def delete_data(self, data_id, var_name, phase):
backend = self._get_backend(data_id, var_name, phase)
if data_id not in self._db[backend].get_data_ids():
logger.info(
f'data_id:{data_id} does not exist in backend:{backend}')
return
self._db[backend].delete_data(data_id, var_name, phase)
def setup_tensorflow(seed=None, igpu=0):
# Tensorflow
import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)
warnings.simplefilter(action="ignore", category=DeprecationWarning)
import os
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '1'
os.environ['CUDA_DEVICE_ORDER'] = 'PCI_BUS_ID'
import tensorflow as tf
tf.compat.v1.logging.set_verbosity(tf.compat.v1.logging.ERROR)
# This is necessary for K.random_normal
# tf.compat.v1.disable_eager_execution()
physical_devices = tf.config.list_physical_devices('GPU')
useGPU = len(physical_devices) > 0
from multiml import logger
logger.info(f"useGPU = {useGPU}")
if isinstance(igpu, int):
igpu = [igpu]
# GPU memory option
if useGPU:
if tf.__version__[0] == '2':
gpus = [physical_devices[i] for i in igpu]
tf.config.set_visible_devices(gpus, 'GPU')
for gpu in gpus:
tf.config.experimental.set_memory_growth(gpu, True)
logical_gpus = tf.config.list_logical_devices('GPU')
print('available GPU:', logical_gpus)
else:
tf_config = tf.ConfigProto(gpu_options=tf.GPUOptions(
allow_growth=True))
from keras import backend as K
sess = tf.Session(config=tf_config)
K.set_session(sess)
# Random seed
import random
import numpy as np
if seed is None:
random.seed(None)
np.random.seed(None)
if tf.__version__[0] == '2':
tf.random.set_seed(None)
else:
tf.set_random_seed(None)
else:
random.seed(1234 + seed)
np.random.seed(12345 + seed)
if tf.__version__[0] == '2':
tf.random.set_seed(123456 + seed)
else:
tf.set_random_seed(123456 + seed)
def _get_best_submodels(alphas):
import tensorflow as tf
subtask_index = []
for var in alphas:
if tf.executing_eagerly():
values = var.numpy().reshape(-1)
else:
values = tf.keras.backend.eval(var).reshape(-1)
idx_max = values.argmax()
subtask_index.append(idx_max)
logger.info(f'darts_final_alpha_index_{var.name}: {idx_max}')
return subtask_index
def _dump_keras(self, key, model=None, model_path=None, **kwargs):
"""Dump keras model and parameters.
"""
kwargs = self._get_basic_kwargs(**kwargs)
kwargs['model_type'] = 'keras'
kwargs['timestamp'] = logger.get_now()
if model is not None:
if model_path is None:
model_path = f'{self._save_dir}/{key}'
logger.info(f'keras model saved path = {model_path}')
model.save_weights(model_path, save_format='tf')
# model.save(model_path, save_format='tf') # not work if the model is complicated
kwargs['model_path'] = model_path
self[key] = kwargs
def get_best_submodels(self):
""" Returns indices of the best submodels determined by the alpha
Returns:
list (int): list of index of the selected submodels
"""
subtask_ids_best = []
for subtask_env, i_model in zip(self._subtasks,
self._index_of_best_submodels):
subtask_ids_best.append(subtask_env.get_submodel(i_model))
logger.info(
f"Submodels used in DARTS = {[m.subtask_id for m in subtask_env._subtasks]}"
)
logger.info(f" Selected = {subtask_ids_best[-1].subtask_id}")
return subtask_ids_best
def show_info(self):
"""Show information of registered tasks and subtasks.
"""
logger.header2('')
for task_id in self._tasktuples:
in_dag = self._in_dag(task_id)
parents = self.get_parents_task_ids(task_id)
children = self.get_children_task_ids(task_id)
logger.info(
f' task_id: {task_id}, DAG: {in_dag} (parents: {parents}, children: {children}):'
)
for subtask in self._tasktuples[task_id].subtasks:
hp_name = subtask.hps.get_hp_names()
logger.info(
f' subtask_id: {subtask.subtask_id}, hps: {hp_name}')
logger.header2('')
def load_boston(storegate,
target_var_name='true',
phase='train',
shuffle=True):
from sklearn.datasets import load_boston
logger.info(f'Load boston dataset: {target_var_name}')
boston_dataset = load_boston()
feature_names = boston_dataset.feature_names.tolist()
data = boston_dataset.data.astype(np.float32)
target = boston_dataset.target.astype(np.float32)
storegate.add_data(feature_names, data, phase=phase, shuffle=shuffle)
storegate.add_data(target_var_name, target, phase=phase, shuffle=shuffle)
storegate.compile()
def load_iris(storegate,
data_var_name='data',
target_var_name='true',
var_names=None,
phase='train',
shuffle=True):
from sklearn.datasets import load_iris
if var_names is not None:
data_var_name, target_var_name = var_names.split()
logger.info(f'Load iris dataset: {data_var_name}, {target_var_name}')
iris_dataset = load_iris()
data = iris_dataset.data.astype(np.float32)
target = iris_dataset.target
storegate.add_data(data_var_name, data, phase=phase, shuffle=shuffle)
storegate.add_data(target_var_name, target, phase=phase, shuffle=shuffle)
storegate.compile()
def _print_result(self, result):
""" Show result.
"""
logger.header2('Result')
for task_id, subtask_id, subtask_hp in zip(result.task_ids,
result.subtask_ids,
result.subtask_hps):
logger.info(f'task_id {task_id} and subtask_id {subtask_id} with:')
if subtask_hp is None or len(subtask_hp) == 0:
logger.info(' No hyperparameters')
else:
for key, value in subtask_hp.items():
logger.info(f' {key} = {value}')
logger.info(f'Metric ({self._metric.name}) is {result.metric_value}')
def show_info(self):
"""Show information currently registered in storegate.
"""
self._check_valid_data_id()
headers = dict(
phase='phase'.ljust(6),
backend='backend'.ljust(8),
var_names='var_names'.ljust(15),
var_types='var_types'.ljust(15),
total_events='total_events'.ljust(15),
var_shape='var_shape'.ljust(15),
)
is_compiled = self._is_compiled()
logger.header3('')
logger.info(f'data_id : {self._data_id}, compiled : {is_compiled}')
for phase in ['train', 'valid', 'test']:
metadata = self._db.get_metadata(self._data_id, phase)
if not metadata.keys():
continue
logger.header2('')
logger.info(' '.join(headers.values()))
logger.header3('')
for var_name, data in metadata.items():
phase = phase.ljust(6)
backend = data['backend'].ljust(8)
var_name = var_name.ljust(15)
dtype = data['type'].ljust(15)
total_events = str(data["total_events"]).ljust(15)
shape = data["shape"]
logger.info(
f'{phase} {backend} {var_name} {dtype} {total_events} {shape}'
)
logger.header3('')
agent.execute()
with timer(timer_reg, "finalize"):
agent.finalize()
if not args.load_weights:
with open(f"{saver.save_dir}/timer.pkl", 'wb') as f:
import pickle
pickle.dump(timer_reg, f)
# Evaluate the best parameters
result = agent.result
task_scheduler.show_info()
for task_id, subtask_id, params in zip(result['task_ids'],
result['subtask_ids'],
result['subtask_hps']):
subtask = task_scheduler.get_subtask(task_id=task_id,
subtask_id=subtask_id)
params.update(save_weights=False, load_weights=True, phases=['test'])
subtask.env.set_hps(params)
agent._execute_subtask(subtask)
metric.storegate = storegate
result_metric = metric.calculate()
from multiml import logger
logger.info(f'metric = {result_metric}')
from run_utils import postprocessing
postprocessing(saver, storegate, args, do_probability=True, do_tau4vec=True)
def main(conf: str,
seed: int,
gpu_index: int,
data_path: str,
event: int,
weight: float,
load_weights: bool,
nopretraining: bool):
global DEVICE
from utils import load_config
from run_utils import get_multi_loss, set_seed
config = load_config(conf)
if seed is not None:
config.seed = seed
if gpu_index is not None and DEVICE == device('cuda'):
DEVICE = device(f'cuda:{gpu_index}')
if data_path is not None:
config['dataset']['params']['data_path'] = data_path
if event is not None:
config['dataset']['params']['max_events'] = int(event)
set_seed(config.seed)
use_multi_loss, loss_weights = get_multi_loss(weight)
from run_utils import preprocessing
saver, storegate, task_scheduler, metric = preprocessing(
save_dir=save_dir,
config=config,
device=DEVICE,
tau4vec_tasks=['conv2D', 'MLP', 'SF'],
higgsId_tasks=['lstm', 'mlp', 'mass'],
)
# Time measurements
from timer import timer
timer_reg = {}
fix_submodel_weights = False
load_weights = load_weights
nopretraining = nopretraining
phases = ['test'] if load_weights else ['train', 'valid', 'test']
# Agent
from multiml.agent.pytorch import PytorchConnectionGridSearchAgent
with timer(timer_reg, "initialize"):
from my_tasks import mapping_truth_corr
agent = PytorchConnectionGridSearchAgent(
# BaseAgent
saver=saver,
storegate=storegate,
task_scheduler=task_scheduler,
metric=metric,
metric_type='max',
dump_all_results=True,
# ConnectionGridAgent
reuse_pretraining=True,
# ConnectionSimpleAgent
freeze_model_weights=fix_submodel_weights,
do_pretraining=not nopretraining,
connectiontask_args={
"num_epochs": 100,
"max_patience": 10,
"batch_size": 100,
"save_weights": not load_weights,
"load_weights": load_weights,
"phases": phases,
"loss_weights": loss_weights,
"optimizer": "Adam",
"optimizer_args": dict(lr=1e-3),
"variable_mapping": mapping_truth_corr,
"device": DEVICE,
}
)
with timer(timer_reg, "execute"):
agent.execute()
with timer(timer_reg, "finalize"):
agent.finalize()
if not load_weights:
with open(f"{saver.save_dir}/timer.pkl", 'wb') as f:
import pickle
pickle.dump(timer_reg, f)
# Evaluate the best parameters
result, config = agent.get_best_result()
subtasks = []
job_id = None
for task_id, subtask_id, params in zip(result['task_ids'],
result['subtask_ids'],
result['subtask_hps']):
subtask = task_scheduler.get_subtask(task_id=task_id,
subtask_id=subtask_id)
params.update(load_weights=True, phases=['test'])
subtask.env.set_hps(params)
agent._execute_subtask(subtask, is_pretraining=True)
subtasks.append(subtask.env)
job_id = params['job_id']
subtask = agent._build_connected_models(subtasks,
job_id=config["job_id"],
use_task_scheduler=False)
subtask.env.task_id = 'connection'
subtask.env.subtask_id = subtask.env.name
subtask.env.set_hps({"load_weights": True, "phases": ['test']})
agent._execute_subtask(subtask, is_pretraining=False)
metric.storegate = storegate
result_metric = metric.calculate()
from multiml import logger
logger.info(f'metric = {result_metric}')
def training_keras_model(model,
num_epochs,
batch_size,
max_patience,
x_train,
y_train,
x_valid,
y_valid,
chpt_path=None,
tensorboard_path=None):
""" Training keras model
Args:
num_epochs (int): maximum number of epochs
batch_size (int): mini-batch size
max_patience (int): maximum patience for early stopping
x_train (np.darray): input array for training
y_train (np.darray): output array for training
x_valid (np.darray): input array for validation
y_valid (np.darray): output array for validation
chpt_path (str): path for Keras check-point saving. If None, temporary directory will be used.
tensorboard_path (str): Path for tensorboard callbacks. If None, tensorboard callback is not used.
Returns:
dict: training results, which contains loss histories.
"""
if chpt_path is None:
import tempfile
tmpdir = tempfile.TemporaryDirectory()
chpt_path = f'{tmpdir.name}/tf_chpt'
logger.info(f'chpt_path = {chpt_path}')
cbs = []
if max_patience is not None:
from tensorflow.keras.callbacks import EarlyStopping
es_cb = EarlyStopping(monitor='val_loss',
patience=max_patience,
verbose=0,
mode='min',
restore_best_weights=True)
cbs.append(es_cb)
from tensorflow.keras.callbacks import ModelCheckpoint
cp_cb = ModelCheckpoint(filepath=chpt_path,
monitor='val_loss',
verbose=0,
save_best_only=True,
save_weights_only=True,
mode='min')
cbs.append(cp_cb)
if tensorboard_path is not None:
from tensorflow.keras.callbacks import TensorBoard
tb_cb = TensorBoard(log_dir=tensorboard_path,
histogram_freq=1,
profile_batch=5)
cbs.append(tb_cb)
training_verbose_mode = 0
if logger.MIN_LEVEL <= logger.DEBUG:
training_verbose_mode = 1
history = model.fit(x_train,
y_train,
epochs=num_epochs,
batch_size=batch_size,
validation_data=(x_valid, y_valid),
callbacks=cbs,
verbose=training_verbose_mode)
# Save loss history
loss_train = history.history.get('loss', [-1])
loss_valid = history.history.get('val_loss', [-1])
return {
'loss_train': loss_train,
'loss_valid': loss_valid,
}
def load_model(self):
""" Load pre-trained keras model weights.
"""
model_path = super().load_model()
logger.info(f'load {model_path}')
self.ml.model.load_weights(model_path).expect_partial()
def main(opts):
logger.set_level(opts.loglevel)
global DEVICE
from utils import load_config
from run_utils import get_multi_loss, set_seed
config = load_config(opts.config)
verbose = 1
if opts.seed is not None:
config['seed'] = opts.seed
if opts.gpu_index is not None and DEVICE == device('cuda'):
DEVICE = device(f'cuda:{opts.gpu_index}')
if opts.data_path is not None:
config['dataset']['params']['data_path'] = opts.data_path
if opts.event is not None:
config['dataset']['params']['max_events'] = int(opts.event)
if opts.clip_value is not None :
config['ASNG']['clip'] = opts.clip_value
if opts.alpha is not None :
config['ASNG']['alpha'] = opts.alpha
if opts.lam is not None :
config['ASNG']['lam'] = opts.lam
if opts.delta is not None :
config['ASNG']['delta'] = opts.delta
if opts.epochs is not None :
config['ASNG']['epochs'] = opts.epochs
set_seed(config.seed)
if opts.do_pretrain :
jobid = 'pretrain_' + opts.jobid
else :
jobid = 'no_train_' + opts.jobid
save_dir = f'output/{os.path.basename(__file__)[:-3]}_{opts.event}evt_weight{opts.weight}_{jobid}'
use_multi_loss, loss_weights = get_multi_loss(opts.weight)
from run_utils import preprocessing
saver, storegate, task_scheduler, metric = preprocessing(
save_dir=save_dir,
config=config,
device=DEVICE,
tau4vec_tasks=['conv2D', 'MLP', 'SF'],
higgsId_tasks=['lstm', 'mlp', 'mass'],
)
# Time measurements
from timer import timer
timer_reg = {}
phases = ['test'] if opts.load_weights else ['train', 'valid', 'test']
# Agent
logger.info(f'lambda / alpha / delta is {config.ASNG.lam} / {config.ASNG.alpha} / {config.ASNG.delta}')
from multiml.agent.pytorch import PytorchASNGNASAgent
with timer(timer_reg, "initialize"):
from my_tasks import mapping_truth_corr
config['ASNG']['connectiontask_args']['phases'] = phases
config['ASNG']['connectiontask_args']['variable_mapping'] = mapping_truth_corr
config['ASNG']['connectiontask_args']['device'] = DEVICE
config['ASNG']['connectiontask_args']['loss_weights'] = loss_weights
agent = PytorchASNGNASAgent(
verbose = verbose,
num_epochs = config.ASNG.epochs,
max_patience = config.ASNG.patience,
batch_size = config.ASNG.batch_size,
asng_args = config.ASNG.asng_args,
optimizer = config.ASNG.optimizer.name,
optimizer_args = config.ASNG.optimizer.params,
scheduler = config.ASNG.scheduler,
# BaseAgent
saver=saver,
storegate=storegate,
task_scheduler=task_scheduler,
metric=metric,
# EnsembleAgent
# ConnectionSimpleAgent
freeze_model_weights=False,
do_pretraining = opts.do_pretrain,
connectiontask_args= config.ASNG.connectiontask_args,
)
with timer(timer_reg, "execute"):
agent.execute()
with timer(timer_reg, "finalize"):
agent.finalize()
results = agent.results_json
results['walltime'] = timer_reg['execute'][1]
results['timer_reg'] = timer_reg
results['seed'] = opts.seed
results['nevents'] = opts.event*2
def print_dict(key, val) :
if type(val) is dict :
for k, v in val.items():
print_dict( f'{key} {k}', v)
else :
logger.info(f'{key: <30} : {val}')
for key, val in results.items() :
print_dict(key, val)
with open(f'{saver.save_dir}/result.run_connection_asngnas_{opts.event}evt_weight{opts.weight}.json', 'w') as fo :
json.dump([results], fo, indent=2)
if not opts.load_weights:
with open(f"{saver.save_dir}/timer.pkl", 'wb') as f:
import pickle
pickle.dump(timer_reg, f)
### post processing
variables = []
from my_tasks import corr_tau_4vec
variables.extend(corr_tau_4vec)
variables.extend(['probability'])
for phase in phases :
# dump prediction
storegate.set_data_id("")
y_pred = np.array( storegate.get_data(phase = phase, var_names = variables ) )
os.makedirs(f'{saver.save_dir}/pred/{phase}', exist_ok = True )
for i, v in enumerate(variables):
np.save(f'{saver.save_dir}/pred/{phase}/{v}', y_pred[i])
def print_dict(key, val) :
if type(val) is dict :
for k, v in val.items():
print_dict( f'{key} {k}', v)
else :
logger.info(f'{key: <30} : {val}')
