Guangyang Lu

Shenggan Cheng, Xuanlei Zhao, Guangyang Lu et al. · berkeley

Protein structure prediction helps to understand gene translation and protein function, which is of growing interest and importance in structural biology. The AlphaFold model, which used transformer architecture to achieve atomic-level accuracy in protein structure prediction, was a significant breakthrough. However, training and inference of the AlphaFold model are challenging due to its high computation and memory cost. In this work, we present FastFold, an efficient implementation of AlphaFold for both training and inference. We propose Dynamic Axial Parallelism and Duality Async Operations to improve the scaling efficiency of model parallelism. Besides, AutoChunk is proposed to reduce memory cost by over 80% during inference by automatically determining the chunk strategy. Experimental results show that FastFold reduces overall training time from 11 days to 67 hours and achieves 7.5X - 9.5X speedup for long-sequence inference. Furthermore, we scale FastFold to 512 GPUs and achieve an aggregate throughput of 6.02 PetaFLOP/s with 90.1% parallel efficiency.

Jinyi Deng, Xinru Tang, Zhiheng Yue et al.

Given the increasing complexity of AI applications, traditional spatial architectures frequently fall short. Our analysis identifies a pattern of interconnected, multi-faceted tasks encompassing both AI and general computational processes. In response, we have conceptualized "Orchestrated AI Workflows," an approach that integrates various tasks with logic-driven decisions into dynamic, sophisticated workflows. Specifically, we find that the intrinsic Dual Dynamicity of Orchestrated AI Workflows, namely dynamic execution times and frequencies of Task Blocks, can be effectively represented using the Orchestrated Workflow Graph. Furthermore, the intrinsic Dual Dynamicity poses challenges to existing spatial architecture, namely Indiscriminate Resource Allocation, Reactive Load Rebalancing, and Contagious PEA Idleness. To overcome these challenges, we present Octopus, a scale-out spatial architecture and a suite of advanced scheduling strategies optimized for executing Orchestrated AI Workflows, such as the Discriminate Dual-Scheduling Mechanism, Adaptive TBU Scheduling Strategy, and Proactive Cluster Scheduling Strategy. Our evaluations demonstrate that Octopus significantly outperforms traditional architectures in handling the dynamic demands of Orchestrated AI Workflows, and possesses robust scalability in large scale hardware such as wafer-scale chip.

Xuanlei Zhao, Shenggan Cheng, Guangyang Lu et al.

Large deep learning models have achieved impressive performance across a range of applications. However, their large memory requirements, including parameter memory and activation memory, have become a significant challenge for their practical serving. While existing methods mainly address parameter memory, the importance of activation memory has been overlooked. Especially for long input sequences, activation memory is expected to experience a significant exponential growth as the length of sequences increases. In this approach, we propose AutoChunk, an automatic and adaptive compiler system that efficiently reduces activation memory for long sequence inference by chunk strategies. The proposed system generates chunk plans by optimizing through multiple stages. In each stage, the chunk search pass explores all possible chunk candidates and the chunk selection pass identifies the optimal one. At runtime, AutoChunk employs code generation to automatically apply chunk strategies. The experiments demonstrate that AutoChunk can reduce over 80\% of activation memory while maintaining speed loss within 10%, extend max sequence length by 3.2x to 11.7x, and outperform state-of-the-art methods by a large margin.