mating_population,
self.problem,
self.crossover_operator,
self.mutation_operator)
task_pool.add(new_task)
else:
for future in task_pool.futures:
future.cancel()
break
self.evaluations += 1
self.solutions = auxiliar_population
self.update_progress()
self.total_computing_time = time.time() - self.start_computing_time
self.solutions = auxiliar_population
def end(self) -> None:
if not self.client:
raise AirflowException(NOT_STARTED_MESSAGE)
if not self.futures:
raise AirflowException(NOT_STARTED_MESSAGE)
self.client.cancel(list(self.futures.keys()))
for future in as_completed(self.futures.copy()):
self._process_future(future)
def executor_map(func, iterable):
""" orderless parallel map """
# TODO: queues..
import distributed # massively slow to import...
executor = distributed.Executor()
futures = executor.map(func, iterable) # should return immediately
for future in distributed.as_completed(futures): # blocks
assert future.done()
yield future.result()
def mysum():
result = 0
sub_tasks = [delayed(double)(i) for i in range(100)]
with worker_client() as lc:
futures = lc.compute(sub_tasks)
for f in as_completed(futures):
result += f.result()
return result
def mysum():
result = 0
sub_tasks = [delayed(double)(i) for i in range(100)]
with worker_client() as lc:
futures = lc.compute(sub_tasks)
for f in as_completed(futures):
result += f.result()
return result
def eval_solver(self, solver, method_name='MyMethod', add_fields=[]):
"""
solver: The solver to evaluate.
method_name: Name of the method to evaluate, name that will appear in results dataframe.
add_fields: List containing additionnal fields that should be saved. These fields
must be present in the output dict of the solver.
"""
all_outputs = defaultdict(list)
save_fields = ['success', 'n_moves', 'n_collision_checks'
] + list(add_fields)
def run_solver(solver, problem, problem_idx):
outputs = solver(problem)
assert "solved" in outputs
if outputs['solved']:
assert 'actions' in outputs
actions = outputs['actions']
# Verify that the problem is indeed solved.
# This will stop the evaluation if the action sequence found doesn't solve the problem
# or doesn't respect the constraints (objects within workspace and no collisions)
problem.assert_solution_valid(actions)
outputs['n_moves'] = len(actions)
outputs['success'] = True
else:
outputs['success'] = False
outputs['n_moves'] = np.nan
outputs['n_collision_checks'] = np.nan
return outputs, problem_idx
futures = []
print(f"{method_name} evaluation ...")
for row_idx, row in enumerate(self.eval_df.itertuples()):
src = row.src
tgt = row.tgt
problem = RearrangementProblem(src=src,
tgt=tgt,
workspace=self.infos['workspace'],
radius=self.infos['radius'])
fut = self.client.submit(run_solver, solver, problem, row_idx)
futures.append(fut)
for fut in tqdm(as_completed(futures), total=len(futures)):
outputs, problem_idx = fut.result()
all_outputs['problem_idx'].append(problem_idx)
for k in save_fields:
all_outputs[f'{method_name}/{k}'].append(outputs[k])
print("Done")
sort_ids = np.argsort(all_outputs['problem_idx'])
del all_outputs['problem_idx']
all_outputs = pd.DataFrame(all_outputs)
all_outputs = all_outputs.iloc[sort_ids].reset_index(drop=True)
self.eval_df = pd.concat((self.eval_df, all_outputs), axis=1)
return
def test_as_completed(client):
ac = client.submit(Counter, actor=True).result()
futures = [ac.increment() for _ in range(10)]
max = 0
for future in as_completed(futures):
value = future.result()
if value > max:
max = value
assert all(future.done() for future in futures)
assert max == 10
def solve(self):
# start off some particles
futures = []
for particle in self.particles: # [:max(int((self.num_workers + 1) / self.replications), 1)]:
futures.append(self.create_parallel_particle_future(particle.name))
# time.sleep(60)
completed = as_completed(futures, with_results=True)
for batch in completed.batches():
for future, (particle_num, score, position, velocity) in batch:
self.particles[particle_num].update_score_position_velocity(
score, position, velocity)
# particle not running anymore
self.particles_running[particle_num] = False
# update the epoch
self.particle_epochs_completed[particle_num] += 1
# see if there's a new best score
self.update_global(score, position)
# print("-- tassie devil\n{}\n{}\n{}\n".format([particle.name for particle in self.particles],
# self.particle_epochs_completed,
# self.particles_running))
# find the next particle (min epochs done and not currently running)
min_epochs = sys.maxsize
next_particle_pos = -1
for pos, (is_running, epochs_done) in enumerate(
zip(self.particles_running,
self.particle_epochs_completed)):
if not is_running and epochs_done < min_epochs:
min_epochs = epochs_done
next_particle_pos = pos
# print("min: {}".format(min_epochs))
if min_epochs < self.iterations:
# not done yet - find the min particle
particle = self.particles[next_particle_pos]
# print("index={}, particle_num={}".format(particle_num, particle.name))
# update for the next run
particle.update_velocity(self.global_best_position)
particle.update_position()
# score the particle position
completed.add(
self.create_parallel_particle_future(particle_num))
# do something with the results now
print("=========== Done ({}) ===============".format(self.iterations))
print(self)
def test_as_completed_async_for(c, s, a, b):
futures = c.map(inc, range(10))
ac = as_completed(futures)
results = []
async def f():
async for future in ac:
result = await future
results.append(result)
yield f()
assert set(results) == set(range(1, 11))
def test_as_completed_async_for_results(c, s, a, b):
futures = c.map(inc, range(10))
ac = as_completed(futures, with_results=True)
results = []
async def f():
async for future, result in ac:
results.append(result)
yield f()
assert set(results) == set(range(1, 11))
assert not s.counters['op'].components[0]['gather']
def iterate():
locs = map(coords.get_loc, coords.drop_duplicates())
if client is not None:
futures = client.map(
self._compute_anomaly,
[data.isel(**{agedim: sl}) for sl in locs],
**kwargs)
for future, result in distributed.as_completed(
futures, with_results=True):
futures.remove(future)
yield result
else:
for sl in locs:
yield self._compute_anomaly(data.isel(**{agedim: sl}),
**kwargs)
def eval_population(population, client, context=context):
""" Concurrently evaluate all the individuals in the given population
:param population: to be evaluated
:param client: dask client
:param context: for storing count of non-viable individuals
:return: dask distrib iterator for futures
"""
# farm out population to worker nodes for evaluation
worker_futures = client.map(evaluate(context=context),
population,
pure=False)
# We'll need this later to catch eval tasks as they complete, and to
# submit new tasks.
return distributed.as_completed(worker_futures)
def record_dataset_dask(client, ds_dir,
scene_cls, scene_kwargs,
n_chunks, n_frames_per_chunk,
start_seed=0, resume=False):
seeds = set(range(start_seed, start_seed + n_chunks))
if resume:
done_seeds = (ds_dir / 'seeds_recorded.txt').read_text().strip().split('\n')
seeds = set(seeds) - set(map(int, done_seeds))
all_keys = (ds_dir / 'keys_recorded.txt').read_text().strip().split('\n')
else:
all_keys = []
seeds = tuple(seeds)
future_kwargs = []
for seed in seeds:
kwargs = dict(ds_dir=ds_dir, seed=seed,
n_frames=n_frames_per_chunk,
scene_cls=scene_cls,
scene_kwargs=scene_kwargs)
future_kwargs.append(kwargs)
futures = []
for kwargs in future_kwargs:
futures.append(client.submit(record_chunk, **kwargs))
iterator = as_completed(futures)
unit = 'frame'
unit_scale = n_frames_per_chunk
n_futures = len(future_kwargs)
tqdm_iterator = tqdm(iterator, total=n_futures, unit_scale=unit_scale, unit=unit, ncols=80)
seeds_file = open(ds_dir / 'seeds_recorded.txt', 'a')
keys_file = open(ds_dir / 'keys_recorded.txt', 'a')
for future in tqdm_iterator:
keys, seed = future.result()
all_keys += keys
seeds_file.write(f'{seed}\n')
seeds_file.flush()
keys_file.write('\n'.join(keys) + '\n')
keys_file.flush()
client.cancel(future)
seeds_file.close()
keys_file.close()
return all_keys
def pytest_runtestloop(self, session):
if (session.testsfailed
and not session.config.option.continue_on_collection_errors):
raise session.Interrupted("%d errors during collection" %
session.testsfailed)
unregister_plugins = ['debugging', 'terminalreporter']
for p in unregister_plugins:
session.config.pluginmanager.unregister(p)
if session.config.option.collectonly:
return True
def generate_tasks(session):
for i, item in enumerate(session.items):
# @delayed(pure=False)
def run_test(_item):
# ensure that the plugin manager gets recreated appropriately.
_item.config.pluginmanager.__recreate__()
results = self.pytest_runtest_protocol(item=_item,
nextitem=None)
return results
# hook = item.ihook
# try to ensure that the module gets treated as a dynamic module that does not
# exist.
# delattr(item.module, '__file__')
# setup = hook.pytest_runtest_setup
# make_report = hook.pytest_runtest_makereport
fut = self.client.submit(run_test, item, pure=False)
yield fut
with self.remote_syspath_ctx():
tasks = generate_tasks(session)
# log these reports to the console.
for resolved in as_completed(tasks):
t = resolved.result()
for report in t:
session.ihook.pytest_runtest_logreport(report=report)
return True
def run_actions(unit_context,
loop_variable_name=None,
loop_variable_value=None,
in_loop=None,
on_dask=None):
results = []
triggers = []
if in_loop:
if on_dask:
futures = []
client = DaskClient().get_dask_client()
for value in unit_context.stageContext.pipelineContext.variables[
loop_variable_name]:
futures.append(
client.submit(run_actions,
unit_context,
loop_variable_name,
value,
False,
False,
pure=False))
for future in as_completed(futures):
result, trigger_pipeline_data_list = future.result()
results.extend(result)
triggers.extend(trigger_pipeline_data_list)
else:
for value in unit_context.stageContext.pipelineContext.variables[
loop_variable_name]:
result, trigger_pipeline_data_list = run_actions(
unit_context, loop_variable_name, value, False, False)
results.extend(result)
triggers.extend(trigger_pipeline_data_list)
else:
for action in unit_context.unit.do:
action_context = ActionContext(unit_context, action)
if loop_variable_name and loop_variable_value:
action_context.delegateVariableName = loop_variable_name
action_context.delegateValue = loop_variable_value
result, trigger_pipeline_data_list = run_action(action_context)
results.append(result)
triggers.extend(trigger_pipeline_data_list)
return results, triggers
def test_as_completed_async_for_cancel(c, s, a, b):
x = c.submit(inc, 1)
y = c.submit(sleep, 0.3)
ac = as_completed([x, y])
async def _():
await gen.sleep(0.1)
await y.cancel(asynchronous=True)
c.loop.add_callback(_)
L = []
async def f():
async for future in ac:
L.append(future)
yield f()
assert L == [x, y]
def execute_list_of_futures_with_dataset_requirements(tuple_list,
tests_per_batch=None):
"""
:param tuple_list: list tuples (dataset_name, f(dataset_future) -> future
:param tests_per_batch: how much tests per batch you want
:return:
"""
if tests_per_batch is None:
tests_per_batch = len(tuple_list)
with Client(address=SCHEDULER_HOSTNAME) as client:
for chunk in chunks(tuple_list, tests_per_batch):
dataset_dict = scatter_datasets(client)
futures = fill_dataset_requirements(chunk, client, dataset_dict)
for _ in tqdm(distributed.as_completed(futures,
with_results=True,
raise_errors=True),
total=len(futures)):
pass
client.restart()
def execute_list_of_clustering_tasks(clustering_tasks, tests_per_batch=None):
if len(clustering_tasks) == 0:
print("all clustering tasks done")
if tests_per_batch is None:
tests_per_batch = len(clustering_tasks)
with Client(address=SCHEDULER_HOSTNAME) as client:
with tqdm(total=len(clustering_tasks)) as pbar:
tasks_to_still_do = deque(clustering_tasks)
dataset_dict = scatter_datasets(client)
futures = []
for _ in range(min(tests_per_batch, len(clustering_tasks))):
task = tasks_to_still_do.popleft()
futures.append(
client.submit(ClusteringTask.run,
task,
dataset_dict[task.dataset_name],
pure=False))
as_completed_futures = distributed.as_completed(futures,
with_results=True,
raise_errors=False)
for future, _ in as_completed_futures:
pbar.update(1)
f: Future = future
if f.exception() is not None:
t = f.traceback()
# for line in t.format():
# print(line, end = "")
# traceback.print_exception()f.exception()
traceback.print_tb(f.traceback())
print(f.exception())
if len(tasks_to_still_do) > 0:
task = tasks_to_still_do.popleft()
future = client.submit(ClusteringTask.run,
task,
dataset_dict[task.dataset_name],
pure=False)
as_completed_futures.add(future)
def _consume_jobs(self, chunk_size=None):
"""Consumes jobs
If chunk_size is set function consumes specified number of
Finished tasks or less if sent_jobs_ids queue became empty.
If chunk_size is None function consumes jobs until
sent_jobs_ids queue became empty.
Jobs with statuses Cancelled, Abandoned, Terminated will be
resent and their ids added to sent_jobs_ids queue
:param chunk_size: size of consuming chunk
:return: generator on job results
"""
logger.debug("Consuming jobs started")
jobs_to_consume = []
while not self.sent_jobs.empty():
job = self.sent_jobs.get()
jobs_to_consume.append(job)
if chunk_size is not None:
chunk_size -= 1
if chunk_size <= 0:
break
for ready_job in distributed.as_completed(jobs_to_consume):
results = ready_job.result()
self.sent_jobs_count -= 1
for result in results:
(node_id, serialized), exc = result
logger.debug(
"Got ready task for node %s, serialized: %s, "
"error: %s", node_id, serialized, exc)
if exc is not None:
raise exc
yield node_id, serialized
logger.debug("Consuming jobs finished")
def parallelStatsDaskSimple(urlSplits,
ds,
nEpochs,
variable,
mask,
coordinates,
reader,
outHdfsPath,
averagingConfig,
sparkConfig,
accumulators=['count', 'mean', 'M2', 'min',
'max']):
'''Compute N-day climatology statistics in parallel using PySpark or pysparkling.'''
if not sparkConfig.startswith('dask,'):
print("dask: configuration must be of form 'dask,n'", file=sys.stderr)
sys.exit(1)
numPartitions = int(sparkConfig.split(',')[1])
with Timer("Configure Dask distributed"):
from distributed import Client, as_completed
client = Client(DaskClientEndpoint)
print('Starting parallel Stats using Dask . . .', file=sys.stderr)
start = time.time()
futures = client.map(
lambda urls: parallelStatsPipeline(
urls, ds, nEpochs, variable, mask, coordinates, reader,
averagingConfig, outHdfsPath, accumulators), urlSplits)
outputFiles = []
for future in as_completed(futures):
outputFile = future.result()
outputFiles.append(outputFile)
end = time.time()
print("parallelStats: Completed %s in %0.3f seconds." %
(outputFile, (end - start)),
file=sys.stderr)
return outputFiles
def _consume_jobs(self, chunk_size=None):
"""Consumes jobs
If chunk_size is set function consumes specified number of
Finished tasks or less if sent_jobs_ids queue became empty.
If chunk_size is None function consumes jobs until
sent_jobs_ids queue became empty.
Jobs with statuses Cancelled, Abandoned, Terminated will be
resent and their ids added to sent_jobs_ids queue
:param chunk_size: size of consuming chunk
:return: generator on job results
"""
logger.debug("Consuming jobs started")
jobs_to_consume = []
while not self.sent_jobs.empty():
job = self.sent_jobs.get()
jobs_to_consume.append(job)
if chunk_size is not None:
chunk_size -= 1
if chunk_size <= 0:
break
for ready_job in distributed.as_completed(jobs_to_consume):
results = ready_job.result()
self.sent_jobs_count -= 1
for result in results:
(node_id, serialized), exc = result
logger.debug("Got ready task for node %s, serialized: %s, "
"error: %s", node_id, serialized, exc)
if exc is not None:
raise exc
yield node_id, serialized
logger.debug("Consuming jobs finished")
def run(ctx, path, ncores):
path = pathlib.Path(path)
if path.is_dir():
paths = list(path.rglob("*.py"))
else:
paths = [path]
import distributed
with distributed.Client(n_workers=ncores) as client:
print(client)
futures = {}
for p in tqdm.tqdm(sorted(paths), desc="Creating tasks"):
fut = client.submit(run_migrators_on_file, p)
futures[fut] = p
progress_iterator = tqdm.tqdm(desc="Scanning :",
total=len(futures),
miniters=1)
all_changed = set()
for resolved_fut in distributed.as_completed(futures):
path = futures[resolved_fut]
progress_iterator.update(1)
progress_iterator.set_description(f"Scanning: {path}")
try:
changed = resolved_fut.result()
if changed:
all_changed.add(path)
except CantParseException as e:
print(f"Can't parse {path}", file=sys.stderr)
progress_iterator.close()
if len(all_changed):
print("Changed the following files:")
for path in sorted(all_changed):
print(f" {path}")
def _iterate_jobs(self):
"""
Iterate through all jobs until the domain size is depleted or
time runs out.
:return: completed job
"""
backlog_half = self.backlog_per_worker / 2
active_futures = self._init_futures(self.backlog_per_worker)
next_futures = []
try:
while ((self._has_more_work()
or self.index_completed < self.index_scheduled)
and not self.canceled):
iterated = 0
for future in as_completed(active_futures):
job = future.result()
self._mark_job_completed(job)
iterated += 1
self.tracer.trace_job(job)
if iterated >= (backlog_half * self.worker_count):
iterated = 0
if self._has_more_work():
next_futures += self._schedule(backlog_half)
if self._has_more_work():
next_futures += self._schedule(backlog_half)
active_futures = next_futures
next_futures = []
except Exception as e:
haydi_logger.error(traceback.format_exc(e))
self.completed = True
def _iterate_jobs(self):
"""
Iterate through all jobs until the domain size is depleted or
time runs out.
:return: completed job
"""
backlog_half = self.backlog_per_worker / 2
active_futures = self._init_futures(self.backlog_per_worker)
next_futures = []
try:
while ((self._has_more_work() or
self.index_completed < self.index_scheduled) and
not self.canceled):
iterated = 0
for future in as_completed(active_futures):
job = future.result()
self._mark_job_completed(job)
iterated += 1
self.tracer.trace_job(job)
if iterated >= (backlog_half * self.worker_count):
iterated = 0
if self._has_more_work():
next_futures += self._schedule(backlog_half)
if self._has_more_work():
next_futures += self._schedule(backlog_half)
active_futures = next_futures
next_futures = []
except Exception as e:
haydi_logger.error(traceback.format_exc(e))
self.completed = True
printt('[info] master > maxmin finished')
else:
for i in range(num_worker):
chunk_data = client.scatter([anchors, chunks[i]])
workers.append(client.submit(work, chunk_data, f'worker_{i}', cur_iter, *option))
# 이터레이션이 실패할 경우를 대비해 redis 의 값을 백업
#entities_initialized_bak = iter_mget(r, [f'{entity}_v' for entity in entities])
#entities_initialized_bak = np.array([loads(decompress(v)) for v in entities_initialized_bak])
#relations_initialized_bak = iter_mget(r, [f'{relation}_v' for relation in relations])
#relations_initialized_bak = np.array([loads(decompress(v)) for v in relations_initialized_bak])
# client.gather(workers)
# result_iter = [worker.result() for worker in workers]
result_iter = []
ac = as_completed(workers, with_results=True)
for future, result in ac:
result_iter.append(result)
iterTimes.append(timeit.default_timer() - iterStart)
if all([e[0] for e in result_iter]):
# 이터레이션 성공
printt('[info] master > iter %d - time : %f' % (cur_iter, timeit.default_timer() - timeNow))
success = True
trial = 0
cur_iter += 1
workTimes = [e[1] for e in result_iter]
printt('[info] master > Total embedding times : ' + str(workTimes))
# printt('[info] master > Average total embedding time : ' + str(np.mean(workTimes)))
def run(self, domain,
worker_reduce_fn, worker_reduce_init,
global_reduce_fn, global_reduce_init):
size = domain.steps
assert size is not None # TODO: Iterators without size
workers = 0
for name, value in self.executor.ncores().items():
workers += value
if workers == 0:
raise Exception("There are no workers")
batch_count = workers * 4
batch_size = max(int(round(size / float(batch_count))), 1)
batches = self._create_batches(batch_size, size, domain,
worker_reduce_fn, worker_reduce_init)
logging.info("Qit: starting {} batches with size {}".format(
batch_count, batch_size))
if self.job_observer:
self.job_observer.on_computation_start(batch_count, batch_size)
futures = self.executor.map(process_batch, batches)
if self.track_progress:
distributed.diagnostics.progress(futures)
if self.write_partial_results is not None:
result_saver = ResultSaver(self.execution_count,
self.write_partial_results)
else:
result_saver = None
timeouted = False
results = []
for future in as_completed(futures):
job = future.result()
if result_saver:
result_saver.handle_result(job.result)
if self.job_observer:
self.job_observer.on_job_completed(job)
results.append(job.result)
if self.timeout and self.timeout.is_finished():
logging.info("Qit: timeouted after {} seconds".format(
self.timeout.timeout))
timeouted = True
break
# order results
if not timeouted:
results = [j.result for j in self.executor.gather(futures)]
self.execution_count += 1
if worker_reduce_fn is None:
results = list(itertools.chain.from_iterable(results))
logging.info("Qit: finished run with size {} (taking {})".format(
len(results), domain.size))
results = results[:domain.size] # trim results to required size
if global_reduce_fn is None:
return results
else:
if global_reduce_init is None:
return reduce(global_reduce_fn, results)
else:
return reduce(global_reduce_fn, results, global_reduce_init)
def parallel_calculate_chunks(chunks,
features,
approximate,
training_window,
verbose,
save_progress,
entityset,
n_jobs,
no_unapproximated_aggs,
cutoff_df_time_var,
target_time,
pass_columns,
dask_kwargs=None):
from distributed import as_completed
from dask.base import tokenize
client = None
cluster = None
try:
client, cluster = create_client_and_cluster(n_jobs=n_jobs,
num_tasks=len(chunks),
dask_kwargs=dask_kwargs)
# scatter the entityset
# denote future with leading underscore
start = time.time()
es_token = "EntitySet-{}".format(tokenize(entityset))
if es_token in client.list_datasets():
print("Using EntitySet persisted on the cluster as dataset %s" %
(es_token))
_es = client.get_dataset(es_token)
else:
_es = client.scatter([entityset])[0]
client.publish_dataset(**{_es.key: _es})
# save features to a tempfile and scatter it
pickled_feats = cloudpickle.dumps(features)
_saved_features = client.scatter(pickled_feats)
client.replicate([_es, _saved_features])
end = time.time()
scatter_time = end - start
scatter_string = "EntitySet scattered to workers in {:.3f} seconds"
print(scatter_string.format(scatter_time))
# map chunks
# TODO: consider handling task submission dask kwargs
_chunks = client.map(calculate_chunk,
chunks,
features=_saved_features,
entityset=_es,
approximate=approximate,
training_window=training_window,
profile=False,
verbose=False,
save_progress=save_progress,
no_unapproximated_aggs=no_unapproximated_aggs,
cutoff_df_time_var=cutoff_df_time_var,
target_time=target_time,
pass_columns=pass_columns)
feature_matrix = []
iterator = as_completed(_chunks).batches()
if verbose:
pbar_str = ("Elapsed: {elapsed} | Remaining: {remaining} | "
"Progress: {l_bar}{bar}| "
"Calculated: {n}/{total} chunks")
pbar = make_tqdm_iterator(total=len(_chunks), bar_format=pbar_str)
for batch in iterator:
results = client.gather(batch)
for result in results:
feature_matrix.append(result)
if verbose:
pbar.update()
if verbose:
pbar.close()
except Exception:
raise
finally:
if 'cluster' not in dask_kwargs and cluster is not None:
cluster.close()
if client is not None:
client.close()
return feature_matrix
def parallel_calculate_chunks(chunks, features, approximate, training_window,
verbose, save_progress, entityset, n_jobs,
no_unapproximated_aggs, cutoff_df_time_var,
target_time, pass_columns, dask_kwargs=None):
from distributed import as_completed
from dask.base import tokenize
client = None
cluster = None
try:
client, cluster = create_client_and_cluster(n_jobs=n_jobs,
num_tasks=len(chunks),
dask_kwargs=dask_kwargs,
entityset_size=entityset.__sizeof__())
# scatter the entityset
# denote future with leading underscore
if verbose:
start = time.time()
es_token = "EntitySet-{}".format(tokenize(entityset))
if es_token in client.list_datasets():
if verbose:
msg = "Using EntitySet persisted on the cluster as dataset {}"
print(msg.format(es_token))
_es = client.get_dataset(es_token)
else:
_es = client.scatter([entityset])[0]
client.publish_dataset(**{_es.key: _es})
# save features to a tempfile and scatter it
pickled_feats = cloudpickle.dumps(features)
_saved_features = client.scatter(pickled_feats)
client.replicate([_es, _saved_features])
if verbose:
end = time.time()
scatter_time = end - start
scatter_string = "EntitySet scattered to workers in {:.3f} seconds"
print(scatter_string.format(scatter_time))
# map chunks
# TODO: consider handling task submission dask kwargs
_chunks = client.map(calculate_chunk,
chunks,
features=_saved_features,
entityset=_es,
approximate=approximate,
training_window=training_window,
profile=False,
verbose=False,
save_progress=save_progress,
no_unapproximated_aggs=no_unapproximated_aggs,
cutoff_df_time_var=cutoff_df_time_var,
target_time=target_time,
pass_columns=pass_columns)
feature_matrix = []
iterator = as_completed(_chunks).batches()
if verbose:
pbar_str = ("Elapsed: {elapsed} | Remaining: {remaining} | "
"Progress: {l_bar}{bar}| "
"Calculated: {n}/{total} chunks")
pbar = make_tqdm_iterator(total=len(_chunks), bar_format=pbar_str)
for batch in iterator:
results = client.gather(batch)
for result in results:
feature_matrix.append(result)
if verbose:
pbar.update()
if verbose:
pbar.close()
except Exception:
raise
finally:
if 'cluster' not in dask_kwargs and cluster is not None:
cluster.close()
if client is not None:
client.close()
return feature_matrix
def end(self):
for future in distributed.as_completed(self.futures.copy()):
self._process_future(future)
def execute(self):
options = self.config["mitodistances"]
output_dir = self.config["output-directory"]
body_svc, mito_svc = self.init_services()
# Resource manager context must be initialized before resource manager client
# (to overwrite config values as needed)
dvid_mgr_config = self.config["dvid-access-manager"]
dvid_mgr_context = LocalResourceManager(dvid_mgr_config)
dvid_mgr_client = ResourceManagerClient(dvid_mgr_config["server"],
dvid_mgr_config["port"])
syn_server, syn_uuid, syn_instance = (options['synapse-criteria'][k]
for k in ('server', 'uuid',
'instance'))
syn_conf = float(options['synapse-criteria']['confidence'])
syn_types = ['PreSyn', 'PostSyn']
if options['synapse-criteria']['type'] == 'pre':
syn_types = ['PreSyn']
elif options['synapse-criteria']['type'] == 'post':
syn_types = ['PostSyn']
bodies = load_body_list(options["bodies"], False)
skip_flags = [
os.path.exists(f'{output_dir}/{body}.csv') for body in bodies
]
bodies_df = pd.DataFrame({'body': bodies, 'should_skip': skip_flags})
bodies = bodies_df.query('not should_skip')['body']
# Shuffle for better load balance?
# TODO: Would be better to sort by synapse count, and put large bodies first,
# assigned to partitions in round-robin style.
# Then work stealing will be more effective at knocking out the smaller jobs at the end.
# This requires knowing all the body sizes, though.
# Perhaps mito count would be a decent proxy for synapse count, and it's readily available.
#bodies = bodies.sample(frac=1.0).values
os.makedirs('body-logs')
os.makedirs(output_dir, exist_ok=True)
mito_server, mito_uuid, mito_instance = (options['mito-labelmap'][k]
for k in ('server', 'uuid',
'instance'))
@auto_retry(3)
def _fetch_synapses(body):
with dvid_mgr_client.access_context(syn_server, True, 1, 1):
syn_df = fetch_annotation_label(syn_server,
syn_uuid,
syn_instance,
body,
format='pandas')
if len(syn_df) == 0:
return syn_df
syn_types, syn_conf
syn_df = syn_df.query(
'kind in @syn_types and conf >= @syn_conf').copy()
return syn_df[[*'xyz', 'kind', 'conf'
]].sort_values([*'xyz']).reset_index(drop=True)
@auto_retry(3)
def _fetch_mito_ids(body):
with dvid_mgr_client.access_context(mito_server, True, 1, 1):
try:
return fetch_supervoxels(mito_server, mito_uuid,
mito_instance, body)
except HTTPError:
return []
def process_and_save(body):
tbars = _fetch_synapses(body)
valid_mitos = _fetch_mito_ids(body)
# TODO:
# Does the stdout_redirected() mechanism work correctly in the context of multiprocessing?
# If not, I should probably just use a custom logging handler instead.
with open(f"body-logs/{body}.log",
"w") as f, stdout_redirected(f), Timer() as timer:
processed_tbars = []
if len(tbars) == 0:
logging.getLogger(__name__).warning(
f"Body {body}: No synapses found")
if len(valid_mitos) == 0:
logging.getLogger(__name__).warning(
f"Body {body}: Failed to fetch mito supervoxels")
processed_tbars = initialize_results(body, tbars)
if len(valid_mitos) and len(tbars):
processed_tbars = measure_tbar_mito_distances(
body_svc,
mito_svc,
body,
tbars=tbars,
valid_mitos=valid_mitos)
if len(processed_tbars) > 0:
processed_tbars.to_csv(f'{output_dir}/{body}.csv',
header=True,
index=False)
with open(f'{output_dir}/{body}.pkl', 'wb') as f:
pickle.dump(processed_tbars, f)
if len(tbars) == 0:
return (body, 0, 'no-synapses', timer.seconds)
if len(valid_mitos) == 0:
return (body, len(processed_tbars), 'no-mitos', timer.seconds)
return (body, len(tbars), 'success', timer.seconds)
logger.info(
f"Processing {len(bodies)}, skipping {bodies_df['should_skip'].sum()}"
)
def process_batch(bodies):
return [*map(process_and_save, bodies)]
with dvid_mgr_context:
batch_size = max(1, len(bodies) // 10_000)
futures = self.client.map(process_batch,
iter_batches(bodies, batch_size))
# Support synchronous testing with a fake 'as_completed' object
if hasattr(self.client, 'DEBUG'):
ac = as_completed_synchronous(futures, with_results=True)
else:
ac = distributed.as_completed(futures, with_results=True)
try:
results = []
for f, r in tqdm_proxy(ac, total=len(futures)):
results.extend(r)
finally:
results = pd.DataFrame(
results,
columns=['body', 'synapses', 'status', 'processing_time'])
results.to_csv('results-summary.csv', header=True, index=False)
num_errors = len(results.query('status == "error"'))
if num_errors:
logger.warning(
f"Encountered {num_errors} errors. See results-summary.csv"
)
def parallel_calculate_chunks(chunks,
features,
approximate,
training_window,
verbose,
save_progress,
entityset,
n_jobs,
no_unapproximated_aggs,
cutoff_df_time_var,
target_time,
pass_columns,
dask_kwargs=None):
from distributed import Client, LocalCluster, as_completed
from dask.base import tokenize
client = None
cluster = None
try:
if 'cluster' in dask_kwargs:
cluster = dask_kwargs['cluster']
else:
diagnostics_port = None
if 'diagnostics_port' in dask_kwargs:
diagnostics_port = dask_kwargs['diagnostics_port']
del dask_kwargs['diagnostics_port']
workers = n_jobs_to_workers(n_jobs)
workers = min(workers, len(chunks))
cluster = LocalCluster(n_workers=workers,
threads_per_worker=1,
diagnostics_port=diagnostics_port,
**dask_kwargs)
# if cluster has bokeh port, notify user if unxepected port number
if diagnostics_port is not None:
if hasattr(cluster, 'scheduler') and cluster.scheduler:
info = cluster.scheduler.identity()
if 'bokeh' in info['services']:
msg = "Dashboard started on port {}"
print(msg.format(info['services']['bokeh']))
client = Client(cluster)
# scatter the entityset
# denote future with leading underscore
start = time.time()
es_token = "EntitySet-{}".format(tokenize(entityset))
if es_token in client.list_datasets():
print("Using EntitySet persisted on the cluster as dataset %s" %
(es_token))
_es = client.get_dataset(es_token)
else:
_es = client.scatter([entityset])[0]
client.publish_dataset(**{_es.key: _es})
# save features to a tempfile and scatter it
pickled_feats = cloudpickle.dumps(features)
_saved_features = client.scatter(pickled_feats)
client.replicate([_es, _saved_features])
end = time.time()
scatter_time = end - start
scatter_string = "EntitySet scattered to workers in {:.3f} seconds"
print(scatter_string.format(scatter_time))
# map chunks
# TODO: consider handling task submission dask kwargs
_chunks = client.map(calculate_chunk,
chunks,
features=_saved_features,
entityset=_es,
approximate=approximate,
training_window=training_window,
profile=False,
verbose=False,
save_progress=save_progress,
no_unapproximated_aggs=no_unapproximated_aggs,
cutoff_df_time_var=cutoff_df_time_var,
target_time=target_time,
pass_columns=pass_columns)
feature_matrix = []
iterator = as_completed(_chunks).batches()
if verbose:
pbar_str = ("Elapsed: {elapsed} | Remaining: {remaining} | "
"Progress: {l_bar}{bar}| "
"Calculated: {n}/{total} chunks")
pbar = make_tqdm_iterator(total=len(_chunks), bar_format=pbar_str)
for batch in iterator:
results = client.gather(batch)
for result in results:
feature_matrix.append(result)
if verbose:
pbar.update()
if verbose:
pbar.close()
except Exception:
raise
finally:
if 'cluster' not in dask_kwargs and cluster is not None:
cluster.close()
if client is not None:
client.close()
return feature_matrix
def end(self):
for future in distributed.as_completed(self.futures.copy()):
self._process_future(future)
def as_completed(futures):
return distributed.as_completed(futures)
