Title
Power-Efficiency Analysis of Accelerated BWA-MEM Implementations on Heterogeneous Computing Platforms
Author
Houtgast, E.J. (TU Delft Computer Engineering; Bluebee, Rijswijk)
Sima, V.M. (Bluebee, Rijswijk)
Marchiori, G. (Bluebee, Rijswijk)
Bertels, K.L.M. (TU Delft Quantum & Computer Engineering; TU Delft FTQC/Bertels Lab)
Al-Ars, Z. (TU Delft Computer Engineering)
Contributor
Athanas, Peter (editor)
Cumplido, René (editor)
Feregrino, Claudia (editor)
Sass, Ron (editor)
Department
Quantum & Computer Engineering
Date
2016-12
Abstract
Next Generation Sequencing techniques have dramatically reduced the cost of sequencing genetic material, resulting in huge amounts of data being sequenced. The processing of this data poses huge challenges, both from a performance perspective, as well as from a power-efficiency perspective. Heterogeneous computing can help on both fronts, by enabling more performant and more power-efficient solutions. In this paper, power-efficiency of the BWA-MEM algorithm, a popular tool for genomic data mapping, is studied on two heterogeneous architectures. The performance and power-efficiency of an FPGA-based implementation using a single Xilinx Virtex-7 FPGA on the Alpha Data add-in card is compared to a GPU-based implementation using an NVIDIA GeForce GTX 970 and against the software-only baseline system. By offloading the Seed Extension phase on an accelerator, both implementations are able to achieve a two-fold speedup in overall application-level performance over the software-only implementation. Moreover, the highly customizable nature of the FPGA results in much higher power-efficiency, as the FPGA power consumption is less than one fourth of that of the GPU. To facilitate platform and tool-agnostic comparisons, the base pairs per Joule unit is introduced as a measure of power-efficiency. The FPGA design is able to map up to 44 thousand base pairs per Joule, a 2.1x gain in power-efficiency as compared to the software-only baseline.
Subject
read mapping
FPGA
GPU
Next Generation Sequencing
power-efficiency
To reference this document use:
http://resolver.tudelft.nl/uuid:31d95525-9eba-498e-8900-69e80f60b4ce
DOI
https://doi.org/10.1109/ReConFig.2016.7857181
Publisher
IEEE, Danvers, MA
ISBN
978-1-5090-3707-0
Source
2016 International Conference on ReConFigurable Computing and FPGAs (ReConFig)
Event
International Conference on ReConFigurable Computing and FPGAs, ReConFig 2016, 2016-11-30 → 2016-12-02, Cancun, Mexico
Bibliographical note
Accepted Author Manuscript
Part of collection
Institutional Repository
Document type
conference paper
Rights
© 2016 E.J. Houtgast, V.M. Sima, G. Marchiori, K.L.M. Bertels, Z. Al-Ars