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Merge pull request #1570 from explosion/feature/fix-beam-leak 

Fix memory leak in beam parser
This commit is contained in:
Matthew Honnibal 2017-11-15 14:15:05 +01:00 committed by GitHub
parent 2f169fdb0a d274d3a3b9
commit 437ad1a852
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GPG Key ID: 4AEE18F83AFDEB23
7 changed files with 155 additions and 115 deletions
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54
spacy/syntax/_beam_utils.pyx
View File

@ -9,36 +9,31 @@ from thinc.typedefs cimport hash_t, class_t
from thinc.extra.search cimport MaxViolation
from .transition_system cimport TransitionSystem, Transition
from .stateclass cimport StateClass
from ..gold cimport GoldParse
from .stateclass cimport StateC, StateClass
# These are passed as callbacks to thinc.search.Beam
cdef int _transition_state(void* _dest, void* _src, class_t clas, void* _moves) except -1:
dest = <StateClass>_dest
src = <StateClass>_src
dest = <StateC*>_dest
src = <StateC*>_src
moves = <const Transition*>_moves
dest.clone(src)
moves[clas].do(dest.c, moves[clas].label)
dest.c.push_hist(clas)
moves[clas].do(dest, moves[clas].label)
dest.push_hist(clas)
cdef int _check_final_state(void* _state, void* extra_args) except -1:
return (<StateClass>_state).is_final()
def _cleanup(Beam beam):
for i in range(beam.width):
Py_XDECREF(<PyObject*>beam._states[i].content)
Py_XDECREF(<PyObject*>beam._parents[i].content)
state = <StateC*>_state
return state.is_final()
cdef hash_t _hash_state(void* _state, void* _) except 0:
state = <StateClass>_state
if state.c.is_final():
state = <StateC*>_state
if state.is_final():
return 1
else:
return state.c.hash()
return state.hash()
cdef class ParserBeam(object):
@ -55,14 +50,15 @@ cdef class ParserBeam(object):
self.golds = golds
self.beams = []
cdef Beam beam
cdef StateClass state, st
cdef StateClass state
cdef StateC* st
for state in states:
beam = Beam(self.moves.n_moves, width, density)
beam.initialize(self.moves.init_beam_state, state.c.length,
state.c._sent)
for i in range(beam.width):
st = <StateClass>beam.at(i)
st.c.offset = state.c.offset
st = <StateC*>beam.at(i)
st.offset = state.c.offset
self.beams.append(beam)
self.dones = [False] * len(self.beams)
@ -85,14 +81,12 @@ cdef class ParserBeam(object):
self._set_scores(beam, scores[i])
if self.golds is not None:
self._set_costs(beam, self.golds[i], follow_gold=follow_gold)
if follow_gold:
beam.advance(_transition_state, NULL, <void*>self.moves.c)
else:
beam.advance(_transition_state, _hash_state, <void*>self.moves.c)
beam.advance(_transition_state, NULL, <void*>self.moves.c)
beam.check_done(_check_final_state, NULL)
# This handles the non-monotonic stuff for the parser.
if beam.is_done and self.golds is not None:
for j in range(beam.size):
state = <StateClass>beam.at(j)
state = StateClass.borrow(<StateC*>beam.at(j))
if state.is_final():
try:
if self.moves.is_gold_parse(state, self.golds[i]):
@ -107,11 +101,11 @@ cdef class ParserBeam(object):
cdef int nr_state = min(scores.shape[0], beam.size)
cdef int nr_class = scores.shape[1]
for i in range(nr_state):
state = <StateClass>beam.at(i)
state = <StateC*>beam.at(i)
if not state.is_final():
for j in range(nr_class):
beam.scores[i][j] = c_scores[i * nr_class + j]
self.moves.set_valid(beam.is_valid[i], state.c)
self.moves.set_valid(beam.is_valid[i], state)
else:
for j in range(beam.nr_class):
beam.scores[i][j] = 0
@ -119,8 +113,8 @@ cdef class ParserBeam(object):
def _set_costs(self, Beam beam, GoldParse gold, int follow_gold=False):
for i in range(beam.size):
state = <StateClass>beam.at(i)
if not state.c.is_final():
state = StateClass.borrow(<StateC*>beam.at(i))
if not state.is_final():
self.moves.set_costs(beam.is_valid[i], beam.costs[i],
state, gold)
if follow_gold:
@ -157,7 +151,7 @@ def update_beam(TransitionSystem moves, int nr_feature, int max_steps,
pbeam = ParserBeam(moves, states, golds,
width=width, density=density)
gbeam = ParserBeam(moves, states, golds,
width=width, density=0.0)
width=width, density=density)
cdef StateClass state
beam_maps = []
backprops = []
@ -231,7 +225,7 @@ def get_states(pbeams, gbeams, beam_map, nr_update):
p_indices.append([])
g_indices.append([])
for i in range(pbeam.size):
state = <StateClass>pbeam.at(i)
state = StateClass.borrow(<StateC*>pbeam.at(i))
if not state.is_final():
key = tuple([eg_id] + pbeam.histories[i])
assert key not in seen, (key, seen)
@ -240,7 +234,7 @@ def get_states(pbeams, gbeams, beam_map, nr_update):
states.append(state)
beam_map.update(seen)
for i in range(gbeam.size):
state = <StateClass>gbeam.at(i)
state = StateClass.borrow(<StateC*>gbeam.at(i))
if not state.is_final():
key = tuple([eg_id] + gbeam.histories[i])
if key in seen:

28
spacy/syntax/arc_eager.pyx
View File

@ -292,12 +292,16 @@ cdef int _get_root(int word, const GoldParseC* gold) nogil:
cdef void* _init_state(Pool mem, int length, void* tokens) except NULL:
cdef StateClass st = StateClass.init(<const TokenC*>tokens, length)
for i in range(st.c.length):
st.c._sent[i].l_edge = i
st.c._sent[i].r_edge = i
st = new StateC(<const TokenC*>tokens, length)
for i in range(st.length):
if st._sent[i].dep == 0:
st._sent[i].l_edge = i
st._sent[i].r_edge = i
st._sent[i].head = 0
st._sent[i].dep = 0
st._sent[i].l_kids = 0
st._sent[i].r_kids = 0
st.fast_forward()
Py_INCREF(st)
return <void*>st
@ -533,18 +537,18 @@ cdef class ArcEager(TransitionSystem):
assert n_gold >= 1
def get_beam_annot(self, Beam beam):
length = (<StateClass>beam.at(0)).c.length
length = (<StateC*>beam.at(0)).length
heads = [{} for _ in range(length)]
deps = [{} for _ in range(length)]
probs = beam.probs
for i in range(beam.size):
stcls = <StateClass>beam.at(i)
self.finalize_state(stcls.c)
if stcls.is_final():
state = <StateC*>beam.at(i)
self.finalize_state(state)
if state.is_final():
prob = probs[i]
for j in range(stcls.c.length):
head = j + stcls.c._sent[j].head
dep = stcls.c._sent[j].dep
for j in range(state.length):
head = j + state._sent[j].head
dep = state._sent[j].dep
heads[j].setdefault(head, 0.0)
heads[j][head] += prob
deps[j].setdefault(dep, 0.0)

28
spacy/syntax/ner.pyx
View File

@ -123,14 +123,14 @@ cdef class BiluoPushDown(TransitionSystem):
entities = {}
probs = beam.probs
for i in range(beam.size):
stcls = <StateClass>beam.at(i)
if stcls.is_final():
self.finalize_state(stcls.c)
state = <StateC*>beam.at(i)
if state.is_final():
self.finalize_state(state)
prob = probs[i]
for j in range(stcls.c._e_i):
start = stcls.c._ents[j].start
end = stcls.c._ents[j].end
label = stcls.c._ents[j].label
for j in range(state._e_i):
start = state._ents[j].start
end = state._ents[j].end
label = state._ents[j].label
entities.setdefault((start, end, label), 0.0)
entities[(start, end, label)] += prob
return entities
@ -139,15 +139,15 @@ cdef class BiluoPushDown(TransitionSystem):
parses = []
probs = beam.probs
for i in range(beam.size):
stcls = <StateClass>beam.at(i)
if stcls.is_final():
self.finalize_state(stcls.c)
state = <StateC*>beam.at(i)
if state.is_final():
self.finalize_state(state)
prob = probs[i]
parse = []
for j in range(stcls.c._e_i):
start = stcls.c._ents[j].start
end = stcls.c._ents[j].end
label = stcls.c._ents[j].label
for j in range(state._e_i):
start = state._ents[j].start
end = state._ents[j].end
label = state._ents[j].label
parse.append((start, end, self.strings[label]))
parses.append((prob, parse))
return parses

143
spacy/syntax/nn_parser.pyx
View File

@ -17,7 +17,7 @@ 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
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
@ -224,6 +224,16 @@ cdef void cpu_regression_loss(float* d_scores,
d_scores[i] = diff
def _collect_states(beams):
cdef StateClass state
cdef Beam beam
states = []
for beam in beams:
state = StateClass.borrow(<StateC*>beam.at(0))
states.append(state)
return states
cdef class Parser:
"""
Base class of the DependencyParser and EntityRecognizer.
@ -336,7 +346,7 @@ cdef class Parser:
beam_density=beam_density)
beam = beams[0]
output = self.moves.get_beam_annot(beam)
state = <StateClass>beam.at(0)
state = StateClass.borrow(<StateC*>beam.at(0))
self.set_annotations([doc], [state], tensors=tokvecs)
_cleanup(beam)
return output
@ -356,10 +366,10 @@ cdef class Parser:
if beam_density is None:
beam_density = self.cfg.get('beam_density', 0.0)
cdef Doc doc
cdef Beam beam
for batch in cytoolz.partition_all(batch_size, docs):
batch = list(batch)
by_length = sorted(list(batch), key=lambda doc: len(doc))
batch_in_order = list(batch)
by_length = sorted(batch_in_order, key=lambda doc: len(doc))
batch_beams = []
for subbatch in cytoolz.partition_all(8, by_length):
subbatch = list(subbatch)
if beam_width == 1:
@ -369,21 +379,20 @@ cdef class Parser:
beams, tokvecs = self.beam_parse(subbatch,
beam_width=beam_width,
beam_density=beam_density)
parse_states = []
for beam in beams:
parse_states.append(<StateClass>beam.at(0))
self.set_annotations(subbatch, parse_states, tensors=tokvecs)
yield from batch
for beam in beams:
_cleanup(beam)
parse_states = _collect_states(beams)
self.set_annotations(subbatch, parse_states, tensors=None)
for beam in beams:
_cleanup(beam)
for doc in batch_in_order:
yield doc
def parse_batch(self, docs):
cdef:
precompute_hiddens state2vec
StateClass stcls
Pool mem
const float* feat_weights
StateC* st
StateClass stcls
vector[StateC*] states
int guess, nr_class, nr_feat, nr_piece, nr_dim, nr_state, nr_step
int j
@ -476,50 +485,59 @@ cdef class Parser:
cdef np.ndarray scores
cdef Doc doc
cdef int nr_class = self.moves.n_moves
cdef StateClass stcls, output
cuda_stream = util.get_cuda_stream()
(tokvecs, bp_tokvecs), state2vec, vec2scores = self.get_batch_model(
docs, cuda_stream, 0.0)
beams = []
cdef int offset = 0
cdef int j = 0
cdef int k
beams = []
for doc in docs:
beam = Beam(nr_class, beam_width, min_density=beam_density)
beam.initialize(self.moves.init_beam_state, doc.length, doc.c)
for i in range(beam.width):
stcls = <StateClass>beam.at(i)
stcls.c.offset = offset
state = <StateC*>beam.at(i)
state.offset = offset
offset += len(doc)
beam.check_done(_check_final_state, NULL)
while not beam.is_done:
states = []
beams.append(beam)
cdef np.ndarray token_ids
token_ids = numpy.zeros((len(docs) * beam_width, self.nr_feature),
dtype='i', order='C')
todo = [beam for beam in beams if not beam.is_done]
cdef int* c_ids
cdef int nr_feature = self.nr_feature
cdef int n_states
while todo:
todo = [beam for beam in beams if not beam.is_done]
token_ids.fill(-1)
c_ids = <int*>token_ids.data
n_states = 0
for beam in todo:
for i in range(beam.size):
stcls = <StateClass>beam.at(i)
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 stcls.is_final():
states.append(stcls)
token_ids = self.get_token_ids(states)
vectors = state2vec(token_ids)
if self.cfg.get('hist_size', 0):
hists = numpy.asarray([st.history[:self.cfg['hist_size']]
for st in states], dtype='i')
scores = vec2scores((vectors, hists))
else:
scores = vec2scores(vectors)
j = 0
c_scores = <float*>scores.data
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 = state2vec(token_ids[:n_states])
scores = vec2scores(vectors)
c_scores = <float*>scores.data
for beam in todo:
for i in range(beam.size):
stcls = <StateClass>beam.at(i)
if not stcls.is_final():
self.moves.set_valid(beam.is_valid[i], stcls.c)
for k in range(nr_class):
beam.scores[i][k] = c_scores[j * scores.shape[1] + k]
j += 1
beam.advance(_transition_state, _hash_state, <void*>self.moves.c)
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, nr_class * sizeof(float))
c_scores += nr_class
beam.advance(_transition_state, NULL, <void*>self.moves.c)
beam.check_done(_check_final_state, NULL)
beams.append(beam)
tokvecs = self.model[0].ops.unflatten(tokvecs,
[len(doc) for doc in docs])
return beams, tokvecs
@ -527,7 +545,7 @@ cdef class Parser:
def update(self, docs, golds, drop=0., sgd=None, losses=None):
if not any(self.moves.has_gold(gold) for gold in golds):
return None
if self.cfg.get('beam_width', 1) >= 2 and numpy.random.random() >= 0.5:
if self.cfg.get('beam_width', 1) >= 2 and numpy.random.random() >= 0.0:
return self.update_beam(docs, golds,
self.cfg['beam_width'], self.cfg['beam_density'],
drop=drop, sgd=sgd, losses=losses)
@ -965,27 +983,40 @@ cdef int arg_max_if_valid(const weight_t* scores, const int* is_valid, int n) no
# These are passed as callbacks to thinc.search.Beam
cdef int _transition_state(void* _dest, void* _src, class_t clas, void* _moves) except -1:
dest = <StateClass>_dest
src = <StateClass>_src
dest = <StateC*>_dest
src = <StateC*>_src
moves = <const Transition*>_moves
dest.clone(src)
moves[clas].do(dest.c, moves[clas].label)
dest.c.push_hist(clas)
moves[clas].do(dest, moves[clas].label)
dest.push_hist(clas)
cdef int _check_final_state(void* _state, void* extra_args) except -1:
return (<StateClass>_state).is_final()
state = <StateC*>_state
return state.is_final()
def _cleanup(Beam beam):
cdef StateC* state
# Once parsing has finished, states in beam may not be unique. Is this
# correct?
seen = set()
for i in range(beam.width):
Py_XDECREF(<PyObject*>beam._states[i].content)
Py_XDECREF(<PyObject*>beam._parents[i].content)
cdef hash_t _hash_state(void* _state, void* _) except 0:
state = <StateClass>_state
if state.c.is_final():
return 1
else:
return state.c.hash()
addr = <size_t>beam._parents[i].content
if addr not in seen:
state = <StateC*>addr
del state
seen.add(addr)
else:
print(i, addr)
print(seen)
raise Exception
addr = <size_t>beam._states[i].content
if addr not in seen:
state = <StateC*>addr
del state
seen.add(addr)
else:
print(i, addr)
print(seen)
raise Exception

10
spacy/syntax/stateclass.pxd
View File

@ -13,12 +13,22 @@ from ._state cimport StateC
cdef class StateClass:
cdef Pool mem
cdef StateC* c
cdef int _borrowed
@staticmethod
cdef inline StateClass init(const TokenC* sent, int length):
cdef StateClass self = StateClass()
self.c = new StateC(sent, length)
return self
@staticmethod
cdef inline StateClass borrow(StateC* ptr):
cdef StateClass self = StateClass()
del self.c
self.c = ptr
self._borrowed = 1
return self
@staticmethod
cdef inline StateClass init_offset(const TokenC* sent, int length, int

4
spacy/syntax/stateclass.pyx
View File

@ -11,12 +11,14 @@ cdef class StateClass:
def __init__(self, Doc doc=None, int offset=0):
cdef Pool mem = Pool()
self.mem = mem
self._borrowed = 0
if doc is not None:
self.c = new StateC(doc.c, doc.length)
self.c.offset = offset
def __dealloc__(self):
del self.c
if self._borrowed != 1:
del self.c
@property
def stack(self):

3
spacy/syntax/transition_system.pyx
View File

@ -23,8 +23,7 @@ class OracleError(Exception):
cdef void* _init_state(Pool mem, int length, void* tokens) except NULL:
cdef StateClass st = StateClass.init(<const TokenC*>tokens, length)
Py_INCREF(st)
cdef StateC* st = new StateC(<const TokenC*>tokens, length)
return <void*>st