Source code for modelzoo.transformers.data_processing.HDF5IterableDataset

# Copyright 2022 Cerebras Systems.
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"""PyTorch HDF5 Dataset"""

import json
import math
import os
import random
from pathlib import Path

import h5py
import numpy as np
import torch

from cerebras_pytorch.distributed import get_worker_state
from modelzoo.common.pytorch.input_utils import get_streaming_batch_size
from modelzoo.transformers.pytorch.input_utils import (
    cluster_config,
    shard_list_of_chunks_contiguous,
)


[docs]class RestartableDataLoader(torch.utils.data.DataLoader): """ This custom dataloader class specifies the 'state_dict', 'aggregate_state_dict', 'load_state_dict' and 'deaggregate_state_dict' methods. These methods dictate what worker state information is stored (local or global streaming info) and how it is to be aggregated and retrieved. To deterministically restart an instance of HDF5IterableDataset, it requires the number of samples already seen in the previous run. This info is stored in the `samples_streamed` key inside the worker state dict. Upon restart, the `load_state_dict` method sets the `samples_seen` class variable which determines the number of samples to be skipped. """
[docs] def __init__(self, *args, **kwargs): # keep track of how many samples were streamed in the previous portion # of the run so that we can track cumulative samples streamed in the # state_dict self.previous_samples_streamed = 0 super().__init__(*args, **kwargs)
def state_dict(self): worker_state = get_worker_state() return { "samples_streamed": worker_state.samples_streamed + self.previous_samples_streamed, "shard_index": self.dataset.shard_index, } def load_state_dict(self, state_dict): if ( len(state_dict) != 2 or "samples_streamed" not in state_dict or "shard_index" not in state_dict ): raise RuntimeError( "The state dict must contain keys `samples_streamed` and `shard_index`, " f"but found {state_dict.keys()}. This means that the dataloader " "state in the checkpoint being loaded from is not compatible " "with the dataloader currently in use. Consider re-running " "without loading the dataloader state." ) self.previous_samples_streamed = state_dict["samples_streamed"] self.dataset.set_state( state_dict["samples_streamed"], state_dict["shard_index"] ) def aggregate_state_dict(self, worker_states): worker_states.sort(key=lambda x: x["shard_index"]) return {"all_worker_states": worker_states} def deaggregate_state_dict(self, aggregated_state_dict): if ( len(aggregated_state_dict) != 1 or "all_worker_states" not in aggregated_state_dict ): raise RuntimeError( "The aggregated state dict must contain a single key " f"'all_worker_states', found {aggregated_state_dict.keys()}. " "This means that the dataloader state in the checkpoint you are " "loading from is not compatible with the dataloader currently " "in use. Consider re-running without loading the dataloader " "state." ) all_worker_states = aggregated_state_dict["all_worker_states"] # For deterministic restart to work, the num_tasks for the previous run should # match with the restart run's num_tasks. If that condition is not met, # the dataloader would start from sample `0`. num_tasks_prev_run = len(all_worker_states) num_tasks = self.dataset.num_tasks task_id = self.dataset.task_id if num_tasks != num_tasks_prev_run: raise RuntimeError( "Unable to deterministically restart the dataloader. The total number " f"of workers for the initial run, {num_tasks_prev_run}, does not match " f"number of workers in the current run, {num_tasks}. This is currently " "not supported by the dataloader for the `HDF5IterableDataset`. Please " "ensure that `num_csx * num_workers_per_csx` is fixed across runs, or " "consider opting out of loading dataloader state via `runconfig.load_checkpoint_states`." ) worker_index_offset = None min_samples = None for i, sd in enumerate(all_worker_states): if ( worker_index_offset is None or sd["samples_streamed"] < min_samples ): worker_index_offset = i min_samples = sd["samples_streamed"] return all_worker_states[(task_id + worker_index_offset) % num_tasks]
[docs]class HDF5IterableDataset(torch.utils.data.IterableDataset): """ A HDF5 dataset processor. Loads data from HDF5 files. :param dict params: dict containing training input parameters for creating dataset. Expects the following fields: - "data_dir" (str or list of str): Path to dataset HDF5 files - "batch_size" (int): Batch size. - "shuffle" (bool): Flag to enable data shuffling. - "shuffle_seed" (int): Shuffle seed. - "num_workers" (int): How many subprocesses to use for data loading. - "drop_last" (bool): If True and the dataset size is not divisible by the batch size, the last incomplete batch will be dropped. - "use_vsl" (bool): Flag to enable variable sequence length training. It requires the dataset to have two extra features: the `attention_span` of keys and the `position_ids` of tokens. Defaults to `False`. """
[docs] def __init__(self, params): super(HDF5IterableDataset, self).__init__() self.data_dir = params["data_dir"] self.batch_size = get_streaming_batch_size(params["batch_size"]) self.shuffle = params["shuffle"] self.shuffle_seed = params.get("shuffle_seed", None) self.num_workers = params.get("num_workers", 0) self.drop_last = params.get("drop_last", True) self.use_vsl = params.get("use_vsl", False) self.num_feature_groups = 1 # Load feature names from data_params.json, if present and # has the correct format (generated by HF > HDF5 converter script) if not isinstance(self.data_dir, list) and os.path.exists( os.path.join(self.data_dir, "data_params.json") ): try: with open( os.path.join(self.data_dir, "data_params.json"), 'r' ) as _fin: data_params = json.load(_fin) if "features" in data_params: self.features_list = data_params["features"] elif "data_0_features" in data_params: self.features_list = [data_params["data_0_features"]] i = 1 while f"data_{i}_features" in data_params: self.features_list.append( data_params[f"data_{i}_features"] ) i += 1 self.num_feature_groups = i else: self.features_list = [ "input_ids", "attention_mask", "labels", ] except: self.features_list = ["input_ids", "attention_mask", "labels"] else: self.features_list = ["input_ids", "attention_mask", "labels"] if self.use_vsl: self.features_list = [ "input_ids", "attention_mask", "labels", "attention_span", "position_ids", ] if self.batch_size <= 0: raise ValueError( f"Batch size should be a positive number, but got value {self.batch_size}." ) if not isinstance(self.data_dir, list): self.data_dir = [self.data_dir] self.files = [] for directory in self.data_dir: p = Path(directory) if not p.is_dir(): raise FileNotFoundError( f"The path {directory} does not exist or is not a directory." ) self.files.extend(p.glob('*.h5')) self.files = sorted(self.files) if not self.files: raise RuntimeError("No .h5 dataset files found.") cluster_spec, worker_spec = cluster_config() self.num_tasks = cluster_spec.num_tasks() self.task_id = worker_spec.rank # initialize state with 0 samples seen and shard_index = task_id self.set_state(0, self.task_id)
[docs] def set_state(self, samples_seen, shard_index): """ This method sets the state of the dataloader's samples_seen variable that controls how many samples are to be skipped for determinisitic restart. This is called by the load_state_dict method of the RestartableDataLoader. Args: samples_seen (int): number of samples streamed by the dataloader shard_index (int): the index of the shard of data that this worker is responsible for streaming """ self._samples_seen = samples_seen self.shard_index = shard_index # Shard H5 files between the tasks and resolve the paths files_in_this_task = [ str(file.resolve()) for file in self.files[shard_index :: self.num_tasks] ] self.files_in_this_task = [] self.num_examples_in_this_task = 0 for file_path in files_in_this_task: with h5py.File(file_path, mode='r') as h5_file: num_examples_in_file = h5_file.attrs["n_examples"] self.files_in_this_task.append( (file_path, num_examples_in_file) ) self.num_examples_in_this_task += num_examples_in_file if self.shuffle: random.seed(self.shuffle_seed) random.shuffle(self.files_in_this_task)
@property def samples_seen(self): return self._samples_seen % self.__len__() def _load_buffer(self, data_partitions): # partition id should default to 0 if not reading iter from file self.prev_worker_iter_index = self.samples_seen // self.batch_size restart_iter_partition_id = 0 restart_iter_start_idx = 0 # start_idx should default to 0 if self.prev_worker_iter_index > 0: # check total number of iterations/steps in the data partitions # This is required to determine the epoch of the restart iter worker_num_iters = self.num_examples_in_this_task // self.batch_size self.prev_worker_iter_index %= worker_num_iters iters_until_current_partition = 0 prev_partition_offset_start_idx = 0 current_partition_offset_start_idx = 0 for partition_idx, partition_specs in enumerate(data_partitions): start_idx = partition_specs[1] num_examples = partition_specs[2] if partition_idx > 0: num_examples_prev_partition = ( data_partitions[partition_idx - 1][2] - prev_partition_offset_start_idx ) if ( num_examples_prev_partition - (num_examples_prev_partition // self.batch_size) * self.batch_size ) > 0: current_partition_offset_start_idx = self.batch_size - ( num_examples_prev_partition - (num_examples_prev_partition // self.batch_size) * self.batch_size ) else: current_partition_offset_start_idx = 0 prev_partition_offset_start_idx = ( current_partition_offset_start_idx ) num_examples_curr_partition = ( num_examples - current_partition_offset_start_idx ) else: num_examples_curr_partition = num_examples current_partition_offset_start_idx = 0 iters_until_current_partition += np.ceil( num_examples_curr_partition / self.batch_size ) if ( self.prev_worker_iter_index <= iters_until_current_partition - 1 ): restart_iter_partition_id = partition_idx restart_iter_start_idx = int( self.batch_size * ( self.prev_worker_iter_index - ( iters_until_current_partition - np.ceil( num_examples_curr_partition / self.batch_size ) ) ) ) restart_iter_start_idx += current_partition_offset_start_idx break for partition_idx, partition_specs in enumerate( data_partitions[restart_iter_partition_id:] ): file_path = partition_specs[0] start_idx_org = partition_specs[1] num_examples = partition_specs[2] if self.prev_worker_iter_index > 0: if restart_iter_partition_id >= 0 and partition_idx == 0: start_idx = restart_iter_start_idx else: start_idx = start_idx_org else: start_idx = start_idx_org with h5py.File(file_path, mode='r') as h5_file: if self.use_vsl and h5_file["data"].shape[1] != 5: raise ValueError( f"Expected all dataset H5 files to have 5 features for " f"variable sequence length training, but got " f"{h5_file['data'].shape[1]} features in {file_path}." ) for idx in range( start_idx, start_idx_org + num_examples, self.batch_size ): load_len = min( self.batch_size, start_idx_org + num_examples - idx ) if self.num_feature_groups == 1: load_data = h5_file["data"][idx : idx + load_len] for i in range(load_len): yield load_data[i] else: load_data = [None] * self.num_feature_groups for i in range(self.num_feature_groups): load_data[i] = h5_file[f"data_{i}"][ idx : idx + load_len ] for i in range(load_len): yield tuple( [ load_data[j][i] for j in range(self.num_feature_groups) ] ) l = self.__len__() self._samples_seen = l * math.ceil((self._samples_seen + 1) / l) def __iter__(self): """ Iterating over the data to construct input features. """ worker_info = torch.utils.data.get_worker_info() if worker_info is not None: worker_id = worker_info.id num_workers = worker_info.num_workers else: # Single-process worker_id = 0 num_workers = 1 data_partitions = shard_list_of_chunks_contiguous( self.files_in_this_task, worker_id, num_workers ) for example in self._load_buffer(data_partitions): if self.num_feature_groups == 1: yield { feature: np.array(example[i], np.int32) for i, feature in enumerate(self.features_list) } else: sample = {} for j in range(self.num_feature_groups): sample.update( { feature: np.array(example[j][i], np.int32) for i, feature in enumerate(self.features_list[j]) } ) yield sample def __len__(self): """ Returns the len of dataset on the task process """ return self.num_examples_in_this_task