spaCy/spacy/syntax/nn_parser.pyx
Matthew Honnibal 2c37e0ccf6
💫 Use Blis for matrix multiplications (#2966)
Our epic matrix multiplication odyssey is drawing to a close...

I've now finally got the Blis linear algebra routines in a self-contained Python package, with wheels for Windows, Linux and OSX. The only missing platform at the moment is Windows Python 2.7. The result is at https://github.com/explosion/cython-blis

Thinc v7.0.0 will make the change to Blis. I've put a Thinc v7.0.0.dev0 up on PyPi so that we can test these changes with the CI, and even get them out to spacy-nightly, before Thinc v7.0.0 is released. This PR also updates the other dependencies to be in line with the current versions master is using. I've also resolved the msgpack deprecation problems, and gotten spaCy and Thinc up to date with the latest Cython.

The point of switching to Blis is to have control of how our matrix multiplications are executed across platforms. When we were using numpy for this, a different library would be used on pip and conda, OSX would use Accelerate, etc. This would open up different bugs and performance problems, especially when multi-threading was introduced.

With the change to Blis, we now strictly single-thread the matrix multiplications. This will make it much easier to use multiprocessing to parallelise the runtime, since we won't have nested parallelism problems to deal with.

* Use blis

* Use -2 arg to Cython

* Update dependencies

* Fix requirements

* Update setup dependencies

* Fix requirement typo

* Fix msgpack errors

* Remove Python27 test from Appveyor, until Blis works there

* Auto-format setup.py

* Fix murmurhash version
2018-11-27 00:44:04 +01:00

593 lines
25 KiB
Cython

# cython: infer_types=True
# cython: cdivision=True
# cython: boundscheck=False
# coding: utf-8
from __future__ import unicode_literals, print_function
from collections import OrderedDict
import ujson
import json
import numpy
cimport cython.parallel
import cytoolz
import numpy.random
cimport numpy as np
from cpython.ref cimport PyObject, Py_XDECREF
from cpython.exc cimport PyErr_CheckSignals, PyErr_SetFromErrno
from libc.math cimport exp
from libcpp.vector cimport vector
from libc.string cimport memset, memcpy
from libc.stdlib cimport calloc, free
from cymem.cymem cimport Pool
from thinc.typedefs cimport weight_t, class_t, hash_t
from thinc.extra.search cimport Beam
from thinc.api import chain, clone
from thinc.v2v import Model, Maxout, Affine
from thinc.misc import LayerNorm
from thinc.neural.ops import CupyOps
from thinc.neural.util import get_array_module
from thinc.linalg cimport Vec, VecVec
from ._parser_model cimport resize_activations, predict_states, arg_max_if_valid
from ._parser_model cimport WeightsC, ActivationsC, SizesC, cpu_log_loss
from ._parser_model cimport get_c_weights, get_c_sizes
from ._parser_model import ParserModel
from .._ml import zero_init, PrecomputableAffine, Tok2Vec, flatten
from .._ml import link_vectors_to_models, create_default_optimizer
from ..compat import json_dumps, copy_array
from ..tokens.doc cimport Doc
from ..gold cimport GoldParse
from ..errors import Errors, TempErrors
from .. import util
from .stateclass cimport StateClass
from ._state cimport StateC
from .transition_system cimport Transition
from . cimport _beam_utils
from . import _beam_utils
from . import nonproj
cdef class Parser:
"""
Base class of the DependencyParser and EntityRecognizer.
"""
@classmethod
def Model(cls, nr_class, **cfg):
depth = util.env_opt('parser_hidden_depth', cfg.get('hidden_depth', 1))
subword_features = util.env_opt('subword_features',
cfg.get('subword_features', True))
conv_depth = util.env_opt('conv_depth', cfg.get('conv_depth', 4))
bilstm_depth = util.env_opt('bilstm_depth', cfg.get('bilstm_depth', 0))
if depth != 1:
raise ValueError(TempErrors.T004.format(value=depth))
parser_maxout_pieces = util.env_opt('parser_maxout_pieces',
cfg.get('maxout_pieces', 2))
token_vector_width = util.env_opt('token_vector_width',
cfg.get('token_vector_width', 128))
hidden_width = util.env_opt('hidden_width', cfg.get('hidden_width', 128))
embed_size = util.env_opt('embed_size', cfg.get('embed_size', 5000))
pretrained_vectors = cfg.get('pretrained_vectors', None)
tok2vec = Tok2Vec(token_vector_width, embed_size,
conv_depth=conv_depth,
subword_features=subword_features,
pretrained_vectors=pretrained_vectors,
bilstm_depth=bilstm_depth)
tok2vec = chain(tok2vec, flatten)
lower = PrecomputableAffine(hidden_width,
nF=cls.nr_feature, nI=token_vector_width,
nP=parser_maxout_pieces)
lower.nP = parser_maxout_pieces
with Model.use_device('cpu'):
upper = zero_init(Affine(nr_class, hidden_width, drop_factor=0.0))
cfg = {
'nr_class': nr_class,
'hidden_depth': depth,
'token_vector_width': token_vector_width,
'hidden_width': hidden_width,
'maxout_pieces': parser_maxout_pieces,
'pretrained_vectors': pretrained_vectors,
'bilstm_depth': bilstm_depth
}
return ParserModel(tok2vec, lower, upper), cfg
name = 'base_parser'
def __init__(self, Vocab vocab, moves=True, model=True, **cfg):
"""Create a Parser.
vocab (Vocab): The vocabulary object. Must be shared with documents
to be processed. The value is set to the `.vocab` attribute.
moves (TransitionSystem): Defines how the parse-state is created,
updated and evaluated. The value is set to the .moves attribute
unless True (default), in which case a new instance is created with
`Parser.Moves()`.
model (object): Defines how the parse-state is created, updated and
evaluated. The value is set to the .model attribute. If set to True
(default), a new instance will be created with `Parser.Model()`
in parser.begin_training(), parser.from_disk() or parser.from_bytes().
**cfg: Arbitrary configuration parameters. Set to the `.cfg` attribute
"""
self.vocab = vocab
if moves is True:
self.moves = self.TransitionSystem(self.vocab.strings)
else:
self.moves = moves
if 'beam_width' not in cfg:
cfg['beam_width'] = util.env_opt('beam_width', 1)
if 'beam_density' not in cfg:
cfg['beam_density'] = util.env_opt('beam_density', 0.0)
cfg.setdefault('cnn_maxout_pieces', 3)
self.cfg = cfg
self.model = model
self._multitasks = []
def __reduce__(self):
return (Parser, (self.vocab, self.moves, self.model), None, None)
@property
def tok2vec(self):
return self.model.tok2vec
@property
def move_names(self):
names = []
for i in range(self.moves.n_moves):
name = self.moves.move_name(self.moves.c[i].move, self.moves.c[i].label)
names.append(name)
return names
nr_feature = 8
@property
def labels(self):
class_names = [self.moves.get_class_name(i) for i in range(self.moves.n_moves)]
return class_names
@property
def tok2vec(self):
'''Return the embedding and convolutional layer of the model.'''
return None if self.model in (None, True, False) else self.model.tok2vec
@property
def postprocesses(self):
# Available for subclasses, e.g. to deprojectivize
return []
def add_label(self, label):
resized = False
for action in self.moves.action_types:
added = self.moves.add_action(action, label)
if added:
resized = True
if self.model not in (True, False, None) and resized:
self.model.resize_output(self.moves.n_moves)
def add_multitask_objective(self, target):
# Defined in subclasses, to avoid circular import
raise NotImplementedError
def init_multitask_objectives(self, get_gold_tuples, pipeline, **cfg):
'''Setup models for secondary objectives, to benefit from multi-task
learning. This method is intended to be overridden by subclasses.
For instance, the dependency parser can benefit from sharing
an input representation with a label prediction model. These auxiliary
models are discarded after training.
'''
pass
def preprocess_gold(self, docs_golds):
for doc, gold in docs_golds:
yield doc, gold
def use_params(self, params):
# Can't decorate cdef class :(. Workaround.
with self.model.use_params(params):
yield
def __call__(self, Doc doc, beam_width=None):
"""Apply the parser or entity recognizer, setting the annotations onto
the `Doc` object.
doc (Doc): The document to be processed.
"""
if beam_width is None:
beam_width = self.cfg.get('beam_width', 1)
beam_density = self.cfg.get('beam_density', 0.)
states = self.predict([doc], beam_width=beam_width,
beam_density=beam_density)
self.set_annotations([doc], states, tensors=None)
return doc
def pipe(self, docs, int batch_size=256, int n_threads=2, beam_width=None):
"""Process a stream of documents.
stream: The sequence of documents to process.
batch_size (int): Number of documents to accumulate into a working set.
n_threads (int): The number of threads with which to work on the buffer
in parallel.
YIELDS (Doc): Documents, in order.
"""
if beam_width is None:
beam_width = self.cfg.get('beam_width', 1)
beam_density = self.cfg.get('beam_density', 0.)
cdef Doc doc
for batch in cytoolz.partition_all(batch_size, docs):
batch_in_order = list(batch)
by_length = sorted(batch_in_order, key=lambda doc: len(doc))
for subbatch in cytoolz.partition_all(8, by_length):
subbatch = list(subbatch)
parse_states = self.predict(subbatch, beam_width=beam_width,
beam_density=beam_density)
self.set_annotations(subbatch, parse_states, tensors=None)
for doc in batch_in_order:
yield doc
def predict(self, docs, beam_width=1, beam_density=0.0, drop=0.):
if isinstance(docs, Doc):
docs = [docs]
if not any(len(doc) for doc in docs):
return self.moves.init_batch(docs)
if beam_width < 2:
return self.greedy_parse(docs, drop=drop)
else:
return self.beam_parse(docs, beam_width=beam_width,
beam_density=beam_density, drop=drop)
def greedy_parse(self, docs, drop=0.):
cdef vector[StateC*] states
cdef StateClass state
model = self.model(docs)
batch = self.moves.init_batch(docs)
weights = get_c_weights(model)
for state in batch:
if not state.is_final():
states.push_back(state.c)
sizes = get_c_sizes(model, states.size())
with nogil:
self._parseC(&states[0],
weights, sizes)
return batch
def beam_parse(self, docs, int beam_width, float drop=0., beam_density=0.):
cdef Beam beam
cdef Doc doc
cdef np.ndarray token_ids
model = self.model(docs)
beams = self.moves.init_beams(docs, beam_width, beam_density=beam_density)
token_ids = numpy.zeros((len(docs) * beam_width, self.nr_feature),
dtype='i', order='C')
cdef int* c_ids
cdef int nr_feature = self.nr_feature
cdef int n_states
model = self.model(docs)
todo = [beam for beam in beams if not beam.is_done]
while todo:
token_ids.fill(-1)
c_ids = <int*>token_ids.data
n_states = 0
for beam in todo:
for i in range(beam.size):
state = <StateC*>beam.at(i)
# This way we avoid having to score finalized states
# We do have to take care to keep indexes aligned, though
if not state.is_final():
state.set_context_tokens(c_ids, nr_feature)
c_ids += nr_feature
n_states += 1
if n_states == 0:
break
vectors = model.state2vec(token_ids[:n_states])
scores = model.vec2scores(vectors)
todo = self.transition_beams(todo, scores)
return beams
cdef void _parseC(self, StateC** states,
WeightsC weights, SizesC sizes) nogil:
cdef int i, j
cdef vector[StateC*] unfinished
cdef ActivationsC activations
memset(&activations, 0, sizeof(activations))
while sizes.states >= 1:
predict_states(&activations,
states, &weights, sizes)
# Validate actions, argmax, take action.
self.c_transition_batch(states,
activations.scores, sizes.classes, sizes.states)
for i in range(sizes.states):
if not states[i].is_final():
unfinished.push_back(states[i])
for i in range(unfinished.size()):
states[i] = unfinished[i]
sizes.states = unfinished.size()
unfinished.clear()
def set_annotations(self, docs, states_or_beams, tensors=None):
cdef StateClass state
cdef Beam beam
cdef Doc doc
states = []
beams = []
for state_or_beam in states_or_beams:
if isinstance(state_or_beam, StateClass):
states.append(state_or_beam)
else:
beam = state_or_beam
state = StateClass.borrow(<StateC*>beam.at(0))
states.append(state)
beams.append(beam)
for i, (state, doc) in enumerate(zip(states, docs)):
self.moves.finalize_state(state.c)
for j in range(doc.length):
doc.c[j] = state.c._sent[j]
self.moves.finalize_doc(doc)
for hook in self.postprocesses:
hook(doc)
for beam in beams:
_beam_utils.cleanup_beam(beam)
def transition_states(self, states, float[:, ::1] scores):
cdef StateClass state
cdef float* c_scores = &scores[0, 0]
cdef vector[StateC*] c_states
for state in states:
c_states.push_back(state.c)
self.c_transition_batch(&c_states[0], c_scores, scores.shape[1], scores.shape[0])
return [state for state in states if not state.c.is_final()]
cdef void c_transition_batch(self, StateC** states, const float* scores,
int nr_class, int batch_size) nogil:
cdef int[500] is_valid # TODO: Unhack
cdef int i, guess
cdef Transition action
for i in range(batch_size):
self.moves.set_valid(is_valid, states[i])
guess = arg_max_if_valid(&scores[i*nr_class], is_valid, nr_class)
action = self.moves.c[guess]
action.do(states[i], action.label)
states[i].push_hist(guess)
def transition_beams(self, beams, float[:, ::1] scores):
cdef Beam beam
cdef float* c_scores = &scores[0, 0]
for beam in beams:
for i in range(beam.size):
state = <StateC*>beam.at(i)
if not state.is_final():
self.moves.set_valid(beam.is_valid[i], state)
memcpy(beam.scores[i], c_scores, scores.shape[1] * sizeof(float))
c_scores += scores.shape[1]
beam.advance(_beam_utils.transition_state, NULL, <void*>self.moves.c)
beam.check_done(_beam_utils.check_final_state, NULL)
return [b for b in beams if not b.is_done]
def update(self, docs, golds, drop=0., sgd=None, losses=None):
if isinstance(docs, Doc) and isinstance(golds, GoldParse):
docs = [docs]
golds = [golds]
if len(docs) != len(golds):
raise ValueError(Errors.E077.format(value='update', n_docs=len(docs),
n_golds=len(golds)))
if losses is None:
losses = {}
losses.setdefault(self.name, 0.)
# The probability we use beam update, instead of falling back to
# a greedy update
beam_update_prob = self.cfg.get('beam_update_prob', 1.0)
if self.cfg.get('beam_width', 1) >= 2 and numpy.random.random() < beam_update_prob:
return self.update_beam(docs, golds, self.cfg.get('beam_width', 1),
drop=drop, sgd=sgd, losses=losses,
beam_density=self.cfg.get('beam_density', 0.0))
# Chop sequences into lengths of this many transitions, to make the
# batch uniform length.
cut_gold = numpy.random.choice(range(20, 100))
states, golds, max_steps = self._init_gold_batch(docs, golds, max_length=cut_gold)
states_golds = [(s, g) for (s, g) in zip(states, golds)
if not s.is_final() and g is not None]
# Prepare the stepwise model, and get the callback for finishing the batch
model, finish_update = self.model.begin_update(docs, drop=drop)
for _ in range(max_steps):
if not states_golds:
break
states, golds = zip(*states_golds)
scores, backprop = model.begin_update(states, drop=drop)
d_scores = self.get_batch_loss(states, golds, scores, losses)
backprop(d_scores, sgd=sgd)
# Follow the predicted action
self.transition_states(states, scores)
states_golds = [eg for eg in states_golds if not eg[0].is_final()]
# Do the backprop
finish_update(golds, sgd=sgd)
return losses
def update_beam(self, docs, golds, width, drop=0., sgd=None, losses=None,
beam_density=0.0):
lengths = [len(d) for d in docs]
states = self.moves.init_batch(docs)
for gold in golds:
self.moves.preprocess_gold(gold)
model, finish_update = self.model.begin_update(docs, drop=drop)
states_d_scores, backprops, beams = _beam_utils.update_beam(
self.moves, self.nr_feature, 10000, states, golds, model.state2vec,
model.vec2scores, width, drop=drop, losses=losses,
beam_density=beam_density)
for i, d_scores in enumerate(states_d_scores):
losses[self.name] += (d_scores**2).sum()
ids, bp_vectors, bp_scores = backprops[i]
d_vector = bp_scores(d_scores, sgd=sgd)
if isinstance(model.ops, CupyOps) \
and not isinstance(ids, model.state2vec.ops.xp.ndarray):
model.backprops.append((
util.get_async(model.cuda_stream, ids),
util.get_async(model.cuda_stream, d_vector),
bp_vectors))
else:
model.backprops.append((ids, d_vector, bp_vectors))
model.make_updates(sgd)
cdef Beam beam
for beam in beams:
_beam_utils.cleanup_beam(beam)
def _init_gold_batch(self, whole_docs, whole_golds, min_length=5, max_length=500):
"""Make a square batch, of length equal to the shortest doc. A long
doc will get multiple states. Let's say we have a doc of length 2*N,
where N is the shortest doc. We'll make two states, one representing
long_doc[:N], and another representing long_doc[N:]."""
cdef:
StateClass state
Transition action
whole_states = self.moves.init_batch(whole_docs)
max_length = max(min_length, min(max_length, min([len(doc) for doc in whole_docs])))
max_moves = 0
states = []
golds = []
for doc, state, gold in zip(whole_docs, whole_states, whole_golds):
gold = self.moves.preprocess_gold(gold)
if gold is None:
continue
oracle_actions = self.moves.get_oracle_sequence(doc, gold)
start = 0
while start < len(doc):
state = state.copy()
n_moves = 0
while state.B(0) < start and not state.is_final():
action = self.moves.c[oracle_actions.pop(0)]
action.do(state.c, action.label)
state.c.push_hist(action.clas)
n_moves += 1
has_gold = self.moves.has_gold(gold, start=start,
end=start+max_length)
if not state.is_final() and has_gold:
states.append(state)
golds.append(gold)
max_moves = max(max_moves, n_moves)
start += min(max_length, len(doc)-start)
max_moves = max(max_moves, len(oracle_actions))
return states, golds, max_moves
def get_batch_loss(self, states, golds, float[:, ::1] scores, losses):
cdef StateClass state
cdef GoldParse gold
cdef Pool mem = Pool()
cdef int i
is_valid = <int*>mem.alloc(self.moves.n_moves, sizeof(int))
costs = <float*>mem.alloc(self.moves.n_moves, sizeof(float))
cdef np.ndarray d_scores = numpy.zeros((len(states), self.moves.n_moves),
dtype='f', order='C')
c_d_scores = <float*>d_scores.data
for i, (state, gold) in enumerate(zip(states, golds)):
memset(is_valid, 0, self.moves.n_moves * sizeof(int))
memset(costs, 0, self.moves.n_moves * sizeof(float))
self.moves.set_costs(is_valid, costs, state, gold)
cpu_log_loss(c_d_scores,
costs, is_valid, &scores[i, 0], d_scores.shape[1])
c_d_scores += d_scores.shape[1]
if losses is not None:
losses.setdefault(self.name, 0.)
losses[self.name] += (d_scores**2).sum()
return d_scores
def create_optimizer(self):
return create_default_optimizer(self.model.ops,
**self.cfg.get('optimizer', {}))
def begin_training(self, get_gold_tuples, pipeline=None, sgd=None, **cfg):
if 'model' in cfg:
self.model = cfg['model']
if not hasattr(get_gold_tuples, '__call__'):
gold_tuples = get_gold_tuples
get_gold_tuples = lambda: gold_tuples
cfg.setdefault('min_action_freq', 30)
actions = self.moves.get_actions(gold_parses=get_gold_tuples(),
min_freq=cfg.get('min_action_freq', 30))
previous_labels = dict(self.moves.labels)
self.moves.initialize_actions(actions)
for action, label_freqs in previous_labels.items():
for label in label_freqs:
self.moves.add_action(action, label)
cfg.setdefault('token_vector_width', 128)
if self.model is True:
self.model, cfg = self.Model(self.moves.n_moves, **cfg)
if sgd is None:
sgd = self.create_optimizer()
doc_sample = []
gold_sample = []
for raw_text, annots_brackets in cytoolz.take(1000, get_gold_tuples()):
for annots, brackets in annots_brackets:
ids, words, tags, heads, deps, ents = annots
doc_sample.append(Doc(self.vocab, words=words))
gold_sample.append(GoldParse(doc_sample[-1], words=words, tags=tags,
heads=heads, deps=deps, ents=ents))
self.model.begin_training(doc_sample, gold_sample)
if pipeline is not None:
self.init_multitask_objectives(get_gold_tuples, pipeline, sgd=sgd, **cfg)
link_vectors_to_models(self.vocab)
else:
if sgd is None:
sgd = self.create_optimizer()
self.model.begin_training([])
self.cfg.update(cfg)
return sgd
def to_disk(self, path, **exclude):
serializers = {
'model': lambda p: (self.model.to_disk(p) if self.model is not True else True),
'vocab': lambda p: self.vocab.to_disk(p),
'moves': lambda p: self.moves.to_disk(p, strings=False),
'cfg': lambda p: p.open('w').write(json_dumps(self.cfg))
}
util.to_disk(path, serializers, exclude)
def from_disk(self, path, **exclude):
deserializers = {
'vocab': lambda p: self.vocab.from_disk(p),
'moves': lambda p: self.moves.from_disk(p, strings=False),
'cfg': lambda p: self.cfg.update(util.read_json(p)),
'model': lambda p: None
}
util.from_disk(path, deserializers, exclude)
if 'model' not in exclude:
path = util.ensure_path(path)
if self.model is True:
self.model, cfg = self.Model(**self.cfg)
else:
cfg = {}
with (path / 'model').open('rb') as file_:
bytes_data = file_.read()
self.model.from_bytes(bytes_data)
self.cfg.update(cfg)
return self
def to_bytes(self, **exclude):
serializers = OrderedDict((
('model', lambda: (self.model.to_bytes() if self.model is not True else True)),
('vocab', lambda: self.vocab.to_bytes()),
('moves', lambda: self.moves.to_bytes(strings=False)),
('cfg', lambda: json.dumps(self.cfg, indent=2, sort_keys=True))
))
return util.to_bytes(serializers, exclude)
def from_bytes(self, bytes_data, **exclude):
deserializers = OrderedDict((
('vocab', lambda b: self.vocab.from_bytes(b)),
('moves', lambda b: self.moves.from_bytes(b, strings=False)),
('cfg', lambda b: self.cfg.update(json.loads(b))),
('model', lambda b: None)
))
msg = util.from_bytes(bytes_data, deserializers, exclude)
if 'model' not in exclude:
# TODO: Remove this once we don't have to handle previous models
if self.cfg.get('pretrained_dims') and 'pretrained_vectors' not in self.cfg:
self.cfg['pretrained_vectors'] = self.vocab.vectors.name
if self.model is True:
self.model, cfg = self.Model(**self.cfg)
else:
cfg = {}
if 'model' in msg:
self.model.from_bytes(msg['model'])
self.cfg.update(cfg)
return self