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Scaling read aligners to hundreds of threads on general-purpose processors

BIOINFORMATICS 2019年第3期35卷 421-432页

作者： Langmead, Ben Wilks, Christopher Antonescu, Valentin Charles, Rone Johns Hopkins Univ Dept Comp Sci Baltimore MD 21205 USA Johns Hopkins Univ Ctr Computat Biol Baltimore MD 21205 USA

Motivation: General-purpose processors can now contain many dozens of processor cores and support hundreds of simultaneous threads of execution. To make best use of these threads, genomics software must contend with new and subtle computer architecture issues. We discuss some of these and propose methods for improving thread scaling in tools that analyze each read independently, such as read aligners. Results: We implement these methods in new versions of Bowtie, Bowtie 2 and HISAT. We greatly improve thread scaling in many scenarios, including on the recent Intel Xeon Phi architecture. We also highlight how bottlenecks are exacerbated by variable-record-length file formats like FASTQ and suggest changes that enable superior scaling.

关键词： BIOINFORMATICS simultaneous multithreading processors COMPUTER architecture MULTIprocessors GENOMICS

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Intention preservation in deterministic multithreading: a partial solution

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IET SOFTWARE 2016年第6期10卷 155-163页

作者： Zhao, Wenbing Luo, Xiong Zhu, Yueqin Chai, Hua Cleveland State Univ Dept Elect Engn & Comp Sci Cleveland OH 44115 USA Univ Sci & Technol Beijing Sch Comp & Commun Engn Beijing 100083 Peoples R China China Geol Survey Dev Res Ctr Beijing 100037 Peoples R China Minist Land & Resources Key Lab Geol Informat Technol Beijing 100037 Peoples R China Hyland Software Inc 28500 Clemens Rd Westlake OH 44145 USA

Deterministic multithreading is a promising new research area that aims to enable reproducible deterministic execution of multithreaded applications. Some of the proposed approaches can render data races deterministic. In this study, the authors introduce the intention preservation problem in multithreaded applications and point out that existing deterministic multithreading approaches do not always preserve the program intention. While it is desirable to automatically capture the full intention of a program and preserve it in deterministic multithreading, it might be an intractable problem. Instead, they provide a partial solution for two specific cases. In the first case, they aim to preserve the program intention for read and write operations on primitive types by tracking read-write causality. In the second case, they preserve the program intention for concurrent write operations on ordered collection types by applying an operational transformation.

关键词： simultaneous multithreading processors COMPUTER programming COMPUTER software execution COMPUTER science COMPUTER research

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multithreading with C# Cookbook - Second Edition 2

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2016年

作者： Eugene Agafonov

ISBN: (数字)9781785884009

ISBN: (纸本)9781785881251

Over 70 recipes to get you writing powerful and efficient multithreaded, asynchronous, and parallel programs in C# 6.0 About This Book • Rewritten and updated to take advantage of the latest C# 6 features • Learn about multithreaded, asynchronous, and parallel programming through hands-on, code-first examples • Use these recipes to build fast, scalable, and reliable applications in C# Who This Book Is For This book is aimed at those who are new to multithreaded programming, and who are looking for a quick and easy way to get started. It is assumed that you have some experience in C# and .NET already, and you should also be familiar with basic computer science terminology and basic algorithms and data structures. What You Will Learn • Use C# 6.0 asynchronous language features • Work with raw threads, synchronize threads, and coordinate their work • Develop your own asynchronous API with Task Parallel Library • Work effectively with a thread pool • Scale up your server application with I/O threads • Parallelize your LINQ queries with PLINQ • Use common concurrent collections • Apply different parallel programming patterns • Use Reactive Extensions to run asynchronous operations and manage their options In Detail Multi-core processors are synonymous with computing speed and power in today’s world, which is why multithreading has become a key concern for C# developers. Multithreaded code helps you create effective, scalable, and responsive applications. This is an easy-to-follow guide that will show you difficult programming problems in context. You will learn how to solve them with practical, hands-on, recipes. With these recipes, you’ll be able to start creating your own scalable and reliable multithreaded applications. Starting from learning what a thread is, we guide you through the basics and then move on to more advanced concepts such as task parallel libraries, C# asynchronous functions, and much more. Rewritten to the latest C# specification, C# 6, and u

关键词： Parallel programming (Computer science) Threads (Computer programs) C# (Computer program language) simultaneous multithreading processors

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Performance Evaluation of Multithreaded Geant4 Simulations Using an Intel Xeon Phi Cluster

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SCIENTIFIC PROGRAMMING 2015年第1期2015卷 1-10页

作者： Schweitzer, P. Cipiere, S. Dufaure, A. Payno, H. Perrot, Y. Hill, D. R. C. Maigne, L. Univ Blaise Pascal Univ Clermont Auvergne Phys Corpusculaire Lab F-63000 Clermont Ferrand France CNRS UMR 6158 LIMOS F-63178 Clermont Ferrand France Inst Super Informat Modelisat & Leurs Applicat ISIMA F-63178 Aubiere France CNRS UMR 6533 LPC F-63178 Clermont Ferrand France

The objective of this study is to evaluate the performances of Intel Xeon Phi hardware accelerators for Geant4 simulations, especially formultithreaded applications. We present the completemethodology to guide users for the compilation of their Geant4 applications on Phi processors. Then, we propose series of benchmarks to compare the performance of Xeon CPUs and Phi processors for aGeant4 example dedicated to the simulation of electron dose point kernels, the TestEm12 example. First, we compare a distributed execution of a sequential version of the Geant4 example on both architectures before evaluating the multithreaded version of the Geant4 example. If Phi processors demonstrated their ability to accelerate computing time (till a factor 3.83) when distributing sequential Geant4 simulations, we do not reach the same level of speedup when considering themultithreaded version of the Geant4 example.

关键词： INTEL microprocessors COMPUTER simulation CLUSTER analysis (Statistics) COMPUTER input-output equipment CENTRAL processing units (Computers) simultaneous multithreading processors

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Parallel deblocking filter for HEVC on many-core processor

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ELECTRONICS LETTERS 2014年第5期50卷 367-+页

作者： Yan, Chenggang Zhang, Yongdong Dai, Feng Wang, Xi Li, Liang Dai, Qionghai Chinese Acad Sci Inst Comp Technol Beijing Peoples R China Tsinghua Univ Beijing 100084 Peoples R China

High-efficiency video coding (HEVC) is the next generation standard of video coding. The deblocking filter (DF) constitutes a significant part of the HEVC decoder complexity. A three-step parallel framework (TPF) is proposed for the H. 264/AVC DF, which is also suitable for HEVC except the third step. The third step of the TPF is replaced with a directed acyclic graph-based order. Experiments show that the proposed method dramatically accelerates more than the state-of-the-art parallel method.

关键词： BLOCKING oscillators FILTERS & filtration simultaneous multithreading processors EXPERIMENTS COMPLEXITY (Philosophy)

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Making Parallel Programs Reliable with Stable multithreading

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COMMUNICATIONS OF THE ACM 2014年第3期57卷 58-69页

作者： Yang, Junfeng Cui, Heming Wu, Jingyue Tang, Yang Hu, Gang Columbia Univ Dept Comp Sci Software Syst Lab New York NY 10027 USA

Stable multithreading dramatically simplifies the interleaving behaviors of parallel programs, offering new hope for making parallel programming easier.

关键词： Parallel processing (Electronic computers) Operating systems (Computers) simultaneous multithreading processors Multicore processors (Computers) Trends -- Social aspects Online social networks Compilers (Computer programs)

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multithreading in C# 5.0 Cookbook 1

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2013年

作者： Eugene Agafonov

ISBN: (数字)9781849697651

ISBN: (纸本)1849697647;9781849697644

Over 70 recipes to help you learn asynchronous and parallel programming with C# 5.0 quickly and efficiently Overview Delve deep into the .NET threading infrastructure and use Task Parallel Library for asynchronous programming Scale out your server applications effectively Master C# 5.0 asynchronous operations language support In Detail In an age when computer processors are being developed to contain more and more cores, multithreading is a key factor for creating scalable, effective, and responsive applications. If you fail to do it correctly, it can lead to puzzling problems that take a huge amount of time to resolve. Therefore, having a solid understanding of multithreading is a must for the modern application developer. multithreading in C# 5.0 Cookbook is an easy-to-understand guide to the most puzzling programming problems. This book will guide you through practical examples dedicated to various aspects of multithreading in C# on Windows and will give you a good basis of practical knowledge which you can then use to program your own scalable and reliable multithreaded applications. This book guides you through asynchronous and parallel programming from basic examples to practical, real-world solutions to complex problems. You will start from the very beginning, learning what a thread is, and then proceed to learn new concepts based on the information you get from the previous examples. After describing the basics of threading, you will be able to grasp more advanced concepts like Task Parallel Library and C# asynchronous functions. Then, we move towards parallel programming, starting with basic data structures and gradually progressing to the more advanced patterns. The book concludes with a discussion of the specifics of Windows 8 application programming, giving you a complete understanding of how Windows 8 applications are different and how to program asynchronous applications for Windows 8. What you will learn from this book Work with raw threads, synchroni

关键词： Parallel programming (Computer science) Threads (Computer programs) simultaneous multithreading processors C# (Computer program language)

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Conceptual characteristic features of fault-free hardware design

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AUTOMATION AND REMOTE CONTROL 2012年第7期73卷 1202-1215页

作者： Dianov, V. N. Moscow State Ind Univ Moscow Russia

We consider the concept of active diagnostics for detecting and registering hardware faults in computers, sensors, executive mechanisms, and optical electronic systems. We propose a collection of informative features to detect and register sources of the faults: connectors, contacting units of large integral circuits (LIC) and super-large integral circuits (SLIC), contacting conductors on printed circuit boards (including multilayered ones), interface buses, unshielded single- and multicore wires, grounding and power buses, connector blocks, brazing joints. Based on these new properties of passive elements in radioelectronic hardware, and in keeping with the notion of "fail-safeness," we propose a new notion of reliability, "fault-safeness," that establishes a connection between hardware faults and its hidden defects.

关键词： ELECTRIC circuits MULTICORE processors (Computers) COMPUTER architecture PARALLEL computers simultaneous multithreading processors ELECTRONIC circuits SEALING (Technology) BRAZING

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An efficient adaptive software-implemented technique to detect control-flow errors in multi-core architectures

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MICROELECTRONICS RELIABILITY 2012年第11期52卷 2812-2828页

作者： Maghsoudloo, Mohammad Zarandi, Hamid R. Khoshavi, Navid Amirkabir Univ Technol Tehran Polytech Dept Comp Engn & Informat Technol Tehran Iran Inst Res Fundamental Sci IPM Sch Comp Sci Tehran Iran

In this paper, a software behavior-based technique is presented to detect control-flow errors in multi-core architectures. The analysis of two key points leads to introduce the proposed technique: (i) employing under-utilized CPU resources in multi-core processors to check the execution flow of the programs in parallel with their executions to moderate the performance overhead of previous software-based techniques, and to enhance the applicability of them in current architectures. (ii) Adjusting the locations of additional statements in a given program in order to increase the ability of detecting possible control-flow errors along with significant reduction in overheads. To evaluate the proposed technique, a quad-core processor system is used as the simulation environment, and the behavior of several well-known single- and multi-threaded benchmarks have been studied. The experimental results, regarding to both detection coverage and performance overhead, demonstrate that on average about 93% of the control-flow errors can be detected by the proposed technique with just about 10% performance overhead, compared to at least 30% imposed by the previous techniques. (C) 2012 Elsevier Ltd. All rights reserved.

关键词： SELF-adaptive software MULTICORE processors (Computers) CENTRAL processing units (Computers) PERFORMANCE evaluation SIMULATION methods & models simultaneous multithreading processors

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Extending the Semantics of Scheduling Priorities

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COMMUNICATIONS OF THE ACM 2012年第8期55卷 48-52页

作者： Polanczyk, Rafael Vanoni Oracle

Increasing parallelism demands new paradigms.

关键词： COMPUTER operating systems management MULTICORE processors (Computers) CENTRAL processing units (Computers) LOAD balancing (Computer networks) simultaneous multithreading processors CHARTS, diagrams, etc.

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