ThunderGNN: Unlocking Tensor Cores for Graph Neural Networks

Graph Neural Networks (GNNs) have emerged as the state-of-the-art methodology for learning on graph-structured data, yet their performance is severely constrained by a fundamental mismatch between irregular graph sparsity and the rigid parallelism of modern hardware. While modern GPUs rely on Tensor Cores (TCs) to deliver massive computational throughput, these units demand strictly tiled, dense inputs—a requirement that conflicts with the extreme sparsity of real-world graphs. Existing frameworks fail to resolve this design conflict: they either fallback to legacy SIMT cores, leaving TCs underutilized, or they incur prohibitive memory bloat by forcing sparse data into dense tiles via excessive padding. To bridge this gap, we propose ThunderGNN, a hardware-aware acceleration system designed to reconcile graph irregularity with Tensor Core rigidity. ThunderGNN employs a unified co-design strategy comprising three key optimizations: (1) a sparsity-aware reordering algorithm that logically groups graph rows to maximize local density; (2) a Condensed Binarized Abstraction (CBA) storage layout that physically organizes the adjacency matrix into TC-aligned blocks without explicit zero-padding; and (3) a hardware-aware execution engine that efficiently streams compressed blocks directly into TCs. Extensive experiments on NVIDIA A100 GPUs demonstrate that ThunderGNN significantly outperforms state-of-the-art systems, achieving geometric mean speedups of 1.89× over DGL and 2.59× over PyG.