peacock-data-public-datasets-idc-mint
/
docker
/bloom13b
/Model-References
/TensorFlow
/nlp
/bert
/run_squad.py
# coding=utf-8 | |
# Copyright 2018 The Google AI Language Team 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 | |
# | |
# http://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. | |
############################################################################### | |
# Copyright (C) 2020-2022 Habana Labs, Ltd. an Intel Company | |
# | |
# Changes: | |
# - Added stdout/stderr flush in main | |
# - Added default values for environment variables: | |
# - HABANA_INITIAL_WORKSPACE_SIZE_MB | |
# - TF_DISABLE_MKL | |
# - TF_BF16_CONVERSION | |
# - TF_PRELIMINARY_CLUSTER_SIZE | |
# - TF_DISABLE_SCOPED_ALLOCATOR | |
# - Added command-line flags: | |
# - num_train_steps | |
# - deterministic_run | |
# - deterministic_seed | |
# - Added prefetch of dataset | |
# - Added support for HPU profiling (command-line flag - `profile`). | |
# - Added line tf.get_logger().propagate = False | |
############################################################################### | |
"""Run BERT on SQuAD 1.1 and SQuAD 2.0.""" | |
from __future__ import division | |
from __future__ import print_function | |
from __future__ import absolute_import | |
import json | |
import os | |
import sys | |
import socket | |
curr_path = os.path.abspath(os.path.dirname(__file__)) | |
sys.path.append(os.path.join(curr_path, '..')) | |
import tensorflow as tf | |
import six | |
import TensorFlow.nlp.bert.utils.habana_hooks as habana_hooks | |
import TensorFlow.nlp.bert.data_preprocessing.tokenization as tokenization | |
import TensorFlow.nlp.bert.optimization as optimization | |
import TensorFlow.nlp.bert.modeling as modeling | |
import numpy as np | |
import random | |
import math | |
import json | |
import collections | |
from TensorFlow.common.tb_utils import write_hparams_v1, TBSummary, TensorBoardHook | |
from TensorFlow.common.debug import dump_callback | |
from habana_frameworks.tensorflow import load_habana_module | |
try: | |
import horovod.tensorflow as hvd | |
except ImportError: | |
hvd = None | |
def horovod_enabled(): | |
return hvd is not None and hvd.is_initialized() | |
tf.get_logger().propagate = False | |
flags = tf.compat.v1.flags | |
FLAGS = flags.FLAGS | |
def init_squad_flags(): | |
# Required parameters | |
flags.DEFINE_string( | |
"bert_config_file", None, | |
"The config json file corresponding to the pre-trained BERT model. " | |
"This specifies the model architecture.") | |
flags.DEFINE_string("vocab_file", None, | |
"The vocabulary file that the BERT model was trained on.") | |
flags.DEFINE_string( | |
"output_dir", None, | |
"The output directory where the model checkpoints will be written.") | |
# Other parameters | |
flags.DEFINE_string("train_file", None, | |
"SQuAD json for training. E.g., train-v1.1.json") | |
flags.DEFINE_string( | |
"predict_file", None, | |
"SQuAD json for predictions. E.g., dev-v1.1.json or test-v1.1.json") | |
flags.DEFINE_string( | |
"init_checkpoint", None, | |
"Initial checkpoint (usually from a pre-trained BERT model).") | |
flags.DEFINE_bool( | |
"do_lower_case", True, | |
"Whether to lower case the input text. Should be True for uncased " | |
"models and False for cased models.") | |
flags.DEFINE_integer( | |
"max_seq_length", 384, | |
"The maximum total input sequence length after WordPiece tokenization. " | |
"Sequences longer than this will be truncated, and sequences shorter " | |
"than this will be padded.") | |
flags.DEFINE_integer( | |
"doc_stride", 128, | |
"When splitting up a long document into chunks, how much stride to " | |
"take between chunks.") | |
flags.DEFINE_integer( | |
"max_query_length", 64, | |
"The maximum number of tokens for the question. Questions longer than " | |
"this will be truncated to this length.") | |
flags.DEFINE_bool("do_train", False, "Whether to run training.") | |
flags.DEFINE_bool("do_predict", False, "Whether to run eval on the dev set.") | |
flags.DEFINE_bool("do_eval", False, "Whether to run eval on the dev set.") | |
flags.DEFINE_integer("train_batch_size", 32, | |
"Total batch size for training.") | |
flags.DEFINE_integer("predict_batch_size", 8, | |
"Total batch size for predictions.") | |
flags.DEFINE_float("learning_rate", 5e-5, | |
"The initial learning rate for Adam.") | |
flags.DEFINE_float("num_train_epochs", 3.0, | |
"Total number of training epochs to perform.") | |
flags.DEFINE_float("num_train_steps", None, | |
"Total number of training steps to perform.") | |
flags.DEFINE_float( | |
"warmup_proportion", 0.1, | |
"Proportion of training to perform linear learning rate warmup for. " | |
"E.g., 0.1 = 10% of training.") | |
flags.DEFINE_integer("save_checkpoints_steps", 1000, | |
"How often to save the model checkpoint.") | |
flags.DEFINE_integer("save_summary_steps", 1, | |
"How often to save the summary data.") | |
flags.DEFINE_integer("iterations_per_loop", 1000, | |
"How many steps to make in each estimator call.") | |
flags.DEFINE_integer( | |
"n_best_size", 20, | |
"The total number of n-best predictions to generate in the " | |
"nbest_predictions.json output file.") | |
flags.DEFINE_integer( | |
"max_answer_length", 30, | |
"The maximum length of an answer that can be generated. This is needed " | |
"because the start and end predictions are not conditioned on one another.") | |
flags.DEFINE_bool("use_tpu", False, "Whether to use TPU or GPU/CPU.") | |
flags.DEFINE_string( | |
"tpu_name", None, | |
"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.") | |
flags.DEFINE_string( | |
"tpu_zone", None, | |
"[Optional] GCE zone where the Cloud TPU is located in. If not " | |
"specified, we will attempt to automatically detect the GCE project from " | |
"metadata.") | |
flags.DEFINE_string( | |
"gcp_project", None, | |
"[Optional] Project name for the Cloud TPU-enabled project. If not " | |
"specified, we will attempt to automatically detect the GCE project from " | |
"metadata.") | |
flags.DEFINE_string("master", None, "[Optional] TensorFlow master URL.") | |
flags.DEFINE_integer( | |
"num_tpu_cores", 8, | |
"Only used if `use_tpu` is True. Total number of TPU cores to use.") | |
flags.DEFINE_bool( | |
"verbose_logging", False, | |
"If true, all of the warnings related to data processing will be printed. " | |
"A number of warnings are expected for a normal SQuAD evaluation.") | |
flags.DEFINE_bool( | |
"version_2_with_negative", False, | |
"If true, the SQuAD examples contain some that do not have an answer.") | |
flags.DEFINE_float( | |
"null_score_diff_threshold", 0.0, | |
"If null_score - best_non_null is greater than the threshold predict null.") | |
flags.DEFINE_bool("cpu_only", False, "Whether to run on CPU.") | |
flags.DEFINE_bool("deterministic_run", False, "If set run will be deterministic (set random seed, read dataset in single thread, disable dropout)") | |
flags.DEFINE_integer("deterministic_seed", 1, "Seed vaule to be used in deterministic mode for all pseudorandom sequences") | |
flags.DEFINE_bool("use_horovod", False, "Run training using horovod.") | |
flags.DEFINE_integer('horovod_fusion_threshold', 256, "Horovod Fusion Buffer size in MB.") | |
flags.DEFINE_string("bf16_config_path", None, "Defines config for tensor converson to bf16 data type") | |
flags.DEFINE_bool('enable_scoped_allocator', False, "Enable scoped allocator optimization") | |
flags.DEFINE_string("profile", "", "Profile Steps range X-Y (e.g. --profile 7,10)") | |
def set_random_seed(seed): | |
tf.compat.v1.set_random_seed(seed) | |
tf.random.set_seed(seed) | |
random.seed(seed) | |
np.random.seed(seed) | |
class SquadExample(object): | |
"""A single training/test example for simple sequence classification. | |
For examples without an answer, the start and end position are -1. | |
""" | |
def __init__(self, | |
qas_id, | |
question_text, | |
doc_tokens, | |
orig_answer_text=None, | |
start_position=None, | |
end_position=None, | |
is_impossible=False): | |
self.qas_id = qas_id | |
self.question_text = question_text | |
self.doc_tokens = doc_tokens | |
self.orig_answer_text = orig_answer_text | |
self.start_position = start_position | |
self.end_position = end_position | |
self.is_impossible = is_impossible | |
def __str__(self): | |
return self.__repr__() | |
def __repr__(self): | |
s = "" | |
s += "qas_id: %s" % (tokenization.printable_text(self.qas_id)) | |
s += ", question_text: %s" % ( | |
tokenization.printable_text(self.question_text)) | |
s += ", doc_tokens: [%s]" % (" ".join(self.doc_tokens)) | |
if self.start_position: | |
s += ", start_position: %d" % (self.start_position) | |
if self.start_position: | |
s += ", end_position: %d" % (self.end_position) | |
if self.start_position: | |
s += ", is_impossible: %r" % (self.is_impossible) | |
return s | |
class InputFeatures(object): | |
"""A single set of features of data.""" | |
def __init__(self, | |
unique_id, | |
example_index, | |
doc_span_index, | |
tokens, | |
token_to_orig_map, | |
token_is_max_context, | |
input_ids, | |
input_mask, | |
segment_ids, | |
start_position=None, | |
end_position=None, | |
is_impossible=None): | |
self.unique_id = unique_id | |
self.example_index = example_index | |
self.doc_span_index = doc_span_index | |
self.tokens = tokens | |
self.token_to_orig_map = token_to_orig_map | |
self.token_is_max_context = token_is_max_context | |
self.input_ids = input_ids | |
self.input_mask = input_mask | |
self.segment_ids = segment_ids | |
self.start_position = start_position | |
self.end_position = end_position | |
self.is_impossible = is_impossible | |
def read_squad_examples(input_file, is_training, version_2_with_negative): | |
"""Read a SQuAD json file into a list of SquadExample.""" | |
with tf.io.gfile.GFile(input_file, "r") as reader: | |
input_data = json.load(reader)["data"] | |
def is_whitespace(c): | |
if c == " " or c == "\t" or c == "\r" or c == "\n" or ord(c) == 0x202F: | |
return True | |
return False | |
examples = [] | |
for entry in input_data: | |
for paragraph in entry["paragraphs"]: | |
paragraph_text = paragraph["context"] | |
doc_tokens = [] | |
char_to_word_offset = [] | |
prev_is_whitespace = True | |
for c in paragraph_text: | |
if is_whitespace(c): | |
prev_is_whitespace = True | |
else: | |
if prev_is_whitespace: | |
doc_tokens.append(c) | |
else: | |
doc_tokens[-1] += c | |
prev_is_whitespace = False | |
char_to_word_offset.append(len(doc_tokens) - 1) | |
for qa in paragraph["qas"]: | |
qas_id = qa["id"] | |
question_text = qa["question"] | |
start_position = None | |
end_position = None | |
orig_answer_text = None | |
is_impossible = False | |
if is_training: | |
if version_2_with_negative: | |
is_impossible = qa["is_impossible"] | |
if (len(qa["answers"]) != 1) and (not is_impossible): | |
raise ValueError( | |
"For training, each question should have exactly 1 answer.") | |
if not is_impossible: | |
answer = qa["answers"][0] | |
orig_answer_text = answer["text"] | |
answer_offset = answer["answer_start"] | |
answer_length = len(orig_answer_text) | |
start_position = char_to_word_offset[answer_offset] | |
end_position = char_to_word_offset[answer_offset + answer_length - | |
1] | |
# Only add answers where the text can be exactly recovered from the | |
# document. If this CAN'T happen it's likely due to weird Unicode | |
# stuff so we will just skip the example. | |
# | |
# Note that this means for training mode, every example is NOT | |
# guaranteed to be preserved. | |
actual_text = " ".join( | |
doc_tokens[start_position:(end_position + 1)]) | |
cleaned_answer_text = " ".join( | |
tokenization.whitespace_tokenize(orig_answer_text)) | |
if actual_text.find(cleaned_answer_text) == -1: | |
tf.compat.v1.logging.warning("Could not find answer: '%s' vs. '%s'", | |
actual_text, cleaned_answer_text) | |
continue | |
else: | |
start_position = -1 | |
end_position = -1 | |
orig_answer_text = "" | |
example = SquadExample( | |
qas_id=qas_id, | |
question_text=question_text, | |
doc_tokens=doc_tokens, | |
orig_answer_text=orig_answer_text, | |
start_position=start_position, | |
end_position=end_position, | |
is_impossible=is_impossible) | |
examples.append(example) | |
return examples | |
def convert_examples_to_features(examples, tokenizer, max_seq_length, | |
doc_stride, max_query_length, is_training, | |
output_fn): | |
"""Loads a data file into a list of `InputBatch`s.""" | |
unique_id = 1000000000 | |
for (example_index, example) in enumerate(examples): | |
query_tokens = tokenizer.tokenize(example.question_text) | |
if len(query_tokens) > max_query_length: | |
query_tokens = query_tokens[0:max_query_length] | |
tok_to_orig_index = [] | |
orig_to_tok_index = [] | |
all_doc_tokens = [] | |
for (i, token) in enumerate(example.doc_tokens): | |
orig_to_tok_index.append(len(all_doc_tokens)) | |
sub_tokens = tokenizer.tokenize(token) | |
for sub_token in sub_tokens: | |
tok_to_orig_index.append(i) | |
all_doc_tokens.append(sub_token) | |
tok_start_position = None | |
tok_end_position = None | |
if is_training and example.is_impossible: | |
tok_start_position = -1 | |
tok_end_position = -1 | |
if is_training and not example.is_impossible: | |
tok_start_position = orig_to_tok_index[example.start_position] | |
if example.end_position < len(example.doc_tokens) - 1: | |
tok_end_position = orig_to_tok_index[example.end_position + 1] - 1 | |
else: | |
tok_end_position = len(all_doc_tokens) - 1 | |
(tok_start_position, tok_end_position) = _improve_answer_span( | |
all_doc_tokens, tok_start_position, tok_end_position, tokenizer, | |
example.orig_answer_text) | |
# The -3 accounts for [CLS], [SEP] and [SEP] | |
max_tokens_for_doc = max_seq_length - len(query_tokens) - 3 | |
# We can have documents that are longer than the maximum sequence length. | |
# To deal with this we do a sliding window approach, where we take chunks | |
# of the up to our max length with a stride of `doc_stride`. | |
_DocSpan = collections.namedtuple( # pylint: disable=invalid-name | |
"DocSpan", ["start", "length"]) | |
doc_spans = [] | |
start_offset = 0 | |
while start_offset < len(all_doc_tokens): | |
length = len(all_doc_tokens) - start_offset | |
if length > max_tokens_for_doc: | |
length = max_tokens_for_doc | |
doc_spans.append(_DocSpan(start=start_offset, length=length)) | |
if start_offset + length == len(all_doc_tokens): | |
break | |
start_offset += min(length, doc_stride) | |
for (doc_span_index, doc_span) in enumerate(doc_spans): | |
tokens = [] | |
token_to_orig_map = {} | |
token_is_max_context = {} | |
segment_ids = [] | |
tokens.append("[CLS]") | |
segment_ids.append(0) | |
for token in query_tokens: | |
tokens.append(token) | |
segment_ids.append(0) | |
tokens.append("[SEP]") | |
segment_ids.append(0) | |
for i in range(doc_span.length): | |
split_token_index = doc_span.start + i | |
token_to_orig_map[len(tokens)] = tok_to_orig_index[split_token_index] | |
is_max_context = _check_is_max_context(doc_spans, doc_span_index, | |
split_token_index) | |
token_is_max_context[len(tokens)] = is_max_context | |
tokens.append(all_doc_tokens[split_token_index]) | |
segment_ids.append(1) | |
tokens.append("[SEP]") | |
segment_ids.append(1) | |
input_ids = tokenizer.convert_tokens_to_ids(tokens) | |
# The mask has 1 for real tokens and 0 for padding tokens. Only real | |
# tokens are attended to. | |
input_mask = [1] * len(input_ids) | |
# Zero-pad up to the sequence length. | |
while len(input_ids) < max_seq_length: | |
input_ids.append(0) | |
input_mask.append(0) | |
segment_ids.append(0) | |
assert len(input_ids) == max_seq_length | |
assert len(input_mask) == max_seq_length | |
assert len(segment_ids) == max_seq_length | |
start_position = None | |
end_position = None | |
if is_training and not example.is_impossible: | |
# For training, if our document chunk does not contain an annotation | |
# we throw it out, since there is nothing to predict. | |
doc_start = doc_span.start | |
doc_end = doc_span.start + doc_span.length - 1 | |
out_of_span = False | |
if not (tok_start_position >= doc_start and | |
tok_end_position <= doc_end): | |
out_of_span = True | |
if out_of_span: | |
start_position = 0 | |
end_position = 0 | |
else: | |
doc_offset = len(query_tokens) + 2 | |
start_position = tok_start_position - doc_start + doc_offset | |
end_position = tok_end_position - doc_start + doc_offset | |
if is_training and example.is_impossible: | |
start_position = 0 | |
end_position = 0 | |
if example_index < 20: | |
tf.compat.v1.logging.info("*** Example ***") | |
tf.compat.v1.logging.info("unique_id: %s" % (unique_id)) | |
tf.compat.v1.logging.info("example_index: %s" % (example_index)) | |
tf.compat.v1.logging.info("doc_span_index: %s" % (doc_span_index)) | |
tf.compat.v1.logging.info("tokens: %s" % " ".join( | |
[tokenization.printable_text(x) for x in tokens])) | |
tf.compat.v1.logging.info("token_to_orig_map: %s" % " ".join( | |
["%d:%d" % (x, y) for (x, y) in six.iteritems(token_to_orig_map)])) | |
tf.compat.v1.logging.info("token_is_max_context: %s" % " ".join([ | |
"%d:%s" % (x, y) for (x, y) in six.iteritems(token_is_max_context) | |
])) | |
tf.compat.v1.logging.info("input_ids: %s" % " ".join([str(x) for x in input_ids])) | |
tf.compat.v1.logging.info( | |
"input_mask: %s" % " ".join([str(x) for x in input_mask])) | |
tf.compat.v1.logging.info( | |
"segment_ids: %s" % " ".join([str(x) for x in segment_ids])) | |
if is_training and example.is_impossible: | |
tf.compat.v1.logging.info("impossible example") | |
if is_training and not example.is_impossible: | |
answer_text = " ".join(tokens[start_position:(end_position + 1)]) | |
tf.compat.v1.logging.info("start_position: %d" % (start_position)) | |
tf.compat.v1.logging.info("end_position: %d" % (end_position)) | |
tf.compat.v1.logging.info( | |
"answer: %s" % (tokenization.printable_text(answer_text))) | |
feature = InputFeatures( | |
unique_id=unique_id, | |
example_index=example_index, | |
doc_span_index=doc_span_index, | |
tokens=tokens, | |
token_to_orig_map=token_to_orig_map, | |
token_is_max_context=token_is_max_context, | |
input_ids=input_ids, | |
input_mask=input_mask, | |
segment_ids=segment_ids, | |
start_position=start_position, | |
end_position=end_position, | |
is_impossible=example.is_impossible) | |
# Run callback | |
output_fn(feature) | |
unique_id += 1 | |
def _improve_answer_span(doc_tokens, input_start, input_end, tokenizer, | |
orig_answer_text): | |
"""Returns tokenized answer spans that better match the annotated answer.""" | |
# The SQuAD annotations are character based. We first project them to | |
# whitespace-tokenized words. But then after WordPiece tokenization, we can | |
# often find a "better match". For example: | |
# | |
# Question: What year was John Smith born? | |
# Context: The leader was John Smith (1895-1943). | |
# Answer: 1895 | |
# | |
# The original whitespace-tokenized answer will be "(1895-1943).". However | |
# after tokenization, our tokens will be "( 1895 - 1943 ) .". So we can match | |
# the exact answer, 1895. | |
# | |
# However, this is not always possible. Consider the following: | |
# | |
# Question: What country is the top exporter of electornics? | |
# Context: The Japanese electronics industry is the lagest in the world. | |
# Answer: Japan | |
# | |
# In this case, the annotator chose "Japan" as a character sub-span of | |
# the word "Japanese". Since our WordPiece tokenizer does not split | |
# "Japanese", we just use "Japanese" as the annotation. This is fairly rare | |
# in SQuAD, but does happen. | |
tok_answer_text = " ".join(tokenizer.tokenize(orig_answer_text)) | |
for new_start in range(input_start, input_end + 1): | |
for new_end in range(input_end, new_start - 1, -1): | |
text_span = " ".join(doc_tokens[new_start:(new_end + 1)]) | |
if text_span == tok_answer_text: | |
return (new_start, new_end) | |
return (input_start, input_end) | |
def _check_is_max_context(doc_spans, cur_span_index, position): | |
"""Check if this is the 'max context' doc span for the token.""" | |
# Because of the sliding window approach taken to scoring documents, a single | |
# token can appear in multiple documents. E.g. | |
# Doc: the man went to the store and bought a gallon of milk | |
# Span A: the man went to the | |
# Span B: to the store and bought | |
# Span C: and bought a gallon of | |
# ... | |
# | |
# Now the word 'bought' will have two scores from spans B and C. We only | |
# want to consider the score with "maximum context", which we define as | |
# the *minimum* of its left and right context (the *sum* of left and | |
# right context will always be the same, of course). | |
# | |
# In the example the maximum context for 'bought' would be span C since | |
# it has 1 left context and 3 right context, while span B has 4 left context | |
# and 0 right context. | |
best_score = None | |
best_span_index = None | |
for (span_index, doc_span) in enumerate(doc_spans): | |
end = doc_span.start + doc_span.length - 1 | |
if position < doc_span.start: | |
continue | |
if position > end: | |
continue | |
num_left_context = position - doc_span.start | |
num_right_context = end - position | |
score = min(num_left_context, num_right_context) + 0.01 * doc_span.length | |
if best_score is None or score > best_score: | |
best_score = score | |
best_span_index = span_index | |
return cur_span_index == best_span_index | |
def create_model(bert_config, is_training, input_ids, input_mask, segment_ids, | |
use_one_hot_embeddings): | |
"""Creates a classification model.""" | |
model = modeling.BertModel( | |
config=bert_config, | |
is_training=is_training, | |
input_ids=input_ids, | |
input_mask=input_mask, | |
token_type_ids=segment_ids, | |
use_one_hot_embeddings=use_one_hot_embeddings) | |
final_hidden = model.get_sequence_output() | |
final_hidden_shape = modeling.get_shape_list(final_hidden, expected_rank=3) | |
batch_size = final_hidden_shape[0] | |
seq_length = final_hidden_shape[1] | |
hidden_size = final_hidden_shape[2] | |
output_weights = tf.compat.v1.get_variable( | |
"cls/squad/output_weights", [2, hidden_size], | |
initializer=tf.compat.v1.truncated_normal_initializer(stddev=0.02)) | |
output_bias = tf.compat.v1.get_variable( | |
"cls/squad/output_bias", [2], initializer=tf.compat.v1.zeros_initializer()) | |
final_hidden_matrix = tf.reshape(final_hidden, | |
[batch_size * seq_length, hidden_size]) | |
logits = tf.matmul(final_hidden_matrix, output_weights, transpose_b=True) | |
logits = tf.nn.bias_add(logits, output_bias) | |
logits = tf.reshape(logits, [batch_size, seq_length, 2]) | |
logits = tf.transpose(a=logits, perm=[2, 0, 1]) | |
unstacked_logits = tf.unstack(logits, axis=0) | |
(start_logits, end_logits) = (unstacked_logits[0], unstacked_logits[1]) | |
return (start_logits, end_logits) | |
def model_fn_builder(bert_config, init_checkpoint, learning_rate, | |
num_train_steps, num_warmup_steps, use_tpu, | |
use_one_hot_embeddings): | |
"""Returns `model_fn` closure for TPUEstimator.""" | |
def model_fn(features, labels, mode, params): # pylint: disable=unused-argument | |
"""The `model_fn` for TPUEstimator.""" | |
tf.compat.v1.logging.info("*** Features ***") | |
for name in sorted(features.keys()): | |
tf.compat.v1.logging.info(" name = %s, shape = %s" % (name, features[name].shape)) | |
unique_ids = features["unique_ids"] | |
input_ids = features["input_ids"] | |
input_mask = features["input_mask"] | |
segment_ids = features["segment_ids"] | |
is_training = (mode == tf.estimator.ModeKeys.TRAIN) | |
(start_logits, end_logits) = create_model( | |
bert_config=bert_config, | |
is_training=is_training, | |
input_ids=input_ids, | |
input_mask=input_mask, | |
segment_ids=segment_ids, | |
use_one_hot_embeddings=use_one_hot_embeddings) | |
tvars = tf.compat.v1.trainable_variables() | |
initialized_variable_names = {} | |
scaffold_fn = None | |
if init_checkpoint: | |
(assignment_map, initialized_variable_names | |
) = modeling.get_assignment_map_from_checkpoint(tvars, init_checkpoint) | |
if use_tpu: | |
def tpu_scaffold(): | |
tf.compat.v1.train.init_from_checkpoint(init_checkpoint, assignment_map) | |
return tf.compat.v1.train.Scaffold() | |
scaffold_fn = tpu_scaffold | |
else: | |
tf.compat.v1.train.init_from_checkpoint(init_checkpoint, assignment_map) | |
tf.compat.v1.logging.info("**** Trainable Variables ****") | |
for var in tvars: | |
init_string = "" | |
if var.name in initialized_variable_names: | |
init_string = ", *INIT_FROM_CKPT*" | |
tf.compat.v1.logging.info(" name = %s, shape = %s%s", var.name, var.shape, | |
init_string) | |
output_spec = None | |
if mode == tf.estimator.ModeKeys.TRAIN: | |
seq_length = modeling.get_shape_list(input_ids)[1] | |
def compute_loss(logits, positions): | |
one_hot_positions = tf.one_hot( | |
positions, depth=seq_length, dtype=tf.float32) | |
log_probs = tf.nn.log_softmax(logits, axis=-1) | |
loss = -tf.reduce_mean( | |
input_tensor=tf.reduce_sum(input_tensor=one_hot_positions * log_probs, axis=-1)) | |
return loss | |
start_positions = features["start_positions"] | |
end_positions = features["end_positions"] | |
start_loss = compute_loss(start_logits, start_positions) | |
end_loss = compute_loss(end_logits, end_positions) | |
total_loss = (start_loss + end_loss) / 2.0 | |
total_loss = tf.compat.v1.Print(total_loss, [total_loss], message="LOSS: ") | |
train_op = optimization.create_optimizer( | |
total_loss, learning_rate, num_train_steps, num_warmup_steps, use_tpu) | |
output_spec = tf.compat.v1.estimator.tpu.TPUEstimatorSpec( | |
mode=mode, | |
loss=total_loss, | |
train_op=train_op, | |
scaffold_fn=scaffold_fn) | |
elif mode == tf.estimator.ModeKeys.PREDICT: | |
predictions = { | |
"unique_ids": unique_ids, | |
"start_logits": start_logits, | |
"end_logits": end_logits, | |
} | |
output_spec = tf.compat.v1.estimator.tpu.TPUEstimatorSpec( | |
mode=mode, predictions=predictions, scaffold_fn=scaffold_fn) | |
else: | |
raise ValueError( | |
"Only TRAIN and PREDICT modes are supported: %s" % (mode)) | |
return output_spec | |
return model_fn | |
def input_fn_builder(input_file, seq_length, is_training, drop_remainder): | |
"""Creates an `input_fn` closure to be passed to TPUEstimator.""" | |
name_to_features = { | |
"unique_ids": tf.io.FixedLenFeature([], tf.int64), | |
"input_ids": tf.io.FixedLenFeature([seq_length], tf.int64), | |
"input_mask": tf.io.FixedLenFeature([seq_length], tf.int64), | |
"segment_ids": tf.io.FixedLenFeature([seq_length], tf.int64), | |
} | |
if is_training: | |
name_to_features["start_positions"] = tf.io.FixedLenFeature([], tf.int64) | |
name_to_features["end_positions"] = tf.io.FixedLenFeature([], tf.int64) | |
def _decode_record(record, name_to_features): | |
"""Decodes a record to a TensorFlow example.""" | |
example = tf.io.parse_single_example(serialized=record, features=name_to_features) | |
# tf.Example only supports tf.int64, but the TPU only supports tf.int32. | |
# So cast all int64 to int32. | |
for name in list(example.keys()): | |
t = example[name] | |
if t.dtype == tf.int64: | |
t = tf.cast(t, dtype=tf.int32) | |
example[name] = t | |
return example | |
def input_fn(params): | |
"""The actual input function.""" | |
batch_size = params["batch_size"] | |
# For training, we want a lot of parallel reading and shuffling. | |
# For eval, we want no shuffling and parallel reading doesn't matter. | |
d = tf.data.TFRecordDataset(input_file) | |
if FLAGS.deterministic_run: | |
d = d.repeat() | |
d = d.shuffle(buffer_size=100, seed=FLAGS.deterministic_seed) | |
d = d.apply( | |
tf.data.experimental.map_and_batch( | |
lambda record: _decode_record(record, name_to_features), | |
batch_size=batch_size, | |
num_parallel_calls=1, | |
drop_remainder=drop_remainder)) | |
else: | |
if is_training: | |
if horovod_enabled(): | |
d = d.shard(hvd.local_size(), hvd.local_rank()) | |
d = d.repeat() | |
d = d.shuffle(buffer_size=100) | |
d = d.apply( | |
tf.data.experimental.map_and_batch( | |
lambda record: _decode_record(record, name_to_features), | |
batch_size=batch_size, | |
drop_remainder=drop_remainder)) | |
d = d.prefetch(tf.data.experimental.AUTOTUNE) | |
return d | |
return input_fn | |
RawResult = collections.namedtuple("RawResult", | |
["unique_id", "start_logits", "end_logits"]) | |
def write_predictions(all_examples, all_features, all_results, n_best_size, | |
max_answer_length, do_lower_case, output_prediction_file, | |
output_nbest_file, output_null_log_odds_file, version_2_with_negative, | |
verbose_logging): | |
"""Write final predictions to the json file and log-odds of null if needed.""" | |
tf.compat.v1.logging.info("Writing predictions to: %s" % (output_prediction_file)) | |
tf.compat.v1.logging.info("Writing nbest to: %s" % (output_nbest_file)) | |
example_index_to_features = collections.defaultdict(list) | |
for feature in all_features: | |
example_index_to_features[feature.example_index].append(feature) | |
unique_id_to_result = {} | |
for result in all_results: | |
unique_id_to_result[result.unique_id] = result | |
_PrelimPrediction = collections.namedtuple( # pylint: disable=invalid-name | |
"PrelimPrediction", | |
["feature_index", "start_index", "end_index", "start_logit", "end_logit"]) | |
all_predictions = collections.OrderedDict() | |
all_nbest_json = collections.OrderedDict() | |
scores_diff_json = collections.OrderedDict() | |
for (example_index, example) in enumerate(all_examples): | |
features = example_index_to_features[example_index] | |
prelim_predictions = [] | |
# keep track of the minimum score of null start+end of position 0 | |
score_null = 1000000 # large and positive | |
min_null_feature_index = 0 # the paragraph slice with min mull score | |
null_start_logit = 0 # the start logit at the slice with min null score | |
null_end_logit = 0 # the end logit at the slice with min null score | |
for (feature_index, feature) in enumerate(features): | |
result = unique_id_to_result[feature.unique_id] | |
start_indexes = _get_best_indexes(result.start_logits, n_best_size) | |
end_indexes = _get_best_indexes(result.end_logits, n_best_size) | |
# if we could have irrelevant answers, get the min score of irrelevant | |
if version_2_with_negative: | |
feature_null_score = result.start_logits[0] + result.end_logits[0] | |
if feature_null_score < score_null: | |
score_null = feature_null_score | |
min_null_feature_index = feature_index | |
null_start_logit = result.start_logits[0] | |
null_end_logit = result.end_logits[0] | |
for start_index in start_indexes: | |
for end_index in end_indexes: | |
# We could hypothetically create invalid predictions, e.g., predict | |
# that the start of the span is in the question. We throw out all | |
# invalid predictions. | |
if start_index >= len(feature.tokens): | |
continue | |
if end_index >= len(feature.tokens): | |
continue | |
if start_index not in feature.token_to_orig_map: | |
continue | |
if end_index not in feature.token_to_orig_map: | |
continue | |
if not feature.token_is_max_context.get(start_index, False): | |
continue | |
if end_index < start_index: | |
continue | |
length = end_index - start_index + 1 | |
if length > max_answer_length: | |
continue | |
prelim_predictions.append( | |
_PrelimPrediction( | |
feature_index=feature_index, | |
start_index=start_index, | |
end_index=end_index, | |
start_logit=result.start_logits[start_index], | |
end_logit=result.end_logits[end_index])) | |
if version_2_with_negative: | |
prelim_predictions.append( | |
_PrelimPrediction( | |
feature_index=min_null_feature_index, | |
start_index=0, | |
end_index=0, | |
start_logit=null_start_logit, | |
end_logit=null_end_logit)) | |
prelim_predictions = sorted( | |
prelim_predictions, | |
key=lambda x: (x.start_logit + x.end_logit), | |
reverse=True) | |
_NbestPrediction = collections.namedtuple( # pylint: disable=invalid-name | |
"NbestPrediction", ["text", "start_logit", "end_logit"]) | |
seen_predictions = {} | |
nbest = [] | |
for pred in prelim_predictions: | |
if len(nbest) >= n_best_size: | |
break | |
feature = features[pred.feature_index] | |
if pred.start_index > 0: # this is a non-null prediction | |
tok_tokens = feature.tokens[pred.start_index:(pred.end_index + 1)] | |
orig_doc_start = feature.token_to_orig_map[pred.start_index] | |
orig_doc_end = feature.token_to_orig_map[pred.end_index] | |
orig_tokens = example.doc_tokens[orig_doc_start:(orig_doc_end + 1)] | |
tok_text = " ".join(tok_tokens) | |
# De-tokenize WordPieces that have been split off. | |
tok_text = tok_text.replace(" ##", "") | |
tok_text = tok_text.replace("##", "") | |
# Clean whitespace | |
tok_text = tok_text.strip() | |
tok_text = " ".join(tok_text.split()) | |
orig_text = " ".join(orig_tokens) | |
final_text = get_final_text(tok_text, orig_text, do_lower_case, verbose_logging) | |
if final_text in seen_predictions: | |
continue | |
seen_predictions[final_text] = True | |
else: | |
final_text = "" | |
seen_predictions[final_text] = True | |
nbest.append( | |
_NbestPrediction( | |
text=final_text, | |
start_logit=pred.start_logit, | |
end_logit=pred.end_logit)) | |
# if we didn't inlude the empty option in the n-best, inlcude it | |
if version_2_with_negative: | |
if "" not in seen_predictions: | |
nbest.append( | |
_NbestPrediction( | |
text="", start_logit=null_start_logit, | |
end_logit=null_end_logit)) | |
# In very rare edge cases we could have no valid predictions. So we | |
# just create a nonce prediction in this case to avoid failure. | |
if not nbest: | |
nbest.append( | |
_NbestPrediction(text="empty", start_logit=0.0, end_logit=0.0)) | |
assert len(nbest) >= 1 | |
total_scores = [] | |
best_non_null_entry = None | |
for entry in nbest: | |
total_scores.append(entry.start_logit + entry.end_logit) | |
if not best_non_null_entry: | |
if entry.text: | |
best_non_null_entry = entry | |
probs = _compute_softmax(total_scores) | |
nbest_json = [] | |
for (i, entry) in enumerate(nbest): | |
output = collections.OrderedDict() | |
output["text"] = entry.text | |
output["probability"] = probs[i] | |
output["start_logit"] = entry.start_logit | |
output["end_logit"] = entry.end_logit | |
nbest_json.append(output) | |
assert len(nbest_json) >= 1 | |
if not version_2_with_negative: | |
all_predictions[example.qas_id] = nbest_json[0]["text"] | |
else: | |
# predict "" iff the null score - the score of best non-null > threshold | |
score_diff = score_null - best_non_null_entry.start_logit - ( | |
best_non_null_entry.end_logit) | |
scores_diff_json[example.qas_id] = score_diff | |
if score_diff > FLAGS.null_score_diff_threshold: | |
all_predictions[example.qas_id] = "" | |
else: | |
all_predictions[example.qas_id] = best_non_null_entry.text | |
all_nbest_json[example.qas_id] = nbest_json | |
with tf.io.gfile.GFile(output_prediction_file, "w") as writer: | |
writer.write(json.dumps(all_predictions, indent=4) + "\n") | |
with tf.io.gfile.GFile(output_nbest_file, "w") as writer: | |
writer.write(json.dumps(all_nbest_json, indent=4) + "\n") | |
if version_2_with_negative: | |
with tf.io.gfile.GFile(output_null_log_odds_file, "w") as writer: | |
writer.write(json.dumps(scores_diff_json, indent=4) + "\n") | |
return [all_predictions, all_nbest_json, scores_diff_json] | |
def get_final_text(pred_text, orig_text, do_lower_case, verbose_logging): | |
"""Project the tokenized prediction back to the original text.""" | |
# When we created the data, we kept track of the alignment between original | |
# (whitespace tokenized) tokens and our WordPiece tokenized tokens. So | |
# now `orig_text` contains the span of our original text corresponding to the | |
# span that we predicted. | |
# | |
# However, `orig_text` may contain extra characters that we don't want in | |
# our prediction. | |
# | |
# For example, let's say: | |
# pred_text = steve smith | |
# orig_text = Steve Smith's | |
# | |
# We don't want to return `orig_text` because it contains the extra "'s". | |
# | |
# We don't want to return `pred_text` because it's already been normalized | |
# (the SQuAD eval script also does punctuation stripping/lower casing but | |
# our tokenizer does additional normalization like stripping accent | |
# characters). | |
# | |
# What we really want to return is "Steve Smith". | |
# | |
# Therefore, we have to apply a semi-complicated alignment heruistic between | |
# `pred_text` and `orig_text` to get a character-to-charcter alignment. This | |
# can fail in certain cases in which case we just return `orig_text`. | |
def _strip_spaces(text): | |
ns_chars = [] | |
ns_to_s_map = collections.OrderedDict() | |
for (i, c) in enumerate(text): | |
if c == " ": | |
continue | |
ns_to_s_map[len(ns_chars)] = i | |
ns_chars.append(c) | |
ns_text = "".join(ns_chars) | |
return (ns_text, ns_to_s_map) | |
# We first tokenize `orig_text`, strip whitespace from the result | |
# and `pred_text`, and check if they are the same length. If they are | |
# NOT the same length, the heuristic has failed. If they are the same | |
# length, we assume the characters are one-to-one aligned. | |
tokenizer = tokenization.BasicTokenizer(do_lower_case=do_lower_case) | |
tok_text = " ".join(tokenizer.tokenize(orig_text)) | |
start_position = tok_text.find(pred_text) | |
if start_position == -1: | |
if verbose_logging: | |
tf.compat.v1.logging.info( | |
"Unable to find text: '%s' in '%s'" % (pred_text, orig_text)) | |
return orig_text | |
end_position = start_position + len(pred_text) - 1 | |
(orig_ns_text, orig_ns_to_s_map) = _strip_spaces(orig_text) | |
(tok_ns_text, tok_ns_to_s_map) = _strip_spaces(tok_text) | |
if len(orig_ns_text) != len(tok_ns_text): | |
if verbose_logging: | |
tf.compat.v1.logging.info("Length not equal after stripping spaces: '%s' vs '%s'", | |
orig_ns_text, tok_ns_text) | |
return orig_text | |
# We then project the characters in `pred_text` back to `orig_text` using | |
# the character-to-character alignment. | |
tok_s_to_ns_map = {} | |
for (i, tok_index) in six.iteritems(tok_ns_to_s_map): | |
tok_s_to_ns_map[tok_index] = i | |
orig_start_position = None | |
if start_position in tok_s_to_ns_map: | |
ns_start_position = tok_s_to_ns_map[start_position] | |
if ns_start_position in orig_ns_to_s_map: | |
orig_start_position = orig_ns_to_s_map[ns_start_position] | |
if orig_start_position is None: | |
if verbose_logging: | |
tf.compat.v1.logging.info("Couldn't map start position") | |
return orig_text | |
orig_end_position = None | |
if end_position in tok_s_to_ns_map: | |
ns_end_position = tok_s_to_ns_map[end_position] | |
if ns_end_position in orig_ns_to_s_map: | |
orig_end_position = orig_ns_to_s_map[ns_end_position] | |
if orig_end_position is None: | |
if verbose_logging: | |
tf.compat.v1.logging.info("Couldn't map end position") | |
return orig_text | |
output_text = orig_text[orig_start_position:(orig_end_position + 1)] | |
return output_text | |
def _get_best_indexes(logits, n_best_size): | |
"""Get the n-best logits from a list.""" | |
index_and_score = sorted(enumerate(logits), key=lambda x: x[1], reverse=True) | |
best_indexes = [] | |
for i in range(len(index_and_score)): | |
if i >= n_best_size: | |
break | |
best_indexes.append(index_and_score[i][0]) | |
return best_indexes | |
def _compute_softmax(scores): | |
"""Compute softmax probability over raw logits.""" | |
if not scores: | |
return [] | |
max_score = None | |
for score in scores: | |
if max_score is None or score > max_score: | |
max_score = score | |
exp_scores = [] | |
total_sum = 0.0 | |
for score in scores: | |
x = math.exp(score - max_score) | |
exp_scores.append(x) | |
total_sum += x | |
probs = [] | |
for score in exp_scores: | |
probs.append(score / total_sum) | |
return probs | |
class FeatureWriter(object): | |
"""Writes InputFeature to TF example file.""" | |
def __init__(self, filename, is_training): | |
self.filename = filename | |
self.is_training = is_training | |
self.num_features = 0 | |
self._writer = tf.io.TFRecordWriter(filename) | |
def process_feature(self, feature): | |
"""Write a InputFeature to the TFRecordWriter as a tf.train.Example.""" | |
self.num_features += 1 | |
def create_int_feature(values): | |
feature = tf.train.Feature( | |
int64_list=tf.train.Int64List(value=list(values))) | |
return feature | |
features = collections.OrderedDict() | |
features["unique_ids"] = create_int_feature([feature.unique_id]) | |
features["input_ids"] = create_int_feature(feature.input_ids) | |
features["input_mask"] = create_int_feature(feature.input_mask) | |
features["segment_ids"] = create_int_feature(feature.segment_ids) | |
if self.is_training: | |
features["start_positions"] = create_int_feature([feature.start_position]) | |
features["end_positions"] = create_int_feature([feature.end_position]) | |
impossible = 0 | |
if feature.is_impossible: | |
impossible = 1 | |
features["is_impossible"] = create_int_feature([impossible]) | |
tf_example = tf.train.Example(features=tf.train.Features(feature=features)) | |
self._writer.write(tf_example.SerializeToString()) | |
def close(self): | |
self._writer.close() | |
def validate_flags_or_throw(bert_config): | |
"""Validate the input FLAGS or throw an exception.""" | |
tokenization.validate_case_matches_checkpoint(FLAGS.do_lower_case, | |
FLAGS.init_checkpoint) | |
if not FLAGS.do_train and not FLAGS.do_predict: | |
raise ValueError("At least one of `do_train` or `do_predict` must be True.") | |
if FLAGS.do_train: | |
if not FLAGS.train_file: | |
raise ValueError( | |
"If `do_train` is True, then `train_file` must be specified.") | |
if FLAGS.do_predict: | |
if not FLAGS.predict_file: | |
raise ValueError( | |
"If `do_predict` is True, then `predict_file` must be specified.") | |
if FLAGS.max_seq_length > bert_config.max_position_embeddings: | |
raise ValueError( | |
"Cannot use sequence length %d because the BERT model " | |
"was only trained up to sequence length %d" % | |
(FLAGS.max_seq_length, bert_config.max_position_embeddings)) | |
if FLAGS.max_seq_length <= FLAGS.max_query_length + 3: | |
raise ValueError( | |
"The max_seq_length (%d) must be greater than max_query_length " | |
"(%d) + 3" % (FLAGS.max_seq_length, FLAGS.max_query_length)) | |
def main(_): | |
tf.compat.v1.logging.set_verbosity(tf.compat.v1.logging.INFO) | |
bert_config = modeling.BertConfig.from_json_file(FLAGS.bert_config_file) | |
validate_flags_or_throw(bert_config) | |
tf.io.gfile.makedirs(FLAGS.output_dir) | |
tokenizer = tokenization.FullTokenizer( | |
vocab_file=FLAGS.vocab_file, do_lower_case=FLAGS.do_lower_case) | |
tpu_cluster_resolver = None | |
if FLAGS.use_tpu and FLAGS.tpu_name: | |
tpu_cluster_resolver = tf.distribute.cluster_resolver.TPUClusterResolver( | |
FLAGS.tpu_name, zone=FLAGS.tpu_zone, project=FLAGS.gcp_project) | |
model_dir = FLAGS.output_dir | |
if horovod_enabled(): | |
model_dir = os.path.join(FLAGS.output_dir, "worker_" + str(hvd.rank())) | |
is_per_host = tf.compat.v1.estimator.tpu.InputPipelineConfig.PER_HOST_V2 | |
# The Scoped Allocator Optimization is enabled by default unless disabled by a flag. | |
if FLAGS.enable_scoped_allocator: | |
from tensorflow.core.protobuf import rewriter_config_pb2 # pylint: disable=import-error | |
session_config = tf.compat.v1.ConfigProto() | |
session_config.graph_options.rewrite_options.scoped_allocator_optimization = rewriter_config_pb2.RewriterConfig.ON | |
enable_op = session_config.graph_options.rewrite_options.scoped_allocator_opts.enable_op | |
del enable_op[:] | |
enable_op.append("HorovodAllreduce") | |
else: | |
session_config = None | |
run_config = tf.compat.v1.estimator.tpu.RunConfig( | |
cluster=tpu_cluster_resolver, | |
master=FLAGS.master, | |
model_dir=model_dir, | |
keep_checkpoint_max=1, | |
save_checkpoints_steps=FLAGS.save_checkpoints_steps, | |
save_summary_steps=FLAGS.save_summary_steps, | |
tpu_config=tf.compat.v1.estimator.tpu.TPUConfig( | |
iterations_per_loop=FLAGS.iterations_per_loop, | |
num_shards=FLAGS.num_tpu_cores, | |
per_host_input_for_training=is_per_host), | |
session_config=session_config) | |
train_examples = None | |
num_train_steps = None | |
num_warmup_steps = None | |
train_batch_size = FLAGS.train_batch_size | |
if horovod_enabled(): | |
train_batch_size = train_batch_size * hvd.size() | |
if FLAGS.do_train: | |
train_examples = read_squad_examples( | |
input_file=FLAGS.train_file, is_training=True, version_2_with_negative=FLAGS.version_2_with_negative) | |
if FLAGS.num_train_steps is not None: | |
num_train_steps = FLAGS.num_train_steps | |
else: | |
num_train_steps = int( | |
len(train_examples) / train_batch_size * FLAGS.num_train_epochs) | |
num_warmup_steps = int(num_train_steps * FLAGS.warmup_proportion) | |
# Pre-shuffle the input to avoid having to make a very large shuffle | |
# buffer in in the `input_fn`. | |
rng = random.Random(12345) | |
rng.shuffle(train_examples) | |
start_index = 0 | |
end_index = len(train_examples) | |
per_worker_filenames = [os.path.join(FLAGS.output_dir, "train.tf_record")] | |
worker_id = 0 | |
if horovod_enabled(): | |
per_worker_filenames = [os.path.join(FLAGS.output_dir, "train.tf_record_{}".format(i)) | |
for i in range(hvd.local_size())] | |
num_examples_per_rank = len(train_examples) // hvd.size() | |
remainder = len(train_examples) % hvd.size() | |
worker_id = hvd.rank() | |
if worker_id < remainder: | |
start_index = worker_id * (num_examples_per_rank + 1) | |
end_index = start_index + num_examples_per_rank + 1 | |
else: | |
start_index = worker_id * num_examples_per_rank + remainder | |
end_index = start_index + (num_examples_per_rank) | |
learning_rate = FLAGS.learning_rate | |
if horovod_enabled(): | |
learning_rate = learning_rate * hvd.size() | |
model_fn = model_fn_builder( | |
bert_config=bert_config, | |
init_checkpoint=FLAGS.init_checkpoint, | |
learning_rate=FLAGS.learning_rate, | |
num_train_steps=num_train_steps, | |
num_warmup_steps=num_warmup_steps, | |
use_tpu=FLAGS.use_tpu, | |
use_one_hot_embeddings=FLAGS.use_tpu) | |
# If TPU is not available, this will fall back to normal Estimator on CPU | |
# or GPU. | |
estimator = tf.compat.v1.estimator.tpu.TPUEstimator( | |
use_tpu=FLAGS.use_tpu, | |
model_fn=model_fn, | |
config=run_config, | |
train_batch_size=FLAGS.train_batch_size, | |
predict_batch_size=FLAGS.predict_batch_size) | |
write_hparams_v1(FLAGS.output_dir, { | |
'batch_size': FLAGS.train_batch_size, | |
**{x: getattr(FLAGS, x) for x in FLAGS} | |
}) | |
if FLAGS.do_train: | |
# We write to a temporary file to avoid storing very large constant tensors | |
# in memory. | |
train_writer = FeatureWriter( | |
filename=per_worker_filenames[hvd.local_rank() if horovod_enabled() else worker_id], | |
is_training=True) | |
convert_examples_to_features( | |
examples=train_examples[start_index:end_index], | |
tokenizer=tokenizer, | |
max_seq_length=FLAGS.max_seq_length, | |
doc_stride=FLAGS.doc_stride, | |
max_query_length=FLAGS.max_query_length, | |
is_training=True, | |
output_fn=train_writer.process_feature) | |
train_writer.close() | |
num_features = train_writer.num_features | |
tf.compat.v1.logging.info("***** Running training *****") | |
tf.compat.v1.logging.info(" Num orig examples = %d", len(train_examples)) | |
tf.compat.v1.logging.info(" Num split examples = %d", num_features) | |
tf.compat.v1.logging.info(" Per-worker batch size = %d", FLAGS.train_batch_size) | |
tf.compat.v1.logging.info(" Total batch size = %d", train_batch_size) | |
tf.compat.v1.logging.info(" Num steps = %d", num_train_steps) | |
del train_examples | |
train_input_fn = input_fn_builder( | |
input_file=per_worker_filenames, | |
seq_length=FLAGS.max_seq_length, | |
is_training=True, | |
drop_remainder=True) | |
train_hooks = [habana_hooks.PerfLoggingHook(batch_size=train_batch_size, mode="train")] | |
if len(FLAGS.profile) > 0: | |
train_hooks.append(TensorBoardHook(output_dir=FLAGS.output_dir,profile_steps=FLAGS.profile)) | |
if horovod_enabled(): | |
train_hooks.append(hvd.BroadcastGlobalVariablesHook(0)) | |
with dump_callback(): | |
estimator.train(input_fn=train_input_fn, max_steps=num_train_steps, hooks=train_hooks) | |
if FLAGS.do_predict: | |
eval_examples = read_squad_examples( | |
input_file=FLAGS.predict_file, is_training=False, version_2_with_negative=FLAGS.version_2_with_negative) | |
eval_writer = FeatureWriter( | |
filename=os.path.join(model_dir, "eval.tf_record"), | |
is_training=False) | |
eval_features = [] | |
def append_feature(feature): | |
eval_features.append(feature) | |
eval_writer.process_feature(feature) | |
convert_examples_to_features( | |
examples=eval_examples, | |
tokenizer=tokenizer, | |
max_seq_length=FLAGS.max_seq_length, | |
doc_stride=FLAGS.doc_stride, | |
max_query_length=FLAGS.max_query_length, | |
is_training=False, | |
output_fn=append_feature) | |
eval_writer.close() | |
tf.compat.v1.logging.info("***** Running predictions *****") | |
tf.compat.v1.logging.info(" Num orig examples = %d", len(eval_examples)) | |
tf.compat.v1.logging.info(" Num split examples = %d", len(eval_features)) | |
tf.compat.v1.logging.info(" Batch size = %d", FLAGS.predict_batch_size) | |
all_results = [] | |
predict_input_fn = input_fn_builder( | |
input_file=eval_writer.filename, | |
seq_length=FLAGS.max_seq_length, | |
is_training=False, | |
drop_remainder=False) | |
eval_hooks = [habana_hooks.PerfLoggingHook(batch_size=FLAGS.predict_batch_size, mode="eval")] | |
# If running eval on the TPU, you will need to specify the number of | |
# steps. | |
all_results = [] | |
for result in estimator.predict( | |
predict_input_fn, yield_single_examples=True, hooks=eval_hooks): | |
if len(all_results) % 1000 == 0: | |
tf.compat.v1.logging.info("Processing example: %d" % (len(all_results))) | |
unique_id = int(result["unique_ids"]) | |
start_logits = [float(x) for x in result["start_logits"].flat] | |
end_logits = [float(x) for x in result["end_logits"].flat] | |
all_results.append( | |
RawResult( | |
unique_id=unique_id, | |
start_logits=start_logits, | |
end_logits=end_logits)) | |
output_prediction_file = os.path.join(model_dir, "predictions.json") | |
output_nbest_file = os.path.join(model_dir, "nbest_predictions.json") | |
output_null_log_odds_file = os.path.join(model_dir, "null_odds.json") | |
all_predictions, all_nbest_json, scores_diff_json = write_predictions( | |
eval_examples, eval_features, all_results, | |
FLAGS.n_best_size, FLAGS.max_answer_length, | |
FLAGS.do_lower_case, output_prediction_file, | |
output_nbest_file, output_null_log_odds_file, | |
FLAGS.version_2_with_negative, | |
FLAGS.verbose_logging) | |
if FLAGS.do_eval: | |
if FLAGS.version_2_with_negative: | |
tf.compat.v1.logging.fatal("Eval for v2 is not supported") | |
pass | |
else: | |
with tf.io.gfile.GFile(FLAGS.predict_file, 'r') as reader: | |
dataset_json = json.load(reader) | |
pred_dataset = dataset_json['data'] | |
f1 = exact_match = total = 0 | |
for article in pred_dataset: | |
for paragraph in article["paragraphs"]: | |
for qa in paragraph["qas"]: | |
total += 1 | |
if qa["id"] not in all_predictions: | |
message = "Unanswered question " + qa["id"] + " will receive score 0." | |
tf.compat.v1.logging.error(message) | |
continue | |
ground_truths = [entry["text"] for entry in qa["answers"]] | |
prediction = all_predictions[qa["id"]] | |
exact_match += _metric_max_over_ground_truths(_exact_match_score, | |
prediction, ground_truths) | |
f1 += _metric_max_over_ground_truths(_f1_score, prediction, | |
ground_truths) | |
exact_match = exact_match / total | |
f1 = f1 / total | |
tf.compat.v1.logging.warning("Exact matches %s" % str(exact_match)) | |
tf.compat.v1.logging.warning("Final accuracy %s" % str(f1)) | |
with TBSummary(os.path.join(model_dir, 'eval')) as summary_writer: | |
summary_writer.add_scalar('accuracy', f1, 0) | |
summary_writer.add_scalar('exact_matches', exact_match, 0) | |
def _metric_max_over_ground_truths(metric_fn, prediction, ground_truths): | |
"""Computes the max over all metric scores.""" | |
scores_for_ground_truths = [] | |
for ground_truth in ground_truths: | |
score = metric_fn(prediction, ground_truth) | |
scores_for_ground_truths.append(score) | |
return max(scores_for_ground_truths) | |
def _exact_match_score(prediction, ground_truth): | |
"""Checks if predicted answer exactly matches ground truth answer.""" | |
return _normalize_answer(prediction) == _normalize_answer(ground_truth) | |
def _f1_score(prediction, ground_truth): | |
"""Computes F1 score by comparing prediction to ground truth.""" | |
prediction_tokens = _normalize_answer(prediction).split() | |
ground_truth_tokens = _normalize_answer(ground_truth).split() | |
prediction_counter = collections.Counter(prediction_tokens) | |
ground_truth_counter = collections.Counter(ground_truth_tokens) | |
common = prediction_counter & ground_truth_counter | |
num_same = sum(common.values()) | |
if num_same == 0: | |
return 0 | |
precision = 1.0 * num_same / len(prediction_tokens) | |
recall = 1.0 * num_same / len(ground_truth_tokens) | |
f1 = (2 * precision * recall) / (precision + recall) | |
return f1 | |
def _normalize_answer(s): | |
"""Lowers text and remove punctuation, articles and extra whitespace.""" | |
def remove_articles(text): | |
import re | |
return re.sub(r"\b(a|an|the)\b", " ", text) | |
def white_space_fix(text): | |
return " ".join(text.split()) | |
def remove_punc(text): | |
import string | |
exclude = set(string.punctuation) | |
return "".join(ch for ch in text if ch not in exclude) | |
def lower(text): | |
return text.lower() | |
return white_space_fix(remove_articles(remove_punc(lower(s)))) | |
if __name__ == "__main__": | |
init_squad_flags() | |
tf.compat.v1.enable_resource_variables() | |
flags.mark_flag_as_required("vocab_file") | |
flags.mark_flag_as_required("bert_config_file") | |
flags.mark_flag_as_required("output_dir") | |
if FLAGS.deterministic_run: | |
set_random_seed(FLAGS.deterministic_seed) | |
modeling.dropout = lambda input_tensor, dropout_prob: input_tensor # disable dropout | |
if FLAGS.bf16_config_path is None: | |
os.environ.setdefault('HABANA_INITIAL_WORKSPACE_SIZE_MB', '13271') | |
else: | |
os.environ['TF_BF16_CONVERSION'] = FLAGS.bf16_config_path | |
os.environ.setdefault('HABANA_INITIAL_WORKSPACE_SIZE_MB', '17371') | |
os.environ.setdefault("TF_DISABLE_MKL", "1") | |
bert_config = json.load(open(FLAGS.bert_config_file, 'r')) | |
if 'hidden_size' in bert_config: | |
if bert_config['hidden_size'] == 768: | |
# cluster slicing optimization tested for bert base, works well with this size | |
os.environ.setdefault('TF_PRELIMINARY_CLUSTER_SIZE', '1000') | |
elif bert_config['hidden_size'] >= 1024: | |
if FLAGS.bf16_config_path is None: | |
os.environ.setdefault('HABANA_INITIAL_WORKSPACE_SIZE_MB', '17257') | |
else: | |
os.environ.setdefault('HABANA_INITIAL_WORKSPACE_SIZE_MB', '21393') | |
if not FLAGS.cpu_only: | |
load_habana_module() | |
from habana_frameworks.tensorflow.habana_device import get_type | |
if get_type() == 'GAUDI2': | |
os.environ['HOROVOD_FUSION_THRESHOLD'] = str(FLAGS.horovod_fusion_threshold) | |
if FLAGS.use_horovod: | |
assert not FLAGS.cpu_only, "Horovod without HPU is not supported in helpers." | |
if hvd is None: | |
raise RuntimeError( | |
"Problem encountered during Horovod import. Please make sure that habana-horovod package is installed.") | |
hvd.init() | |
host_name = socket.gethostname() | |
vmulti = os.environ.get('MULTI_HLS_IPS') | |
v1 = os.environ.get('HABANA_INITIAL_WORKSPACE_SIZE_MB') | |
v2 = os.environ.get('TF_BF16_CONVERSION') | |
print(f"{host_name}: MULTI_HLS_IPS = {vmulti}") | |
print(f"{host_name}: HABANA_INITIAL_WORKSPACE_SIZE_MB = {v1}") | |
print(f"{host_name}: TF_BF16_CONVERSION = {v2}") | |
sys.stdout.flush() | |
sys.stderr.flush() | |
tf.compat.v1.app.run() | |