GenDRAM:Hardware-Software Co-Design of General Platform in DRAM

Abstract: Dynamic programming (DP) algorithms, such as All-Pairs Shortest Path (APSP) and genomic sequence alignment, are fundamental to many scientific domains but are severely bottlenecked by data movement on conventional architectures. While Processing-in-Memory (PIM) offers a promising solution, existing accelerators often address only a fraction of the work-flow, creating new system-level bottlenecks in host-accelerator communication and off-chip data streaming. In this work, we propose GenDRAM, a massively parallel PIM accelerator that overcomes these limitations. GenDRAM leverages the immense capacity and internal bandwidth of monolithic 3D DRAM(M3D DRAM) to integrate entire data-intensive pipelines, such as the full genomics workflow from seeding to alignment, onto a single heterogeneous chip. At its core is a novel architecture featuring specialized Search PUs for memory-intensive tasks and universal, multiplier-less Compute PUs for diverse DP calculations. This is enabled by a 3D-aware data mapping strategy that exploits the tiered latency of M3D DRAM for performance optimization. Through comprehensive simulation, we demonstrate that GenDRAM achieves a transformative performance leap, outperforming state-of-the-art GPU systems by over 68x on APSP and over 22x on the end-to-end genomics pipeline.