GenDRAM:Hardware-Software Co-Design of General Platform in DRAM
Tsung-Han Lu, Weihong Xu, Tajana Rosing

TL;DR
GenDRAM is a novel PIM accelerator leveraging monolithic 3D DRAM to perform entire data-intensive workflows like genomics and APSP on a single chip, significantly surpassing GPU performance.
Contribution
It introduces a hardware-software co-designed architecture with specialized processing units and a 3D-aware data mapping for efficient in-memory computation of complex algorithms.
Findings
Over 68x faster than GPUs on APSP
Over 22x faster on genomics pipeline
Effective integration of full data workflows on a single chip
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…
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Taxonomy
TopicsParallel Computing and Optimization Techniques · Genomics and Phylogenetic Studies · Graph Theory and Algorithms
