arXiv subjects

Sreenivas Subramoney

Publications and source records attributed to Sreenivas Subramoney.

21 records · Page 2Linked to original sources

arXiv2020

GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis

Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. Unfortunately, it is currently bottlenecked by the computational power and memory bandwidth limitations of existing systems, as many of the steps in genome sequence analysis must process a large amount of data. A major contributor to this bottleneck is approximate string matching (ASM). We propose GenASM, the first ASM acceleration framework for genome sequence analysis. We modify the underlying ASM algorithm (Bitap) to significantly increase its parallelism and reduce its memory footprint, and we design the first hardware accelerator for Bitap. Our hardware accelerator consists of specialized compute units and on-chip SRAMs that are designed to match the rate of computation with memory capacity and bandwidth. We demonstrate that GenASM is a flexible, high-performance, and low-power framework, which provides significant performance and power benefits for three different use cases in genome sequence analysis: 1) GenASM accelerates read alignment for both long reads and short reads. For long reads, GenASM outperforms state-of-the-art software and hardware accelerators by 116x and 3.9x, respectively, while consuming 37x and 2.7x less power. For short reads, GenASM outperforms state-of-the-art software and hardware accelerators by 111x and 1.9x. 2) GenASM accelerates pre-alignment filtering for short reads, with 3.7x the performance of a state-of-the-art pre-alignment filter, while consuming 1.7x less power and significantly improving the filtering accuracy. 3) GenASM accelerates edit distance calculation, with 22-12501x and 9.3-400x speedups over the state-of-the-art software library and FPGA-based accelerator, respectively, while consuming 548-582x and 67x less power.

cs.AR↗

arXiv2019

DSPatch: Dual Spatial Pattern Prefetcher

High main memory latency continues to limit performance of modern high-performance out-of-order cores. While DRAM latency has remained nearly the same over many generations, DRAM bandwidth has grown significantly due to higher frequencies, newer architectures (DDR4, LPDDR4, GDDR5) and 3D-stacked memory packaging (HBM). Current state-of-the-art prefetchers do not do well in extracting higher performance when higher DRAM bandwidth is available. Prefetchers need the ability to dynamically adapt to available bandwidth, boosting prefetch count and prefetch coverage when headroom exists and throttling down to achieve high accuracy when the bandwidth utilization is close to peak. To this end, we present the Dual Spatial Pattern Prefetcher (DSPatch) that can be used as a standalone prefetcher or as a lightweight adjunct spatial prefetcher to the state-of-the-art delta-based Signature Pattern Prefetcher (SPP). DSPatch builds on a novel and intuitive use of modulated spatial bit-patterns. The key idea is to: (1) represent program accesses on a physical page as a bit-pattern anchored to the first "trigger" access, (2) learn two spatial access bit-patterns: one biased towards coverage and another biased towards accuracy, and (3) select one bit-pattern at run-time based on the DRAM bandwidth utilization to generate prefetches. Across a diverse set of workloads, using only 3.6KB of storage, DSPatch improves performance over an aggressive baseline with a PC-based stride prefetcher at the L1 cache and the SPP prefetcher at the L2 cache by 6% (9% in memory-intensive workloads and up to 26%). Moreover, the performance of DSPatch+SPP scales with increasing DRAM bandwidth, growing from 6% over SPP to 10% when DRAM bandwidth is doubled.

cs.AR↗

arXiv2018

MARS: Memory Aware Reordered Source

Memory bandwidth is critical in today's high performance computing systems. The bandwidth is particularly paramount for GPU workloads such as 3D Gaming, Imaging and Perceptual Computing, GPGPU due to their data-intensive nature. As the number of threads and data streams in the GPUs increases with each generation, along with a high available memory bandwidth, memory efficiency is also crucial in order to achieve desired performance. In presence of multiple concurrent data streams, the inherent locality in a single data stream is often lost as these streams are interleaved while moving through multiple levels of memory system. In DRAM based main memory, the poor request locality reduces row-buffer reuse resulting in underutilized and inefficient memory bandwidth. In this paper we propose Memory-Aware Reordered Source (\textit{MARS}) architecture to address memory inefficiency arising from highly interleaved data streams. The key idea of \textit{MARS} is that with a sufficiently large lookahead before the main memory, data streams can be reordered based on their row-buffer address to regain the lost locality and improve memory efficiency. We show that \textit{MARS} improves achieved memory bandwidth by 11\% for a set of synthetic microbenchmarks. Moreover, MARS does so without any specific knowledge of the memory configuration.

cs.PF↗