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3D-Stacked Many-Core Architecture for Biological Sequence Analysis Problems
KTH, School of Information and Communication Technology (ICT), Electronics.
KTH, School of Information and Communication Technology (ICT), Electronics.ORCID iD: 0000-0003-0565-9376
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2017 (English)In: International journal of parallel programming, ISSN 0885-7458, E-ISSN 1573-7640, Vol. 45, no 6, p. 1420-1460Article in journal (Refereed) Published
Abstract [en]

Sequence analysis plays extremely important role in bioinformatics, and most applications of which have compute intensive kernels consuming over 70% of total execution time. By exploiting the compute intensive execution stages of popular sequence analysis applications, we present and evaluate a VLSI architecture with a focus on those that target at biological sequences directly, including pairwise sequence alignment, multiple sequence alignment, database search, and short read sequence mappings. Based on coarse grained reconfigurable array we propose the use of many-core and 3D-stacked technologies to gain further improvement over memory subsystem, which gives another order of magnitude speedup from high bandwidth and low access latency. We analyze our approach in terms of its throughput and efficiency for different application mappings. Initial experimental results are evaluated from a stripped down implementation in a commodity FPGA, and then we scale the results to estimate the performance of our architecture with 9 layers of stacked wafers in 45-nm process. We demonstrate numerous estimated speedups better than corresponding existed hardware accelerator platforms for at least 40 times for the entire range of applications and datasets of interest. In comparison, the alternative FPGA based accelerators deliver only improvement for single application, while GPGPUs perform not well enough on accelerating program kernel with random memory access and integer addition/comparison operations.

Place, publisher, year, edition, pages
SPRINGER/PLENUM PUBLISHERS , 2017. Vol. 45, no 6, p. 1420-1460
Keyword [en]
Accelerator architectures, Application specific integrated circuits, Bioinformatics, Computational biology, Coprocessors, Reconfigurable architectures, Three-dimensional integrated circuits
National Category
Computer and Information Sciences
Identifiers
URN: urn:nbn:se:kth:diva-215775DOI: 10.1007/s10766-017-0495-0ISI: 000411558500010Scopus ID: 2-s2.0-85017448393OAI: oai:DiVA.org:kth-215775DiVA, id: diva2:1151182
Note

QC 20171023

Available from: 2017-10-23 Created: 2017-10-23 Last updated: 2018-01-13Bibliographically approved

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Hemani, Ahmed

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