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13th ACM SIGPLAN/SIGBED International Conference on Languages, Compilers, Tools and Theory for Embedded Systems

作者： Aslam, Faisal Baig, Ghufran Qureshi, Mubashir Adnan Uzmi, Zartash Afzal Fennell, Luminous Thiemann, Peter Schindelhauer, Christian Haussmann, Elmar Punjab Univ Coll Informat Technol Lahore Pakistan Lahore Univ Management Sci DHA Lahore 54792 Pakistan Univ Freiburg D-79110 Freiburg Germany

ISBN: (纸本)9781450312127

The ability of tiny embedded devices to run large feature-rich programs is typically constrained by the amount of memory installed on such devices. Furthermore, the useful operation of these devices in wireless sensor applications is limited by their battery life. This paper presents a call stack redesign targeted at an efficient use of RAM storage and CPU cycles by a java program running on a wireless sensor mote. Without compromising the application programs, our call stack redesign saves 30% of RAM, on average, evaluated over a large number of benchmarks. On the same set of benchmarks, our design also avoids frequent RAM allocations and deallocations, resulting in average 80% fewer memory operations and 23% faster program execution. These may be critical improvements for tiny embedded devices that are equipped with small amount of RAM and limited battery life. However, our call stack redesign is equally effective for any complex multi-threaded object oriented program developed for desktop computers. We describe the redesign, measure its performance and report the resulting savings in RAM and execution time for a wide variety of programs.

关键词： Algorithms Design Experimentation Performance Wireless Sensor Networks Call Stack Memory Management JVM java virtual machine TakaTuka

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Sharing Programming Resources Between Bio* Projects Through Remote Procedure Call and Native Call Stack Strategies

Sharing Programming Resources Between Bio* Projects Through ...

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作者： Pjotr Prins Naohisa Goto Andrew Yates Laurent Gautier Scooter Willis Christopher Fields Toshiaki Katayama

Open-source software (OSS) encourages computer programmers to reuse software components written by others. In evolutionary bioinformatics, OSS comes in a broad range of programming languages, including C/C++, Perl, Python, Ruby, java, and R. To avoid writing the same functionality multiple times for different languages, it is possible to share components by bridging computer languages and Bio* projects, such as BioPerl, Biopython, BioRuby, Biojava, and R/Bioconductor. In this chapter, we compare the two principal approaches for sharing software between different programming languages: either by remote procedure call (RPC) or by sharing a local call stack. RPC provides a language-independent protocol over a network interface; examples are RSOAP and Rserve. The local call stack provides a between-language mapping not over the network interface, but directly in computer memory; examples are R bindings, RPy, and languages sharing the java virtual machine stack. This functionality provides strategies for sharing of software between Bio* projects, which can be exploited more often. Here, we present cross-language examples for sequence translation, and measure throughput of the different options. We compare calling into R through native R, RSOAP, Rserve, and RPy interfaces, with the performance of native BioPerl, Biopython, Biojava, and BioRuby implementations, and with call stack bindings to Biojava and the European Molecular Biology Open Software Suite. In general, call stack approaches outperform native Bio* implementations and these, in turn, outperform RPC-based approaches. To test and compare strategies, we provide a downloadable BioNode image with all examples, tools, and libraries included. The BioNode image can be run on virtualBox-supported operating systems, including Windows, OSX, and Linux. less

关键词： Python R Bioinformatics BioPerl BioRuby Biopython Biojava Web services Remote procedure call java virtual machine

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Performance optimization of java virtual machine on dual-core technology for web services - Aa study

Performance optimization of Java Virtual Machine on dual-cor...

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9th International Conference on Advanced Communication Technology (ICACT 2007)

作者： Mun, Chong Kam KrishnaRao, G. S. V. R. Lam, Hai-Shuan Eswaran, C. Phon-Amnuaisuk, Somnuk Multimedia Univ Fac Informat Technol Cyberjaya Malaysia

ISBN: (纸本)9788955191318

How well the web applications handle the workload is a key factor in determining the performance of the web service. Due to its support for multithreading at language level, java is becoming a popular language for web application. The performance of java application is greatly dependent on java virtual machine (JVM). Performance of multithreaded java application can be enhanced by fully utilizing the computing resources of dual-core processor. This paper targets in optimizing the JVM to take advantage on dual-core processor. With the optimization, the web service is expected to have a marked performance gain.

关键词： web service dual-core technology java virtual machine thread scheduling throughput benchmarking

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Space-and-Time Efficient Parallel Garbage Collector for Data-Intensive Applications

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INTERNATIONAL JOURNAL OF PARALLEL PROGRAMMING 2011年第4期39卷 451-472页

作者： Liu, Shaoshan Wang, Ligang Li, Xiao-Feng Gaudiot, Jean-Luc Univ Calif Irvine Irvine CA 92717 USA Intel China Res Ctr Beijing Peoples R China

As multithreaded server applications and runtime systems prevail, garbage collection is becoming an essential feature to support high performance systems, especially those running data-intensive applications. The fundamental issue of garbage collector (GC) design is to maximize the recycled space with minimal time overhead. This paper proposes two innovative solutions: one to improve space efficiency, and the other to improve time efficiency. To achieve space efficiency, we propose the Space Tuner that utilizes the novel concept of allocation speed to reduce wasted space. Conventional static space partitioning techniques often lead to inefficient space utilization. The Space Tuner adjusts the heap partitioning dynamically such that when a collection is triggered, all space partitions are fully filled. To achieve time efficiency, we propose a novel parallelization method that reduces the compacting GC parallelization problem into a tree traversal parallelization problem. This method can be applied for both normal and large object compaction. Object compaction is hard to parallelize due to strong data dependencies such that the source object can not be moved to its target location until the object originally in the target location has been moved out. Our proposed algorithm overcomes the difficulties by dividing the heap into equal-sized blocks and parallelizing the movement of the independent blocks. It is noteworthy that these proposed algorithms are generic such that they can be utilized in different GC designs. The proposed techniques have been implemented in Apache Harmony JVM and we evaluated the proposed algorithms with SPECjbb and Dacapo benchmark suites. The experiment results demonstrate that our proposed algorithms greatly improve space utilization and the corresponding parallelization schemes are scalable, which brings time efficiency.

关键词： java virtual machine Garbage collection

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Flexible and efficient profiling with aspect-oriented programming

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CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE 2011年第15期23卷 1749-1773页

作者： Binder, Walter Ansaloni, Danilo Villazon, Alex Moret, Philippe Univ Lugano Fac Informat CH-6900 Lugano Switzerland UPB CINTI Cochabamba Bolivia

Many profilers for virtual execution environments, such as the java virtual machine (JVM), are implemented with low-level bytecode instrumentation techniques, which is tedious, error-prone, and complicates maintenance and extension of the tools. In order to reduce the development time and cost, we promote building profilers for the JVM using high-level aspect-oriented programming (AOP). We show that the use of aspects yields concise profilers that are easy to develop, extend, and maintain, because low-level instrumentation details are hidden from the tool developer. In order to build efficient profilers, we introduce inter-advice communication, an extension to common AOP languages that enables efficient data passing between advices that are woven into the same method using local variables. We illustrate our approach with two case studies. First, we show that an existing, instrumentation-based tool for listener latency profiling can be easily recast as an aspect. Second, we present an aspect for comprehensive calling context profiling. In order to reduce profiling overhead, our aspect parallelizes application execution and profile creation, resulting in a speedup of 110% on a machine with more than two cores, compared with a primitive, non-parallel approach. Copyright (C) 2011 John Wiley & Sons, Ltd.

关键词： profiling aspect-oriented programming aspect weaving bytecode instrumentation calling context tree concurrency multicores java virtual machine

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New developments on the cheminformatics open workflow environment CDK-Taverna

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JOURNAL OF CHEMINFORMATICS 2011年第1期3卷 1-10页

作者： Truszkowski, Andreas Jayaseelan, Kalai Vanii Neumann, Stefan Willighagen, Egon L. Zielesny, Achim Steinbeck, Christoph EBI Cambridge England Univ Appl Sci Gelsenkirchen Inst Bioinformat & Cheminformat Recklinghausen Germany GNWI Gesell Nat Wissenschaftliche Informat mbH Oer Erkenschwick Germany Karolinska Inst Inst Environm Med Div Mol Toxicol S-10401 Stockholm Sweden

Background: The computational processing and analysis of small molecules is at heart of cheminformatics and structural bioinformatics and their application in e. g. metabolomics or drug discovery. Pipelining or workflow tools allow for the Lego (TM)-like, graphical assembly of I/O modules and algorithms into a complex workflow which can be easily deployed, modified and tested without the hassle of implementing it into a monolithic application. The CDK-Taverna project aims at building a free open-source cheminformatics pipelining solution through combination of different open-source projects such as Taverna, the Chemistry Development Kit (CDK) or the Waikato Environment for Knowledge Analysis (WEKA). A first integrated version 1.0 of CDK-Taverna was recently released to the public. Results: The CDK-Taverna project was migrated to the most up-to-date versions of its foundational software libraries with a complete re-engineering of its worker's architecture (version 2.0). 64-bit computing and multi-core usage by paralleled threads are now supported to allow for fast in-memory processing and analysis of large sets of molecules. Earlier deficiencies like workarounds for iterative data reading are removed. The combinatorial chemistry related reaction enumeration features are considerably enhanced. Additional functionality for calculating a natural product likeness score for small molecules is implemented to identify possible drug candidates. Finally the data analysis capabilities are extended with new workers that provide access to the open-source WEKA library for clustering and machine learning as well as training and test set partitioning. The new features are outlined with usage scenarios. Conclusions: CDK-Taverna 2.0 as an open-source cheminformatics workflow solution matured to become a freely available and increasingly powerful tool for the biosciences. The combination of the new CDK-Taverna worker family with the already available workflows developed by a lively Ta

关键词： java virtual machine Atom Signature Public Void Configuration Panel Taverna Workbench

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OSCAR4: a flexible architecture for chemical text-mining

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JOURNAL OF CHEMINFORMATICS 2011年第1期3卷 1-12页

作者： Jessop, David M. Adams, Sam E. Willighagen, Egon L. Hawizy, Lezan Murray-Rust, Peter Univ Cambridge Dept Chem Unilever Ctr Mol Sci Informat Cambridge CB2 1EW England

The Open-Source Chemistry Analysis Routines (OSCAR) software, a toolkit for the recognition of named entities and data in chemistry publications, has been developed since 2002. Recent work has resulted in the separation of the core OSCAR functionality and its release as the OSCAR4 library. This library features a modular API (based on reduction of surface coupling) that permits client programmers to easily incorporate it into external applications. OSCAR4 offers a domain-independent architecture upon which chemistry specific text-mining tools can be built, and its development and usage are discussed.

关键词： Plain Text European Patent Office European Bioinformatics Institute java virtual machine Client Programmer

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Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on

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JOURNAL OF CHEMINFORMATICS 2011年第1期3卷 1-15页

作者： O'Boyle, Noel M. Guha, Rajarshi Willighagen, Egon L. Adams, Samuel E. Alvarsson, Jonathan Bradley, Jean-Claude Filippov, Igor V. Hanson, Robert M. Hanwell, Marcus D. Hutchison, Geoffrey R. James, Craig A. Jeliazkova, Nina Lang, Andrew S. I. D. Langner, Karol M. Lonie, David C. Lowe, Daniel M. Pansanel, Jerome Pavlov, Dmitry Spjuth, Ola Steinbeck, Christoph Tenderholt, Adam L. Theisen, Kevin J. Murray-Rust, Peter Natl Univ Ireland Univ Coll Cork Analyt & Biol Chem Res Facil Cork Ireland NIH Ctr Translat Therapeut Rockville MD 20878 USA Karolinska Inst Inst Environm Med Div Mol Toxicol S-17177 Stockholm Sweden Univ Cambridge Dept Chem Unilever Ctr Mol Sci Informat Cambridge CB2 1EW England Uppsala Univ Dept Pharmaceut Biosci S-75124 Uppsala Sweden Drexel Univ Dept Chem Philadelphia PA 19104 USA NCI Biol Chem Lab Basic Res Program SAIC Frederick Inc Frederick MD 21702 USA St Olaf Coll Northfield MN 55057 USA Kitware Inc Clifton Pk NY 12065 USA Univ Pittsburgh Dept Chem Pittsburgh PA 15260 USA eMolecules Inc Solana Beach CA 92075 USA Ideaconsult Ltd Sofia 1000 Bulgaria Oral Roberts Univ Dept Engn Comp Sci Phys & Math Tulsa OK 74171 USA Leiden Univ Leiden Inst Chem NL-2333 CC Leiden Netherlands SUNY Buffalo Dept Chem Buffalo NY 14260 USA Univ Strasbourg IPHC CNRS UMR7178 F-67037 Strasbourg France GGA Software Serv LLC St Petersburg 194342 Russia EBI Cheminformat & Metab Team Cambridge England Univ Washington Dept Chem Seattle WA 98195 USA iChemLabs Piscataway NJ 08854 USA

Background: The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and Open Standards. Results: This contribution looks back on the work carried out by the Blue Obelisk in the past 5 years and surveys progress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry. Conclusions: We show that the Blue Obelisk has been very successful in bringing together researchers and developers with common interests in ODOSOS, leading to development of many useful resources freely available to the chemistry community.

关键词： Open Source Open Data Resource Description Framework java virtual machine Chemical Markup Language

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Comprehensive aspect weaving for java

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SCIENCE OF COMPUTER PROGRAMMING 2011年第11期76卷 1015-1036页

作者： Villazon, Alex Binder, Walter Moret, Philippe Ansaloni, Danilo Univ Lugano Fac Informat CH-6900 Lugano Switzerland

Aspect-oriented programming (AOP) has been successfully applied to application code thanks to techniques such as java bytecode instrumentation. Unfortunately, with existing AOP frameworks for java such as AspectJ, aspects cannot be woven into the standard java class library. This restriction is particularly unfortunate for aspects that would benefit from comprehensive aspect weaving with complete method coverage, such as profiling or debugging aspects. In this article we present MAJOR, a new tool for comprehensive aspect weaving, which ensures that aspects are woven into all classes loaded in a java virtual machine, including those in the standard java class library. MAJOR includes the pluggable module CARAJillo, which supports efficient access to a complete and customizable calling context representation. We validate our approach with three case studies. Firstly, we weave existing profiling aspects with MAJOR which otherwise would generate incomplete profiles. Secondly, we introduce an aspect for memory leak detection that also benefits from comprehensive weaving. Thirdly, we present an aspect subsuming the functionality of ReCrash, an existing tool based on low-level bytecode instrumentation techniques that generates unit tests to reproduce program failures. Our aspect-based tools are concisely implemented in a few lines of code, and leverage MAJOR and CARAJillo for comprehensive aspect weaving and for efficient access to calling context information. (C) 2010 Elsevier B.V. All rights reserved.

关键词： Aspect-oriented programming Aspect weaving Bytecode instrumentation Profiling Debugging Detecting memory leaks Recreating crashing conditions java virtual machine

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A Step Towards Transparent Integration of Input-Consciousness into Dynamic Program Optimizations 11

A Step Towards Transparent Integration of Input-Consciousnes...

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2th ACM International Conference on Systems, Programming, Languages, and Applications: Software for Humanity (SPLASH)

作者： Tian, Kai Zhang, Eddy Z. Shen, Xipeng Coll William & Mary Dept Comp Sci Williamsburg VA 23185 USA

ISBN: (纸本)9781450309400

Dynamic program optimizations are critical for the efficiency of applications in managed programming languages and scripting languages. Recent studies have shown that exploitation of program inputs may enhance the effectiveness of dynamic optimizations significantly. However, current solutions for enabling the exploitation require either programmers' annotations or intensive offline profiling, impairing the practical adoption of the techniques. This current work examines the basic feasibility of transparent integration of input-consciousness into dynamic program optimizations, particularly in managed execution environments. It uses transparent learning across production runs as the basic vehicle, and investigates the implications of cross-run learning on each main component of input-conscious dynamic optimizations. It proposes several techniques to address some key challenges for the transparent integration, including randomized inspection-instrumentation for cross-user data collection, a sparsity-tolerant algorithm for input characterization, and selective prediction for efficiency protection. These techniques make it possible to automatically recognize the relations between the inputs to a program and the appropriate ways to optimize it. The whole process happens transparently across production runs;no need for offline profiling or programmer intervention. Experiments on a number of java programs demonstrate the effectiveness of the techniques in enabling input-consciousness for dynamic optimizations, revealing the feasibility and potential benefits of the new optimization paradigm in some basic settings.

关键词： Program inputs Dynamic optimizations java virtual machine Proactivity Seminal behaviors Dynamic version selection Just-In-Time Compilation

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