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Comput Biol Med. 2018 Oct 1;101:163-173. doi: 10.1016/j.compbiomed.2018.08.015. Epub 2018 Aug 16.

GPU-DAEMON: GPU algorithm design, data management & optimization template for array based big omics data.

Author information

1
Department of Computer Science, Western Michigan University, Kalamazoo, MI, USA.
2
School of Computing and Information Sciences, Florida International University, Miami, FL, USA. Electronic address: fsaeed@fiu.edu.

Abstract

In the age of ever increasing data, faster and more efficient data processing algorithms are needed. Graphics Processing Units (GPU) are emerging as a cost-effective alternative architecture for high-end computing. The optimal design of GPU algorithms is a challenging task which requires thorough understanding of the high performance computing architecture as well as the algorithmic design. The steep learning curve needed for effective GPU-centric algorithm design and implementation requires considerable expertise, time, and resources. In this paper, we present GPU-DAEMON, a GPU Data Management, Algorithm Design and Optimization technique suitable for processing array based big omics data. Our proposed GPU algorithm design template outlines and provides generic methods to tackle critical bottlenecks which can be followed to implement high performance, scalable GPU algorithms for given big data problem. We study the capability of GPU-DAEMON by reviewing the implementation of GPU-DAEMON based algorithms for three different big data problems. Speed up of as large as 386x (over the sequential version) and 50x (over naive GPU design methods) are observed using the proposed GPU-DAEMON. GPU-DAEMON template is available at https://github.com/pcdslab/GPU-DAEMON and the source codes for GPU-ArraySort, G-MSR and GPU-PCC are available at https://github.com/pcdslab.

KEYWORDS:

Big-data; CUDA; GPU; High-performance-computing; Omics-data

PMID:
30145436
PMCID:
PMC6400487
[Available on 2019-10-01]
DOI:
10.1016/j.compbiomed.2018.08.015

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