# Copyright 2024 ByteDance and/or its affiliates. # # 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. import math from typing import Iterator, Optional, Sequence import torch import torch.distributed as dist from ml_collections.config_dict import ConfigDict from torch.utils.data import DataLoader, DistributedSampler, Sampler from protenix.data.dataset import Dataset, get_datasets from protenix.utils.logger import get_logger logger = get_logger(__name__) class WeightedSampler(Sampler): """ A weighted sampler for single node. """ def __init__( self, weights: Sequence[float], num_samples: int, replacement: bool, seed: int = 0, ): """ Args: weights (list or numpy array): A list or numpy array of weights. num_samples (int): The number of samples to be drawn. replacement (bool): Whether sampling is done with replacement. seed (int): The seed for the random number generator. """ self.weights = torch.as_tensor(weights, dtype=torch.double) self.replacement = replacement self.seed = seed self.epoch = 0 self.num_samples = num_samples def __iter__(self) -> Iterator[int]: """ Generates an iterator over the sampled indices. This method uses a random number generator to sample indices based on the provided weights. The generator is seeded with the current seed and epoch to ensure reproducibility. Returns: iter: An iterator over the sampled indices. """ g = torch.Generator() g.manual_seed(self.seed + self.epoch) indices = torch.multinomial( self.weights, self.num_samples, self.replacement, generator=g ).tolist() return iter(indices) def __len__(self) -> int: return self.num_samples def set_epoch(self, epoch: int) -> None: self.epoch = epoch class DistributedWeightedSampler(DistributedSampler): """ A distributed weighted sampler for multiple nodes. """ def __init__( self, dataset: Dataset, weights: Sequence[float], num_samples: int, num_replicas: Optional[int] = None, rank: Optional[int] = None, replacement: bool = True, seed: int = 0, ): """ Args: dataset (Dataset): The dataset to be loaded. weights (list): The weights associated with the dataset. num_samples (int): The total number of samples to be drawn. num_replicas (int, optional): The number of replicas to use for distributed sampling. Defaults to None. rank (int, optional): The rank of the current process in a distributed environment. Defaults to None. replacement (bool, optional): Whether to sample with replacement. Defaults to True. seed (int, optional): The random seed for reproducibility. Defaults to 0. """ super().__init__(dataset, num_replicas=num_replicas, rank=rank, shuffle=False) self.weights = torch.as_tensor(weights, dtype=torch.double) self.replacement = replacement self.seed = seed self.epoch = 0 self.num_samples = num_samples self.num_samples_per_replica = int( math.ceil(self.num_samples / self.num_replicas) ) self.total_size = self.num_samples_per_replica * self.num_replicas def __iter__(self) -> Iterator[int]: """ Generates an iterator over the sampled indices for the current process in a distributed environment. This method uses a random number generator to sample indices based on the provided weights. The generator is seeded with the current seed and epoch to ensure reproducibility. The sampled indices are then distributed across the replicas according to the rank of the current process. Returns: iter: An iterator over the sampled indices for the current process. """ g = torch.Generator() g.manual_seed(self.seed + self.epoch) indices = torch.multinomial( self.weights, self.num_samples, self.replacement, generator=g ).tolist() indices = indices[self.rank : self.total_size : self.num_replicas] return iter(indices) def __len__(self) -> int: return self.num_samples // self.num_replicas def set_epoch(self, epoch: int) -> None: self.epoch = epoch class KeySumBalancedSampler(Sampler): def __init__( self, dataset: Dataset, key: str, value_scale: float = 1.0, seed: Optional[int] = None, num_replicas: Optional[int] = None, rank: Optional[int] = None, ): """ This method initializes the KeySumBalancedSampler. It calls the `get_balanced_assignments` method to distribute the dataset indices across workers based on the key sum. Args: dataset (Dataset): The dataset to sample from. key (str): The key by which data will be balanced (integer value). value_scale (float): The multiplier of key value when computing the worker assignment weight num_replicas (int, optional): Number of processes participating in distributed training. rank (int, optional): Rank of the current process within num_replicas. """ self.dataset = dataset self.key = key self.value_scale = value_scale self.seed = seed self.num_replicas = num_replicas or dist.get_world_size() self.rank = rank or dist.get_rank() # Get indices for this process after balancing by key sum worker_assignments = self.get_balanced_assignments() self.indices = worker_assignments[self.rank] def get_balanced_assignments(self): """ Distribute dataset indices across workers such that the sum of key values assigned to each worker is as balanced as possible. """ if self.seed is not None: # deterministically shuffle based on seed g = torch.Generator() g.manual_seed(self.seed) indices = torch.randperm(len(self.dataset), generator=g).tolist() else: indices = list(range(len(self.dataset))) # pad for len(dataset) to self.num_replicas if len(dataset) < self.num_replicas while len(indices) < self.num_replicas: indices += indices[: (self.num_replicas - len(indices))] if isinstance(self.dataset.indices_list, list): # e.g. recentPDB test set dataset_values = [ x[self.key].astype(int)[0] for x in self.dataset.indices_list ] else: # e.g. posebuster test set dataset_values = self.dataset.indices_list[self.key].astype(int).to_numpy() # Sort indices by key value key_value_pairs = [(idx, dataset_values[idx]) for idx in indices] key_value_pairs.sort(key=lambda x: x[1], reverse=True) # Calculate the target number of samples per worker num_samples_per_worker = len(self.dataset) // self.num_replicas # Initialize containers for worker assignments and their current key sum worker_assignments = [[] for _ in range(self.num_replicas)] worker_sums = [0] * self.num_replicas total_samples = num_samples_per_worker * self.num_replicas # Distribute samples using a greedy strategy to balance the key sum for idx, key_value in key_value_pairs[:total_samples]: # Find the worker with the smallest sum that hasn't exceeded its target sample count min_worker = min( range(self.num_replicas), key=lambda i: ( worker_sums[i] if len(worker_assignments[i]) < num_samples_per_worker else float("inf") ), ) worker_assignments[min_worker].append(idx) worker_sums[min_worker] += key_value**2 # Fix any discrepancies in the number of samples all_indices = [idx for idx, _ in key_value_pairs] # Assign remaining samples if the dataset isn't divisible perfectly if len(all_indices) > total_samples: for i in range(len(all_indices) - total_samples): worker_assignments[i % self.num_replicas].append( all_indices[total_samples + i] ) # Return the indices assigned to the current worker return worker_assignments def __iter__(self): return iter(self.indices) def __len__(self): return len(self.indices) class IterDataLoader(DataLoader): """ Iterative dataloader for single node. """ def __init__(self, *args, **kwargs): super(IterDataLoader, self).__init__(*args, **kwargs) assert self.sampler is not None self.counter = 0 def __iter__(self): self.sampler.set_epoch(self.counter) self.counter += 1 _iterator = super(IterDataLoader, self).__iter__() return _iterator class DistributedDataLoader(DataLoader): """ Distributed dataloader for multiple nodes. """ def __init__( self, dataset: Dataset, batch_size: int, num_workers: int = 0, collate_fn=None, seed: int = 42, drop_last: bool = True, shuffle: bool = True, sampler: Sampler = None, ): if sampler is not None: self.sampler = sampler else: self.sampler = DistributedSampler( dataset, shuffle=shuffle, seed=seed, drop_last=drop_last ) super(DistributedDataLoader, self).__init__( dataset=dataset, batch_size=batch_size, num_workers=num_workers, sampler=self.sampler, shuffle=False, collate_fn=collate_fn, ) self.counter = 0 def __iter__(self): self.sampler.set_epoch(self.counter) self.counter += 1 _iterator = super(DistributedDataLoader, self).__iter__() return _iterator def get_dataloaders( configs: ConfigDict, world_size: int, seed: int, error_dir: Optional[str] = None ): """ Generate data loaders for training and testing based on the given configurations and seed. Args: configs (ConfigDict): An object containing the data configuration information. world_size (int): The number of processes in the distributed environment. seed (int): The random seed used for data sampling. error_dir (str, optional): The directory to store error information. Defaults to None. Returns: tuple: A tuple containing the training data loader and a dictionary of testing data loaders. """ train_dataset, test_datasets = get_datasets(configs, error_dir) if world_size > 1: train_sampler = DistributedWeightedSampler( train_dataset, train_dataset.merged_datapoint_weights, num_samples=configs.data.epoch_size, replacement=True, seed=seed, ) train_dl = DistributedDataLoader( dataset=train_dataset, batch_size=1, shuffle=False, num_workers=configs.data.num_dl_workers, collate_fn=lambda batch: batch[0], sampler=train_sampler, ) else: train_sampler = WeightedSampler( weights=train_dataset.merged_datapoint_weights, num_samples=configs.data.epoch_size, replacement=True, seed=seed, ) train_dl = IterDataLoader( dataset=train_dataset, batch_size=1, shuffle=False, num_workers=configs.data.num_dl_workers, collate_fn=lambda batch: batch[0], sampler=train_sampler, ) test_dls = {} test_dataset_sizes = {} for test_name, test_dataset in test_datasets.items(): test_dataset_sizes[test_name] = len(test_dataset) test_sampler = ( KeySumBalancedSampler(test_dataset, key="num_tokens", seed=configs.seed) if world_size > 1 else None ) test_dls[test_name] = DataLoader( test_dataset, batch_size=1, shuffle=False, num_workers=configs.data.num_dl_workers, sampler=test_sampler, collate_fn=lambda batch: batch[0], ) logger.info( f"train data size: {len(train_dataset)}, test size: {test_dataset_sizes}" ) return train_dl, test_dls