Daily Papers

Recent years have seen a surge in deep learning approaches to accelerate numerical solvers, which provide faithful but computationally intensive simulations of the physical world. These deep surrogates are generally trained in a supervised manner from limited amounts of data slowly generated by the same solver they intend to accelerate. We propose an open-source framework that enables the online training of these models from a large ensemble run of simulations. It leverages multiple levels of parallelism to generate rich datasets. The framework avoids I/O bottlenecks and storage issues by directly streaming the generated data. A training reservoir mitigates the inherent bias of streaming while maximizing GPU throughput. Experiment on training a fully connected network as a surrogate for the heat equation shows the proposed approach enables training on 8TB of data in 2 hours with an accuracy improved by 47% and a batch throughput multiplied by 13 compared to a traditional offline procedure.

Large Language Models (LLMs) face challenges for on-device inference due to high memory demands. Traditional methods to reduce memory usage often compromise performance and lack adaptability. We propose FlexInfer, an optimized offloading framework for on-device inference, addressing these issues with techniques like asynchronous prefetching, balanced memory locking, and flexible tensor preservation. These strategies enhance memory efficiency and mitigate I/O bottlenecks, ensuring high performance within user-specified resource constraints. Experiments demonstrate that FlexInfer significantly improves throughput under limited resources, achieving up to 12.5 times better performance than existing methods and facilitating the deployment of large models on resource-constrained devices.

The Transformer architecture has significantly advanced natural language processing (NLP) and has been foundational in developing large language models (LLMs) such as LLaMA and OPT, which have come to dominate a broad range of NLP tasks. Despite their superior accuracy, LLMs present unique challenges in practical inference, concerning the compute and memory-intensive nature. Thanks to the autoregressive characteristic of LLM inference, KV caching for the attention layers in Transformers can effectively accelerate LLM inference by substituting quadratic-complexity computation with linear-complexity memory accesses. Yet, this approach requires increasing memory as demand grows for processing longer sequences. The overhead leads to reduced throughput due to I/O bottlenecks and even out-of-memory errors, particularly on resource-constrained systems like a single commodity GPU. In this paper, we propose ALISA, a novel algorithm-system co-design solution to address the challenges imposed by KV caching. On the algorithm level, ALISA prioritizes tokens that are most important in generating a new token via a Sparse Window Attention (SWA) algorithm. SWA introduces high sparsity in attention layers and reduces the memory footprint of KV caching at negligible accuracy loss. On the system level, ALISA employs three-phase token-level dynamical scheduling and optimizes the trade-off between caching and recomputation, thus maximizing the overall performance in resource-constrained systems. In a single GPU-CPU system, we demonstrate that under varying workloads, ALISA improves the throughput of baseline systems such as FlexGen and vLLM by up to 3X and 1.9X, respectively.

In recent times, the emergence of Large Language Models (LLMs) has resulted in increasingly larger model size, posing challenges for inference on low-resource devices. Prior approaches have explored offloading to facilitate low-memory inference but often suffer from efficiency due to I/O bottlenecks. To achieve low-latency LLMs inference on resource-constrained devices, we introduce HeteGen, a novel approach that presents a principled framework for heterogeneous parallel computing using CPUs and GPUs. Based on this framework, HeteGen further employs heterogeneous parallel computing and asynchronous overlap for LLMs to mitigate I/O bottlenecks. Our experiments demonstrate a substantial improvement in inference speed, surpassing state-of-the-art methods by over 317% at most.

Vision-language models (VLMs) show remarkable performance in multimodal tasks. However, excessively long multimodal inputs lead to oversized Key-Value (KV) caches, resulting in significant memory consumption and I/O bottlenecks. Previous KV quantization methods for Large Language Models (LLMs) may alleviate these issues but overlook the attention saliency differences of multimodal tokens, resulting in suboptimal performance. In this paper, we investigate the attention-aware token saliency patterns in VLM and propose AKVQ-VL. AKVQ-VL leverages the proposed Text-Salient Attention (TSA) and Pivot-Token-Salient Attention (PSA) patterns to adaptively allocate bit budgets. Moreover, achieving extremely low-bit quantization requires effectively addressing outliers in KV tensors. AKVQ-VL utilizes the Walsh-Hadamard transform (WHT) to construct outlier-free KV caches, thereby reducing quantization difficulty. Evaluations of 2-bit quantization on 12 long-context and multimodal tasks demonstrate that AKVQ-VL maintains or even improves accuracy, outperforming LLM-oriented methods. AKVQ-VL can reduce peak memory usage by 2.13x, support up to 3.25x larger batch sizes and 2.46x throughput.

AlphaFold predicts protein structures from the amino acid sequence at or near experimental resolution, solving the 50-year-old protein folding challenge, leading to progress by transforming large-scale genomics data into protein structures. AlphaFold will also greatly change the scientific research model from low-throughput to high-throughput manner. The AlphaFold framework is a mixture of two types of workloads: MSA construction based on CPUs and model inference on GPUs. The first CPU stage dominates the overall runtime, taking hours for a single protein due to the large database sizes and I/O bottlenecks. However, GPUs in this CPU stage remain idle, resulting in low GPU utilization and restricting the capacity of large-scale structure predictions. Therefore, we proposed ParaFold, an open-source parallel version of AlphaFold for high throughput protein structure predictions. ParaFold separates the CPU and GPU parts to enable large-scale structure predictions. ParaFold also effectively reduces the CPU and GPU runtime with two optimizations without compromising the quality of prediction results: using multi-threaded parallelism on CPUs and using optimized JAX compilation on GPUs. We evaluated ParaFold with three datasets of different size and protein lengths. We evaluated the accuracy and efficiency of optimizations on CPUs and GPUs, and showed the large-scale prediction capability by running ParaFold inferences of 19,704 small proteins in five hours on one NVIDIA DGX-2. Using the JAX compile optimization, ParaFold attained a 13.8X average speedup over AlphaFold. ParaFold offers a rapid and effective approach for high-throughput structure predictions, leveraging the predictive power by running on supercomputers, with shorter time, and at a lower cost. The development of ParaFold will greatly speed up high-throughput studies and render the protein "structure-omics" feasible.

Convolution models with long filters have demonstrated state-of-the-art reasoning abilities in many long-sequence tasks but lag behind the most optimized Transformers in wall-clock time. A major bottleneck is the Fast Fourier Transform (FFT)--which allows long convolutions to run in O(N logN) time in sequence length N but has poor hardware utilization. In this paper, we study how to optimize the FFT convolution. We find two key bottlenecks: the FFT does not effectively use specialized matrix multiply units, and it incurs expensive I/O between layers of the memory hierarchy. In response, we propose FlashFFTConv. FlashFFTConv uses a matrix decomposition that computes the FFT using matrix multiply units and enables kernel fusion for long sequences, reducing I/O. We also present two sparse convolution algorithms--1) partial convolutions and 2) frequency-sparse convolutions--which can be implemented simply by skipping blocks in the matrix decomposition, enabling further opportunities for memory and compute savings. FlashFFTConv speeds up exact FFT convolutions by up to 7.93times over PyTorch and achieves up to 4.4times speedup end-to-end. Given the same compute budget, FlashFFTConv allows Hyena-GPT-s to achieve 2.3 points better perplexity on the PILE and M2-BERT-base to achieve 3.3 points higher GLUE score--matching models with twice the parameter count. FlashFFTConv also achieves 96.1% accuracy on Path-512, a high-resolution vision task where no model had previously achieved better than 50%. Furthermore, partial convolutions enable longer-sequence models--yielding the first DNA model that can process the longest human genes (2.3M base pairs)--and frequency-sparse convolutions speed up pretrained models while maintaining or improving model quality.

While frontier large language models (LLMs) continue to push capability boundaries, their deployment remains confined to GPU-powered cloud infrastructure. We challenge this paradigm with SmallThinker, a family of LLMs natively designed - not adapted - for the unique constraints of local devices: weak computational power, limited memory, and slow storage. Unlike traditional approaches that mainly compress existing models built for clouds, we architect SmallThinker from the ground up to thrive within these limitations. Our innovation lies in a deployment-aware architecture that transforms constraints into design principles. First, We introduce a two-level sparse structure combining fine-grained Mixture-of-Experts (MoE) with sparse feed-forward networks, drastically reducing computational demands without sacrificing model capacity. Second, to conquer the I/O bottleneck of slow storage, we design a pre-attention router that enables our co-designed inference engine to prefetch expert parameters from storage while computing attention, effectively hiding storage latency that would otherwise cripple on-device inference. Third, for memory efficiency, we utilize NoPE-RoPE hybrid sparse attention mechanism to slash KV cache requirements. We release SmallThinker-4B-A0.6B and SmallThinker-21B-A3B, which achieve state-of-the-art performance scores and even outperform larger LLMs. Remarkably, our co-designed system mostly eliminates the need for expensive GPU hardware: with Q4_0 quantization, both models exceed 20 tokens/s on ordinary consumer CPUs, while consuming only 1GB and 8GB of memory respectively. SmallThinker is publicly available at hf.co/PowerInfer/SmallThinker-4BA0.6B-Instruct and hf.co/PowerInfer/SmallThinker-21BA3B-Instruct.

The spatiotemporal resolution of Partial Differential Equations (PDEs) plays important roles in the mathematical description of the world's physical phenomena. In general, scientists and engineers solve PDEs numerically by the use of computationally demanding solvers. Recently, deep learning algorithms have emerged as a viable alternative for obtaining fast solutions for PDEs. Models are usually trained on synthetic data generated by solvers, stored on disk and read back for training. This paper advocates that relying on a traditional static dataset to train these models does not allow the full benefit of the solver to be used as a data generator. It proposes an open source online training framework for deep surrogate models. The framework implements several levels of parallelism focused on simultaneously generating numerical simulations and training deep neural networks. This approach suppresses the I/O and storage bottleneck associated with disk-loaded datasets, and opens the way to training on significantly larger datasets. Experiments compare the offline and online training of four surrogate models, including state-of-the-art architectures. Results indicate that exposing deep surrogate models to more dataset diversity, up to hundreds of GB, can increase model generalization capabilities. Fully connected neural networks, Fourier Neural Operator (FNO), and Message Passing PDE Solver prediction accuracy is improved by 68%, 16% and 7%, respectively.

Self-attention is at the heart of the popular Transformer architecture, yet suffers from quadratic time and memory complexity. The breakthrough FlashAttention algorithm revealed I/O complexity as the true bottleneck in scaling Transformers. Given two levels of memory hierarchy, a fast cache (e.g. GPU on-chip SRAM) and a slow memory (e.g. GPU high-bandwidth memory), the I/O complexity measures the number of accesses to memory. FlashAttention computes attention using N^2d^2{M} I/O operations where N is the dimension of the attention matrix, d the head-dimension and M the cache size. However, is this I/O complexity optimal? The known lower bound only rules out an I/O complexity of o(Nd) when M=Theta(Nd), since the output that needs to be written to slow memory is Omega(Nd). This leads to the main question of our work: Is FlashAttention I/O optimal for all values of M? We resolve the above question in its full generality by showing an I/O complexity lower bound that matches the upper bound provided by FlashAttention for any values of M geq d^2 within any constant factors. Further, we give a better algorithm with lower I/O complexity for M < d^2, and show that it is optimal as well. Moreover, our lower bounds do not rely on using combinatorial matrix multiplication for computing the attention matrix. We show even if one uses fast matrix multiplication, the above I/O complexity bounds cannot be improved. We do so by introducing a new communication complexity protocol for matrix compression, and connecting communication complexity to I/O complexity. To the best of our knowledge, this is the first work to establish a connection between communication complexity and I/O complexity, and we believe this connection could be of independent interest and will find many more applications in proving I/O complexity lower bounds in the future.

Checkpointing to preserve training states is crucial during the development of Large Foundation Models (LFMs), for training resumption upon various failures or changes in GPU resources and parallelism configurations. In addition, saved checkpoints are dispatched to evaluation tasks or transferred across different training stages (e.g., from pre-training to post-training). All these scenarios require resharding distributed checkpoints from one parallelism to another. In production environments, different LFMs are trained with various frameworks and storage backends, depending on model sizes and training scales. A high-performance checkpointing system is needed to enable efficient checkpoint management at scale throughout the lifecycle of LFM development. We introduce ByteCheckpoint, an industrial-grade checkpointing system for large-scale LFM training. ByteCheckpoint features: a parallelism-agnostic checkpoint representation that enables efficient load-time checkpoint resharding; a generic checkpoint saving/loading workflow to accommodate multiple training frameworks and support different storage backends; full-stack optimizations to ensure high I/O efficiency and scalability; a suite of monitoring tools to streamline large-scale performance analysis and bottleneck detection. Compared to existing open-source checkpointing systems [52, 58], ByteCheckpoint significantly reduces runtime checkpoint stalls, achieving an average reduction of 54.20x. For saving and loading times, ByteCheckpoint achieves improvements of up to 9.96x and 8.80x, respectively.

Clustering non-Euclidean data is difficult, and one of the most used algorithms besides hierarchical clustering is the popular algorithm Partitioning Around Medoids (PAM), also simply referred to as k-medoids clustering. In Euclidean geometry the mean-as used in k-means-is a good estimator for the cluster center, but this does not exist for arbitrary dissimilarities. PAM uses the medoid instead, the object with the smallest dissimilarity to all others in the cluster. This notion of centrality can be used with any (dis-)similarity, and thus is of high relevance to many domains and applications. A key issue with PAM is its high run time cost. We propose modifications to the PAM algorithm that achieve an O(k)-fold speedup in the second ("SWAP") phase of the algorithm, but will still find the same results as the original PAM algorithm. If we relax the choice of swaps performed (while retaining comparable quality), we can further accelerate the algorithm by eagerly performing additional swaps in each iteration. With the substantially faster SWAP, we can now explore faster initialization strategies, because (i) the classic ("BUILD") initialization now becomes the bottleneck, and (ii) our swap is fast enough to compensate for worse starting conditions. We also show how the CLARA and CLARANS algorithms benefit from the proposed modifications. While we do not study the parallelization of our approach in this work, it can easily be combined with earlier approaches to use PAM and CLARA on big data (some of which use PAM as a subroutine, hence can immediately benefit from these improvements), where the performance with high k becomes increasingly important. In experiments on real data with k=100,200, we observed a 458x respectively 1191x speedup compared to the original PAM SWAP algorithm, making PAM applicable to larger data sets, and in particular to higher k.