Zhongming Yu

Haotian Tang, Shang Yang, Zhijian Liu et al. · mit

Sparse convolution plays a pivotal role in emerging workloads, including point cloud processing in AR/VR, autonomous driving, and graph understanding in recommendation systems. Since the computation pattern is sparse and irregular, specialized high-performance kernels are required. Existing GPU libraries offer two dataflow types for sparse convolution. The gather-GEMM-scatter dataflow is easy to implement but not optimal in performance, while the dataflows with overlapped computation and memory access (e.g.implicit GEMM) are highly performant but have very high engineering costs. In this paper, we introduce TorchSparse++, a new GPU library that achieves the best of both worlds. We create a highly efficient Sparse Kernel Generator that generates performant sparse convolution kernels at less than one-tenth of the engineering cost of the current state-of-the-art system. On top of this, we design the Sparse Autotuner, which extends the design space of existing sparse convolution libraries and searches for the best dataflow configurations for training and inference workloads. Consequently, TorchSparse++ achieves 2.9x, 3.3x, 2.2x and 1.7x measured end-to-end speedup on an NVIDIA A100 GPU over state-of-the-art MinkowskiEngine, SpConv 1.2, TorchSparse and SpConv v2 in inference; and is 1.2-1.3x faster than SpConv v2 in mixed precision training across seven representative autonomous driving benchmarks. It also seamlessly supports graph convolutions, achieving 2.6-7.6x faster inference speed compared with state-of-the-art graph deep learning libraries.

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.

Yuwei Hu, Jiajie Li, Zhongming Yu et al.

Graph neural networks (GNNs), which have emerged as an effective method for handling machine learning tasks on graphs, bring a new approach to building recommender systems, where the task of recommendation can be formulated as the link prediction problem on user-item bipartite graphs. Training GNN-based recommender systems (GNNRecSys) on large graphs incurs a large memory footprint, easily exceeding the DRAM capacity on a typical server. Existing solutions resort to distributed subgraph training, which is inefficient due to the high cost of dynamically constructing subgraphs and significant redundancy across subgraphs. The emerging persistent memory technologies provide a significantly larger memory capacity than DRAMs at an affordable cost, making single-machine GNNRecSys training feasible, which eliminates the inefficiencies in distributed training. One major concern of using persistent memory devices for GNNRecSys is their relatively low bandwidth compared with DRAMs. This limitation can be particularly detrimental to achieving high performance for GNNRecSys workloads since their dominant compute kernels are sparse and memory access intensive. To understand whether persistent memory is a good fit for GNNRecSys training, we perform an in-depth characterization of GNNRecSys workloads and a comprehensive analysis of their performance on a persistent memory device, namely, Intel Optane. Based on the analysis, we provide guidance on how to configure Optane for GNNRecSys workloads. Furthermore, we present techniques for large-batch training to fully realize the advantages of single-machine GNNRecSys training. Our experiment results show that with the tuned batch size and optimal system configuration, Optane-based single-machine GNNRecSys training outperforms distributed training by a large margin, especially when handling deep GNN models.

Zhongming Yu, Hejia Zhang, Yujie Zhao et al.

Recent developments in Large Language Model (LLM) agents are revolutionizing Autonomous Software Engineering (ASE), enabling automated coding, problem fixes, and feature improvements. However, localization -- precisely identifying software problems by navigating to relevant code sections -- remains a significant challenge. Current approaches often yield suboptimal results due to a lack of effective integration between LLM agents and precise code search mechanisms. This paper introduces OrcaLoca, an LLM agent framework that improves accuracy for software issue localization by integrating priority-based scheduling for LLM-guided action, action decomposition with relevance scoring, and distance-aware context pruning. Experimental results demonstrate that OrcaLoca becomes the new open-source state-of-the-art (SOTA) in function match rate (65.33%) on SWE-bench Lite. It also improves the final resolved rate of an open-source framework by 6.33 percentage points through its patch generation integration.

Yujie Zhao, Hejia Zhang, Hanxian Huang et al.

The automatic generation of RTL code (e.g., Verilog) through natural language instructions has emerged as a promising direction with the advancement of large language models (LLMs). However, producing RTL code that is both syntactically and functionally correct remains a significant challenge. Existing single-LLM-agent approaches face substantial limitations because they must navigate between various programming languages and handle intricate generation, verification, and modification tasks. To address these challenges, this paper introduces MAGE, the first open-source multi-agent AI system designed for robust and accurate Verilog RTL code generation. We propose a novel high-temperature RTL candidate sampling and debugging system that effectively explores the space of code candidates and significantly improves the quality of the candidates. Furthermore, we design a novel Verilog-state checkpoint checking mechanism that enables early detection of functional errors and delivers precise feedback for targeted fixes, significantly enhancing the functional correctness of the generated RTL code. MAGE achieves a 95.7% rate of syntactic and functional correctness code generation on VerilogEval-Human 2 benchmark, surpassing the state-of-the-art Claude-3.5-sonnet by 23.3 %, demonstrating a robust and reliable approach for AI-driven RTL design workflows.

Yujie Zhao, Zhijing Wu, Hejia Zhang et al.

LLM-assisted hardware verification is gaining substantial attention due to its potential to significantly reduce the cost and effort of crafting effective testbenches. It also serves as a critical enabler for LLM-aided end-to-end hardware language design. However, existing current LLMs often struggle with Register Transfer Level (RTL) code generation, resulting in testbenches that exhibit functional errors in Hardware Description Languages (HDL) logic. Motivated by the strong performance of LLMs in Python code generation under inference-time sampling strategies, and their promising capabilities as judge agents, we propose PRO-V a fully program generation multi-agent system for robust RTL verification. Pro-V incorporates an efficient best-of-n iterative sampling strategy to enhance the correctness of generated testbenches. Moreover, it introduces an LLM-as-a-judge aid validation framework featuring an automated prompt generation pipeline. By converting rule-based static analysis from the compiler into natural language through in-context learning, this pipeline enables LLMs to assist the compiler in determining whether verification failures stem from errors in the RTL design or the testbench. PRO-V attains a verification accuracy of 87.17% on golden RTL implementations and 76.28% on RTL mutants. Our code is open-sourced at https://github.com/stable-lab/Pro-V.

Zhongming Yu, Genghan Zhang, Hanxian Huang et al.

In recent years, Graph Neural Networks (GNNs) have ignited a surge of innovation, significantly enhancing the processing of geometric data structures such as graphs, point clouds, and meshes. As the domain continues to evolve, a series of frameworks and libraries are being developed to push GNN efficiency to new heights. While graph-centric libraries have achieved success in the past, the advent of efficient tensor compilers has highlighted the urgent need for tensor-centric libraries. Yet, efficient tensor-centric frameworks for GNNs remain scarce due to unique challenges and limitations encountered when implementing segment reduction in GNN contexts. We introduce GeoT, a cutting-edge tensor-centric library designed specifically for GNNs via efficient segment reduction. GeoT debuts innovative parallel algorithms that not only introduce new design principles but also expand the available design space. Importantly, GeoT is engineered for straightforward fusion within a computation graph, ensuring compatibility with contemporary tensor-centric machine learning frameworks and compilers. Setting a new performance benchmark, GeoT marks a considerable advancement by showcasing an average operator speedup of 1.80x and an end-to-end speedup of 1.68x.

Hengrui Zhang, Zhongming Yu, Guohao Dai et al.

Graph Neural Networks (GNNs) have been widely used in various domains, and GNNs with sophisticated computational graph lead to higher latency and larger memory consumption. Optimizing the GNN computational graph suffers from: (1) Redundant neural operator computation. The same data are propagated through the graph structure to perform the same neural operation multiple times in GNNs, leading to redundant computation which accounts for 92.4% of total operators. (2) Inconsistent thread mapping. Efficient thread mapping schemes for vertex-centric and edge-centric operators are different. This inconsistency prohibits operator fusion to reduce memory IO. (3) Excessive intermediate data. For GNN training which is usually performed concurrently with inference, intermediate data must be stored for the backward pass, consuming 91.9% of the total memory requirement. To tackle these challenges, we propose following designs to optimize the GNN computational graph from a novel coordinated computation, IO, and memory perspective: (1) Propagation-postponed operator reorganization. We reorganize operators to perform neural operations before the propagation, thus the redundant computation is eliminated. (2) Unified thread mapping for fusion. We propose a unified thread mapping scheme for both vertex- and edge-centric operators to enable fusion and reduce IO. (3) Intermediate data recomputation. Intermediate data are recomputed during the backward pass to reduce the total memory consumption. Extensive experimental results on three typical GNN models show that, we achieve up to 2.75x end-to-end speedup, 6.89x less memory IO, and 7.73x less memory consumption over state-of-the-art frameworks.

Yukuo Cen, Zhenyu Hou, Yan Wang et al.

Graph neural networks (GNNs) have attracted tremendous attention from the graph learning community in recent years. It has been widely adopted in various real-world applications from diverse domains, such as social networks and biological graphs. The research and applications of graph deep learning present new challenges, including the sparse nature of graph data, complicated training of GNNs, and non-standard evaluation of graph tasks. To tackle the issues, we present CogDL, a comprehensive library for graph deep learning that allows researchers and practitioners to conduct experiments, compare methods, and build applications with ease and efficiency. In CogDL, we propose a unified design for the training and evaluation of GNN models for various graph tasks, making it unique among existing graph learning libraries. By utilizing this unified trainer, CogDL can optimize the GNN training loop with several training techniques, such as mixed precision training. Moreover, we develop efficient sparse operators for CogDL, enabling it to become the most competitive graph library for efficiency. Another important CogDL feature is its focus on ease of use with the aim of facilitating open and reproducible research of graph learning. We leverage CogDL to report and maintain benchmark results on fundamental graph tasks, which can be reproduced and directly used by the community.