def init_dist(args, backend="nccl"):
if mp.get_start_method(allow_none=True) is None:
mp.set_start_method("spawn")
if not dist.is_available():
args.launcher = "none"
if args.launcher == "pytorch":
# DDP
init_dist_pytorch(args, backend)
return True
elif args.launcher == "slurm":
# DDP
init_dist_slurm(args, backend)
return True
elif args.launcher == "none":
# DataParallel or single GPU
if 'CUDA_VISIBLE_DEVICES' in os.environ.keys():
args.total_gpus = len(os.environ['CUDA_VISIBLE_DEVICES'].split(','))
else:
args.total_gpus = torch.cuda.device_count()
if args.total_gpus > 1:
warnings.warn(
"It is highly recommended to use DistributedDataParallel by setting "
"args.launcher as 'slurm' or 'pytorch'."
)
return False
else:
raise ValueError("Invalid launcher type: {}".format(args.launcher))
def set_mp_start_method() -> None:
"""
Sets the multiprocessing start method.
"""
start_method = _get_start_method()
if not start_method:
return
import multiprocessing
import multiprocess
multiprocessing.set_start_method(start_method)
multiprocess.set_start_method(start_method)
def run_safely(f, x):
"""Runs f(args) in a separate process."""
# f_global = f # globalize(f)
# mp.freeze_support()
mp.set_start_method("spawn")
q = mp.Queue()
p = Process(target=with_queue, args=(f, q, x))
p.start()
p.join()
if p.exception:
error, traceback = p.exception
print(traceback)
raise error
try:
out = q.get(False, 2.0) # Non-blocking mode
except queue.Empty:
print("Empty queue!")
print("Exit code: ", p.exitcode)
raise MemoryError()
return out
def train_parallel_trpo(
env_id,
predictor,
make_env=gym.make,
summary_writer=None,
workers=1,
runtime=1800,
max_timesteps_per_episode=None,
timesteps_per_batch=5000,
max_kl=0.001,
seed=0,
discount_factor=0.995,
cg_damping=0.1,
):
# Tensorflow is not fork-safe, so we must use spawn instead
# https://github.com/tensorflow/tensorflow/issues/5448#issuecomment-258934405
# We use multiprocess rather than multiprocessing because Keras sets a multiprocessing context
if not os.environ.get("SET_PARALLEL_TRPO_START_METHOD"
): # Use an env variable to prevent double-setting
multiprocess.set_start_method('spawn')
os.environ['SET_PARALLEL_TRPO_START_METHOD'] = "1"
run_indefinitely = (runtime <= 0)
if max_timesteps_per_episode is None:
max_timesteps_per_episode = gym.spec(env_id).timestep_limit
learner = TRPO(env_id,
make_env,
max_kl=max_kl,
discount_factor=discount_factor,
cg_damping=cg_damping)
rollouts = ParallelRollout(env_id, make_env, predictor, workers,
max_timesteps_per_episode, seed)
iteration = 0
start_time = time()
while run_indefinitely or time() < start_time + runtime:
iteration += 1
# update the weights
weights = learner.get_policy()
rollouts.set_policy_weights(weights)
# run a bunch of async processes that collect rollouts
paths, rollout_time = rollouts.rollout(timesteps_per_batch)
# learn from that data
stats, learn_time = learner.learn(paths)
# output stats
print("-------- Iteration %d ----------" % iteration)
frames_gathered_per_second = stats["Frames gathered"] / rollout_time
stats["Frames gathered/second"] = int(frames_gathered_per_second)
stats['Time spent gathering rollouts'] = rollout_time
stats['Time spent updating weights'] = learn_time
total_elapsed_seconds = time() - start_time
stats["Total time"] = total_elapsed_seconds
##### HACK #####
stats[
"Predictor iteration"] = predictor.predictor._elapsed_predictor_training_iters
if predictor.entropy_alpha is not None:
stats["Predictor Entropy Alpha"] = predictor.entropy_alpha
if predictor.softmax_beta is not None:
stats["Predictor Softmax Beta"] = predictor.softmax_beta
print_stats(stats)
if summary_writer:
# Log results to tensorboard
mean_reward = np.mean(
np.array([path["original_rewards"].sum() for path in paths]))
summary = tf.Summary(value=[
tf.Summary.Value(tag="parallel_trpo/mean_reward",
simple_value=mean_reward),
tf.Summary.Value(tag="parallel_trpo/elapsed_seconds",
simple_value=total_elapsed_seconds),
tf.Summary.Value(
tag="parallel_trpo/frames_gathered_per_second",
simple_value=frames_gathered_per_second),
])
summary_writer.add_summary(summary, global_step=iteration)
rollouts.end()
def main(global_config, **settings):
""" This function returns a Pyramid WSGI application.
"""
multiprocess.set_start_method("spawn")
engine = engine_from_config(settings, 'sqlalchemy.')
DBSession.configure(bind=engine)
Base.metadata.bind = engine
from pyramid.config import Configurator
config_file = global_config['__file__']
parser = ConfigParser()
parser.read(config_file)
# TODO: DANGER
storage = dict()
for k, v in parser.items('backend:storage'):
storage[k] = v
settings['storage'] = storage
if parser.has_section('app:desktop'):
for k, v in parser.items('app:desktop'):
storage[k] = v
settings['desktop'] = storage
config = Configurator(settings=settings)
log = logging.getLogger(__name__)
# TODO: Find a more neat way
try:
cache_kwargs = dict()
for k, v in parser.items('cache:dogpile'):
cache_kwargs[k] = v
cache_args = dict()
for k, v in parser.items('cache:dogpile:args'):
cache_args[k] = v
cache_kwargs['arguments'] = cache_args
if 'expiration_time' in cache_kwargs:
cache_kwargs['expiration_time'] = int(cache_kwargs['expiration_time'])
if 'redis_expiration_time' in cache_kwargs:
cache_kwargs['redis_expiration_time'] = int(cache_kwargs['redis_expiration_time'])
except NoSectionError:
log.warn("No 'cache:dogpile' or/and 'cache:dogpile:args' sections in config; disabling caching")
initialize_cache(None)
else:
initialize_cache(cache_kwargs)
# config.configure_celery('development_test.ini')
authentication_policy = AuthTktAuthenticationPolicy(settings['secret'],
hashalg='sha512', callback=groupfinder)
authorization_policy = ACLAuthorizationPolicy()
config.set_authentication_policy(authentication_policy)
config.set_authorization_policy(authorization_policy)
config.include('pyramid_chameleon')
config.add_static_view(settings['storage']['static_route'], path=settings['storage']['path'], cache_max_age=3600)
config.add_static_view('static', path='lingvodoc:static', cache_max_age=3600)
configure_routes(config)
config.add_route('testing', '/testing')
# config.add_route('example', 'some/route/{object_id}/{client_id}/of/perspective', factory = 'lingvodoc.models.DictAcl')
# config.add_route('home', '/')
# config.add_route('login', 'login')
# config.add_route('logout', 'logout')
# config.add_route('register', 'register')
# config.add_route('acquire_client_key', 'acquire_client_key')
# config.add_route('dictionaries.list', 'dictionaries', factory='lingvodoc.models.DictionariesACL')
# config.add_route('dictionary', 'dictionary')
# config.add_route('metaword', 'dictionary/{dictionary_id}/etymology/metaword')
config.scan('.views')
return config.make_wsgi_app()
visualize.plot_species(stats, view=True)
# p = neat.Checkpointer.restore_checkpoint('neat-checkpoint-4')
# p.run(eval_genomes, 10)
def start_sim(self, cmd):
proc = sp.Popen(cmd, shell=False, stdout=sp.DEVNULL)
def conn_sim(self, connection_string, sims, index):
self.sims[index] = Simulation(connection_string,
targets_amount=5,
speedup=Const.SPEED_UP)
if __name__ == '__main__':
mp.set_start_method('spawn', True)
# parse input
parser = argparse.ArgumentParser(
description='Train a NN with the NEAT algorithm.')
parser.add_argument('-n_sims',
type=int,
default=1,
help='Amount of simulators to run in parallel')
parser.add_argument('-start_sims',
type=bool,
default=1,
help='Set to False if sims are already running')
args = parser.parse_args()
NeatEvolver(args.n_sims, args.start_sims)
def train_parallel_trpo(
env_id,
predictor,
make_env=gym.make,
summary_writer=None,
workers=1,
runtime=1800,
max_timesteps_per_episode=None,
timesteps_per_batch=5000,
max_kl=0.001,
seed=0,
discount_factor=0.995,
cg_damping=0.1,
save_freq=100,
save_dir=None,
load=False,
iteration=0,
):
# Tensorflow is not fork-safe, so we must use spawn instead
# https://github.com/tensorflow/tensorflow/issues/5448#issuecomment-258934405
# We use multiprocess rather than multiprocessing because Keras sets a multiprocessing context
if not os.environ.get("SET_PARALLEL_TRPO_START_METHOD"): # Use an env variable to prevent double-setting
multiprocess.set_start_method('spawn')
os.environ['SET_PARALLEL_TRPO_START_METHOD'] = "1"
run_indefinitely = (runtime <= 0)
if max_timesteps_per_episode is None:
max_timesteps_per_episode = gym.spec(env_id).timestep_limit
learner = TRPO(
env_id, make_env,
max_kl=max_kl,
discount_factor=discount_factor,
cg_damping=cg_damping)
if predictor.sess:
predictor.sess.run(tf.initializers.variables(tf.get_collection(tf.GraphKeys.GLOBAL_VARIABLES, scope='policy')))
if load:
print("Loading Learner...")
learner.load_session(save_dir)
# with open(os.path.join(save_dir,'loaded_weights.txt'), 'w+') as f:
# f.write(str(learner.get_policy()))
print("Loading Predictor...")
predictor.load_session(save_dir)
rollouts = ParallelRollout(env_id, make_env, predictor, workers, max_timesteps_per_episode, seed)
start_time = time()
while run_indefinitely or time() < start_time + runtime:
iteration += 1
# update the weights
weights = learner.session.run(learner.get_policy)
#weights = learner.get_policy()
rollouts.set_policy_weights(weights)
# run a bunch of async processes that collect rollouts
paths, rollout_time = rollouts.rollout(timesteps_per_batch)
# learn from that data
stats, learn_time = learner.learn(paths)
if iteration % save_freq == 0:
# Saving learner
fpath = os.path.join(save_dir, 'learner')
learner.save_session(save_dir, global_step=iteration)
#op with open(fpath + '_saved_weights_{}.txt'.format(iteration), 'w+') as f:
# f.write(str(learner.get_policy()))
# Saving predictor
predictor.save_session(save_dir, global_step=iteration)
tf.summary.FileWriter(os.path.join(save_dir, 'learner_graph'), learner.session.graph)
#tf.summary.FileWriter(os.path.join(save_dir, 'predictor_graph'), predictor.sess.graph)
# output stats
print("-------- Iteration %d ----------" % iteration)
frames_gathered_per_second = stats["Frames gathered"] / rollout_time
stats["Frames gathered/second"] = int(frames_gathered_per_second)
stats['Time spent gathering rollouts'] = rollout_time
stats['Time spent updating weights'] = learn_time
total_elapsed_seconds = time() - start_time
stats["Total time"] = total_elapsed_seconds
if predictor.comparison_collector:
stats["Collected Comparisons"] = len(predictor.comparison_collector)
print_stats(stats)
if summary_writer:
# Log results to tensorboard
mean_reward = np.mean(np.array([path["original_rewards"].sum() for path in paths]))
summary = tf.Summary(value=[
tf.Summary.Value(tag="parallel_trpo/mean_reward", simple_value=mean_reward),
tf.Summary.Value(tag="parallel_trpo/elapsed_seconds", simple_value=total_elapsed_seconds),
tf.Summary.Value(tag="parallel_trpo/frames_gathered_per_second", simple_value=frames_gathered_per_second),
])
summary_writer.add_summary(summary, global_step=iteration)
rollouts.end()
def train_parallel_trpo(env_id,
predictor,
num_r,
make_env=gym.make,
summary_writer=None,
workers=1,
runtime=1800,
max_timesteps_per_episode=None,
timesteps_per_batch=5000,
max_kl=0.001,
seed=0,
discount_factor=0.995,
cg_damping=0.1,
num_policy=0,
exploration=False):
# Tensorflow is not fork-safe, so we must use spawn instead
# https://github.com/tensorflow/tensorflow/issues/5448#issuecomment-258934405
# We use multiprocess rather than multiprocessing because Keras sets a multiprocessing context
if not os.environ.get("SET_PARALLEL_TRPO_START_METHOD"
): # Use an env variable to prevent double-setting
multiprocess.set_start_method('spawn')
os.environ['SET_PARALLEL_TRPO_START_METHOD'] = "1"
run_indefinitely = (runtime <= 0)
if max_timesteps_per_episode is None:
max_timesteps_per_episode = gym.spec(env_id).timestep_limit
# explorations
learners_policy = []
if exploration:
for i in range(num_policy):
_learner = TRPO(env_id,
make_env,
max_kl=max_kl,
discount_factor=discount_factor,
cg_damping=cg_damping,
policy_name='policy' + str(i))
learners_policy.append(_learner)
learner = TRPO(env_id,
make_env,
max_kl=max_kl,
discount_factor=discount_factor,
cg_damping=cg_damping,
policy_name='baseline')
if exploration:
rollouts = ParallelRollout_1(env_id, make_env, predictor, workers,
max_timesteps_per_episode, seed, num_r,
num_policy)
else:
rollouts = ParallelRollout(env_id, make_env, predictor, workers,
max_timesteps_per_episode, seed, num_r)
iteration = 0
start_time = time()
num_chosen_paths = 4
while run_indefinitely or time() < start_time + runtime:
iteration += 1
# exploration
if exploration:
weights_list = []
for i in range(num_policy):
weights_list.append(learners_policy[i].get_policy())
# update the weights for the baseline policy
weights = learner.get_policy()
weights_list.append(weights)
rollouts.set_policy_weights(weights_list)
# run a bunch of async processes that collect rollouts
paths, rollout_time = rollouts.rollout(timesteps_per_batch)
# learn from that data
for i in range(num_policy):
stats, learn_time = learners_policy[i].learn(
random.choice(paths, num_chosen_paths))
stats, learn_time = learner.learn(
random.choice(paths, num_chosen_paths))
else:
weights = learner.get_policy()
rollouts.set_policy_weights(weights)
# run a bunch of async processes that collect rollouts
paths, rollout_time = rollouts.rollout(timesteps_per_batch)
# learn from that data
stats, learn_time = learner.learn(
random.choice(paths, num_chosen_paths))
# output stats
print("-------- Iteration %d ----------" % iteration)
frames_gathered_per_second = stats["Frames gathered"] / rollout_time
stats["Frames gathered/second"] = int(frames_gathered_per_second)
stats['Time spent gathering rollouts'] = rollout_time
stats['Time spent updating weights'] = learn_time
total_elapsed_seconds = time() - start_time
stats["Total time"] = total_elapsed_seconds
print_stats(stats)
if summary_writer:
# Log results to tensorboard
mean_reward = np.mean(
np.array([path["original_rewards"].sum() for path in paths]))
summary = tf.Summary(value=[
tf.Summary.Value(tag="parallel_trpo/mean_reward",
simple_value=mean_reward),
tf.Summary.Value(tag="parallel_trpo/elapsed_seconds",
simple_value=total_elapsed_seconds),
tf.Summary.Value(
tag="parallel_trpo/frames_gathered_per_second",
simple_value=frames_gathered_per_second),
])
summary_writer.add_summary(summary, global_step=iteration)
rollouts.end()
# Use thread to speed up processing (multithreading)
# thread1 = threading.Thread(None, target=classic_gen_time_Sample1,
# name="1",
# args=[5, queue1],
# daemon=True, )
# Use thread to speed up processing (multithreading)
# thread2 = threading.Thread(None, target=classic_gen_time_Sample2,
# name="2",
# args=[5, [], queue2],
# daemon=True, )
# queue1 = _Queue.Queue(0)
# queue2 = _Queue.Queue(0)
if __name__ == '__main__':
mp.set_start_method('spawn')
start_sampling = threading.Event()
queue2 = Queue()
queue1 = Queue()
maxSample = Value('d', 2.0)
p1 = Process(target=process_thread_1, name="p1", args=(maxSample, ))
# thread1 = threading.Thread(None, target=classic_gen_time_Sample1,
# name="1",
# args=[maxSample, queue1],
# daemon=True, )
p2 = Process(target=process_thread_2, name="p2", args=(maxSample, ))
# thread2 = threading.Thread(None, target=classic_gen_time_Sample2,
# name="2",
# args=[maxSample, [], queue2],
# daemon=True, )
# PosLbl module for microscopy data.
# Contains all single TP FrameLbls for a specific well/position
# Deals with tracking
# AOY
import sys
import os
import pandas as pd
import numpy as np
from skimage import measure
from oyLabImaging import Metadata
import multiprocess as mp #import Pool, set_start_method
mp.set_start_method('spawn',force=True)
from functools import partial
from oyLabImaging.Processing import FrameLbl
from scipy.spatial import KDTree
import lap
from tqdm import tqdm
class PosLbl(object):
"""
Class for data from a single position (multi timepoint, position, single experiment, multi channel). Handles image tracking.
Parameters
----------
MD : relevant metadata OR
pth : str path to relevant metadata
Attributes
----------
Pos : position name
acq : acquisition name
print()
stopTraining()
response = "success"
else:
try:
stopBot()
base_model = request.form['base_model']
new_model = request.form['new_model']
startTraining(base_model, new_model)
response = "success"
except:
response = "failure"
return response, 200
## Due to debug mode being on, the app reloads and startBot messes up,
## unless use_reloader is set to false, or startBot is placed inside the below:
# @app.before_first_request
# def setup():
# if botPid is None:
# startBot()
if __name__ == "__main__":
import multiprocess
multiprocess.set_start_method('spawn')
app.secret_key = os.urandom(12)
app.run(debug=app.config['DEBUG'],
host='0.0.0.0',
port=app.config['WEBSITEPORT']) #, use_reloader=False
