# Copyright 2022 Cerebras Systems.
#
# 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.
"""
This module implements a generic data preprocessor called `DataPreprocessor`.
It internally uses `DataFrame` and `DataReader` to read and process data.
"""
import glob
import importlib
import json
import logging
import math
import multiprocessing
import os
import shutil
import sys
import time
from collections import defaultdict
from functools import partial
from multiprocessing import Event, Lock, Process, Queue, Value, cpu_count
from multiprocessing.synchronize import Event
from threading import Event, Thread
from typing import Any, Dict, List, Optional, Tuple
import h5py
import numpy as np
import psutil
from datasets import load_dataset
from PIL import Image
from tqdm import tqdm
from cerebras.modelzoo.common.utils.utils import check_and_create_output_dirs
from cerebras.modelzoo.data_preparation.data_preprocessing.data_reader import (
DataFrame,
Reader,
optional_lock,
)
from cerebras.modelzoo.data_preparation.data_preprocessing.pretraining_token_generator import (
PretrainingTokenGenerator,
)
from cerebras.modelzoo.data_preparation.data_preprocessing.utils import (
dump_args,
get_files,
get_size,
)
from cerebras.modelzoo.data_preparation.data_preprocessing.dpo_token_generator import ( # noqa
DPOTokenGenerator,
)
from cerebras.modelzoo.data_preparation.data_preprocessing.fim_token_generator import ( # noqa
FIMTokenGenerator,
)
from cerebras.modelzoo.data_preparation.data_preprocessing.finetuning_token_generator import ( # noqa
FinetuningTokenGenerator,
)
from cerebras.modelzoo.data_preparation.data_preprocessing.multimodal_finetuning_token_generator import ( # noqa
MultiModalFinetuningTokenGenerator,
)
from cerebras.modelzoo.data_preparation.data_preprocessing.multimodal_pretraining_token_generator import ( # noqa
MultiModalPretrainingTokenGenerator,
)
from cerebras.modelzoo.data_preparation.data_preprocessing.nlg_token_generator import ( # noqa
NLGTokenGenerator,
)
from cerebras.modelzoo.data_preparation.data_preprocessing.vsl_finetuning_token_generator import ( # noqa
VSLFinetuningTokenGenerator,
)
from cerebras.modelzoo.data_preparation.data_preprocessing.vsl_pretraining_token_generator import ( # noqa
VSLPretrainingTokenGenerator,
)
logging.basicConfig()
logger = logging.getLogger(__file__)
logger.setLevel(logging.INFO)
[docs]def get_available_memory():
"""
Returns available memory in bytes.
"""
mem = psutil.virtual_memory()
return mem.available
[docs]def get_compression_factor(filename: str) -> int:
"""
Calculate and return the compression factor based on a file's extension.
Args:
filename (str): The name of the file.
Returns:
int: Compression factor. Returns 3 for all compressed and parquet formats,
otherwise returns 1 for uncompressed formats.
"""
compressed_formats = [
".jsonl.zst",
".jsonl.zst.tar",
".json.gz",
".parquet",
]
for format in compressed_formats:
if filename.endswith(format):
return 3 # compression factor for compressed/parquet formats
return 1 # default factor for uncompressed formats
[docs]def update_progress(
pbar: tqdm,
progress_counter: Value,
total_chunks: int,
start_time: float,
stop_event: Event,
) -> None:
"""
Update the progress bar based on the current progress.
Args:
pbar (tqdm): The progress bar instance.
progress_counter (Value): A shared counter to track progress across processes.
total_chunks (int): Total chunks to process.
start_time (float): The start time of the process.
stop_event (Event): Event to signal when to stop updating progress.
Returns:
None
"""
while not stop_event.is_set():
progress = progress_counter.value
if progress > pbar.n:
num_processed = progress - pbar.n
pbar.update(num_processed)
elapsed_time = time.time() - start_time
avg_time_per_chunk = elapsed_time / pbar.n
estimated_remaining = avg_time_per_chunk * (total_chunks - pbar.n)
formatted_estimated_remaining = format_time(estimated_remaining)
# Update progress bar description with processed/total chunks
pbar.set_description(f"Processing {pbar.n}/{total_chunks} chunks")
# Update the progress bar postfix with avg processing time and estimated time
pbar.set_postfix(
avg_time=f"{avg_time_per_chunk:.4f}s/chunk",
est_remaining=formatted_estimated_remaining,
refresh=True,
)
time.sleep(0.5)
[docs]def check_and_create_dir(dir: Optional[str], split_dir: Optional[str]) -> str:
"""
Ensures a directory exists, optionally handling a subdirectory. It prompts
the user for action if the directory already has files.
Args:
dir (Optional[str]): Base directory path. Defaults to 'input_dir' in cwd.
split_dir (Optional[str]): Subdirectory to add to the base directory.
Returns:
str: The final directory path ensured to exist.
"""
# Set default directory if none provided
if dir is None:
dir = os.path.join(os.getcwd(), 'input_dir')
# Append subdirectory if provided
if split_dir:
dir = os.path.join(dir, split_dir)
# Check for existing files and handle existing files
if os.path.isdir(dir) and os.listdir(dir):
_in = input(
"Input directory already contains file(s). Do you want to delete "
"the folder and download the dataset again? "
"(yes/no): "
)
if _in.lower() in ["y", "yes"]:
shutil.rmtree(dir)
os.makedirs(dir) # Recreate directory after removal
elif _in.lower() in ["n", "no"]:
return dir
else:
raise ValueError(
f"Inputs can be yes, no, y, or n. Received {_in}!!"
)
else:
# Create directory if it does not exist
os.makedirs(dir, exist_ok=True)
return dir
[docs]def default_hook(x):
return x
[docs]def save_image_locally(example, idx, image_key, image_dir):
image_data = example[image_key]
if isinstance(image_data, list):
image_paths = []
for i, img_data in enumerate(image_data):
if img_data is None:
image_paths.append(None)
else:
image_path = os.path.join(image_dir, f"{idx}_{i}.png")
if img_data is None:
image_paths.append(None)
continue
if isinstance(img_data, Image.Image):
img_data.save(image_path)
image_paths.append(f"{idx}_{i}.png")
elif isinstance(img_data, str):
image_paths.append(img_data)
else:
raise ValueError(
f" Image data format - {type(image_data)} is not supported"
)
example[image_key] = image_paths
else:
if image_data is None:
example[image_key] = None
else:
image_path = os.path.join(image_dir, f"{idx}.png")
if isinstance(image_data, Image.Image):
image_data.save(image_path)
example[image_key] = f"{idx}.png"
elif isinstance(image_data, str):
example[image_key] = image_data
else:
raise ValueError(
f" Image data format - {type(image_data)} is not supported"
)
return example
[docs]class DataPreprocessor:
def __init__(self, params):
"""
Initialize the class with given parameters.
Args:
params (dict): Configuration parameters.
"""
self.params = params
self.json_params_file = None
self.running_avg_processing_time = 0
self.chunks_processed = 0
self.process_params()
[docs] def load_dataset(self, input_data_params: Dict[str, Optional[str]]) -> str:
"""
Loads a dataset from a specified source and saves it in a specified format
in the given directory, potentially within a subdirectory denoted by a 'split'.
Args:
input_data_params (Dict[str, Optional[str]]): Parameters for dataset loading
including 'source', 'split' (optional), and 'format'.
Returns:
str: The directory where the dataset has been saved.
Raises:
ValueError: If the specified format is not supported.
"""
split_type = input_data_params.pop('split', None)
cache_dir = input_data_params.pop('cache_dir', None)
cache_dir = check_and_create_dir(cache_dir, split_type)
source_dataset = input_data_params.pop('source')
input_data_params = (
{} if input_data_params is None else input_data_params
)
# Load the dataset with or without the split
if split_type is not None:
dataset = load_dataset(
source_dataset,
split=split_type,
cache_dir=cache_dir,
**input_data_params,
)
else:
dataset = load_dataset(
source_dataset, cache_dir=cache_dir, **input_data_params
)
if self.data_keys.get("image_key") in dataset.column_names:
process_images_fn = partial(
save_image_locally,
image_key=self.data_keys.get("image_key"),
image_dir=self.image_dir,
)
dataset = dataset.map(
process_images_fn, with_indices=True, num_proc=self.processes
)
# Determine the file path based on format
format_type = input_data_params.get('format', 'parquet')
file_path = os.path.join(cache_dir, "data", f"dataset.{format_type}")
# Save the dataset in the desired format
if format_type == 'parquet':
dataset.to_parquet(file_path)
elif format_type == 'jsonl':
dataset.to_json(file_path, orient='records', lines=True)
else:
ValueError(
f"{format_type} is not supported by the data preprocessor."
)
logger.info(f"Dataset saved in {format_type} format at {file_path}")
return os.path.join(cache_dir, "data")
[docs] def process_params(self) -> None:
"""
Process parameters by calling various initialization methods.
"""
self.setup_output_directory()
self.process_setup_params()
self.process_dataset_params()
self.process_processing_params()
self.handle_input_files()
self.initialize_miscellaneous_attributes()
self.check_unused_params()
[docs] def setup_output_directory(self) -> None:
"""
Set up the output directory based on provided configuration.
"""
self.output_dir = self.params["setup"].get("output_dir", "./output/")
if not self.params["processing"].get("resume_from_checkpoint", False):
check_and_create_output_dirs(self.output_dir, filetype="h5")
logger.info(f"\nWriting data to {self.output_dir}.\n")
self.json_params_file = os.path.join(
self.output_dir, "data_params.json"
)
self.checkpoint_path = os.path.join(self.output_dir, "checkpoint.txt")
dump_args(self.params, self.json_params_file)
[docs] def process_setup_params(self) -> None:
"""
Setup the number of processes based on provided configuration.
"""
self.processes = self.params["setup"].pop("processes", 0)
if self.processes == 0:
self.processes = cpu_count()
self.mode = self.params["setup"].pop("mode", None)
assert (
self.mode is not None
), "Data preprocessing mode is not set. Please set it. "
if self.mode == 'custom':
logger.info(f"Initializing custom processing mode")
self.token_generator_name = self.params["setup"][
"token_generator"
].split(":")[1]
[docs] def check_unused_params(self) -> None:
"""
Check for any unused parameters and log them as warnings.
"""
unused_setup_params = [
key for key in self.params["setup"].keys() if key != "output_dir"
]
if unused_setup_params:
logger.warning(
f"\nThe following setup params are unused: {', '.join(unused_setup_params)}"
)
if self.params["dataset"]:
logger.warning(
"The following dataset params are unused: "
+ ", ".join(self.params["dataset"].keys())
)
[docs] def process_dataset_params(self) -> None:
"""
Process dataset specific parameters.
"""
dataset_params = self.params["dataset"]
use_vsl = dataset_params.pop("use_vsl", False)
self.multimodal = dataset_params.pop("is_multimodal", False)
self.training_objective = dataset_params.get("training_objective", None)
# Set the token generator name
if self.mode == "pretraining":
if self.multimodal:
logger.info(f"Initializing multimodal pretraining mode")
self.token_generator_name = (
"MultiModalPretrainingTokenGenerator"
)
elif self.training_objective == 'fim':
logger.info(f"Initializing fill in the middle pretraining mode")
self.token_generator_name = "FIMTokenGenerator"
else:
if use_vsl:
logger.info(f"Initializing VSL pretraining mode")
else:
logger.info(f"Initializing pretraining mode")
self.token_generator_name = (
"VSLPretrainingTokenGenerator"
if use_vsl
else "PretrainingTokenGenerator"
)
elif self.mode == "finetuning":
if self.multimodal:
logger.info(f"Initializing multimodal finetuning mode")
self.token_generator_name = "MultiModalFinetuningTokenGenerator"
else:
if use_vsl:
logger.info(f"Initializing VSL finetuning mode")
else:
logger.info(f"Initializing finetuning mode")
self.token_generator_name = (
"VSLFinetuningTokenGenerator"
if use_vsl
else "FinetuningTokenGenerator"
)
elif self.mode == "dpo":
logger.info(f"Initializing dpo mode")
self.token_generator_name = "DPOTokenGenerator"
elif self.mode == "nlg":
logger.info(f"Initializing dpo mode")
self.token_generator_name = "NLGTokenGenerator"
else:
if self.mode != "custom":
ValueError(
f"Invalid processor mode specified. The modes can be ['pretraining', 'finetuning', 'dpo', 'nlg', 'custom']"
)
if self.multimodal:
self.image_dir = dataset_params.get("image_dir", None)
os.makedirs(self.image_dir, exist_ok=True)
if not self.image_dir:
raise ValueError(
"Image directory path has not been provided through the data config. Please pass it in the dataset section."
)
## initialize the final data statistics
self.final_data_stats = defaultdict(int)
# Initialize checkpoint data stats
self.checkpoint_data_stats = defaultdict(int)
[docs] def estimate_queue_size(self, fraction_of_memory=0.5):
"""
Estimates an optimal queue size based on the max_chunk_size and a fraction of available system memory.
Args:
- fraction_of_memory: Fraction of available system memory to be used for queues.
Returns:
- An integer representing the optimal queue size.
"""
available_memory = get_available_memory()
memory_for_queues = available_memory * fraction_of_memory
queue_size = int(
memory_for_queues
/ (self.read_chunk_size * (self.processes - 1) * 2)
)
return queue_size
[docs] def process_processing_params(self) -> None:
"""
Process the processing parameters and initialize relevant class attributes.
"""
processing_params = self.params["processing"]
self.output_name = processing_params.pop("output_name", "examples")
self.resume_from_checkpoint = processing_params.pop(
"resume_from_checkpoint", False
)
self.max_seq_length = processing_params.get("max_seq_length", 2048)
self.read_chunk_size = (
processing_params.pop("read_chunk_size", 1024) * 1024
) # By default, set to 1 MB.
self.write_chunk_size = (
processing_params.pop("write_chunk_size", 1024) * 1024
) # write_chunk_size is given in KB.
formatted_max_chunk_size = self.human_readable_size(
self.read_chunk_size
)
logger.info(f"\nChunk size : {formatted_max_chunk_size}.\n")
self.write_in_batch = processing_params.pop("write_in_batch", False)
self.format_hook_path = processing_params.pop("read_hook", None)
self.format_hook_kwargs = processing_params.pop("read_hook_kwargs", {})
self.data_keys = self.format_hook_kwargs.get("data_keys")
assert (
self.data_keys is not None
), "Data keys is missing inside the read_hook_kwargs section."
self.format_hook_fn = self.load_format_hook_fn()
self.shuffle = processing_params.get("shuffle", False)
if self.shuffle:
self.shuffle_seed = processing_params.get("shuffle_seed", 0)
self.writer_process_num = (self.processes - 1) // 2
else:
self.writer_process_num = math.ceil((self.processes - 1) / 10)
self.tokenize_process_num = self.processes - 1 - self.writer_process_num
self.initialize_tokenizer(processing_params)
# Create tokenizer queues for each tokenizer process
self.tokenizer_queues = None
if self.tokenize_process_num > 0:
# Set up communication queues
self.fraction_of_RAM_alloted = processing_params.get(
"fraction_of_RAM_alloted", 0.7
)
queue_size = min(
self.estimate_queue_size(
fraction_of_memory=self.fraction_of_RAM_alloted
),
50,
)
if queue_size == 0:
raise ValueError(
"""
The max_chunk_size set at present exceeds what can be allocated in memory.
To carry out this preprocessing task, it's necessary to reduce the max_chunk_size.
"""
)
self.tokenizer_queues = [
Queue(maxsize=queue_size)
for _ in range(self.tokenize_process_num)
]
self.writer_queues = [
Queue(maxsize=queue_size)
for _ in range(self.tokenize_process_num)
]
self.stats_queue = Queue()
if isinstance(
self.token_generator, PretrainingTokenGenerator
) and not isinstance(
self.token_generator, VSLPretrainingTokenGenerator
):
self.prefix_queue = Queue()
def load_format_hook_fn(self):
from functools import partial
if self.format_hook_path is None:
if self.multimodal:
raise ValueError(
"A format hook function is required for preprocessing multimodal datasets. Please provide it."
)
else:
return default_hook
module_name, func_name = self.format_hook_path.rsplit(':', 1)
mod = importlib.import_module(module_name)
func = getattr(mod, func_name)
# Use functools.partial to bind the kwargs to the function
format_hook_fn = partial(func, **self.format_hook_kwargs)
return format_hook_fn
[docs] def initialize_tokenizer(self, processing_params: Dict[str, Any]) -> None:
"""
Initialize tokenizer based on the provided `tokenizer_type` parameter.
Args:
processing_params (Dict[str, Any]): Dictionary of processing parameters.
"""
hf_tokenizer = processing_params.pop("huggingface_tokenizer", None)
custom_tokenizer = processing_params.pop("custom_tokenizer", None)
if hf_tokenizer:
hf_tokenizer = hf_tokenizer.lower()
if custom_tokenizer:
# We do not want to convert to lowercase in case it is a custom tokenizer as it would be a path.
if (
custom_tokenizer.casefold() == "gpt2tokenizer"
or custom_tokenizer.casefold() == "neoxtokenizer"
):
custom_tokenizer = custom_tokenizer.lower()
if hf_tokenizer and custom_tokenizer:
raise ValueError(
f"Both custom and huggingface tokenizer cannot be provided. Please provide one tokenizer"
)
tokenizer_params = processing_params.pop("tokenizer_params", None)
is_gpt2_tokenizer = False
if hf_tokenizer:
self.initialize_huggingfacetokenizer(hf_tokenizer, tokenizer_params)
else:
if custom_tokenizer == "gpt2tokenizer":
is_gpt2_tokenizer = True
self.initialize_gpt2tokenizer(tokenizer_params)
elif custom_tokenizer == "neoxtokenizer":
self.initialize_neoxtokenizer(tokenizer_params)
else:
logger.info(
"Initializing the tokenizer as a custom tokenizer..."
)
self.initialize_customtokenizer(
custom_tokenizer, tokenizer_params
)
# Override eos id and pad id from user args
if (
processing_params.get("eos_id") is not None
): # important as id could be set to 0
logger.info(
f"Overriding the eos id {self.eos_id} from the tokenizer with supplied eos id: {processing_params['eos_id']}."
)
self.eos_id = processing_params["eos_id"]
self.pad_id = processing_params[
"eos_id"
] # set pad id same as eos id
if processing_params.get("pad_id") is not None:
logger.info(
f"Overriding the pad id {self.pad_id} from the tokenizer with supplied pad id: {processing_params['pad_id']}."
)
self.pad_id = processing_params["pad_id"]
if self.pad_id != self.eos_id and is_gpt2_tokenizer:
logger.info(
f"Pad id {self.pad_id} supplied from command line is different from eos id {self.eos_id}. For GPT2 tokenizer, pad id and eos id must be the same. Setting pad id to eos id."
)
self.pad_id = self.eos_id
if self.mode == "custom":
module_path, class_name = (
self.params["setup"].pop("token_generator").split(":")
)
module = importlib.import_module(module_path)
TokenGeneratorClass = getattr(module, class_name)
self.token_generator = TokenGeneratorClass(
self.params, self.tokenizer, self.eos_id, self.pad_id
)
else:
if self.token_generator_name == "NLGTokenGenerator":
self.token_generator = getattr(
sys.modules[__name__], self.token_generator_name
)(self.max_seq_length)
else:
self.token_generator = getattr(
sys.modules[__name__], self.token_generator_name
)(self.params, self.tokenizer, self.eos_id, self.pad_id)
[docs] def initialize_gpt2tokenizer(
self, tokenizer_params: Dict[str, Any]
) -> None:
"""
Initialize GPT-2 tokenizer.
Args:
processing_params (Dict[str, Any]): Dictionary of processing parameters.
"""
vocab_file = tokenizer_params.pop("encoder_file", None)
encoder_file = tokenizer_params.pop("vocab_file", None)
assert (
vocab_file
), "`vocab_file` is missing, please provide it using `args.vocab_file`."
assert (
encoder_file
), "`encoder_file` is missing, please provide it using `args.encoder_file`."
tokenizer_params = {} if tokenizer_params is None else tokenizer_params
from transformers import GPT2TokenizerFast
self.tokenizer = GPT2TokenizerFast(
vocab_file=vocab_file,
merges_file=encoder_file,
name_or_path="gpt2-tokenizer",
**tokenizer_params,
)
self.eos_id = self.tokenizer.convert_tokens_to_ids("<|endoftext|>")
self.pad_id = self.tokenizer.convert_tokens_to_ids("<|endoftext|>")
[docs] def initialize_neoxtokenizer(
self, tokenizer_params: Dict[str, Any]
) -> None:
"""
Initialize Neox tokenizer.
Args:
processing_params (Dict[str, Any]): Dictionary of processing parameters.
"""
from tokenizers import Tokenizer
from transformers import PreTrainedTokenizerFast
encoder_file = tokenizer_params.pop("encoder_file", None)
assert (
encoder_file
), "`encoder_file` is missing, please provide it using `args.encoder_file`."
tokenizer_params = {} if tokenizer_params is None else tokenizer_params
tokenizer_model = Tokenizer.from_file(encoder_file)
self.tokenizer = PreTrainedTokenizerFast(
tokenizer_object=tokenizer_model,
name_or_path="neox-tokenizer",
**tokenizer_params,
)
self.eos_id = self.tokenizer.convert_tokens_to_ids("<|endoftext|>")
self.pad_id = self.tokenizer.convert_tokens_to_ids("<|padding|>")
if self.pad_id is None:
self.pad_id = self.eos_id
[docs] def initialize_huggingfacetokenizer(
self, hf_tokenizer: str, tokenizer_params: Dict[str, Any]
) -> None:
"""
Initialize Hugging Face tokenizer.
Args:
hf_tokenizer: str: HuggingFace tokenizer name.
processing_params (Dict[str, Any]): Dictionary of processing parameters.
"""
from transformers import AutoTokenizer
tokenizer_params = {} if tokenizer_params is None else tokenizer_params
self.tokenizer = AutoTokenizer.from_pretrained(
pretrained_model_name_or_path=hf_tokenizer,
**tokenizer_params,
)
self.eos_id = self.tokenizer.eos_token_id
self.pad_id = (
self.eos_id
if self.tokenizer.pad_token_id is None
else self.tokenizer.pad_token_id
)
[docs] def initialize_customtokenizer(
self,
custom_tokenizer,
tokenizer_params: Dict[str, Any],
) -> None:
"""
Initialize custom tokenizer.
Args:
custom_tokenizer: str: Path to implemenation of custom tokenizer.
tokenizer_params: (Dict[str, Any]): Dictionary of tokenizer parameters.
"""
tokenizer_params = {} if tokenizer_params is None else tokenizer_params
module, class_name = custom_tokenizer.rsplit(':', 1)
module = importlib.import_module(module)
TokenizerClass = getattr(module, class_name)
self.tokenizer = TokenizerClass(**tokenizer_params)
self.eos_id = self.tokenizer.eos_token_id
self.pad_id = self.tokenizer.pad_token_id
[docs] def initialize_miscellaneous_attributes(self) -> None:
"""
Initialize miscellaneous attributes.
"""
self.n_examples = (
0 ## stores the total number of sequences in the current dataset
)
[docs] def get_params_file(self) -> str:
"""
Retrieve the path to the JSON parameters file.
Returns:
str: Path to the JSON parameters file.
"""
return self.json_params_file
[docs] def get_output_dir(self) -> str:
"""
Retrieve the output directory path.
Returns:
str: Path to the output directory.
"""
return self.output_dir
[docs] def calculate_total_size(self) -> int:
"""
Calculate the total size of all input files, taking compression
factors into consideration.
Returns:
int: The total size of all input files in bytes.
"""
total_size = sum(
os.path.getsize(file) * get_compression_factor(file)
for file in self.input_files
)
return total_size
[docs] def human_readable_size(self, size, decimal_places=2):
"""
Convert a size in bytes to a human-readable format (e.g., KB, MB, GB).
Args:
size (int): Size in bytes.
decimal_places (int): Number of decimal places for rounding.
Returns:
str: Formatted size string.
"""
for unit in ["B", "KB", "MB", "GB", "TB"]:
if size < 1024.0 or unit == "TB":
break
size /= 1024.0
return f"{size:.{decimal_places}f} {unit}"
[docs] def calculate_total_chunks(self, total_size: int) -> int:
"""
Calculate the total number of chunks based on the given total size
and the predefined max chunk size.
Parameters:
total_size (int): The total size of the data in bytes.
Returns:
int: Total number of chunks.
"""
max_chunk_size_bytes = self.read_chunk_size
return math.ceil(total_size / max_chunk_size_bytes)
[docs] def read_checkpoint(self, num_writers) -> List[Tuple[int, int, int]]:
"""
This function reads the checkpoint args from the created checkpoint file.
Parameters:
num_writers: The number of writer processes
"""
# Collect all the stats from previous processing
# Pattern to find checkpoint stats JSON files
checkpoint_pattern = os.path.join(
self.output_dir, 'checkpoint_process_stats*.json'
)
# Read and aggregate stats from each file
for stats_file in glob.glob(checkpoint_pattern):
with open(stats_file, 'r') as file:
stats_data = json.load(file)
for key in self.checkpoint_data_stats:
if key in stats_data:
self.checkpoint_data_stats[key] += stats_data[key]
process_checkpoints = [
(0, 0, 0, 0, 0) for process in range(num_writers)
]
root, extension = os.path.splitext(self.checkpoint_path)
for pid in range(num_writers):
process_checkpoint_path = root + f'_process_{pid}.txt'
if self.resume_from_checkpoint and os.path.isfile(
process_checkpoint_path
):
try:
with open(process_checkpoint_path, "r") as file:
(
file_idx,
doc_idx,
start_chunk_number,
num_chunks_written,
num_sequences_written,
) = [int(i) for i in file.read().split(", ")]
process_checkpoints[pid] = (
file_idx,
doc_idx,
start_chunk_number,
num_chunks_written,
num_sequences_written,
)
logger.info(
f"Process {pid} resuming from file number: {file_idx}, "
f"and number of hdf5 files written = {num_chunks_written}"
)
except Exception as e:
# if checkpoint path is at initialization,
# file may exist, but no data might be written in the file
# in that event, do not do anything, go to the final return
logger.error(e)
return process_checkpoints
[docs] def write_remaining_prefix(self, chunk_locks, pid) -> Tuple[int, Dict]:
"""
This function writes the prefix remaining after processing LMData when pack_sequences is set to true.
Parameters:
chunk_locks : List of locks for appending to hdf5 files during shuffling
pid: Process id of the current process
"""
root, _ = os.path.splitext(self.checkpoint_path)
process_checkpoint_path = root + f'_process_{pid}.txt'
## write remaining prefix from all processes for LMData tasks when pack sequences is set to true
if not (
self.token_generator_name == "PretrainingTokenGenerator"
or self.token_generator_name == "FIMTokenGenerator"
):
return
else:
output_file_name = os.path.join(
self.output_dir,
f"output_chunk_{pid}_{0}_{0}_{0}.h5",
)
prefix_sequences = 0
prefix_stats = {
"num_pad_tokens": 0,
"non_pad_tokens": 0,
"num_masked_tokens": 0,
"loss_valid_tokens": 0,
"num_tokens": 0,
}
if self.shuffle:
np.random.seed(self.shuffle_seed)
prefix = []
sentinels_received = 0
while True:
curr_prefix = self.prefix_queue.get()
if curr_prefix is None:
sentinels_received += 1
if sentinels_received == self.tokenize_process_num:
break
else:
prefix = prefix + curr_prefix
if len(prefix) > 0:
(
encoded_prefix,
prefix_stats,
) = self.token_generator.encode_leftover_prefix(prefix)
if len(encoded_prefix) > 0:
base_name, extension = os.path.splitext(output_file_name)
chunk_number = int(base_name.split('_')[-1])
df_chunk = DataFrame(self.data_keys)
for key, value in encoded_prefix.items():
df_chunk.tokenized_data[key].append(value)
chunk_data = chunk_number, df_chunk
if not self.shuffle:
buffer = {}
for data_label, data in df_chunk.tokenized_data.items():
data = np.concatenate(data, axis=0)
buffer.setdefault(data_label, []).append(data)
with h5py.File(output_file_name, "w") as h5f:
self.save_buffer_to_hdf5(
h5f, buffer, self.write_in_batch
)
prefix_sequences += int(h5f.attrs["n_examples"])
else:
chunk_buffer = [chunk_data]
n_examples = self.append_buffer_to_hdf5(
chunk_buffer,
self.output_dir,
chunk_locks,
)
prefix_sequences += n_examples
for key in prefix_stats:
self.final_data_stats[key] += prefix_stats[key]
self.final_data_stats["examples"] += prefix_sequences
[docs] def shuffle_second_pass(self, file_list, progress_counter, pid) -> None:
"""
This function performs the second pass of shuffling.
Parameters:
file_list: List of hdf5 file paths to shuffle
progress_counter: A shared counter to track progress across processes.
"""
np.random.seed(self.shuffle_seed + pid)
for file_path in file_list:
with h5py.File(file_path, 'r+') as hf:
data = hf["data"]
data_array = data[:]
np.random.shuffle(data_array)
data[...] = data_array
progress_counter.value += 1
[docs] def split_shuffle_second_pass(self):
"""
This function divides the output hdf5 files into different processes and prepares them for the
second pass of shuffling.
"""
## Perform the second pass of shuffling:
logger.info("The second pass of shuffling has started")
hdf5_file_list = sorted(
glob.glob(os.path.join(self.output_dir, "*.h5"))
)
hdf5_file_list_length = len(hdf5_file_list)
chunk_size = hdf5_file_list_length // self.processes
file_list_per_process = [
hdf5_file_list[i * chunk_size : (i + 1) * chunk_size]
for i in range(self.processes)
]
remainder = hdf5_file_list_length % self.processes
for i in range(remainder):
file_list_per_process[i].append(
hdf5_file_list[self.processes * chunk_size + i]
)
progress_counter = multiprocessing.Value("i", 0)
start_time = time.time()
shuffle_processes = [
Process(
target=self.shuffle_second_pass,
args=(
file_list_per_process[i],
progress_counter,
i,
),
)
for i in range(self.processes)
]
for proc in shuffle_processes:
proc.start()
with tqdm(
total=hdf5_file_list_length, desc="Processing", dynamic_ncols=True
) as pbar:
stop_event = Event()
progress_thread = Thread(
target=update_progress,
args=(
pbar,
progress_counter,
hdf5_file_list_length,
start_time,
stop_event,
),
)
progress_thread.start()
for i, proc in enumerate(shuffle_processes):
proc.join()
stop_event.set()
progress_thread.join()
[docs] def stats_collation(self, num_writer_processes) -> None:
"""
This function collates the stats obtained from the different writer processes into a combined final stats
Parameters:
num_writer_processes: Number of writer processes
"""
sentinels_received = 0
while True:
data_stats = self.stats_queue.get()
if data_stats == None:
sentinels_received += 1
if sentinels_received == num_writer_processes:
break # Exit loop after receiving all sentinels
else:
for key in data_stats:
self.final_data_stats[key] += data_stats[key]
if self.resume_from_checkpoint:
# Update final_data_stats with aggregated values
for key in self.checkpoint_data_stats:
self.final_data_stats[key] += self.checkpoint_data_stats[key]
def average_chars_and_bytes(self) -> None:
if self.final_data_stats["examples"] > 0:
self.final_data_stats["average_chars_per_sequence"] = math.ceil(
self.final_data_stats["raw_chars_count"]
/ self.final_data_stats["examples"]
)
self.final_data_stats["average_bytes_per_sequence"] = math.ceil(
self.final_data_stats["raw_bytes_count"]
/ self.final_data_stats["examples"]
)
[docs] def process_files(
self,
file_paths,
process_idx,
checkpoint_args,
progress_counter,
chunk_locks,
) -> None:
"""
Process the given files, tokenize the data chunks, and save to HDF5 format.
Parameters:
file_paths: list of file_paths.
process_idx: Index of current process among all process spawned for file split
checkpoint_args (Tuple[int, int, int]): File index, doc start index, and hdf5 index.
progress_counter (Value[int]): Shared counter tracking number of processed chunks.
chunk_locks : List of locks for appending to hdf5 files during shuffling
"""
cum_data_stats = defaultdict(int)
if self.shuffle:
np.random.seed(self.shuffle_seed + process_idx)
# Initial setup
reader = Reader(
file_paths,
max_chunk_size=self.read_chunk_size,
keys=self.data_keys,
format_hook_fn=self.format_hook_fn,
)
(
file_idx,
doc_start_idx,
start_chunk_number,
num_chunks_written,
num_sequences_written,
) = checkpoint_args
process_chunk_number = start_chunk_number
checkpoint_args = (file_idx, doc_start_idx)
root, extension = os.path.splitext(self.checkpoint_path)
process_checkpoint_path = root + f'_process_{process_idx}.txt'
process_stats_path = root + f'_process_stats_{process_idx}.json'
buffer = {}
chunk_buffer = []
for df_chunk in reader.stream_data(checkpoint_args):
# Tokenize chunk
df_chunk.tokenize(self.token_generator)
for key in df_chunk.data_stats:
cum_data_stats[key] += df_chunk.data_stats[key]
if df_chunk.tokenized_data == {}:
process_chunk_number += 1
progress_counter.value += 1
continue
checkpoint_doc_idx = df_chunk.end_doc_idx + 1
if isinstance(
self.token_generator,
(VSLPretrainingTokenGenerator, VSLFinetuningTokenGenerator),
):
checkpoint_doc_idx = df_chunk.start_doc_idx
if not self.shuffle:
for data_label, data in df_chunk.tokenized_data.items():
data = np.concatenate(data, axis=0)
if data_label not in buffer:
buffer[data_label] = []
buffer[data_label].append(data)
if get_size(buffer) >= self.write_chunk_size:
output_file_name = os.path.join(
self.output_dir,
f"output_chunk_{process_idx}_{df_chunk.file_idx}_{df_chunk.start_doc_idx}_{process_chunk_number}.h5",
)
with h5py.File(output_file_name, "w") as h5f:
self.save_buffer_to_hdf5(
h5f, buffer, self.write_in_batch
)
cum_data_stats["examples"] += int(
h5f.attrs["n_examples"]
)
num_chunks_written += 1
buffer = {}
else:
chunk_buffer.append((process_chunk_number, df_chunk))
if get_size(buffer) >= self.write_chunk_size:
n_examples = self.append_buffer_to_hdf5(
chunk_buffer,
self.output_dir,
chunk_locks,
)
# Update progress counter
num_chunks_written += 1
cum_data_stats["examples"] += n_examples
chunk_buffer = []
progress_counter.value += 1
process_chunk_number += 1
checkpoint_data = [
df_chunk.file_idx,
checkpoint_doc_idx,
process_chunk_number,
num_chunks_written,
0,
]
self.update_checkpoint(process_checkpoint_path, checkpoint_data)
if len(buffer) != 0 or len(chunk_buffer) != 0:
output_file_name = os.path.join(
self.output_dir,
f"output_chunk_{process_idx}_{df_chunk.file_idx}_{df_chunk.start_doc_idx}_{process_chunk_number}.h5",
)
if not self.shuffle:
with h5py.File(output_file_name, "w") as h5f:
self.save_buffer_to_hdf5(h5f, buffer, self.write_in_batch)
cum_data_stats["examples"] += int(h5f.attrs["n_examples"])
else:
n_examples = self.append_buffer_to_hdf5(
chunk_buffer,
self.output_dir,
chunk_locks,
)
cum_data_stats["examples"] += n_examples
num_chunks_written += 1
checkpoint_data = [
df_chunk.file_idx,
checkpoint_doc_idx,
process_chunk_number,
num_chunks_written,
0,
]
self.update_checkpoint(process_checkpoint_path, checkpoint_data)
dump_args(cum_data_stats, process_stats_path)
if isinstance(
self.token_generator, PretrainingTokenGenerator
) and not isinstance(
self.token_generator, VSLPretrainingTokenGenerator
):
if self.token_generator.prefix != []:
self.prefix_queue.put(self.token_generator.prefix)
self.prefix_queue.put(None)
self.stats_queue.put(cum_data_stats)
self.stats_queue.put(None)
[docs] def file_split_process_dataset(self) -> None:
"""
Process the dataset by splitting files across multiple processes.
"""
start_time = time.time()
self.tokenize_process_num = self.processes
total_size = self.calculate_total_size()
self.total_chunks = self.calculate_total_chunks(total_size)
self.total_output_files = math.ceil(total_size / self.write_chunk_size)
process_file_lists = [[] for _ in range(self.processes)]
process_checkpoints = self.read_checkpoint(self.processes)
num_chunks_written = sum(
[checkpoint_args[-2] for checkpoint_args in process_checkpoints]
)
for idx, file in enumerate(self.input_files):
target_process = idx % self.processes
process_file_lists[target_process].append(file)
# Setup the shared progress counter
progress_counter = multiprocessing.Value("i", num_chunks_written)
if self.shuffle and self.processes > 1:
lock_pool_size = cpu_count()
chunk_locks = [Lock() for _ in range(lock_pool_size)]
else:
chunk_locks = None
processes = [
Process(
target=self.process_files,
args=(
files,
pid,
process_checkpoints[pid],
progress_counter,
chunk_locks,
),
)
for pid, files in enumerate(process_file_lists)
]
for p in processes:
p.start()
# Using tqdm for progress bar
with tqdm(
total=self.total_chunks, desc="Processing", dynamic_ncols=True
) as pbar:
stop_event = (
Event()
) # To signal the progress update thread when to stop
progress_thread = Thread(
target=update_progress,
args=(
pbar,
progress_counter,
self.total_chunks,
start_time,
stop_event,
),
)
progress_thread.start()
self.stats_collation(self.processes)
self.write_remaining_prefix(chunk_locks, self.processes)
self.average_chars_and_bytes()
# Wait for all processes to finish
for p in processes:
# TODO: We had to add a timeout here
# as a workaround to avoid hanging at the
# join. We need to figure out a better
# solution.
p.join(timeout=1e-6)
end_time = time.time()
elapsed_time = end_time - start_time
stop_event.set() # Signal the progress update thread to stop
progress_thread.join() # Wait for the progress update thread to finish
if self.shuffle:
self.split_shuffle_second_pass()
end_time = time.time()
elapsed_time = end_time - start_time
logger.info(
f"The process_dataset function took {elapsed_time:.2f} seconds to complete."
)
[docs] def reader_process(self, process_checkpoints: List[Tuple]) -> None:
"""
Reads data from input files and distributes them to the tokenizer queues.
Args:
checkpoint_args (List[Tuple[int, int, int, int, int]]): List of File index, doc start index, start_chunk_nuber,
num_chunks_written, num_sequences_written
"""
reader = Reader(
self.input_files,
max_chunk_size=self.read_chunk_size,
keys=self.data_keys,
format_hook_fn=self.format_hook_fn,
)
sorted_process_checkpoints = sorted(
process_checkpoints, key=lambda x: x[2]
)
(
file_idx,
doc_start_idx,
start_chunk_number,
num_chunks_written,
num_sequences_written,
) = sorted_process_checkpoints[0]
checkpoint_args = (file_idx, doc_start_idx)
chunk_number = start_chunk_number # Initialize chunk number counter
for df_chunk in reader.stream_data(checkpoint_args):
tokenizer_index = (chunk_number - start_chunk_number) % (
self.tokenize_process_num
)
writer_index = tokenizer_index % self.writer_process_num
if chunk_number < process_checkpoints[writer_index][2]:
chunk_number += 1
continue
# Distribute chunks in a round-robin fashion across tokenizer queues
# while making sure the first chunk is given to first tokenizer process
tokenizer_queue = self.tokenizer_queues[tokenizer_index]
tokenizer_queue.put(
(chunk_number, df_chunk)
) # Send chunk number with df_chunk
chunk_number += 1
# Place sentinel values in each tokenizer queue to indicate end of reading
for tq in self.tokenizer_queues:
tq.put(None)
[docs] def tokenizer_process(self, idx: int) -> None:
"""
Tokenizes data and forwards the tokenized data to the writer queue.
Args:
idx (int): Queue ID to forward tokenized chunks of data.
"""
while True:
try:
chunk_data = self.tokenizer_queues[idx].get()
if chunk_data is None: # Sentinel value indicates termination
if isinstance(
self.token_generator, PretrainingTokenGenerator
) and not isinstance(
self.token_generator, VSLPretrainingTokenGenerator
):
if self.token_generator.prefix != []:
self.prefix_queue.put(self.token_generator.prefix)
self.prefix_queue.put(None)
self.writer_queues[idx].put(None)
break
(
chunk_number,
df_chunk,
) = chunk_data # Unpack chunk number and data frame chunk
df_chunk.tokenize(self.token_generator)
self.writer_queues[idx].put((chunk_number, df_chunk))
except Exception as e:
logger.error(
f'Exception in tokenizer process {os.getpid()}: {e}'
)
[docs] def writer_process(
self,
progress_counter: "Value[int]",
num_sentinels: int,
writer_idx: int,
chunk_locks: List[Lock],
process_checkpoints: Tuple,
) -> None:
"""
Process that writes tokenized data to HDF5 format.
Args:
progress_counter (Value[int]): Shared counter tracking number of processed chunks.
num_sentinels : Number of sentinels to be received for the current writer process
writer_idx : The index of the current writer process
chunk_locks : List of locks for appending to hdf5 files during shuffling
process_checkpoints: Checkpoint for the current process. This is used for resuming from checkpoint.
"""
cum_data_stats = defaultdict(int)
sentinels_received = 0
tokenizer_idx = writer_idx
num_chunks_written = process_checkpoints[-2]
root, extension = os.path.splitext(self.checkpoint_path)
process_checkpoint_path = root + f'_process_{writer_idx}.txt'
process_stats_path = root + f'_process_stats_{writer_idx}.json'
if self.shuffle:
np.random.seed(self.shuffle_seed + writer_idx)
buffer = {}
chunk_buffer = []
while True:
try:
chunk_data = self.writer_queues[tokenizer_idx].get()
## We need to allocate the writer queues to writer processes in a round robin fashion.
## When the writer queue index (aka tokenizer_idx) goes beyond the total writer queues(aka self.tokenize_process_num) reset it to the current writer process index(aka writer_idx).
tokenizer_idx = tokenizer_idx + self.writer_process_num
if tokenizer_idx >= self.tokenize_process_num:
tokenizer_idx = writer_idx
if chunk_data is None:
sentinels_received += 1
if sentinels_received == num_sentinels:
break
continue
chunk_number, df_chunk = chunk_data
for key in df_chunk.data_stats:
cum_data_stats[key] += df_chunk.data_stats[key]
if df_chunk.tokenized_data == {}:
progress_counter.value += 1
continue
else:
checkpoint_doc_idx = df_chunk.end_doc_idx + 1
if isinstance(
self.token_generator,
(
VSLPretrainingTokenGenerator,
VSLFinetuningTokenGenerator,
),
):
checkpoint_doc_idx = df_chunk.start_doc_idx
if not self.shuffle:
for data_label, data in df_chunk.tokenized_data.items():
data = np.concatenate(data, axis=0)
if data_label not in buffer:
buffer[data_label] = []
buffer[data_label].append(data)
if get_size(buffer) >= self.write_chunk_size:
output_file_name = os.path.join(
self.output_dir,
f"output_chunk_{writer_idx}_{df_chunk.file_idx}_{df_chunk.start_doc_idx}_{chunk_number}.h5",
)
with h5py.File(output_file_name, "w") as h5f:
self.save_buffer_to_hdf5(
h5f, buffer, self.write_in_batch
)
cum_data_stats["examples"] += int(
h5f.attrs["n_examples"]
)
num_chunks_written += 1
buffer = {}
else:
chunk_buffer.append(chunk_data)
if get_size(buffer) >= self.write_chunk_size:
n_examples = self.append_buffer_to_hdf5(
chunk_buffer,
self.output_dir,
chunk_locks,
process_checkpoint_path,
)
cum_data_stats["examples"] += n_examples
num_chunks_written += 1
chunk_buffer = []
progress_counter.value += 1
checkpoint_data = [
df_chunk.file_idx,
checkpoint_doc_idx,
chunk_number + 1,
num_chunks_written,
0,
]
self.update_checkpoint(
process_checkpoint_path, checkpoint_data
)
except Exception as e:
logger.error(f'Exception in writer process {os.getpid()}: {e}')
if len(buffer) != 0 or len(chunk_buffer) != 0:
output_file_name = os.path.join(
self.output_dir,
f"output_chunk_remaining_{df_chunk.file_idx}_{df_chunk.start_doc_idx}.h5",
)
if not self.shuffle:
with h5py.File(output_file_name, "w") as h5f:
self.save_buffer_to_hdf5(h5f, buffer, self.write_in_batch)
cum_data_stats["examples"] += int(h5f.attrs["n_examples"])
else:
n_examples = self.append_buffer_to_hdf5(
chunk_buffer,
self.output_dir,
chunk_locks,
process_checkpoint_path,
)
cum_data_stats["examples"] += n_examples
num_chunks_written += 1
checkpoint_data = [
df_chunk.file_idx,
checkpoint_doc_idx,
chunk_number + 1,
num_chunks_written,
0,
]
self.update_checkpoint(process_checkpoint_path, checkpoint_data)
dump_args(cum_data_stats, process_stats_path)
self.stats_queue.put(cum_data_stats)
self.stats_queue.put(None)
[docs] def task_split_process_dataset(self) -> None:
"""
Split the dataset processing tasks across multiple processes.
"""
start_time = time.time()
total_size = self.calculate_total_size()
readable_size = self.human_readable_size(total_size)
logger.info(f"Total size of dataset: {readable_size}")
self.total_chunks = self.calculate_total_chunks(total_size)
self.total_output_files = math.ceil(total_size / self.write_chunk_size)
logger.info(
f"Approximate number of chunks to process: {self.total_chunks}"
)
process_checkpoints = self.read_checkpoint(self.writer_process_num)
total_num_chunks_written = sum(
[checkpoint_args[-2] for checkpoint_args in process_checkpoints]
)
progress_counter = multiprocessing.Value("i", total_num_chunks_written)
# Log process information
logger.info(f"Total processes: {self.processes}")
logger.info(f"Reader processes: 1")
logger.info(f"Tokenizer processes: {self.tokenize_process_num}")
logger.info(f"Writer processes: {self.writer_process_num}")
if self.shuffle and self.writer_process_num > 1:
lock_pool_size = 128
chunk_locks = [Lock() for _ in range(lock_pool_size)]
else:
chunk_locks = None
chunks_per_writer = [
(
(self.tokenize_process_num // self.writer_process_num + 1)
if i < self.tokenize_process_num % self.writer_process_num
else (self.tokenize_process_num // self.writer_process_num)
)
for i in range(self.writer_process_num)
]
# Initialize and start processes
tokenizers = [
Process(
target=self.tokenizer_process,
args=(idx,),
)
for idx in range(self.tokenize_process_num)
]
writers = []
for idx in range(self.writer_process_num):
writers.append(
Process(
target=self.writer_process,
args=(
progress_counter,
chunks_per_writer[idx],
idx,
chunk_locks,
process_checkpoints[idx],
),
)
)
for t in tokenizers:
t.start()
for w in writers:
w.start()
# Use tqdm for the progress bar
with tqdm(
total=self.total_chunks, desc="Processing", dynamic_ncols=True
) as pbar:
stop_event = Event()
progress_thread = Thread(
target=update_progress,
args=(
pbar,
progress_counter,
self.total_chunks,
start_time,
stop_event,
),
)
progress_thread.start()
self.reader_process(process_checkpoints)
for t in tokenizers:
# TODO: We had to add a timeout here
# as a workaround to avoid hanging at the
# join. We need to figure out a better
# solution.
t.join(timeout=1e-6)
self.stats_collation(self.writer_process_num)
self.write_remaining_prefix(chunk_locks, self.writer_process_num)
self.average_chars_and_bytes()
for w in writers:
w.join()
stop_event.set()
progress_thread.join()
if self.shuffle:
self.split_shuffle_second_pass()
end_time = time.time()
elapsed_time = end_time - start_time
logger.info(
f"The process_dataset function took {format_time(elapsed_time)} to complete."
)
[docs] def process_dataset(self) -> dict:
"""
Process the dataset either through file split or task split methods.
"""
data_stats = None
if self.processes < 3:
self.file_split_process_dataset()
else:
self.task_split_process_dataset()
self.final_data_stats["sample_features"] = getattr(
self.token_generator, 'sample_features', []
)
return self.final_data_stats
[docs] def get_vocab_size(self):
"""Get tokenizer vocabulary size
Returns:
vocab_size (int): text to tokenize
"""
return len(self.tokenizer)
def save_buffer_to_hdf5(
self, h5file, buffer, write_in_batch, dtype="i4", compression="gzip"
):
n_examples = 0
for data_label in [*buffer]:
data = np.concatenate(buffer[data_label], axis=0)
if data.dtype.kind == 'S':
dtype = h5py.string_dtype(encoding='utf-8')
elif data.dtype == np.bool_:
dtype = np.bool_
else:
dtype = "i4"
if len(data.shape) > 1:
chunks_shape = (
1,
*data.shape[1:],
) # Set chunk shape for multidimensional data
else:
chunks_shape = None
n_examples = data.shape[0]
dset = h5file.create_dataset(
data_label,
data=data,
dtype=dtype,
chunks=chunks_shape,
compression=compression,
)
if not write_in_batch:
for idx, f in enumerate(data):
dset[idx] = f
h5file.attrs["n_examples"] = n_examples
[docs] def append_buffer_to_hdf5(
self,
buffer,
output_dir,
chunk_locks,
dtype="i4",
compression="gzip",
):
"""
Appends an entire buffer of chunk to multiple HDF5 files. This method
is called as part of the shuffling process.
"""
if len(buffer) == 0:
return 0
n_examples = 0
for chunk_number, chunk in buffer:
sample_key = next(iter(chunk.tokenized_data.keys()))
n_examples += np.concatenate(
chunk.tokenized_data[sample_key], axis=0
).shape[0]
shuffled_indices = np.random.choice(
np.arange(self.total_output_files), n_examples
)
for chunk_number, chunk in buffer:
for i, (data_label, data) in enumerate(
chunk.tokenized_data.items()
):
data = np.concatenate(data, axis=0)
if data.dtype.kind == 'S':
dtype = h5py.string_dtype(encoding='utf-8')
elif data.dtype == np.bool_:
dtype = np.bool_
else:
dtype = "i4"
if len(data.shape) > 1:
chunks_shape = (
1,
*data.shape[1:],
) # Set chunk shape for multidimensional data
maxshape = (None, *data.shape[1:])
else:
chunks_shape = None
maxshape = None
for idx, element in enumerate(data):
idx_seq = shuffled_indices[idx]
output_file_name = os.path.join(
output_dir, f"output_chunk_{idx_seq}.h5"
)
if chunk_locks:
lock = chunk_locks[idx_seq % len(chunk_locks)]
else:
lock = None
with optional_lock(lock):
with h5py.File(output_file_name, "a") as h5f:
element = np.expand_dims(element, axis=0)
if data_label not in h5f:
h5f.create_dataset(
data_label,
data=element,
dtype=dtype,
chunks=chunks_shape,
maxshape=maxshape,
compression=compression,
)
h5f.attrs["n_examples"] = 1
else:
h5f[data_label].resize(
(h5f[data_label].shape[0] + 1), axis=0
)
h5f[data_label][-1:] = element
h5f.attrs["n_examples"] += 1
return n_examples
def update_checkpoint(
self,
process_checkpoint_path,
checkpoint_data,
):
with open(process_checkpoint_path, "w") as file:
file.write(
f"{checkpoint_data[0]}, {checkpoint_data[1]}, {checkpoint_data[2]}, {checkpoint_data[3]}, {checkpoint_data[4]}"
)
file.flush()