PIM-Aligner: A Processing-in-MRAM Platform for Biological Sequence Alignment
PIM-Aligner: A Processing-in-MRAM Platform for Biological Sequence Alignment
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DOI：
10.23919/date48585.2020.9116303
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发表时间：
2020-03
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影响因子：
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通讯作者：
Shaahin Angizi;Jiao-Jin Sun;Wei Zhang;Deliang Fan
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文献类型：
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作者：
Shaahin Angizi;Jiao-Jin Sun;Wei Zhang;Deliang Fan
在本文中，我们提出了一个高吞吐量和节能的内存处理加速器（PIM-Aligner）执行DNA短读比对的基础上优化和硬件友好的比对算法。首先，我们重建现有的序列比对算法的基础上BWT和FM索引，使它可以完全实现在PIM平台。它支持精确对齐，还可以处理不匹配以减少过多的回溯。然后，我们开发了PIM-Aligner平台，将SOT-MRAM阵列转换为潜在的计算存储器，以加速重建的存储器中存储算法，从而在原始SOT-MRAM芯片的基础上降低成本（不到芯片面积的10%）。因此，我们提出了一个本地数据分区，映射和管道技术，以最大限度地提高并行多个计算子阵列，同时做对齐任务。仿真结果表明，PIM-Aligner的性能优于基于动态规划的最新平台，每瓦吞吐量提高了2.31倍。此外，与基于FM索引的ASIC和ReRAM处理设计相比，PIM-Aligner将每瓦每平方毫米的短读对齐吞吐量分别提高了1.9倍和1.9倍。
In this paper, we propose a high-throughput and energy-efficient Processing-in-Memory accelerator (PIM-Aligner) to execute DNA short read alignment based on an optimized and hardware-friendly alignment algorithm. We first reconstruct the existing sequence alignment algorithm based on BWT and FM-index such that it can be fully implemented in PIM platforms. It supports exact alignment and also handles mismatches to reduce excessive backtracking. We then develop PIM-Aligner platform that transforms SOT-MRAM array to a potential computational memory to accelerate the reconstructed alignment-in-memory algorithm incurring a low cost on top of original SOT-MRAM chips (less than 10% of chip area). Accordingly, we present a local data partitioning, mapping, and pipeline technique to maximize the parallelism in multiple computational sub-array while doing the alignment task. The simulation results show that PIM-Aligner outperforms recent platforms based on dynamic programming with ∼ 3.1× higher throughput per Watt. Besides, PIM-Aligner improves the short read alignment throughput per Watt per mm2 by ∼ 9× and 1.9× compared to FM-index-based ASIC and processing-in-ReRAM designs, respectively.