def get_query_encoder(args):
saved_state = load_states_from_checkpoint(args.model_file)
set_encoder_params_from_state(saved_state.encoder_params, args)
print_args(args)
tensorizer, encoder, _ = init_biencoder_components(args.encoder_model_type,
args,
inference_only=True)
encoder = encoder.question_model
#encoder, _ = setup_for_distributed_mode(encoder, None, args.device, args.n_gpu,
# args.local_rank,
# args.fp16,
# args.fp16_opt_level)
#encoder.eval()
logger.info(args.__dict__)
# load weights from the model file
model_to_load = get_model_obj(encoder)
logger.info('Loading saved model state ...')
logger.debug('saved model keys =%s', saved_state.model_dict.keys())
prefix_len = len('question_model.')
ctx_state = {
key[prefix_len:]: value
for (key, value) in saved_state.model_dict.items()
if key.startswith('question_model.')
}
model_to_load.load_state_dict(ctx_state)
return model_to_load
def _load_saved_state(self, saved_state: CheckpointStateOFA):
epoch = saved_state.epoch
# offset is currently ignored since all checkpoints are made after full epochs
offset = saved_state.offset
if offset == 0: # epoch has been completed
epoch += 1
logger.info("Loading checkpoint @ batch=%s and epoch=%s", offset, epoch)
if self.cfg.ignore_checkpoint_offset:
self.start_epoch = 0
self.start_batch = 0
else:
self.start_epoch = epoch
# TODO: offset doesn't work for multiset currently
self.start_batch = 0 # offset
model_to_load = get_model_obj(self.model)
logger.info("Loading saved model state ...")
model_to_load.load_state(saved_state)
if not self.cfg.ignore_checkpoint_optimizer:
if saved_state.biencoder_optimizer_dict:
logger.info("Loading saved biencoder optimizer state ...")
self.biencoder_optimizer.load_state_dict(saved_state.biencoder_optimizer_dict)
if saved_state.biencoder_scheduler_dict:
self.biencoder_scheduler_state = saved_state.biencoder_scheduler_dict
if saved_state.reader_optimizer_dict:
logger.info("Loading saved reader optimizer state ...")
self.reader_optimizer.load_state_dict(saved_state.reader_optimizer_dict)
if saved_state.reader_scheduler_dict:
self.reader_scheduler_state = saved_state.reader_scheduler_dict
def main(args):
saved_state = load_states_from_checkpoint(args.model_file)
set_encoder_params_from_state(saved_state.encoder_params, args)
print_args(args)
tensorizer, encoder, _ = init_biencoder_components(args.encoder_model_type,
args,
inference_only=True)
encoder = encoder.ctx_model
encoder, _ = setup_for_distributed_mode(encoder, None, args.device,
args.n_gpu, args.local_rank,
args.fp16, args.fp16_opt_level)
encoder.eval()
# load weights from the model file
model_to_load = get_model_obj(encoder)
logger.info('Loading saved model state ...')
logger.debug('saved model keys =%s', saved_state.model_dict.keys())
prefix_len = len('ctx_model.')
ctx_state = {
key[prefix_len:]: value
for (key, value) in saved_state.model_dict.items()
if key.startswith('ctx_model.')
}
model_to_load.load_state_dict(ctx_state)
logger.info('reading data from file=%s', args.ctx_file)
rows = []
with open(args.ctx_file) as tsvfile:
reader = csv.reader(tsvfile, delimiter='\t')
# file format: doc_id, doc_text, title
rows.extend([(row[0], row[1], row[2]) for row in reader
if row[0] != 'id'])
shard_size = int(len(rows) / args.num_shards)
start_idx = args.shard_id * shard_size
end_idx = start_idx + shard_size
logger.info(
'Producing encodings for passages range: %d to %d (out of total %d)',
start_idx, end_idx, len(rows))
rows = rows[start_idx:end_idx]
data = gen_ctx_vectors(rows, encoder, tensorizer, True)
file = args.out_file + '_' + str(args.shard_id)
pathlib.Path(os.path.dirname(file)).mkdir(parents=True, exist_ok=True)
logger.info('Writing results to %s' % file)
with open(file, mode='wb') as f:
pickle.dump(data, f)
logger.info('Total passages processed %d. Written to %s', len(data), file)
def __init__(self, name, **config):
super().__init__(name)
self.args = argparse.Namespace(**config)
saved_state = load_states_from_checkpoint(self.args.model_file)
set_encoder_params_from_state(saved_state.encoder_params, self.args)
tensorizer, encoder, _ = init_biencoder_components(
self.args.encoder_model_type, self.args, inference_only=True)
encoder = encoder.question_model
encoder, _ = setup_for_distributed_mode(
encoder,
None,
self.args.device,
self.args.n_gpu,
self.args.local_rank,
self.args.fp16,
)
encoder.eval()
# load weights from the model file
model_to_load = get_model_obj(encoder)
prefix_len = len("question_model.")
question_encoder_state = {
key[prefix_len:]: value
for (key, value) in saved_state.model_dict.items()
if key.startswith("question_model.")
}
model_to_load.load_state_dict(question_encoder_state)
vector_size = model_to_load.get_out_size()
index_buffer_sz = self.args.index_buffer
if self.args.hnsw_index:
index = DenseHNSWFlatIndexer(vector_size)
index.deserialize_from(self.args.hnsw_index_path)
else:
index = DenseFlatIndexer(vector_size)
self.retriever = DenseRetriever(encoder, self.args.batch_size,
tensorizer, index)
# index all passages
ctx_files_pattern = self.args.encoded_ctx_file
input_paths = glob.glob(ctx_files_pattern)
if not self.args.hnsw_index:
self.retriever.index_encoded_data(input_paths,
buffer_size=index_buffer_sz)
# not needed for now
self.all_passages = load_passages(self.args.ctx_file)
self.KILT_mapping = None
if self.args.KILT_mapping:
self.KILT_mapping = pickle.load(open(self.args.KILT_mapping, "rb"))
def get_retriever(args):
saved_state = load_states_from_checkpoint(args.model_file)
set_encoder_params_from_state(saved_state.encoder_params, args)
tensorizer, encoder, _ = init_biencoder_components(args.encoder_model_type,
args,
inference_only=True)
encoder = encoder.question_model
encoder, _ = setup_for_distributed_mode(encoder, None, args.device,
args.n_gpu, args.local_rank,
args.fp16)
encoder.eval()
# load weights from the model file
model_to_load = get_model_obj(encoder)
logger.info('Loading saved model state ...')
prefix_len = len('question_model.')
question_encoder_state = {
key[prefix_len:]: value
for (key, value) in saved_state.model_dict.items()
if key.startswith('question_model.')
}
model_to_load.load_state_dict(question_encoder_state)
vector_size = model_to_load.get_out_size()
logger.info('Encoder vector_size=%d', vector_size)
index_buffer_sz = args.index_buffer
if args.hnsw_index:
index = DenseHNSWFlatIndexer(vector_size)
index_buffer_sz = -1 # encode all at once
else:
index = DenseFlatIndexer(vector_size)
retriever = DenseRetriever(encoder, args.batch_size, tensorizer, index,
args.device)
# index all passages
if len(args.encoded_ctx_file) > 0:
ctx_files_pattern = args.encoded_ctx_file
input_paths = glob.glob(ctx_files_pattern)
index_path = "_".join(input_paths[0].split("_")[:-1])
if args.save_or_load_index and os.path.exists(index_path):
retriever.index.deserialize(index_path)
else:
logger.info('Reading all passages data from files: %s',
input_paths)
retriever.index_encoded_data(input_paths,
buffer_size=index_buffer_sz)
if args.save_or_load_index:
retriever.index.serialize(index_path)
# get questions & answers
return retriever
def load_saved_state_into_model(encoder, prefix="ctx_model."):
encoder.eval()
model_to_load = get_model_obj(encoder)
prefix_len = len(prefix)
encoder_state = {
key[prefix_len:]: value
for (key, value) in saved_state.model_dict.items()
if key.startswith(prefix)
}
model_to_load.load_state_dict(encoder_state)
return model_to_load
def main(args):
saved_state = load_states_from_checkpoint(args.model_file)
set_encoder_params_from_state(saved_state.encoder_params, args)
print_args(args)
tensorizer, encoder, _ = init_biencoder_components(args.encoder_model_type,
args,
inference_only=True)
encoder = encoder.ctx_model
encoder, _ = setup_for_distributed_mode(encoder, None, args.device,
args.n_gpu, args.local_rank,
args.fp16, args.fp16_opt_level)
encoder.eval()
# load weights from the model file
model_to_load = get_model_obj(encoder)
logger.info('Loading saved model state ...')
logger.debug('saved model keys =%s', saved_state.model_dict.keys())
prefix_len = len('ctx_model.')
ctx_state = {
key[prefix_len:]: value
for (key, value) in saved_state.model_dict.items()
if key.startswith('ctx_model.')
}
model_to_load.load_state_dict(ctx_state)
logger.info('reading data from file=%s', args.ctx_file)
rows = []
with open(args.ctx_file) as jsonfile:
blob = json.load(jsonfile)
for paper in blob.values():
s2_id = paper["paper_id"]
title = paper.get("title") or ""
abstract = paper.get("abstract") or ""
rows.append((s2_id, abstract, title))
data = gen_ctx_vectors(rows, encoder, tensorizer, True)
file = args.out_file
pathlib.Path(os.path.dirname(file)).mkdir(parents=True, exist_ok=True)
logger.info('Writing results to %s' % file)
with open(file, "w+") as f:
for (s2_id, vec) in data:
out = {"paper_id": s2_id, "embedding": vec.tolist()}
f.write(json.dumps(out) + "\n")
logger.info('Total passages processed %d. Written to %s', len(data), file)
def _load_saved_state(self, saved_state: CheckpointState):
epoch = saved_state.epoch
offset = saved_state.offset
if offset == 0: # epoch has been completed
epoch += 1
# logger.info('Loading checkpoint @ batch=%s and epoch=%s', offset, epoch)
# self.start_epoch = epoch
# self.start_batch = offset
model_to_load = get_model_obj(self.reader)
if saved_state.model_dict:
logger.info('Loading model weights from saved state ...')
model_to_load.load_state_dict(saved_state.model_dict)
def _save_checkpoint(self, scheduler, epoch: int, offset: int) -> str:
args = self.args
model_to_save = get_model_obj(self.reader)
cp = os.path.join(args.output_dir,
args.checkpoint_file_name + '.' + str(epoch) + ('.' + str(offset) if offset > 0 else ''))
meta_params = get_encoder_params_state(args)
state = CheckpointState(model_to_save.state_dict(), self.optimizer.state_dict(), scheduler.state_dict(), offset,
epoch, meta_params
)
torch.save(state._asdict(), cp)
return cp
def _save_checkpoint(self, scheduler, epoch: int, offset: int) -> str:
cfg = self.cfg
model_to_save = get_model_obj(self.biencoder)
cp = os.path.join(cfg.output_dir, cfg.checkpoint_file_name + "." + str(epoch))
meta_params = get_encoder_params_state_from_cfg(cfg)
state = CheckpointState(
model_to_save.get_state_dict(),
self.optimizer.state_dict(),
scheduler.state_dict(),
offset,
epoch,
meta_params,
)
torch.save(state._asdict(), cp)
logger.info("Saved checkpoint at %s", cp)
return cp
def __init__(self, args, model_file):
self.args = args
saved_state = load_states_from_checkpoint(model_file)
set_encoder_params_from_state(saved_state.encoder_params, args)
tensorizer, reader, optimizer = init_reader_components(
args.encoder_model_type, args)
tensorizer.pad_to_max = False
del optimizer
reader = reader.cuda()
reader = reader.eval()
self.reader = reader
self.tensorizer = tensorizer
model_to_load = get_model_obj(self.reader)
model_to_load.load_state_dict(saved_state.model_dict)
def _load_saved_state(self, saved_state: CheckpointState):
epoch = saved_state.epoch
offset = saved_state.offset
if offset == 0: # epoch has been completed
epoch += 1
logger.info("Loading checkpoint @ batch=%s and epoch=%s", offset, epoch)
self.start_epoch = epoch
self.start_batch = offset
model_to_load = get_model_obj(self.reader)
if saved_state.model_dict:
logger.info("Loading model weights from saved state ...")
model_to_load.load_state_dict(saved_state.model_dict)
logger.info("Loading saved optimizer state ...")
if saved_state.optimizer_dict:
self.optimizer.load_state_dict(saved_state.optimizer_dict)
self.scheduler_state = saved_state.scheduler_dict
def _load_saved_state(self, saved_state: CheckpointState):
epoch = saved_state.epoch
offset = saved_state.offset
if offset == 0: # epoch has been completed
epoch += 1
logger.info('Loading checkpoint @ batch=%s and epoch=%s', offset, epoch)
self.start_epoch = epoch
self.start_batch = offset
model_to_load = get_model_obj(self.biencoder)
logger.info('Loading saved model state ...')
model_to_load.load_state_dict(saved_state.model_dict, strict=False) # set strict=False if you use extra projection
if saved_state.optimizer_dict:
logger.info('Loading saved optimizer state ...')
self.optimizer.load_state_dict(saved_state.optimizer_dict)
if saved_state.scheduler_dict:
self.scheduler_state = saved_state.scheduler_dict
def _save_checkpoint(self, scheduler, epoch: int, offset: int) -> str:
args = self.args
model_to_save = get_model_obj(self.biencoder)
cp = os.path.join(
args.output_dir,
args.checkpoint_file_name + "." + str(epoch) +
("." + str(offset) if offset > 0 else ""),
)
meta_params = get_encoder_params_state(args)
state = CheckpointState(
model_to_save.state_dict(),
self.optimizer.state_dict(),
scheduler.state_dict(),
offset,
epoch,
meta_params,
)
torch.save(state._asdict(), cp)
logger.info("Saved checkpoint at %s", cp)
return cp
def setup_dpr(model_file,
ctx_file,
encoded_ctx_file,
hnsw_index=False,
save_or_load_index=False):
global retriever
global all_passages
global answer_cache
global answer_cache_path
parameter_setting = model_file + ctx_file + encoded_ctx_file
answer_cache_path = hashlib.sha1(
parameter_setting.encode("utf-8")).hexdigest()
if os.path.exists(answer_cache_path):
answer_cache = pickle.load(open(answer_cache_path, 'rb'))
else:
answer_cache = {}
parser = argparse.ArgumentParser()
add_encoder_params(parser)
add_tokenizer_params(parser)
add_cuda_params(parser)
args = parser.parse_args()
args.model_file = model_file
args.ctx_file = ctx_file
args.encoded_ctx_file = encoded_ctx_file
args.hnsw_index = hnsw_index
args.save_or_load_index = save_or_load_index
args.batch_size = 1 # TODO
setup_args_gpu(args)
print_args(args)
saved_state = load_states_from_checkpoint(args.model_file)
set_encoder_params_from_state(saved_state.encoder_params, args)
tensorizer, encoder, _ = init_biencoder_components(args.encoder_model_type,
args,
inference_only=True)
encoder = encoder.question_model
encoder, _ = setup_for_distributed_mode(encoder, None, args.device,
args.n_gpu, args.local_rank,
args.fp16)
encoder.eval()
# load weights from the model file
model_to_load = get_model_obj(encoder)
logger.info("Loading saved model state ...")
prefix_len = len("question_model.")
question_encoder_state = {
key[prefix_len:]: value
for (key, value) in saved_state.model_dict.items()
if key.startswith("question_model.")
}
model_to_load.load_state_dict(question_encoder_state)
vector_size = model_to_load.get_out_size()
logger.info("Encoder vector_size=%d", vector_size)
if args.hnsw_index:
index = DenseHNSWFlatIndexer(vector_size, 50000)
else:
index = DenseFlatIndexer(vector_size, 50000,
"IVF65536,PQ64") #IVF65536
retriever = DenseRetriever(encoder, args.batch_size, tensorizer, index)
# index all passages
ctx_files_pattern = args.encoded_ctx_file
input_paths = glob.glob(ctx_files_pattern)
index_path = "_".join(input_paths[0].split("_")[:-1])
if args.save_or_load_index and (os.path.exists(index_path) or
os.path.exists(index_path + ".index.dpr")):
retriever.index.deserialize_from(index_path)
else:
logger.info("Reading all passages data from files: %s", input_paths)
retriever.index.index_data(input_paths)
if args.save_or_load_index:
retriever.index.serialize(index_path)
# get questions & answers
all_passages = load_passages(args.ctx_file)
def main(cfg: DictConfig):
cfg = setup_cfg_gpu(cfg)
logger.info("CFG (after gpu configuration):")
logger.info("%s", OmegaConf.to_yaml(cfg))
saved_state = load_states_from_checkpoint(cfg.model_file)
set_cfg_params_from_state(saved_state.encoder_params, cfg)
tensorizer, encoder, _ = init_biencoder_components(
cfg.encoder.encoder_model_type, cfg, inference_only=True)
encoder_path = cfg.encoder_path
if encoder_path:
logger.info("Selecting encoder: %s", encoder_path)
encoder = getattr(encoder, encoder_path)
else:
logger.info("Selecting standard question encoder")
encoder = encoder.question_model
encoder, _ = setup_for_distributed_mode(encoder, None, cfg.device,
cfg.n_gpu, cfg.local_rank,
cfg.fp16)
encoder.eval()
# load weights from the model file
model_to_load = get_model_obj(encoder)
logger.info("Loading saved model state ...")
encoder_prefix = (encoder_path if encoder_path else "question_model") + "."
prefix_len = len(encoder_prefix)
logger.info("Encoder state prefix %s", encoder_prefix)
question_encoder_state = {
key[prefix_len:]: value
for (key, value) in saved_state.model_dict.items()
if key.startswith(encoder_prefix)
}
model_to_load.load_state_dict(question_encoder_state)
vector_size = model_to_load.get_out_size()
logger.info("Encoder vector_size=%d", vector_size)
# get questions & answers
questions = []
question_answers = []
if not cfg.qa_dataset:
logger.warning("Please specify qa_dataset to use")
return
ds_key = cfg.qa_dataset
logger.info("qa_dataset: %s", ds_key)
qa_src = hydra.utils.instantiate(cfg.datasets[ds_key])
qa_src.load_data()
for ds_item in qa_src.data:
question, answers = ds_item.query, ds_item.answers
questions.append(question)
question_answers.append(answers)
index = hydra.utils.instantiate(cfg.indexers[cfg.indexer])
logger.info("Index class %s ", type(index))
index_buffer_sz = index.buffer_size
index.init_index(vector_size)
retriever = LocalFaissRetriever(encoder, cfg.batch_size, tensorizer, index)
logger.info("Using special token %s", qa_src.special_query_token)
questions_tensor = retriever.generate_question_vectors(
questions, query_token=qa_src.special_query_token)
if qa_src.selector:
logger.info("Using custom representation token selector")
retriever.selector = qa_src.selector
id_prefixes = []
ctx_sources = []
for ctx_src in cfg.ctx_datatsets:
ctx_src = hydra.utils.instantiate(cfg.ctx_sources[ctx_src])
id_prefixes.append(ctx_src.id_prefix)
ctx_sources.append(ctx_src)
logger.info("id_prefixes per dataset: %s", id_prefixes)
# index all passages
ctx_files_patterns = cfg.encoded_ctx_files
index_path = cfg.index_path
logger.info("ctx_files_patterns: %s", ctx_files_patterns)
if ctx_files_patterns:
assert len(ctx_files_patterns) == len(
id_prefixes), "ctx len={} pref leb={}".format(
len(ctx_files_patterns), len(id_prefixes))
else:
assert (
index_path
), "Either encoded_ctx_files or index_path parameter should be set."
input_paths = []
path_id_prefixes = []
for i, pattern in enumerate(ctx_files_patterns):
pattern_files = glob.glob(pattern)
pattern_id_prefix = id_prefixes[i]
input_paths.extend(pattern_files)
path_id_prefixes.extend([pattern_id_prefix] * len(pattern_files))
logger.info("Embeddings files id prefixes: %s", path_id_prefixes)
if index_path and index.index_exists(index_path):
logger.info("Index path: %s", index_path)
retriever.index.deserialize(index_path)
else:
logger.info("Reading all passages data from files: %s", input_paths)
retriever.index_encoded_data(input_paths,
index_buffer_sz,
path_id_prefixes=path_id_prefixes)
if index_path:
retriever.index.serialize(index_path)
# get top k results
top_ids_and_scores = retriever.get_top_docs(questions_tensor.numpy(),
cfg.n_docs)
# we no longer need the index
retriever = None
all_passages = {}
for ctx_src in ctx_sources:
ctx_src.load_data_to(all_passages)
if len(all_passages) == 0:
raise RuntimeError(
"No passages data found. Please specify ctx_file param properly.")
if cfg.validate_as_tables:
questions_doc_hits = validate_tables(
all_passages,
question_answers,
top_ids_and_scores,
cfg.validation_workers,
cfg.match,
)
else:
questions_doc_hits = validate(
all_passages,
question_answers,
top_ids_and_scores,
cfg.validation_workers,
cfg.match,
)
if cfg.out_file:
save_results(
all_passages,
questions,
question_answers,
top_ids_and_scores,
questions_doc_hits,
cfg.out_file,
)
if cfg.kilt_out_file:
kilt_ctx = next(
iter([
ctx for ctx in ctx_sources if isinstance(ctx, KiltCsvCtxSrc)
]), None)
if not kilt_ctx:
raise RuntimeError("No Kilt compatible context file provided")
assert hasattr(cfg, "kilt_out_file")
kilt_ctx.convert_to_kilt(qa_src.kilt_gold_file, cfg.out_file,
cfg.kilt_out_file)
def main(args):
saved_state = load_states_from_checkpoint(args.model_file)
set_encoder_params_from_state(saved_state.encoder_params, args)
tensorizer, encoder, _ = init_biencoder_components(
args.encoder_model_type, args, inference_only=True)
encoder = encoder.question_model
encoder, _ = setup_for_distributed_mode(encoder, None, args.device, args.n_gpu,
args.local_rank,
args.fp16)
encoder.eval()
# load weights from the model file
model_to_load = get_model_obj(encoder)
logger.info('Loading saved model state ...')
prefix_len = len('question_model.')
question_encoder_state = {key[prefix_len:]: value for (key, value) in saved_state.model_dict.items() if
key.startswith('question_model.')}
model_to_load.load_state_dict(question_encoder_state)
vector_size = model_to_load.get_out_size()
logger.info('Encoder vector_size=%d', vector_size)
if args.hnsw_index:
index = DenseHNSWFlatIndexer(vector_size, args.index_buffer)
else:
index = DenseFlatIndexer(vector_size, args.index_buffer)
retriever = DenseRetriever(encoder, args.batch_size, tensorizer, index)
# index all passages
ctx_files_pattern = args.encoded_ctx_file
input_paths = glob.glob(ctx_files_pattern)
index_path = "_".join(input_paths[0].split("_")[:-1])
if args.save_or_load_index and (os.path.exists(index_path) or os.path.exists(index_path + ".index.dpr")):
retriever.index.deserialize_from(index_path)
else:
logger.info('Reading all passages data from files: %s', input_paths)
retriever.index.index_data(input_paths)
if args.save_or_load_index:
retriever.index.serialize(index_path)
# get questions & answers
questions = []
question_ids = []
for ds_item in parse_qa_csv_file(args.qa_file):
question_id, question = ds_item
question_ids.append(question_id)
questions.append(question)
questions_tensor = retriever.generate_question_vectors(questions)
# get top k results
top_ids_and_scores = retriever.get_top_docs(
questions_tensor.numpy(), args.n_docs)
# all_passages = load_passages(args.ctx_file)
# if len(all_passages) == 0:
# raise RuntimeError(
# 'No passages data found. Please specify ctx_file param properly.')
# questions_doc_hits = validate(all_passages, question_answers, top_ids_and_scores, args.validation_workers,
# args.match)
if args.out_file:
save_results(question_ids,
top_ids_and_scores, args.out_file)
def main(cfg: DictConfig):
cfg = setup_cfg_gpu(cfg)
saved_state = load_states_from_checkpoint(cfg.model_file)
set_cfg_params_from_state(saved_state.encoder_params, cfg)
logger.info("CFG (after gpu configuration):")
logger.info("%s", OmegaConf.to_yaml(cfg))
tensorizer, encoder, _ = init_biencoder_components(
cfg.encoder.encoder_model_type, cfg, inference_only=True)
logger.info("Loading saved model state ...")
encoder.load_state(saved_state, strict=False)
encoder_path = cfg.encoder_path
if encoder_path:
logger.info("Selecting encoder: %s", encoder_path)
encoder = getattr(encoder, encoder_path)
else:
logger.info("Selecting standard question encoder")
encoder = encoder.question_model
encoder, _ = setup_for_distributed_mode(encoder, None, cfg.device,
cfg.n_gpu, cfg.local_rank,
cfg.fp16)
encoder.eval()
model_to_load = get_model_obj(encoder)
vector_size = model_to_load.get_out_size()
logger.info("Encoder vector_size=%d", vector_size)
# get questions & answers
questions = []
questions_text = []
question_answers = []
if not cfg.qa_dataset:
logger.warning("Please specify qa_dataset to use")
return
ds_key = cfg.qa_dataset
logger.info("qa_dataset: %s", ds_key)
qa_src = hydra.utils.instantiate(cfg.datasets[ds_key])
qa_src.load_data()
total_queries = len(qa_src)
for i in range(total_queries):
qa_sample = qa_src[i]
question, answers = qa_sample.query, qa_sample.answers
questions.append(question)
question_answers.append(answers)
logger.info("questions len %d", len(questions))
logger.info("questions_text len %d", len(questions_text))
if cfg.rpc_retriever_cfg_file:
index_buffer_sz = 1000
retriever = DenseRPCRetriever(
encoder,
cfg.batch_size,
tensorizer,
cfg.rpc_retriever_cfg_file,
vector_size,
use_l2_conversion=cfg.use_l2_conversion,
)
else:
index = hydra.utils.instantiate(cfg.indexers[cfg.indexer])
logger.info("Local Index class %s ", type(index))
index_buffer_sz = index.buffer_size
index.init_index(vector_size)
retriever = LocalFaissRetriever(encoder, cfg.batch_size, tensorizer,
index)
logger.info("Using special token %s", qa_src.special_query_token)
questions_tensor = retriever.generate_question_vectors(
questions, query_token=qa_src.special_query_token)
if qa_src.selector:
logger.info("Using custom representation token selector")
retriever.selector = qa_src.selector
index_path = cfg.index_path
if cfg.rpc_retriever_cfg_file and cfg.rpc_index_id:
retriever.load_index(cfg.rpc_index_id)
elif index_path and index.index_exists(index_path):
logger.info("Index path: %s", index_path)
retriever.index.deserialize(index_path)
else:
# send data for indexing
id_prefixes = []
ctx_sources = []
for ctx_src in cfg.ctx_datatsets:
ctx_src = hydra.utils.instantiate(cfg.ctx_sources[ctx_src])
id_prefixes.append(ctx_src.id_prefix)
ctx_sources.append(ctx_src)
logger.info("ctx_sources: %s", type(ctx_src))
logger.info("id_prefixes per dataset: %s", id_prefixes)
# index all passages
ctx_files_patterns = cfg.encoded_ctx_files
logger.info("ctx_files_patterns: %s", ctx_files_patterns)
if ctx_files_patterns:
assert len(ctx_files_patterns) == len(
id_prefixes), "ctx len={} pref leb={}".format(
len(ctx_files_patterns), len(id_prefixes))
else:
assert (
index_path or cfg.rpc_index_id
), "Either encoded_ctx_files or index_path pr rpc_index_id parameter should be set."
input_paths = []
path_id_prefixes = []
for i, pattern in enumerate(ctx_files_patterns):
pattern_files = glob.glob(pattern)
pattern_id_prefix = id_prefixes[i]
input_paths.extend(pattern_files)
path_id_prefixes.extend([pattern_id_prefix] * len(pattern_files))
logger.info("Embeddings files id prefixes: %s", path_id_prefixes)
logger.info("Reading all passages data from files: %s", input_paths)
retriever.index_encoded_data(input_paths,
index_buffer_sz,
path_id_prefixes=path_id_prefixes)
if index_path:
retriever.index.serialize(index_path)
# get top k results
top_results_and_scores = retriever.get_top_docs(questions_tensor.numpy(),
cfg.n_docs)
if cfg.use_rpc_meta:
questions_doc_hits = validate_from_meta(
question_answers,
top_results_and_scores,
cfg.validation_workers,
cfg.match,
cfg.rpc_meta_compressed,
)
if cfg.out_file:
save_results_from_meta(
questions,
question_answers,
top_results_and_scores,
questions_doc_hits,
cfg.out_file,
cfg.rpc_meta_compressed,
)
else:
all_passages = get_all_passages(ctx_sources)
if cfg.validate_as_tables:
questions_doc_hits = validate_tables(
all_passages,
question_answers,
top_results_and_scores,
cfg.validation_workers,
cfg.match,
)
else:
questions_doc_hits = validate(
all_passages,
question_answers,
top_results_and_scores,
cfg.validation_workers,
cfg.match,
)
if cfg.out_file:
save_results(
all_passages,
questions_text if questions_text else questions,
question_answers,
top_results_and_scores,
questions_doc_hits,
cfg.out_file,
)
if cfg.kilt_out_file:
kilt_ctx = next(
iter([
ctx for ctx in ctx_sources if isinstance(ctx, KiltCsvCtxSrc)
]), None)
if not kilt_ctx:
raise RuntimeError("No Kilt compatible context file provided")
assert hasattr(cfg, "kilt_out_file")
kilt_ctx.convert_to_kilt(qa_src.kilt_gold_file, cfg.out_file,
cfg.kilt_out_file)
def main(args):
questions = []
question_answers = []
for i, ds_item in enumerate(parse_qa_csv_file(args.qa_file)):
#if i == 10:
# break
question, answers = ds_item
questions.append(question)
question_answers.append(answers)
if not args.encoder_model_type == 'hf_attention' and not args.encoder_model_type == 'colbert':
saved_state = load_states_from_checkpoint(args.model_file)
set_encoder_params_from_state(saved_state.encoder_params, args)
tensorizer, encoder, _ = init_biencoder_components(args.encoder_model_type, args, inference_only=True)
if not args.encoder_model_type == 'hf_attention' and not args.encoder_model_type == 'colbert':
encoder = encoder.question_model
encoder, _ = setup_for_distributed_mode(encoder, None, args.device, args.n_gpu,
args.local_rank,
args.fp16)
encoder.eval()
if not args.encoder_model_type == 'hf_attention' and not args.encoder_model_type == 'colbert':
# load weights from the model file
model_to_load = get_model_obj(encoder)
logger.info('Loading saved model state ...')
prefix_len = len('question_model.')
question_encoder_state = {key[prefix_len:]: value for (key, value) in saved_state.model_dict.items() if
key.startswith('question_model.')}
model_to_load.load_state_dict(question_encoder_state)
vector_size = model_to_load.get_out_size()
logger.info('Encoder vector_size=%d', vector_size)
else:
vector_size = 16
index_buffer_sz = args.index_buffer
if args.index_type == 'hnsw':
index = DenseHNSWFlatIndexer(vector_size, index_buffer_sz)
index_buffer_sz = -1 # encode all at once
elif args.index_type == 'custom':
index = CustomIndexer(vector_size, index_buffer_sz)
else:
index = DenseFlatIndexer(vector_size)
retriever = DenseRetriever(encoder, args.batch_size, tensorizer, index, args.encoder_model_type=='colbert')
# index all passages
ctx_files_pattern = args.encoded_ctx_file
input_paths = glob.glob(ctx_files_pattern)
#logger.info('Reading all passages data from files: %s', input_paths)
#memmap = retriever.index_encoded_data(input_paths, buffer_size=index_buffer_sz, memmap=args.encoder_model_type=='colbert')
print(input_paths)
index_path = "_".join(input_paths[0].split("_")[:-1])
memmap_path = 'memmap.npy'
print(args.save_or_load_index, os.path.exists(index_path), index_path)
if args.save_or_load_index and os.path.exists(index_path+'.index.dpr'):
#if False:
retriever.index.deserialize_from(index_path)
if args.encoder_model_type=='colbert':
memmap = np.memmap(memmap_path, dtype=np.float32, mode='w+', shape=(21015324, 250, 16))
else:
memmap = None
else:
logger.info('Reading all passages data from files: %s', input_paths)
if args.encoder_model_type=='colbert':
memmap = np.memmap(memmap_path, dtype=np.float32, mode='w+', shape=(21015324, 250, 16))
else:
memmap = None
retriever.index_encoded_data(input_paths, buffer_size=index_buffer_sz, memmap=memmap)
if args.save_or_load_index:
retriever.index.serialize(index_path)
# get questions & answers
questions_tensor = retriever.generate_question_vectors(questions)
# get top k results
top_ids_and_scores = retriever.get_top_docs(questions_tensor.numpy(), args.n_docs, is_colbert=args.encoder_model_type=='colbert')
with open('approx_scores.pkl', 'wb') as f:
pickle.dump(top_ids_and_scores, f)
retriever.index.index.reset()
if args.encoder_model_type=='colbert':
logger.info('Colbert score')
top_ids_and_scores_colbert = retriever.colbert_search(questions_tensor.numpy(), memmap, top_ids_and_scores, args.n_docs)
all_passages = load_passages(args.ctx_file)
if len(all_passages) == 0:
raise RuntimeError('No passages data found. Please specify ctx_file param properly.')
with open('colbert_scores.pkl', 'wb') as f:
pickle.dump(top_ids_and_scores_colbert, f)
questions_doc_hits = validate(all_passages, question_answers, top_ids_and_scores, args.validation_workers,
args.match)
if args.encoder_model_type=='colbert':
questions_doc_hits_colbert = validate(all_passages, question_answers, top_ids_and_scores_colbert, args.validation_workers,
args.match)
if args.out_file:
save_results(all_passages, questions, question_answers, top_ids_and_scores, questions_doc_hits, args.out_file)
if args.encoder_model_type=='colbert':
save_results(all_passages, questions, question_answers, top_ids_and_scores_colbert, questions_doc_hits_colbert, args.out_file+'colbert')
def main(cfg: DictConfig):
assert cfg.model_file, "Please specify encoder checkpoint as model_file param"
assert cfg.ctx_src, "Please specify passages source as ctx_src param"
print(os.getcwd())
cfg = setup_cfg_gpu(cfg)
saved_state = load_states_from_checkpoint(cfg.model_file)
set_cfg_params_from_state(saved_state.encoder_params, cfg)
logger.info("CFG:")
logger.info("%s", OmegaConf.to_yaml(cfg))
tensorizer, encoder, _ = init_biencoder_components(
cfg.encoder.encoder_model_type, cfg, inference_only=True)
encoder = encoder.ctx_model if cfg.encoder_type == "ctx" else encoder.question_model
encoder, _ = setup_for_distributed_mode(
encoder,
None,
cfg.device,
cfg.n_gpu,
cfg.local_rank,
cfg.fp16,
cfg.fp16_opt_level,
)
encoder.eval()
# load weights from the model file
model_to_load = get_model_obj(encoder)
logger.info("Loading saved model state ...")
logger.debug("saved model keys =%s", saved_state.model_dict.keys())
prefix_len = len("ctx_model.")
ctx_state = {
key[prefix_len:]: value
for (key, value) in saved_state.model_dict.items()
if key.startswith("ctx_model.")
}
model_to_load.load_state_dict(ctx_state)
logger.info("reading data source: %s", cfg.ctx_src)
ctx_src = hydra.utils.instantiate(cfg.ctx_sources[cfg.ctx_src])
all_passages_dict = {}
ctx_src.load_data_to(all_passages_dict)
all_passages = [(k, v) for k, v in all_passages_dict.items()]
shard_size = math.ceil(len(all_passages) / cfg.num_shards)
start_idx = cfg.shard_id * shard_size
end_idx = start_idx + shard_size
logger.info(
"Producing encodings for passages range: %d to %d (out of total %d)",
start_idx,
end_idx,
len(all_passages),
)
shard_passages = all_passages[start_idx:end_idx]
data = gen_ctx_vectors(cfg, shard_passages, encoder, tensorizer, True)
file = cfg.out_file + "_" + str(cfg.shard_id)
pathlib.Path(os.path.dirname(file)).mkdir(parents=True, exist_ok=True)
logger.info("Writing results to %s" % file)
with open(file, mode="wb") as f:
pickle.dump(data, f)
logger.info("Total passages processed %d. Written to %s", len(data), file)
from dpr.utils.model_utils import setup_for_distributed_mode, get_model_obj, load_states_from_checkpoint
from dpr.indexer.faiss_indexers import DenseIndexer, DenseHNSWFlatIndexer, DenseFlatIndexer
from dense_retriever import DenseRetriever
saved_state = load_states_from_checkpoint(args.dpr_model_file)
set_encoder_params_from_state(saved_state.encoder_params, args)
tensorizer, encoder, _ = init_biencoder_components(args.encoder_model_type, args, inference_only=True)
encoder = encoder.question_model
setup_args_gpu(args)
encoder, _ = setup_for_distributed_mode(encoder, None, args.device, args.n_gpu,
args.local_rank,
args.fp16)
encoder.eval()
# load weights from the model file
model_to_load = get_model_obj(encoder)
prefix_len = len('question_model.')
question_encoder_state = {key[prefix_len:]: value for (key, value) in saved_state.model_dict.items() if
key.startswith('question_model.')}
model_to_load.load_state_dict(question_encoder_state)
vector_size = model_to_load.get_out_size()
index_buffer_sz = args.index_buffer
if args.hnsw_index:
index = DenseHNSWFlatIndexer(vector_size)
index_buffer_sz = -1 # encode all at once
else:
index = DenseFlatIndexer(vector_size)
retriever = DenseRetriever(encoder, args.batch_size, tensorizer, index)
retriever.index.deserialize_from(args.dense_index_path)
def validate_nll(self) -> float:
logger.info("NLL validation ...")
cfg = self.cfg
self.biencoder.eval()
if not self.dev_iterator:
self.dev_iterator = self.get_data_iterator(
cfg.train.dev_batch_size,
False,
shuffle=False,
rank=cfg.local_rank)
data_iterator = self.dev_iterator
total_loss = 0.0
start_time = time.time()
total_correct_predictions = 0
num_hard_negatives = cfg.train.hard_negatives
num_other_negatives = cfg.train.other_negatives
log_result_step = cfg.train.log_batch_step
batches = 0
dataset = 0
biencoder = get_model_obj(self.biencoder)
for i, samples_batch in enumerate(data_iterator.iterate_ds_data()):
if isinstance(samples_batch, Tuple):
samples_batch, dataset = samples_batch
logger.info("Eval step: %d ,rnk=%s", i, cfg.local_rank)
biencoder_input = biencoder.create_biencoder_input(
samples_batch,
self.tensorizer,
True,
num_hard_negatives,
num_other_negatives,
shuffle=False,
)
# get the token to be used for representation selection
ds_cfg = self.ds_cfg.dev_datasets[dataset]
rep_positions = ds_cfg.selector.get_positions(
biencoder_input.question_ids, self.tensorizer)
encoder_type = ds_cfg.encoder_type
loss, correct_cnt = _do_biencoder_fwd_pass(
self.biencoder,
biencoder_input,
self.tensorizer,
cfg,
encoder_type=encoder_type,
rep_positions=rep_positions,
)
total_loss += loss.item()
total_correct_predictions += correct_cnt
batches += 1
if (i + 1) % log_result_step == 0:
logger.info(
"Eval step: %d , used_time=%f sec., loss=%f ",
i,
time.time() - start_time,
loss.item(),
)
total_loss = total_loss / batches
total_samples = batches * cfg.train.dev_batch_size * self.distributed_factor
correct_ratio = float(total_correct_predictions / total_samples)
logger.info(
"NLL Validation: loss = %f. correct prediction ratio %d/%d ~ %f",
total_loss,
total_correct_predictions,
total_samples,
correct_ratio,
)
return total_loss
def _train_epoch(
self,
scheduler,
epoch: int,
eval_step: int,
train_data_iterator: MultiSetDataIterator,
):
cfg = self.cfg
rolling_train_loss = 0.0
epoch_loss = 0
epoch_correct_predictions = 0
log_result_step = cfg.train.log_batch_step
rolling_loss_step = cfg.train.train_rolling_loss_step
num_hard_negatives = cfg.train.hard_negatives
num_other_negatives = cfg.train.other_negatives
seed = cfg.seed
self.biencoder.train()
epoch_batches = train_data_iterator.max_iterations
data_iteration = 0
biencoder = get_model_obj(self.biencoder)
dataset = 0
for i, samples_batch in enumerate(
train_data_iterator.iterate_ds_data(epoch=epoch)):
if isinstance(samples_batch, Tuple):
samples_batch, dataset = samples_batch
ds_cfg = self.ds_cfg.train_datasets[dataset]
special_token = ds_cfg.special_token
encoder_type = ds_cfg.encoder_type
shuffle_positives = ds_cfg.shuffle_positives
# to be able to resume shuffled ctx- pools
data_iteration = train_data_iterator.get_iteration()
random.seed(seed + epoch + data_iteration)
biencoder_batch = biencoder.create_biencoder_input(
samples_batch,
self.tensorizer,
True,
num_hard_negatives,
num_other_negatives,
shuffle=True,
shuffle_positives=shuffle_positives,
query_token=special_token,
)
# get the token to be used for representation selection
from dpr.utils.data_utils import DEFAULT_SELECTOR
selector = ds_cfg.selector if ds_cfg else DEFAULT_SELECTOR
rep_positions = selector.get_positions(
biencoder_batch.question_ids, self.tensorizer)
loss_scale = cfg.loss_scale_factors[
dataset] if cfg.loss_scale_factors else None
loss, correct_cnt = _do_biencoder_fwd_pass(
self.biencoder,
biencoder_batch,
self.tensorizer,
cfg,
encoder_type=encoder_type,
rep_positions=rep_positions,
loss_scale=loss_scale,
)
epoch_correct_predictions += correct_cnt
epoch_loss += loss.item()
rolling_train_loss += loss.item()
if cfg.fp16:
from apex import amp
with amp.scale_loss(loss, self.optimizer) as scaled_loss:
scaled_loss.backward()
if cfg.train.max_grad_norm > 0:
torch.nn.utils.clip_grad_norm_(
amp.master_params(self.optimizer),
cfg.train.max_grad_norm)
else:
loss.backward()
if cfg.train.max_grad_norm > 0:
torch.nn.utils.clip_grad_norm_(self.biencoder.parameters(),
cfg.train.max_grad_norm)
if (i + 1) % cfg.train.gradient_accumulation_steps == 0:
self.optimizer.step()
scheduler.step()
self.biencoder.zero_grad()
if i % log_result_step == 0:
lr = self.optimizer.param_groups[0]["lr"]
logger.info(
"Epoch: %d: Step: %d/%d, loss=%f, lr=%f",
epoch,
data_iteration,
epoch_batches,
loss.item(),
lr,
)
if (i + 1) % rolling_loss_step == 0:
logger.info("Train batch %d", data_iteration)
latest_rolling_train_av_loss = rolling_train_loss / rolling_loss_step
logger.info(
"Avg. loss per last %d batches: %f",
rolling_loss_step,
latest_rolling_train_av_loss,
)
rolling_train_loss = 0.0
if data_iteration % eval_step == 0:
logger.info(
"rank=%d, Validation: Epoch: %d Step: %d/%d",
cfg.local_rank,
epoch,
data_iteration,
epoch_batches,
)
self.validate_and_save(epoch,
train_data_iterator.get_iteration(),
scheduler)
self.biencoder.train()
logger.info("Epoch finished on %d", cfg.local_rank)
self.validate_and_save(epoch, data_iteration, scheduler)
epoch_loss = (epoch_loss / epoch_batches) if epoch_batches > 0 else 0
logger.info("Av Loss per epoch=%f", epoch_loss)
logger.info("epoch total correct predictions=%d",
epoch_correct_predictions)
def validate_average_rank(self) -> float:
"""
Validates biencoder model using each question's gold passage's rank across the set of passages from the dataset.
It generates vectors for specified amount of negative passages from each question (see --val_av_rank_xxx params)
and stores them in RAM as well as question vectors.
Then the similarity scores are calculted for the entire
num_questions x (num_questions x num_passages_per_question) matrix and sorted per quesrtion.
Each question's gold passage rank in that sorted list of scores is averaged across all the questions.
:return: averaged rank number
"""
logger.info("Average rank validation ...")
cfg = self.cfg
self.biencoder.eval()
distributed_factor = self.distributed_factor
if not self.dev_iterator:
self.dev_iterator = self.get_data_iterator(
cfg.train.dev_batch_size,
False,
shuffle=False,
rank=cfg.local_rank)
data_iterator = self.dev_iterator
sub_batch_size = cfg.train.val_av_rank_bsz
sim_score_f = BiEncoderNllLoss.get_similarity_function()
q_represenations = []
ctx_represenations = []
positive_idx_per_question = []
num_hard_negatives = cfg.train.val_av_rank_hard_neg
num_other_negatives = cfg.train.val_av_rank_other_neg
log_result_step = cfg.train.log_batch_step
dataset = 0
biencoder = get_model_obj(self.biencoder)
for i, samples_batch in enumerate(data_iterator.iterate_ds_data()):
# samples += 1
if len(q_represenations
) > cfg.train.val_av_rank_max_qs / distributed_factor:
break
if isinstance(samples_batch, Tuple):
samples_batch, dataset = samples_batch
biencoder_input = biencoder.create_biencoder_input(
samples_batch,
self.tensorizer,
True,
num_hard_negatives,
num_other_negatives,
shuffle=False,
)
total_ctxs = len(ctx_represenations)
ctxs_ids = biencoder_input.context_ids
ctxs_segments = biencoder_input.ctx_segments
bsz = ctxs_ids.size(0)
# get the token to be used for representation selection
ds_cfg = self.ds_cfg.dev_datasets[dataset]
encoder_type = ds_cfg.encoder_type
rep_positions = ds_cfg.selector.get_positions(
biencoder_input.question_ids, self.tensorizer)
# split contexts batch into sub batches since it is supposed to be too large to be processed in one batch
for j, batch_start in enumerate(range(0, bsz, sub_batch_size)):
q_ids, q_segments = ((biencoder_input.question_ids,
biencoder_input.question_segments)
if j == 0 else (None, None))
if j == 0 and cfg.n_gpu > 1 and q_ids.size(0) == 1:
# if we are in DP (but not in DDP) mode, all model input tensors should have batch size >1 or 0,
# otherwise the other input tensors will be split but only the first split will be called
continue
ctx_ids_batch = ctxs_ids[batch_start:batch_start +
sub_batch_size]
ctx_seg_batch = ctxs_segments[batch_start:batch_start +
sub_batch_size]
q_attn_mask = self.tensorizer.get_attn_mask(q_ids)
ctx_attn_mask = self.tensorizer.get_attn_mask(ctx_ids_batch)
with torch.no_grad():
q_dense, ctx_dense = self.biencoder(
q_ids,
q_segments,
q_attn_mask,
ctx_ids_batch,
ctx_seg_batch,
ctx_attn_mask,
encoder_type=encoder_type,
representation_token_pos=rep_positions,
)
if q_dense is not None:
q_represenations.extend(q_dense.cpu().split(1, dim=0))
ctx_represenations.extend(ctx_dense.cpu().split(1, dim=0))
batch_positive_idxs = biencoder_input.is_positive
positive_idx_per_question.extend(
[total_ctxs + v for v in batch_positive_idxs])
if (i + 1) % log_result_step == 0:
logger.info(
"Av.rank validation: step %d, computed ctx_vectors %d, q_vectors %d",
i,
len(ctx_represenations),
len(q_represenations),
)
ctx_represenations = torch.cat(ctx_represenations, dim=0)
q_represenations = torch.cat(q_represenations, dim=0)
logger.info("Av.rank validation: total q_vectors size=%s",
q_represenations.size())
logger.info("Av.rank validation: total ctx_vectors size=%s",
ctx_represenations.size())
q_num = q_represenations.size(0)
assert q_num == len(positive_idx_per_question)
scores = sim_score_f(q_represenations, ctx_represenations)
values, indices = torch.sort(scores, dim=1, descending=True)
rank = 0
for i, idx in enumerate(positive_idx_per_question):
# aggregate the rank of the known gold passage in the sorted results for each question
gold_idx = (indices[i] == idx).nonzero()
rank += gold_idx.item()
if distributed_factor > 1:
# each node calcuated its own rank, exchange the information between node and calculate the "global" average rank
# NOTE: the set of passages is still unique for every node
eval_stats = all_gather_list([rank, q_num], max_size=100)
for i, item in enumerate(eval_stats):
remote_rank, remote_q_num = item
if i != cfg.local_rank:
rank += remote_rank
q_num += remote_q_num
av_rank = float(rank / q_num)
logger.info("Av.rank validation: average rank %s, total questions=%d",
av_rank, q_num)
return av_rank
