Using the PGAS Programming Paradigm for Biological Sequence Alignment on a Chip Multi-Threading Architecture

被引：0

作者：

Bakhouya, M. ^{[1
]}

Bahra, S. A. ^{[1
]}

El-Ghazawi, T. ^{[1
]}

机构：

[1] George Washington Univ, Dept Elect & Comp Engn, High Performance Comp Lab, Washington, DC 20052 USA

来源：

PROCEEDINGS OF WORLD ACADEMY OF SCIENCE, ENGINEERING AND TECHNOLOGY, VOL 28 | 2008年 / 28卷

关键词：

Partitioned Global Address Space; Unified Parallel C; Multicore machines; Multi-threading Architecture; Sequence alignment;

D O I：

暂无

中图分类号：

TP39 [计算机的应用];

学科分类号：

081203 ; 0835 ;

摘要：

The Partitioned Global Address Space (PGAS) programming paradigm offers ease-of-use in expressing parallelism through a global shared address space while emphasizing performance by providing locality awareness through the partitioning of this address space. Therefore, the interest in PGAS programming languages is growing and many new languages have emerged and are becoming ubiquitously available on nearly all modem parallel architectures. Recently, new parallel machines with multiple cores are designed for targeting high performance applications. Most of the efforts have gone into benchmarking but there are a few examples of real high performance applications running on multicore machines. In this paper, we present and evaluate a parallelization technique for implementing a local DNA sequence alignment algorithm using a PGAS based language, UPC (Unified Parallel C) on a chip multithreading architecture, the UItraSPARC T1.

引用

页码：137 / 141

页数：5

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