arXiv subjects

Junguk Hong

Publications and source records attributed to Junguk Hong.

6 recordsLinked to original sources

arXiv2026

GriNNder: Breaking the Memory Capacity Wall in Full-Graph GNN Training with Storage Offloading

Full-graph training of graph neural networks (GNNs) is widely used as it enables direct validation of algorithmic improvements by preserving complete neighborhood information. However, it typically requires multiple GPUs or servers, incurring substantial hardware and inter-device communication costs. While existing single-server methods reduce infrastructure requirements, they remain constrained by GPU and host memory capacity as graph sizes increase. To address this limitation, we introduce GriNNder, which is the first work to leverage storage devices to enable full-graph training even with limited memory. Because modern NVMe SSDs offer multi-terabyte capacities and bandwidths exceeding 10 GB/s, they provide an appealing option when memory resources are scarce. Yet, directly applying storage-based methods from other domains fails to address the unique access patterns and data dependencies in full-graph GNN training. GriNNder tackles these challenges by structured storage offloading (SSO), a framework that manages the GPU-host-storage hierarchy through coordinated cache, (re)gather, and bypass mechanisms. To realize the framework, we devise (i) a partition-wise caching strategy for host memory that exploits the observation on cross-partition dependencies, (ii) a regathering strategy for gradient computation that eliminates redundant storage operations, and (iii) a lightweight partitioning scheme that mitigates the memory requirements of existing graph partitioners. In experiments performed over various models and datasets, GriNNder achieves up to 9.78x speedup over state-of-the-art baselines and throughput comparable to distributed systems, enabling previously infeasible large-scale full-graph training even on a single GPU.

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arXiv2026

LOCALUT: Harnessing Capacity-Computation Tradeoffs for LUT-Based Inference in DRAM-PIM

Lookup tables (LUTs) have recently gained attention as an alternative compute mechanism that maps input operands to precomputed results, eliminating the need for arithmetic logic. LUTs not only reduce logic complexity, but also naturally support diverse numerical precisions without requiring separate circuits for each bitwidth-an increasingly important feature in quantized DNNs. This creates a favorable tradeoff in PIM: memory capacity can be used in place of logic to increase computational throughput, aligning well with DRAM-PIM architectures that offer high bandwidth and easily available memory but limited logic density. In this work, we explore this capacity-computation tradeoff in LUT-based PIM designs, where memory capacity is traded for performance by packing multiple MAC operations into a single LUT lookup. Building on this insight, we propose LOCALUT, a PIM-based design for efficient low-bit quantized DNN inference using operation-packed LUTs. First, we observe that these LUTs contain extensive redundancy and introduce LUT canonicalization, which eliminates duplicate entries to reduce LUT size. Second, we propose reordering LUT, a lightweight auxiliary LUT that remaps weight vectors to their canonical form required by LUT canonicalization with a simple LUT lookup. Third, we propose LUT slice streaming, a novel execution strategy that exploits the DRAM-buffer hierarchy by streaming only relevant LUT columns into the buffer and reusing them across multiple weight vectors. Evaluated on a real system based on UPMEM devices, we demonstrate a geometric mean speedup of 1.82x across various numeric precisions and DNN models. We believe LOCALUT opens a path toward scalable, low-logic PIM designs tailored for LUT-based DNN inference. Our implementation of LOCALUT is available at https://github.com/AIS-SNU/LoCaLUT.

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arXiv2025

FlexiWalker: Extensible GPU Framework for Efficient Dynamic Random Walks with Runtime Adaptation

Dynamic random walks are fundamental to various graph analysis applications, offering advantages by adapting to evolving graph properties. Their runtime-dependent transition probabilities break down the pre-computation strategy that underpins most existing CPU and GPU static random walk optimizations. This leaves practitioners suffering from suboptimal frameworks and having to write hand-tuned kernels that do not adapt to workload diversity. To handle this issue, we present FlexiWalker, the first GPU framework that delivers efficient, workload-generic support for dynamic random walks. Our design-space study shows that rejection sampling and reservoir sampling are more suitable than other sampling techniques under massive parallelism. Thus, we devise (i) new high-performance kernels for them that eliminate global reductions, redundant memory accesses, and random-number generation. Given the necessity of choosing the best-fitting sampling strategy at runtime, we adopt (ii) a lightweight first-order cost model that selects the faster kernel per node at runtime. To enhance usability, we introduce (iii) a compile-time component that automatically specializes user-supplied walk logic into optimized building blocks. On various dynamic random walk workloads with real-world graphs, FlexiWalker outperforms the best published CPU/GPU baselines by geometric means of 73.44x and 5.91x, respectively, while successfully executing workloads that prior systems cannot support. We open-source FlexiWalker in https://github.com/AIS-SNU/FlexiWalker.

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arXiv2025

PathWeaver: A High-Throughput Multi-GPU System for Graph-Based Approximate Nearest Neighbor Search

Graph-based Approximate Nearest Neighbor Search (ANNS) is widely adopted in numerous applications, such as recommendation systems, natural language processing, and computer vision. While recent works on GPU-based acceleration have significantly advanced ANNS performance, the ever-growing scale of datasets now demands efficient multi-GPU solutions. However, the design of existing works overlooks multi-GPU scalability, resulting in naive approaches that treat additional GPUs as a means to extend memory capacity for large datasets. This inefficiency arises from partitioning the dataset and independently searching for data points similar to the queries in each GPU. We therefore propose PathWeaver, a novel multi-GPU framework designed to scale and accelerate ANNS for large datasets. First, we propose pipelining-based path extension, a GPU-aware pipelining mechanism that reduces prior work's redundant search iterations by leveraging GPU-to-GPU communication. Second, we design ghost staging that leverages a representative dataset to identify optimal query starting points, reducing the search space for challenging queries. Finally, we introduce direction-guided selection, a data selection technique that filters irrelevant points early in the search process, minimizing unnecessary memory accesses and distance computations. Comprehensive evaluations across diverse datasets demonstrate that PathWeaver achieves 3.24$\times$ geomean speedup and up to 5.30$\times$ speedup on 95% recall rate over state-of-the-art multi-GPU-based ANNS frameworks.

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arXiv2024

PID-Comm: A Fast and Flexible Collective Communication Framework for Commodity Processing-in-DIMM Devices

Recent dual in-line memory modules (DIMMs) are starting to support processing-in-memory (PIM) by associating their memory banks with processing elements (PEs), allowing applications to overcome the data movement bottleneck by offloading memory-intensive operations to the PEs. Many highly parallel applications have been shown to benefit from these PIM-enabled DIMMs, but further speedup is often limited by the huge overhead of inter-PE communication. This mainly comes from the slow CPU-mediated inter-PE communication methods which incurs significant performance overheads, making it difficult for PIM-enabled DIMMs to accelerate a wider range of applications. Prior studies have tried to alleviate the communication bottleneck, but they lack enough flexibility and performance to be used for a wide range of applications. In this paper, we present PID-Comm, a fast and flexible collective inter-PE communication framework for commodity PIM-enabled DIMMs. The key idea of PID-Comm is to abstract the PEs as a multi-dimensional hypercube and allow multiple instances of collective inter-PE communication between the PEs belonging to certain dimensions of the hypercube. Leveraging this abstraction, PID-Comm first defines eight collective inter-PE communication patterns that allow applications to easily express their complex communication patterns. Then, PID-Comm provides high-performance implementations of the collective inter-PE communication patterns optimized for the DIMMs. Our evaluation using 16 UPMEM DIMMs and representative parallel algorithms shows that PID-Comm greatly improves the performance by up to 4.20x compared to the existing inter-PE communication implementations. The implementation of PID-Comm is available at https://github.com/AIS-SNU/PID-Comm.

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arXiv2024

AGAThA: Fast and Efficient GPU Acceleration of Guided Sequence Alignment for Long Read Mapping

With the advance in genome sequencing technology, the lengths of deoxyribonucleic acid (DNA) sequencing results are rapidly increasing at lower prices than ever. However, the longer lengths come at the cost of a heavy computational burden on aligning them. For example, aligning sequences to a human reference genome can take tens or even hundreds of hours. The current de facto standard approach for alignment is based on the guided dynamic programming method. Although this takes a long time and could potentially benefit from high-throughput graphic processing units (GPUs), the existing GPU-accelerated approaches often compromise the algorithm's structure, due to the GPU-unfriendly nature of the computational pattern. Unfortunately, such compromise in the algorithm is not tolerable in the field, because sequence alignment is a part of complicated bioinformatics analysis pipelines. In such circumstances, we propose AGAThA, an exact and efficient GPU-based acceleration of guided sequence alignment. We diagnose and address the problems of the algorithm being unfriendly to GPUs, which comprises strided/redundant memory accesses and workload imbalances that are difficult to predict. According to the experiments on modern GPUs, AGAThA achieves 18.8$\times$ speedup against the CPU-based baseline, 9.6$\times$ against the best GPU-based baseline, and 3.6$\times$ against GPU-based algorithms with different heuristics.

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