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Fine-grained parallel application specific computing for RNA secondary structure prediction using SCFGS on FPGA

Fine-grained parallel application specific computing for RNA...

Embedded Systems Week 2009, ESWEEK 2009 - 2009 International Conference on Compilers, Architecture, and Synthesis for Embedded Systems, CASES'09

作者： Dou, Yong Xia, Fei Jiang, Jingfei National Laboratory for Parallel and Distributed Processing National University of Defence Technology 410073 ChangSha China

ISBN: (纸本)9781605586267

In the field of RNA secondary structure prediction, the CYK (Coche-Younger-Kasami) algorithm is a most popular methods using SCFG (stochastic context-free grammars) model. However, general purpose parallel computers including SMP multiprocessors or cluster systems exhibit low parallel efficiency and they are too expensive to be used easily for many research institutes. FPGA chips provide a new approach to accelerate the CYK algorithm by exploiting fine-grained custom design. The CYK algorithm shows complicated data dependence, in which the dependence distance is variable, and the dependence direction is also across two dimensions. We propose a systolic array structure including one master PE and multiple slave PEs for fine grain hardware implementation on FPGA. We partition tasks by columns and assign tasks to PEs for load balance. We exploit data reuse schemes to reduce the need to load matrix from external memory. To our knowledge, our implementation with 16 PEs is the only FPGA accelerator implementing the complete CYK/inside algorithm. The experimental results show a factor of more than 14 speedup over the Infernal-0.55 software running on a PC platform with Pentium 4 2.66GHz CPU. The computational power of our platform with FPGA accelerator is comparable to a PC cluster consisting of 20 Intel-Xeon CPUs for RNA secondary structure prediction using SCFGs, but the hardware cost and power consumption is only about 15% and 10% of the latter respectively. Copyright 2009 ACM.

关键词： Field programmable gate arrays (FPGA)

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Approximating quantified SMT-solving with SAT

Approximating quantified SMT-solving with SAT

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International Conference on Secure Software Integration and Reliability Improvement Companion

作者： Fu, Xianjin Liu, Wanwei Li, Jing National Laboratory for Parallel and Distributed Processing National University of Defense Technology Changsha 410073 China

ISBN: (纸本)9780769544540

Satisfiability Modulo Theories (SMT) is an extension of SAT towards FOL. SMT solvers have proven highly scalable and efficient for problems based on some ground theorems. However, SMT problems involving quantifiers and combination of theorems is a long-standing challenge, which has been a major bottleneck of practical application of SMT solvers in some fields. We reveal a decidable fragment of FOL involving quantifiers, which could not be solved by SMT solvers such as Z3, CVC3, etc., and show how to convert them into model checking problems. © 2011 IEEE.

关键词： Model checking

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Labeled topic detection of open source software from mining mass textual project profiles

Labeled topic detection of open source software from mining ...

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1st International Workshop on Software Mining, SoftwareMining-2012 - Held in Conjunction with the 18th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, KDD-2012

作者： Wang, Tao Yin, Gang Li, Xiang Wang, Huaimin National Laboratory for Parallel and Distributed Processing National University of Defense Technology Changsha 410073 China

ISBN: (纸本)9781450315609

Nowadays open source software has become an indispensable basis for both individual and industrial software engineering. Various kinds of labeling mechanisms like categories and tags are used in open source communities to annotate projects and facilitate the discovery of certain software However as large amounts of software are attached with no/few labels or the existing labels are from different ontology space, it is still hard to retrieve potentially topic-relevant software. This paper highlights the valuable semantic information of project descriptions and labels, proposes labeled software topic detection LSTD a hybrid approach combining topic models and ranking mechanisms to detect and enrich the topics of software by mining the large amount of textual software profiles, which can be employed to do software categorization and tag recommendation. LSTD makes use of labeled LDA to capture the semantic correlations between labels and descriptions and then construct the label-based topic-word matrix. Based on the generated matrix and the generality of labels, LSTD designs a simple yet eficient algorithm to detect the latent topics of software that expressed as relevant and popular labels. Comprehensive evaluations are conducted on the large-scale datasets of representative open source communities and the results validate the effectiveness of LSTD.

关键词： Open source software

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Special-purposed VLIW architecture for IEEE-754 quadruple precision elementary functions on FPGA

Special-purposed VLIW architecture for IEEE-754 quadruple pr...

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29th IEEE International Conference on Computer Design 2011, ICCD 2011

作者： Lei, Yuanwu Dou, Yong Shen, Li Zhou, Jie Guo, Song National Laboratory for Parallel and Distributed Processing National University of Defense Technology Changsha 410073 China

ISBN: (纸本)9781457719523

This work explores the feasibility to implement IEEE-754-2008 standard quadruple precision (Quad) elementary functions on recent FPGAs with plenty of embedded memories and DSP blocks. First, we analysis the implementation algorithm of Quad elementary functions in detail. Then, we present a special-purpose Very Large Instruction Word (VLIW) architecture for Quad elementary function (QE-Processor). The proposed processor uses a unified hardware structure, equipped with multiple basic arithmetic units, to implement various Quad algebraic and transcendental functions, in which several tradeoffs between latency and resource usage are carefully planned to avoid unbalanced resource utilization. The performance is improved through the explicitly parallel technology of custom VLIW instruction. Finally, we create a prototype of QE-Processor into Xilinx Virtex-5 and Virtex-6 FPGA chips. The experimental results show that our design can guarantee that the percentage of correct rounding is more than 99.9%. Moreover, the FPGA implementation on Virtex-6 XC6VLX760-2FF1760 FPGA, running at 220 MHz, outperforms the parallel software approach based on OpenMP running on an Intel Xeon E5620 CPU at 2.40GHz by a factor of 13X-20X for special function applications in Boost library. © 2011 IEEE.

关键词： Field programmable gate arrays (FPGA)

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An abstract domain to infer symbolic ranges over nonnegative parameters

An abstract domain to infer symbolic ranges over nonnegative...

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作者： Wu, Xueguang Chen, Liqian Wang, Ji National Laboratory for Parallel and Distributed Processing National University of Defense Technology Changsha 410073 China

The value range information of program variables is useful in many applications such as compiler optimization and program analysis. In the framework of abstract interpretation, the interval abstract domain infers numerical bounds for each program variable. However, in certain applications such as automatic parallelization, symbolic ranges are often desired. In this paper, we present a new numerical abstract domain, namely the abstract domain of parametric ranges, to infer symbolic ranges over nonnegative parameters for each program variable. The new domain is designed based on the insight that in certain contexts, program procedures often have nonnegative parameters, such as the length of an input list and the size of an input array. The domain of parametric ranges seeks to infer the lower and upper bounds for each program variable where each bound is a linear expression over nonnegative parameters. The time and memory complexity of the domain operations of parametric ranges is O(nm) where n is the number of program variables and m is the number of nonnegative parameters. On this basis, we show the application of parametric ranges to infer symbolic ranges of the sizes of list segments in programs manipulating singly-linked lists. Finally, we show preliminary experimental results. © 2014 Elsevier B.V. All rights reserved.

关键词： Model checking

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Queueing analysis of the decoding process for intra-session network coding with random linear codes

Queueing analysis of the decoding process for intra-session ...

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作者： Yuan, Yuan Huang, Zhen Liu, Shengyun Peng, Yuxing National Laboratory for Parallel and Distributed Processing National University of Defense Technology Changsha 410073 China

ISBN: (纸本)9783642277078

Efficient designs for intra-session network coding based practical applications largely rely on a better understanding on its queueing behaviors. However, few work devote on this topics. In this paper, we build a multi-channel batch service queueing system (MN/Dm/1) with control feedbacks to describe the decoding process of intra-session network coding with random linear codes and try to answer several fundamental questions, including for example, how to analyze braking redundancy? Under what condition is the system stable? How's quantitative relationship between the inter-decoding delay and the generation granularity? © 2012 Springer-Verlag GmbH Berlin Heidelberg.

关键词： Network coding

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Kraken: A continuous incremental data acquisition system for GitHub and git repositories 7

Kraken: A continuous incremental data acquisition system for...

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2017 7th International Workshop on Computer Science and Engineering, WCSE 2017

作者： Zeng, Lingbin Yin, Gang Wang, Tao Yu, Yue Fan, Qiang Li, Zhi-Xing Yu, Jie Wang, H.M. National Laboratory for Parallel and Distributed Processing National University of Defense Technology Changsha410073 China

ISBN: (纸本)9789811136719

With the quick development of open source software, quantity of software is produced in the open source community (OSC) [1]. Lots of researches are launched to study the internal regular patterns of OSC [2], [3]. GitHub is one of the most famous open source community which owns thousands software projects. As a result, there are massive and abundant data of software development activities in GitHub. With the purpose to offer an accuracy and efficient dataset of GitHub, this paper proposes Kraken which is a continuous incremental data acquisition system for GitHub. Kraken contains three main modules which are independent with each other. Kraken gets the data of GitHub from two ways: git repositories and rest API. The final result shows that Kraken could extract the commits information of git repositories and get pull requests(PRs) and issues through rest API. The commits information contains the detail development history of software and the feedbacks and wisdom of software engineers are showed through PRs and issues.

关键词： Open source software

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Accurate and simplified prediction of L2 cache vulnerability for cost-efficient soft error protection

Accurate and simplified prediction of L2 cache vulnerability...

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作者： Cheng, Yu Ma, Anguo Zhang, Minxuan National Laboratory for Parallel and Distributed Processing School of Computer National University of Defense Technology China

Soft errors caused by energetic particle strikes in on-chip cache memories have become a critical challenge for microprocessor design. Architectural vulnerability factor (AVF), which is defined as the probability that a transient fault in the structure would result in a visible error in the final output of a program, has been widely employed for accurate soft error rate estimation. Recent studies have found that designing soft error protection techniques with the awareness of AVF is greatly helpful to achieve a tradeoff between performance and reliability for several structures (i.e., issue queue, reorder buffer). Considering large on-chip L2 cache, redundancy-based protection techniques (such as ECC) have been widely employed for L2 cache data integrity with high costs. Protecting caches without accurate knowledge of the vulnerability characteristics may lead to the over-protection, thus incurring high overheads. Therefore, designing AVF-aware protection techniques would be attractive for designers to achieve a cost-efficient protection for caches, especially at early design stage. In this paper, we propose an improved AVF estimation framework for conducing comprehensive characterization of dynamic behavior and predictability of L2 cache vulnerability. We propose to employ Bayesian Additive Regression Trees (BART) method to accurately model the variation of L2 cache AVF and to quantitatively explain the important effects of several key performance metrics on L2 cache AVF. Then we employ bump hunting technique to extract some simple selecting rules based on several key performance metrics for a simplified and fast estimation of L2 cache AVF. Using the simplified L2 cache AVF estimator, we develop an AVF-aware ECC technique as an example to demonstrate the cost-efficient advantages of the AVF prediction based dynamic fault tolerant techniques. Experimental results show that compared with traditional full ECC technique, AVF-aware ECC technique reduces the L2 cache acc

关键词： Cache memory

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Rev Rec: A two-layer reviewer recommendation algorithm in pull-based development model

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Journal of Central South University 2018年第5期25卷 1129-1143页

作者：杨程张迅晖曾令斌范强王涛余跃尹刚王怀民 National Laboratory for Parallel and Distributed Processing College of ComputerNational University of Defense Technology

Code review is an important process to reduce code defects and improve software quality. In social coding communities like GitHub, as everyone can submit Pull-Requests, code review plays a more important role than ever before, and the process is quite time-consuming. Therefore, finding and recommending proper reviewers for the emerging Pull-Requests becomes a vital task. However, most of the current studies mainly focus on recommending reviewers by checking whether they will participate or not without differentiating the participation types. In this paper, we develop a two-layer reviewer recommendation model to recommend reviewers for Pull-Requests （PRs） in GitHub projects from the technical and managerial perspectives. For the first layer, we recommend suitable developers to review the target PRs based on a hybrid recommendation method. For the second layer, after getting the recommendation results from the first layer, we specify whether the target developer will technically or managerially participate in the reviewing process. We conducted experiments on two popular projects in GitHub, and tested the approach using PRs created between February 2016 and February 2017. The results show that the first layer of our recommendation model performs better than the previous work, and the second layer can effectively differentiate the types of participation.

关键词： Pull-Request code reviewer recommendation GitHub open source community

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Modular heap abstractionion-based code clone detection for heap-manipulating programs

Modular heap abstractionion-based code clone detection for h...

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12th International Conference on Quality Software, QSIC 2012

作者： Dong, Longming Wang, Ji Chen, Liqian National Laboratory for Parallel and Distributed Processing National University of Defense Technology Changsha 410073 China

ISBN: (纸本)9780769548333

Code clone is a prevalent activity during the development of softwares. However, it may be harmful to the maintenance and evolution of softwares. Current techniques for detecting code clones are most syntax-based, and cannot detect all code clones. In this paper, we present a novel semantic-based clone detection technique by obtaining the similarity about the precondition and postcondition of each procedure, which are computed by a context and field sensitive fixpoint iteration algorithm based on modular heap abstraction in heapmanipulating programs. Experimental evaluation about a set of C benchmark programs shows that the proposed approach can be scalable to detect various clones that existing syntax-based clone detectors have missed. © 2012 IEEE.

关键词： Semantics

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