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Technological advances in long read sequences have greatly facilitated the development of genomics. However, managing and analyzing the raw genomic data that outpaces Moore's Law requires extremely high computational efficiency. On the one hand, existing software solutions can take hundreds of CPU hours to complete human genome alignment. On the other hand, the recently proposed hardware platforms achieve low processing throughput with significant overhead. In this paper, we propose PARC, an Processing-in-Memory architecture for long read pairwise alignment leveraging emerging resistive CAM (content-addressable memory) to accelerate the bottleneck chaining step in DNA alignment. Chaining takes 2-tuple anchors as inputs and identifies a set of correlated anchors as potential alignment candidates. Unlike traditional main memory which organizes relational data structure in a linear address space, PARC stores tuples in two neighboring crossbar arrays with shared row decoder such that column-wise in-memory computational operations and row-wise memory accesses can be performed in-situ in a symmetric crossbar structure. Compared to both software tools and state-of-the-art accelerators, PARC shows significant improvement in alignment throughput and energy efficiency, thanks to the in-site computation capability and optimized data mapping.
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On-the-Fly Data Transformation in Action
Transactional and analytical database management systems (DBMS) typically employ different data layouts: row-stores for the first and column-stores for the latter. In order to bridge the requirements of the two without maintaining two systems and two (or more) copies of the data, our proposed system Relational Memory employs specialized hardware that transforms the base row table into arbitrary column groups at query execution time. This approach maximizes the cache locality and is easy to use via a simple abstraction that allows transparent on-the-fly data transformation. Here, we demonstrate how to deploy and use Relational Memory via four representative scenarios. The demonstration uses the full-stack implementation of Relational Memory on the Xilinx Zynq UltraScale+ MPSoC platform. Conference participants will interact with Relational Memory deployed in the actual platform.
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- Award ID(s):
- 2144547
- PAR ID:
- 10503683
- Publisher / Repository:
- VLDB Endowment
- Date Published:
- Journal Name:
- Proceedings of the VLDB Endowment
- Volume:
- 16
- Issue:
- 12
- ISSN:
- 2150-8097
- Page Range / eLocation ID:
- 3950 to 3953
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.14778/3611540.3611593
