Using BatchedPyEnvironment in tf_agents - tensorflow

I am trying to create a batched environment version of an SAC agent example from the Tensorflow Agents library, the original code can be found here. I am also using a custom environment.
I am pursuing a batched environment setup in order to better leverage GPU resources in order to speed up training. My understanding is that by passing batches of trajectories to the GPU, there will be less overhead incurred when passing data from the host (CPU) to the device (GPU).
My custom environment is called SacEnv, and I attempt to create a batched environment like so:
py_envs = [SacEnv() for _ in range(0, batch_size)]
batched_env = batched_py_environment.BatchedPyEnvironment(envs=py_envs)
tf_env = tf_py_environment.TFPyEnvironment(batched_env)
My hope is that this will create a batched environment consisting of a 'batch' of non-batched environments. However I am receiving the following error when running the code:
ValueError: Cannot assign value to variable ' Accumulator:0': Shape mismatch.The variable shape (1,), and the assigned value shape (32,) are incompatible.
with the stack trace:
Traceback (most recent call last):
File "/home/gary/Desktop/code/sac_test/sac_main2.py", line 370, in <module>
app.run(main)
File "/home/gary/anaconda3/envs/py39/lib/python3.9/site-packages/absl/app.py", line 312, in run
_run_main(main, args)
File "/home/gary/anaconda3/envs/py39/lib/python3.9/site-packages/absl/app.py", line 258, in _run_main
sys.exit(main(argv))
File "/home/gary/Desktop/code/sac_test/sac_main2.py", line 366, in main
train_eval(FLAGS.root_dir)
File "/home/gary/anaconda3/envs/py39/lib/python3.9/site-packages/gin/config.py", line 1605, in gin_wrapper
utils.augment_exception_message_and_reraise(e, err_str)
File "/home/gary/anaconda3/envs/py39/lib/python3.9/site-packages/gin/utils.py", line 41, in augment_exception_message_and_reraise
raise proxy.with_traceback(exception.__traceback__) from None
File "/home/gary/anaconda3/envs/py39/lib/python3.9/site-packages/gin/config.py", line 1582, in gin_wrapper
return fn(*new_args, **new_kwargs)
File "/home/gary/Desktop/code/sac_test/sac_main2.py", line 274, in train_eval
results = metric_utils.eager_compute(
File "/home/gary/anaconda3/envs/py39/lib/python3.9/site-packages/gin/config.py", line 1605, in gin_wrapper
utils.augment_exception_message_and_reraise(e, err_str)
File "/home/gary/anaconda3/envs/py39/lib/python3.9/site-packages/gin/utils.py", line 41, in augment_exception_message_and_reraise
raise proxy.with_traceback(exception.__traceback__) from None
File "/home/gary/anaconda3/envs/py39/lib/python3.9/site-packages/gin/config.py", line 1582, in gin_wrapper
return fn(*new_args, **new_kwargs)
File "/home/gary/anaconda3/envs/py39/lib/python3.9/site-packages/tf_agents/eval/metric_utils.py", line 163, in eager_compute
common.function(driver.run)(time_step, policy_state)
File "/home/gary/anaconda3/envs/py39/lib/python3.9/site-packages/tensorflow/python/util/traceback_utils.py", line 153, in error_handler
raise e.with_traceback(filtered_tb) from None
File "/home/gary/anaconda3/envs/py39/lib/python3.9/site-packages/tf_agents/drivers/dynamic_episode_driver.py", line 211, in run
return self._run_fn(
File "/home/gary/anaconda3/envs/py39/lib/python3.9/site-packages/tf_agents/utils/common.py", line 188, in with_check_resource_vars
return fn(*fn_args, **fn_kwargs)
File "/home/gary/anaconda3/envs/py39/lib/python3.9/site-packages/tf_agents/drivers/dynamic_episode_driver.py", line 238, in _run
tf.while_loop(
File "/home/gary/anaconda3/envs/py39/lib/python3.9/site-packages/tf_agents/drivers/dynamic_episode_driver.py", line 154, in loop_body
observer_ops = [observer(traj) for observer in self._observers]
File "/home/gary/anaconda3/envs/py39/lib/python3.9/site-packages/tf_agents/drivers/dynamic_episode_driver.py", line 154, in <listcomp>
observer_ops = [observer(traj) for observer in self._observers]
File "/home/gary/anaconda3/envs/py39/lib/python3.9/site-packages/tf_agents/metrics/tf_metric.py", line 93, in __call__
return self._update_state(*args, **kwargs)
File "/home/gary/anaconda3/envs/py39/lib/python3.9/site-packages/tf_agents/metrics/tf_metric.py", line 81, in _update_state
return self.call(*arg, **kwargs)
ValueError: in user code:
File "/home/gary/anaconda3/envs/py39/lib/python3.9/site-packages/tf_agents/metrics/tf_metrics.py", line 176, in call *
self._return_accumulator.assign(
ValueError: Cannot assign value to variable ' Accumulator:0': Shape mismatch.The variable shape (1,), and the assigned value shape (32,) are incompatible.
In call to configurable 'eager_compute' (<function eager_compute at 0x7fa4d6e5e040>)
In call to configurable 'train_eval' (<function train_eval at 0x7fa4c8622dc0>)
I have dug through the tf_metric.py code to try and understand the error, however I have been unsuccessful. A related issue was solved when I added the batch size (32) to the initializer for the AverageReturnMetric instance, and this issue seems related.
The full code is:
# coding=utf-8
# Copyright 2020 The TF-Agents Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# Lint as: python2, python3
r"""Train and Eval SAC.
All hyperparameters come from the SAC paper
https://arxiv.org/pdf/1812.05905.pdf
To run:
```bash
tensorboard --logdir $HOME/tmp/sac/gym/HalfCheetah-v2/ --port 2223 &
python tf_agents/agents/sac/examples/v2/train_eval.py \
--root_dir=$HOME/tmp/sac/gym/HalfCheetah-v2/ \
--alsologtostderr
\```
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from sac_env import SacEnv
import os
import time
from absl import app
from absl import flags
from absl import logging
import gin
from six.moves import range
import tensorflow as tf # pylint: disable=g-explicit-tensorflow-version-import
from tf_agents.agents.ddpg import critic_network
from tf_agents.agents.sac import sac_agent
from tf_agents.agents.sac import tanh_normal_projection_network
from tf_agents.drivers import dynamic_step_driver
#from tf_agents.environments import suite_mujoco
from tf_agents.environments import tf_py_environment
from tf_agents.environments import batched_py_environment
from tf_agents.eval import metric_utils
from tf_agents.metrics import tf_metrics
from tf_agents.networks import actor_distribution_network
from tf_agents.policies import greedy_policy
from tf_agents.policies import random_tf_policy
from tf_agents.replay_buffers import tf_uniform_replay_buffer
from tf_agents.utils import common
from tf_agents.train.utils import strategy_utils
flags.DEFINE_string('root_dir', os.getenv('TEST_UNDECLARED_OUTPUTS_DIR'),
'Root directory for writing logs/summaries/checkpoints.')
flags.DEFINE_multi_string('gin_file', None, 'Path to the trainer config files.')
flags.DEFINE_multi_string('gin_param', None, 'Gin binding to pass through.')
FLAGS = flags.FLAGS
gpus = tf.config.list_physical_devices('GPU')
if gpus:
try:
for gpu in gpus:
tf.config.experimental.set_memory_growth(gpu, True)
logical_gpus = tf.config.experimental.list_logical_devices('GPU')
print(len(gpus), "Physical GPUs,", len(logical_gpus), "Logical GPUs")
except RuntimeError as e:
print(e)
#gin.configurable
def train_eval(
root_dir,
env_name='SacEnv',
# The SAC paper reported:
# Hopper and Cartpole results up to 1000000 iters,
# Humanoid results up to 10000000 iters,
# Other mujoco tasks up to 3000000 iters.
num_iterations=3000000,
actor_fc_layers=(256, 256),
critic_obs_fc_layers=None,
critic_action_fc_layers=None,
critic_joint_fc_layers=(256, 256),
# Params for collect
# Follow https://github.com/haarnoja/sac/blob/master/examples/variants.py
# HalfCheetah and Ant take 10000 initial collection steps.
# Other mujoco tasks take 1000.
# Different choices roughly keep the initial episodes about the same.
#initial_collect_steps=10000,
initial_collect_steps=2000,
collect_steps_per_iteration=1,
replay_buffer_capacity=31250, # 1000000 / 32
# Params for target update
target_update_tau=0.005,
target_update_period=1,
# Params for train
train_steps_per_iteration=1,
#batch_size=256,
batch_size=32,
actor_learning_rate=3e-4,
critic_learning_rate=3e-4,
alpha_learning_rate=3e-4,
td_errors_loss_fn=tf.math.squared_difference,
gamma=0.99,
reward_scale_factor=0.1,
gradient_clipping=None,
use_tf_functions=True,
# Params for eval
num_eval_episodes=30,
eval_interval=10000,
# Params for summaries and logging
train_checkpoint_interval=50000,
policy_checkpoint_interval=50000,
rb_checkpoint_interval=50000,
log_interval=1000,
summary_interval=1000,
summaries_flush_secs=10,
debug_summaries=False,
summarize_grads_and_vars=False,
eval_metrics_callback=None):
"""A simple train and eval for SAC."""
root_dir = os.path.expanduser(root_dir)
train_dir = os.path.join(root_dir, 'train')
eval_dir = os.path.join(root_dir, 'eval')
train_summary_writer = tf.compat.v2.summary.create_file_writer(
train_dir, flush_millis=summaries_flush_secs * 1000)
train_summary_writer.set_as_default()
eval_summary_writer = tf.compat.v2.summary.create_file_writer(
eval_dir, flush_millis=summaries_flush_secs * 1000)
eval_metrics = [
tf_metrics.AverageReturnMetric(buffer_size=num_eval_episodes),
tf_metrics.AverageEpisodeLengthMetric(buffer_size=num_eval_episodes)
]
global_step = tf.compat.v1.train.get_or_create_global_step()
with tf.compat.v2.summary.record_if(
lambda: tf.math.equal(global_step % summary_interval, 0)):
py_envs = [SacEnv() for _ in range(0, batch_size)]
batched_env = batched_py_environment.BatchedPyEnvironment(envs=py_envs)
tf_env = tf_py_environment.TFPyEnvironment(batched_env)
eval_py_envs = [SacEnv() for _ in range(0, batch_size)]
eval_batched_env = batched_py_environment.BatchedPyEnvironment(envs=eval_py_envs)
eval_tf_env = tf_py_environment.TFPyEnvironment(eval_batched_env)
time_step_spec = tf_env.time_step_spec()
observation_spec = time_step_spec.observation
action_spec = tf_env.action_spec()
strategy = strategy_utils.get_strategy(tpu=False, use_gpu=True)
with strategy.scope():
actor_net = actor_distribution_network.ActorDistributionNetwork(
observation_spec,
action_spec,
fc_layer_params=actor_fc_layers,
continuous_projection_net=tanh_normal_projection_network
.TanhNormalProjectionNetwork)
critic_net = critic_network.CriticNetwork(
(observation_spec, action_spec),
observation_fc_layer_params=critic_obs_fc_layers,
action_fc_layer_params=critic_action_fc_layers,
joint_fc_layer_params=critic_joint_fc_layers,
kernel_initializer='glorot_uniform',
last_kernel_initializer='glorot_uniform')
tf_agent = sac_agent.SacAgent(
time_step_spec,
action_spec,
actor_network=actor_net,
critic_network=critic_net,
actor_optimizer=tf.compat.v1.train.AdamOptimizer(
learning_rate=actor_learning_rate),
critic_optimizer=tf.compat.v1.train.AdamOptimizer(
learning_rate=critic_learning_rate),
alpha_optimizer=tf.compat.v1.train.AdamOptimizer(
learning_rate=alpha_learning_rate),
target_update_tau=target_update_tau,
target_update_period=target_update_period,
td_errors_loss_fn=td_errors_loss_fn,
gamma=gamma,
reward_scale_factor=reward_scale_factor,
gradient_clipping=gradient_clipping,
debug_summaries=debug_summaries,
summarize_grads_and_vars=summarize_grads_and_vars,
train_step_counter=global_step)
tf_agent.initialize()
# Make the replay buffer.
replay_buffer = tf_uniform_replay_buffer.TFUniformReplayBuffer(
data_spec=tf_agent.collect_data_spec,
batch_size=batch_size,
max_length=replay_buffer_capacity,
device="/device:GPU:0")
replay_observer = [replay_buffer.add_batch]
train_metrics = [
tf_metrics.NumberOfEpisodes(),
tf_metrics.EnvironmentSteps(),
tf_metrics.AverageReturnMetric(
buffer_size=num_eval_episodes, batch_size=tf_env.batch_size),
tf_metrics.AverageEpisodeLengthMetric(
buffer_size=num_eval_episodes, batch_size=tf_env.batch_size),
]
eval_policy = greedy_policy.GreedyPolicy(tf_agent.policy)
initial_collect_policy = random_tf_policy.RandomTFPolicy(
tf_env.time_step_spec(), tf_env.action_spec())
collect_policy = tf_agent.collect_policy
train_checkpointer = common.Checkpointer(
ckpt_dir=train_dir,
agent=tf_agent,
global_step=global_step,
metrics=metric_utils.MetricsGroup(train_metrics, 'train_metrics'))
policy_checkpointer = common.Checkpointer(
ckpt_dir=os.path.join(train_dir, 'policy'),
policy=eval_policy,
global_step=global_step)
rb_checkpointer = common.Checkpointer(
ckpt_dir=os.path.join(train_dir, 'replay_buffer'),
max_to_keep=1,
replay_buffer=replay_buffer)
train_checkpointer.initialize_or_restore()
rb_checkpointer.initialize_or_restore()
initial_collect_driver = dynamic_step_driver.DynamicStepDriver(
tf_env,
initial_collect_policy,
observers=replay_observer + train_metrics,
num_steps=initial_collect_steps)
collect_driver = dynamic_step_driver.DynamicStepDriver(
tf_env,
collect_policy,
observers=replay_observer + train_metrics,
num_steps=collect_steps_per_iteration)
if use_tf_functions:
initial_collect_driver.run = common.function(initial_collect_driver.run)
collect_driver.run = common.function(collect_driver.run)
tf_agent.train = common.function(tf_agent.train)
if replay_buffer.num_frames() == 0:
# Collect initial replay data.
logging.info(
'Initializing replay buffer by collecting experience for %d steps '
'with a random policy.', initial_collect_steps)
initial_collect_driver.run()
results = metric_utils.eager_compute(
eval_metrics,
eval_tf_env,
eval_policy,
num_episodes=num_eval_episodes,
train_step=global_step,
summary_writer=eval_summary_writer,
summary_prefix='Metrics',
)
if eval_metrics_callback is not None:
eval_metrics_callback(results, global_step.numpy())
metric_utils.log_metrics(eval_metrics)
time_step = None
policy_state = collect_policy.get_initial_state(tf_env.batch_size)
timed_at_step = global_step.numpy()
time_acc = 0
# Prepare replay buffer as dataset with invalid transitions filtered.
def _filter_invalid_transition(trajectories, unused_arg1):
return ~trajectories.is_boundary()[0]
dataset = replay_buffer.as_dataset(
sample_batch_size=batch_size,
num_steps=2).unbatch().filter(
_filter_invalid_transition).batch(batch_size).prefetch(5)
# Dataset generates trajectories with shape [Bx2x...]
iterator = iter(dataset)
def train_step():
experience, _ = next(iterator)
return tf_agent.train(experience)
if use_tf_functions:
train_step = common.function(train_step)
global_step_val = global_step.numpy()
while global_step_val < num_iterations:
start_time = time.time()
time_step, policy_state = collect_driver.run(
time_step=time_step,
policy_state=policy_state,
)
for _ in range(train_steps_per_iteration):
train_loss = train_step()
time_acc += time.time() - start_time
global_step_val = global_step.numpy()
if global_step_val % log_interval == 0:
logging.info('step = %d, loss = %f', global_step_val,
train_loss.loss)
steps_per_sec = (global_step_val - timed_at_step) / time_acc
logging.info('%.3f steps/sec', steps_per_sec)
tf.compat.v2.summary.scalar(
name='global_steps_per_sec', data=steps_per_sec, step=global_step)
timed_at_step = global_step_val
time_acc = 0
for train_metric in train_metrics:
train_metric.tf_summaries(
train_step=global_step, step_metrics=train_metrics[:2])
if global_step_val % eval_interval == 0:
results = metric_utils.eager_compute(
eval_metrics,
eval_tf_env,
eval_policy,
num_episodes=num_eval_episodes,
train_step=global_step,
summary_writer=eval_summary_writer,
summary_prefix='Metrics',
)
if eval_metrics_callback is not None:
eval_metrics_callback(results, global_step_val)
metric_utils.log_metrics(eval_metrics)
if global_step_val % train_checkpoint_interval == 0:
train_checkpointer.save(global_step=global_step_val)
if global_step_val % policy_checkpoint_interval == 0:
policy_checkpointer.save(global_step=global_step_val)
if global_step_val % rb_checkpoint_interval == 0:
rb_checkpointer.save(global_step=global_step_val)
return train_loss
def main(_):
tf.compat.v1.enable_v2_behavior()
logging.set_verbosity(logging.INFO)
gin.parse_config_files_and_bindings(FLAGS.gin_file, FLAGS.gin_param)
train_eval(FLAGS.root_dir)
if __name__ == '__main__':
flags.mark_flag_as_required('root_dir')
app.run(main)
What is the appropriate way to create a batched environment for a custom, non-batched environment? I can share my custom environment, but I don't believe the issue lies there as the code works fine when using batch sizes of 1.
Also, any tips on increasing GPU utilization in reinforcement learning scenarios would be greatly appreciated. I have examined examples of using tensorboard-profiler to profile GPU utilization, but it seems these require callbacks and a fit function, which doesn't seem to be applicable in RL use-cases.

It turns out I neglected to pass batch_size when initializing the AverageReturnMetric and AverageEpisodeLengthMetric instances.

Related

Incremental PCA on big dataset, with large component demand

I am trying to find the main 200 components of a datasets of 846 images (2048x2048x3 RGB) with sklearn.decomposition.IncrementalPCA.
Data are read by cv2 and reshaped into a 2d np array ([846,2048x2048x3] size, float16)
To ensure a smaller memory cost, I used partial_fit() and divide the original data into smaller chunks (batches) in both partial_fit() and transform() steps.
just like the way in this problem's solution:
Python PCA on Matrix too large to fit into memory
Now my code works well for relative smaller size computations, like computing 20 components for 200 images in the datasets. It outputs right outcomes.
However, the tasks demands me to compute 200 components, which leads to the limit that my batch's size should be larger or at least equal to 200. (according to sklearn's document and the information in the terminal when running the code)
https://scikit-learn.org/stable/modules/generated/sklearn.decomposition.IncrementalPCA.html
With such big chunk size,I can finish the IPCA model set, but always face MemoryError when doing partial_fit()
What's more, another problem is:
I need to use inverse_transform later, I am not sure if I can use chunk-style compute in this step or not. (In the code below I did not use it.)
What can I do to avoid this MemoryError? Or should I replace IncrementalPCA with some other method instead ? (these alternatives should have some method like inverse_transform())
The all memory I can access to is 131661572 kB(~127GB)
My code:
from sklearn.decomposition import PCA, IncrementalPCA
import numpy as np
import cv2
import os
folder_path = "./output_img"
input=[]
for i in range(1, 847):
if i%10 == 0: print("loading",i,"th image")
# if i == 60: continue #special case, should be skipped
image_path = folder_path+f"/{i}neutral.jpg"
img = cv2.imread(image_path)
input.append(img.reshape(-1))
print("Loaded all",i,"images")
# change into numpy matrix
all_image = np.stack(input,axis=0)
# trans to 0-1 format float64
all_image = (all_image.astype(np.float16))
### shape: #_of_imag x image_pixel_num (50331648 for img_normals case)
# print(all_image)
# print(all_image.shape)
# PCA, keeps 200 features
COM_NUM=200
pca=IncrementalPCA(n_components = COM_NUM)
print("finished IPCA model set")
saving_path = "./principle847"
element_num = all_image.shape[0] # how many elements(rows) we have in the dataset
chunk_size = 220 # how many elements we feed to IPCA at a time
for i in range(0, element_num//chunk_size):
pca.partial_fit(all_image[i*chunk_size : (i+1)*chunk_size])
print("finished PCA fit:",i*chunk_size,"to",(i+1)*chunk_size)
pca.partial_fit(all_image[(i+1)*chunk_size : element_num]) #tail
print("finished PCA fit:",(i+1)*chunk_size,"to",element_num)
for i in range(0, element_num//chunk_size):
if i==0:
result = pca.transform(all_image[i*chunk_size : (i+1)*chunk_size])
else:
tmp = pca.transform(all_image[i*chunk_size : (i+1)*chunk_size])
result = np.concatenate((result, tmp), axis=0)
print("finished PCA transform:",i*chunk_size,"to",(i+1)*chunk_size)
tmp = pca.transform(all_image[(i+1)*chunk_size : element_num]) #tail
result = np.concatenate((result, tmp), axis=0)
print("finished PCA transform:",(i+1)*chunk_size,"to",element_num)
result = pca.inverse_transform(result)
print("PCA mean:",pca.mean_)
mean_img = pca.mean_
mean_img = mean_img.reshape(2048,2048,3)
mean_img = mean_img.astype(np.uint8)
cv2.imwrite(os.path.join(saving_path,("mean.png")),mean_img)
result=result.reshape(-1,2048,2048,3)
# result shape: #_of_componets * 2048 * 2048 * 3
dst = result
# dst=result/np.linalg.norm(result,axis=(3),keepdims=True)
for j in range(0,COM_NUM):
reconImage = (dst)[j]
# reconImage = reconImage.reshape(4096,4096,3)
reconImage = np.clip(reconImage,0,255)
reconImage = reconImage.astype(np.uint8)
cv2.imwrite(os.path.join(saving_path,("p"+str(j)+".png")),reconImage)
print("Saved",j+1,"principle imgs")
The error goes like:
File "model_generate.py", line 36, in <module>
pca.partial_fit(all_image[i*chunk_size : (i+1)*chunk_size])
File "/root/anaconda3/envs/PCA/lib/python3.8/site-packages/sklearn/decomposition/_incremental_pca.py", line 299, in partial_fit
U, V = svd_flip(U, V, u_based_decision=False)
File "/root/anaconda3/envs/PCA/lib/python3.8/site-packages/sklearn/utils/extmath.py", line 538, in svd_flip
max_abs_rows = np.argmax(np.abs(v), axis=1)
File "/root/anaconda3/envs/PCA/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 1103, in argmax
return _wrapfunc(a, 'argmax', axis=axis, out=out)
File "/root/anaconda3/envs/PCA/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 56, in _wrapfunc
return getattr(obj, method)(*args, **kwds)
MemoryError

TPUEstimator error -- AttributeError: module 'tensorflow.contrib.tpu.python.ops.tpu_ops' has no attribute 'cross_replica_sum'

I have written a tensorflow code using the TPUEstimator, but I am having problems running it in use_tpu=False mode. I would like to run it on my local computer to make sure that all the operations are TPU-compatible. The code works fine with the normal Estimator. Here is my master code:
import logging
from tensorflow.contrib.tpu.python.tpu import tpu_config, tpu_estimator, tpu_optimizer
from tensorflow.contrib.cluster_resolver import TPUClusterResolver
from capser_7_model_fn import *
from capser_7_input_fn import *
import subprocess
from absl import flags
flags.DEFINE_bool(
'use_tpu', False,
'Use TPUs rather than plain CPUs')
tf.flags.DEFINE_string(
"tpu", default='$TPU_NAME',
help="The Cloud TPU to use for training. This should be either the name "
"used when creating the Cloud TPU, or a grpc://ip.address.of.tpu:8470 "
"url.")
tf.flags.DEFINE_string("model_dir", LOGDIR, "Estimator model_dir")
flags.DEFINE_integer(
'save_checkpoints_secs', 1000,
'Interval (in seconds) at which the model data '
'should be checkpointed. Set to 0 to disable.')
flags.DEFINE_integer(
'save_summary_steps', 100,
'Number of steps which must have run before showing summaries.')
tf.flags.DEFINE_integer("iterations", 1000,
"Number of iterations per TPU training loop.")
tf.flags.DEFINE_integer("num_shards", 8, "Number of shards (TPU chips).")
tf.flags.DEFINE_integer("batch_size", 1024,
"Mini-batch size for the training. Note that this "
"is the global batch size and not the per-shard batch.")
FLAGS = tf.flags.FLAGS
if FLAGS.use_tpu:
my_project_name = subprocess.check_output(['gcloud', 'config', 'get-value', 'project'])
my_zone = subprocess.check_output(['gcloud', 'config', 'get-value', 'compute/zone'])
cluster_resolver = TPUClusterResolver(
tpu=[FLAGS.tpu],
zone=my_zone,
project=my_project_name)
master = TPUClusterResolver(tpu=[os.environ['TPU_NAME']]).get_master()
else:
master = ''
my_tpu_run_config = tpu_config.RunConfig(
master=master,
model_dir=FLAGS.model_dir,
save_checkpoints_secs=FLAGS.save_checkpoints_secs,
save_summary_steps=FLAGS.save_summary_steps,
session_config=tf.ConfigProto(allow_soft_placement=True, log_device_placement=True),
tpu_config=tpu_config.TPUConfig(iterations_per_loop=FLAGS.iterations, num_shards=FLAGS.num_shards),
)
# create estimator for model (the model is described in capser_7_model_fn)
capser = tpu_estimator.TPUEstimator(model_fn=model_fn_tpu,
config=my_tpu_run_config,
use_tpu=FLAGS.use_tpu,
train_batch_size=batch_size,
params={'model_batch_size': batch_size_per_shard})
# train model
logging.getLogger().setLevel(logging.INFO) # to show info about training progress
capser.train(input_fn=train_input_fn_tpu, steps=n_steps)
I have a capsule network defined in model_fn_tpu, which returns the TPUEstimator spec. The optimizer is a standard AdamOptimizer. I have made all the changes explained here https://www.tensorflow.org/guide/using_tpu#optimizer to make my code compatible with TPUEstimator. I get the following error:
Traceback (most recent call last):
File "C:/Users/doerig/PycharmProjects/capser/TPU_playground.py", line 85, in <module>
capser.train(input_fn=train_input_fn_tpu, steps=n_steps)
File "C:\Users\doerig\AppData\Local\Continuum\Anaconda2\envs\tensorflow\lib\site-packages\tensorflow\python\estimator\estimator.py", line 363, in train
loss = self._train_model(input_fn, hooks, saving_listeners)
File "C:\Users\doerig\AppData\Local\Continuum\Anaconda2\envs\tensorflow\lib\site-packages\tensorflow\python\estimator\estimator.py", line 843, in _train_model
return self._train_model_default(input_fn, hooks, saving_listeners)
File "C:\Users\doerig\AppData\Local\Continuum\Anaconda2\envs\tensorflow\lib\site-packages\tensorflow\python\estimator\estimator.py", line 856, in _train_model_default
features, labels, model_fn_lib.ModeKeys.TRAIN, self.config)
File "C:\Users\doerig\AppData\Local\Continuum\Anaconda2\envs\tensorflow\lib\site-packages\tensorflow\python\estimator\estimator.py", line 831, in _call_model_fn
model_fn_results = self._model_fn(features=features, **kwargs)
File "C:\Users\doerig\AppData\Local\Continuum\Anaconda2\envs\tensorflow\lib\site-packages\tensorflow\contrib\tpu\python\tpu\tpu_estimator.py", line 2016, in _model_fn
features, labels, is_export_mode=is_export_mode)
File "C:\Users\doerig\AppData\Local\Continuum\Anaconda2\envs\tensorflow\lib\site-packages\tensorflow\contrib\tpu\python\tpu\tpu_estimator.py", line 1121, in call_without_tpu
return self._call_model_fn(features, labels, is_export_mode=is_export_mode)
File "C:\Users\doerig\AppData\Local\Continuum\Anaconda2\envs\tensorflow\lib\site-packages\tensorflow\contrib\tpu\python\tpu\tpu_estimator.py", line 1317, in _call_model_fn
estimator_spec = self._model_fn(features=features, **kwargs)
File "C:\Users\doerig\PycharmProjects\capser\capser_7_model_fn.py", line 101, in model_fn_tpu
**output_decoder_deconv_params)
File "C:\Users\doerig\PycharmProjects\capser\capser_model.py", line 341, in capser_model
loss_training_op = optimizer.minimize(loss=loss, global_step=tf.train.get_global_step(), name="training_op")
File "C:\Users\doerig\AppData\Local\Continuum\Anaconda2\envs\tensorflow\lib\site-packages\tensorflow\python\training\optimizer.py", line 424, in minimize
name=name)
File "C:\Users\doerig\AppData\Local\Continuum\Anaconda2\envs\tensorflow\lib\site-packages\tensorflow\contrib\tpu\python\tpu\tpu_optimizer.py", line 113, in apply_gradients
summed_grads_and_vars.append((tpu_ops.cross_replica_sum(grad), var))
AttributeError: module 'tensorflow.contrib.tpu.python.ops.tpu_ops' has no attribute 'cross_replica_sum'
Any ideas to solve this problem? Thank you in advance!
I suspect this is either a bug in the version of TensorFlow you are using + Windows, or else an issue with your build of TensorFlow.
For example, when I chase down the file tensorflow\contrib\tpu\python\tpu\tpu_optimizer.py in the TF 1.4 branch, I see that tpu_ops is imported as:
from tensorflow.contrib.tpu.python.ops import tpu_ops
and if you chase that to the relevant file, you see:
if platform.system() != "Windows":
# pylint: disable=wildcard-import,unused-import,g-import-not-at-top
from tensorflow.contrib.tpu.ops.gen_tpu_ops import *
from tensorflow.contrib.util import loader
from tensorflow.python.platform import resource_loader
# pylint: enable=wildcard-import,unused-import,g-import-not-at-top
_tpu_ops = loader.load_op_library(
resource_loader.get_path_to_datafile("_tpu_ops.so"))
else:
# We have already built the appropriate libraries into the binary via CMake
# if we have built contrib, so we don't need this
pass
Following up with the other TF branches that existed at the time of this posting, we see similar comments in 1.5, in 1.6, in 1.7, in 1.8, and in 1.9.
I strongly suspect this would not occur under Linux, but I might test this later and edit this answer.

How to use tf.train.Saver in SessionRunHook?

I have trained many sub-models, each sub-models is a part of the last model. And then I want to use those pretrained sub models to initial the last model's parameters. I try to use SessionRunHook to load other ckpt file's model parameters to initial the last model's.
I tried the follow code but failed. Hope some advices. Thanks!
The error info is:
Traceback (most recent call last):
File "train_high_api_local.py", line 282, in <module>
tf.app.run()
File "/Users/zhouliaoming/anaconda3/envs/tensorflow/lib/python3.6/site-packages/tensorflow/python/platform/app.py", line 124, in run
_sys.exit(main(argv))
File "train_high_api_local.py", line 266, in main
clf_.train(input_fn=lambda: read_file([tables[0]], epochs_per_eval), steps=None, hooks=[hook_test]) # input yield: x, y
File "/Users/zhouliaoming/anaconda3/envs/tensorflow/lib/python3.6/site-packages/tensorflow/python/estimator/estimator.py", line 314, in train
.......
File "/Users/zhouliaoming/anaconda3/envs/tensorflow/lib/python3.6/site-packages/tensorflow/python/training/monitored_session.py", line 674, in create_session
hook.after_create_session(self.tf_sess, self.coord)
File "train_high_api_local.py", line 102, in after_create_session
saver = tf.train.Saver([ti]) # TODO: ERROR INFO: Graph is finalized and cannot be modified.
.......
File "/Users/zhouliaoming/anaconda3/envs/tensorflow/lib/python3.6/site-packages/tensorflow/python/framework/ops.py", line 3135, in create_op
self._check_not_finalized()
File "/Users/zhouliaoming/anaconda3/envs/tensorflow/lib/python3.6/site-packages/tensorflow/python/framework/ops.py", line 2788, in _check_not_finalized
raise RuntimeError("Graph is finalized and cannot be modified.")
RuntimeError: Graph is finalized and cannot be modified.
and the code detail is:
class SetTensor(session_run_hook.SessionRunHook):
""" like tf.train.LoggingTensorHook """
def after_create_session(self, session, coord):
""" Called when new TensorFlow session is created: graph is finalized and ops can no longer be added. """
graph = tf.get_default_graph()
ti = graph.get_tensor_by_name("h_1_15/bias:0")
with session.as_default():
with tf.name_scope("rewrite"):
saver = tf.train.Saver([ti]) # TODO: ERROR INFO: Graph is finalized and cannot be modified.
saver.restore(session, "/Users/zhouliaoming/data/credit_dnn/model_retrain/rm_gene_v2_sall/model.ckpt-2102")
pass
def main(unused_argv):
""" train """
norm_all_func = lambda x: tf.cond(x>1, lambda: tf.log(x), lambda: tf.identity(x))
feature_columns=[[tf.feature_column.numeric_column(COLUMNS[i], shape=fi, normalizer_fn=lambda x: tf.py_func(weight_norm2, [x], tf.float32) )] for i, fi in enumerate(FEA_DIM)] # normlized: running OK!
## use self-defined model
param = {"learning_rate": 0.0001, "feature_columns": feature_columns, "isanalysis": FLAGS.isanalysis, "isall": False}
clf_ = tf.estimator.Estimator(model_fn=model_fn_wide2deep, params=param, model_dir=ckpt_dir)
hook_test = SetTensor(["h_1_15/bias", "h_1_15/kernel"])
epochs_per_eval = 1
for n in range(int(FLAGS.num_epochs/epochs_per_eval)):
# train num_epochs
clf_.train(input_fn=lambda: read_file([tables[0]], epochs_per_eval), steps=None, hooks=[hook_test]) # input yield: x, y
SessionRunHook is not meant for this use case. As the error says, you cannot change the graph once sess.run() has been invoked.
You can assign variables using saver.restore() in your "normal code". You don't have to be inside any hooks.
Also, if you want to restore many variables and can match them to their names and shapes in a checkpoint, you might want to take a look at https://gist.github.com/iganichev/d2d8a0b1abc6b15d4a07de83171163d4. It shows some example code to restore a subset of variables.
You can do this:
class SaveAtEnd(tf.train.SessionRunHook):
def begin(self):
self._saver = # create your saver
def end(self, session):
self._saver.save(session, ...)

Tensorflow serving error when connecting with client "input size does not match signature"

I have gone about exporting the textsum model using the export_textsum.py file shown below and when I connect using the textsumclient.py file below I receive the error:
Traceback (most recent call last): File "textsum_client.py", line
90, in
tf.app.run() File "/usr/local/lib/python2.7/site-packages/tensorflow/python/platform/app.py",
line 48, in run
_sys.exit(main(_sys.argv[:1] + flags_passthrough)) File "textsum_client.py", line 83, in main
FLAGS.concurrency, FLAGS.num_tests) File "textsum_client.py", line 72, in do_singleDecode
result = stub.Predict(request, 5.0) # 5 seconds File "/usr/local/lib/python2.7/site-packages/grpc/beta/_client_adaptations.py",
line 324, in call
self._request_serializer, self._response_deserializer) File "/usr/local/lib/python2.7/site-packages/grpc/beta/_client_adaptations.py",
line 210, in _blocking_unary_unary
raise _abortion_error(rpc_error_call) grpc.framework.interfaces.face.face.AbortionError:
AbortionError(code=StatusCode.INVALID_ARGUMENT, details="input size
does not match signature")
I believe that it may have something to do with the building of tf_example in my export_textsum file but I honestly have not had luck figuring this out as of yet. Anyone with a bit more experience know what I am doing wrong here? If there are any ideas to help me narrow down exactly what is going on here I am open to any advice. Thanks.
textsumclient.py
from __future__ import print_function
import sys
import threading
# This is a placeholder for a Google-internal import.
from grpc.beta import implementations
import numpy
import tensorflow as tf
from datetime import datetime
from tensorflow_serving.apis import predict_pb2
from tensorflow_serving.apis import prediction_service_pb2
#from tensorflow_serving.example import mnist_input_data
tf.app.flags.DEFINE_integer('concurrency', 1,
'maximum number of concurrent inference requests')
tf.app.flags.DEFINE_integer('num_tests', 10, 'Number of test images')
tf.app.flags.DEFINE_string('server', '172.17.0.2:9000', 'PredictionService host:port')
tf.app.flags.DEFINE_string('work_dir', '/tmp', 'Working directory. ')
FLAGS = tf.app.flags.FLAGS
def do_singleDecode(hostport, work_dir, concurrency, num_tests):
#Connect to server
host, port = hostport.split(':')
channel = implementations.insecure_channel(host, int(port))
stub = prediction_service_pb2.beta_create_PredictionService_stub(channel)
#Prepare our request object
request = predict_pb2.PredictRequest()
request.model_spec.name = 'textsum_model'
request.model_spec.signature_name = 'predict'
#Make some test data
test_data_set = ['This is a test','This is a sample']
#Lets test her out
now = datetime.now()
article, abstract = test_data_set
#***** POPULATE REQUEST INPUTS *****
request.inputs['article'].CopyFrom(
tf.contrib.util.make_tensor_proto(test_data_set[0], shape=[len(test_data_set[0])]))
request.inputs['abstract'].CopyFrom(
tf.contrib.util.make_tensor_proto(test_data_set[1], shape=[len(test_data_set[1])]))
result = stub.Predict(request, 5.0) # 5 seconds
waiting = datetime.now() - now
return result, waiting.microseconds
def main(_):
if not FLAGS.server:
print('please specify server host:port')
return
result, waiting = do_singleDecode(FLAGS.server, FLAGS.work_dir,
FLAGS.concurrency, FLAGS.num_tests)
print('\nTextsum result: %s%%' % result)
print('Waiting time is: ', waiting, 'microseconds.')
if __name__ == '__main__':
tf.app.run()
export_textsum.py
decode_mdl_hps = hps
# Only need to restore the 1st step and reuse it since
# we keep and feed in state for each step's output.
decode_mdl_hps = hps._replace(dec_timesteps=1)
model = seq2seq_attention_model.Seq2SeqAttentionModel(
decode_mdl_hps, vocab, num_gpus=FLAGS.num_gpus)
decoder = seq2seq_attention_decode.BSDecoder(model, batcher, hps, vocab)
serialized_output = tf.placeholder(tf.string, name='tf_output')
serialized_tf_example = tf.placeholder(tf.string, name='tf_example')
feature_configs = {
'article': tf.FixedLenFeature(shape=[1], dtype=tf.string),
'abstract': tf.FixedLenFeature(shape=[1], dtype=tf.string),
}
tf_example = tf.parse_example(serialized_tf_example, feature_configs)
saver = tf.train.Saver()
config = tf.ConfigProto(allow_soft_placement = True)
with tf.Session(config = config) as sess:
# Restore variables from training checkpoints.
ckpt = tf.train.get_checkpoint_state(FLAGS.checkpoint_dir)
if ckpt and ckpt.model_checkpoint_path:
saver.restore(sess, ckpt.model_checkpoint_path)
global_step = ckpt.model_checkpoint_path.split('/')[-1].split('-')[-1]
print('Successfully loaded model from %s at step=%s.' %
(ckpt.model_checkpoint_path, global_step))
else:
print('No checkpoint file found at %s' % FLAGS.checkpoint_dir)
return
# ************** EXPORT MODEL ***************
export_path = os.path.join(FLAGS.export_dir,str(FLAGS.export_version))
print('Exporting trained model to %s' % export_path)
#-------------------------------------------
tensor_info_inputs = tf.saved_model.utils.build_tensor_info(serialized_tf_example)
tensor_info_outputs = tf.saved_model.utils.build_tensor_info(serialized_output)
prediction_signature = (
tf.saved_model.signature_def_utils.build_signature_def(
inputs={ tf.saved_model.signature_constants.PREDICT_INPUTS: tensor_info_inputs},
outputs={tf.saved_model.signature_constants.PREDICT_OUTPUTS:tensor_info_outputs},
method_name=tf.saved_model.signature_constants.PREDICT_METHOD_NAME
))
#----------------------------------
legacy_init_op = tf.group(tf.tables_initializer(), name='legacy_init_op')
builder = saved_model_builder.SavedModelBuilder(export_path)
builder.add_meta_graph_and_variables(
sess=sess,
tags=[tf.saved_model.tag_constants.SERVING],
signature_def_map={
'predict':prediction_signature,
},
legacy_init_op=legacy_init_op)
builder.save()
print('Successfully exported model to %s' % export_path)
except:
traceback.print_exc()
pass
def main(_):
Export()
if __name__ == "__main__":
tf.app.run()
It looks like you should specify a shape of [1] both in your client and graph definition.
export_textsum.py
feature_configs = {
'article': tf.FixedLenFeature(shape=[1], dtype=tf.string),
'abstract': tf.FixedLenFeature(shape=[1], dtype=tf.string),
}
textsumclient.py
request.inputs['article'].CopyFrom(
tf.contrib.util.make_tensor_proto([test_data_set[0]], shape=[1]))
request.inputs['abstract'].CopyFrom(
tf.contrib.util.make_tensor_proto([test_data_set[1]], shape=[1]))
Or perhaps using shape=[len(test_data_set[0])] would be more appropriate
QuantumLicht I again just want to thank you for your assistance here as it was one part of my issue. It seemed to have something to do with the keys used in the feature config. I am still using TF 1.2 and I remember reading sometime back that there were some fixes performed for proper key names being able to be used now in newer versions. That said, as I debugged I noticed that it was expecting a single input named "inputs". So I removed "abstract" and set article to inputs. I then had to modify the output of decode and the final issue was related to the fact that I was only loading the model but never running the function against the model to get back the output that I needed to then send into tensor_info_outputs.

Is there a way to get tensorflow tf.Print output to appear in Jupyter Notebook output

I'm using the tf.Print op in a Jupyter notebook. It works as required, but will only print the output to the console, without printing in the notebook. Is there any way to get around this?
An example would be the following (in a notebook):
import tensorflow as tf
a = tf.constant(1.0)
a = tf.Print(a, [a], 'hi')
sess = tf.Session()
a.eval(session=sess)
That code will print 'hi[1]' in the console, but nothing in the notebook.
Update Feb 3, 2017
I've wrapped this into memory_util package. Example usage
# install memory util
import urllib.request
response = urllib.request.urlopen("https://raw.githubusercontent.com/yaroslavvb/memory_util/master/memory_util.py")
open("memory_util.py", "wb").write(response.read())
import memory_util
sess = tf.Session()
a = tf.random_uniform((1000,))
b = tf.random_uniform((1000,))
c = a + b
with memory_util.capture_stderr() as stderr:
sess.run(c.op)
print(stderr.getvalue())
** Old stuff**
You could reuse FD redirector from IPython core. (idea from Mark Sandler)
import os
import sys
STDOUT = 1
STDERR = 2
class FDRedirector(object):
""" Class to redirect output (stdout or stderr) at the OS level using
file descriptors.
"""
def __init__(self, fd=STDOUT):
""" fd is the file descriptor of the outpout you want to capture.
It can be STDOUT or STERR.
"""
self.fd = fd
self.started = False
self.piper = None
self.pipew = None
def start(self):
""" Setup the redirection.
"""
if not self.started:
self.oldhandle = os.dup(self.fd)
self.piper, self.pipew = os.pipe()
os.dup2(self.pipew, self.fd)
os.close(self.pipew)
self.started = True
def flush(self):
""" Flush the captured output, similar to the flush method of any
stream.
"""
if self.fd == STDOUT:
sys.stdout.flush()
elif self.fd == STDERR:
sys.stderr.flush()
def stop(self):
""" Unset the redirection and return the captured output.
"""
if self.started:
self.flush()
os.dup2(self.oldhandle, self.fd)
os.close(self.oldhandle)
f = os.fdopen(self.piper, 'r')
output = f.read()
f.close()
self.started = False
return output
else:
return ''
def getvalue(self):
""" Return the output captured since the last getvalue, or the
start of the redirection.
"""
output = self.stop()
self.start()
return output
import tensorflow as tf
x = tf.constant([1,2,3])
a=tf.Print(x, [x])
redirect=FDRedirector(STDERR)
sess = tf.InteractiveSession()
redirect.start();
a.eval();
print "Result"
print redirect.stop()
I ran into the same problem and got around it by using a function like this in my notebooks:
def tf_print(tensor, transform=None):
# Insert a custom python operation into the graph that does nothing but print a tensors value
def print_tensor(x):
# x is typically a numpy array here so you could do anything you want with it,
# but adding a transformation of some kind usually makes the output more digestible
print(x if transform is None else transform(x))
return x
log_op = tf.py_func(print_tensor, [tensor], [tensor.dtype])[0]
with tf.control_dependencies([log_op]):
res = tf.identity(tensor)
# Return the given tensor
return res
# Now define a tensor and use the tf_print function much like the tf.identity function
tensor = tf_print(tf.random_normal([100, 100]), transform=lambda x: [np.min(x), np.max(x)])
# This will print the transformed version of the tensors actual value
# (which was summarized to just the min and max for brevity)
sess = tf.InteractiveSession()
sess.run([tensor])
sess.close()
FYI, using a logger instead of calling "print" in my custom function worked wonders for me as the stdout is often buffered by jupyter and not shown before "Loss is Nan" kind of errors -- which was the whole point in using that function in the first place in my case.
You can check the terminal where you launched the jupyter notebook to see the message.
import tensorflow as tf
tf.InteractiveSession()
a = tf.constant(1)
b = tf.constant(2)
opt = a + b
opt = tf.Print(opt, [opt], message="1 + 2 = ")
opt.eval()
In the terminal, I can see:
2018-01-02 23:38:07.691808: I tensorflow/core/kernels/logging_ops.cc:79] 1 + 2 = [3]
A simple way, tried it in regular python, but not jupyter yet.
os.dup2(sys.stdout.fileno(), 1)
os.dup2(sys.stdout.fileno(), 2)
Explanation is here: In python, how to capture the stdout from a c++ shared library to a variable
The issue that I faced was that one can't run a session inside a Tensorflow Graph, like in the training or in the evaluation.
That's why the options to use sess.run(opt) or opt.eval() were not a solution for me.
The best thing was to use tf.Print() and redirect the logging to an external file.
I did this using a temporal file, which I transferred to a regular file like this:
STDERR=2
import os
import sys
import tempfile
class captured:
def __init__(self, fd=STDERR):
self.fd = fd
self.prevfd = None
def __enter__(self):
t = tempfile.NamedTemporaryFile()
self.prevfd = os.dup(self.fd)
os.dup2(t.fileno(), self.fd)
return t
def __exit__(self, exc_type, exc_value, traceback):
os.dup2(self.prevfd, self.fd)
with captured(fd=STDERR) as tmp:
...
classifier.evaluate(input_fn=input_fn, steps=100)
with open('log.txt', 'w') as f:
print(open(tmp.name).read(), file=f)
And then in my evaluation I do:
a = tf.constant(1)
a = tf.Print(a, [a], message="a: ")