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StreamFlex: High-throughput stream programming in java

ACM SIGPLAN NOTICES 2007年第10期42卷 211-228页

作者： Spring, Jesper H. Privat, Jean Guerraoui, Rachid Vitek, Jan Ecole Polytech Fed Lausanne Lausanne Switzerland Purdue Univ Dept Comp Sci W Lafayette IN 47907 USA IBM Corp San Jose CA 95114 USA

The stream programming paradigm aims to expose coarse-grained parallelism in applications that must process continuous sequences of events. The appeal of stream programming comes from its conceptual simplicity. A program is a collection of independent filters which communicate by the means of uni-directional data channels. This model lends itself naturally to concurrent and efficient implementations on modern multiprocessors. As the output behavior of filters is determined by the state of their input channels, stream programs have fewer opportunities for the errors (such as data races and deadlocks) that plague shared memory concurrent programming. This paper introduces STREAMFLEX, an extension to java which marries streams with objects and thus enables to combine, in the same java virtual machine, stream processing code with traditional object-oriented components. STREAMFLEX targets high-throughput low-latency applications with stringent quality-of-service requirements. To achieve these goals, it must, at the same time, extend and restrict java. To allow for program optimization and provide latency guarantees, the STREAMFLEX compiler restricts java by imposing a stricter typing discipline on filters. On the other hand, STREAMFLEX extends the java virtual machine with real-time capabilities, transactional memory and type-safe region-based allocation. The result is a rich and expressive language that can be implemented efficiently.

关键词： languages experimentation. real-time systems java virtual machine memory management ownership types stream processing

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Yama: A scalable generational garbage collector for java in multiprocessor systems

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IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS 2006年第2期17卷 148-159页

作者： Muthukumar, RM Janakiram, D Indian Inst Technol Dept Comp Sci & Engn Distributed & Ojbect Syst Lab Madras 600036 Tamil Nadu India

The current state-of-the-art generational garbage collector pauses all the program threads when it performs young and old generation garbage collection. As the number of program threads increases, the delay due to garbage collection also increases, thus restricting the scalability of the collector. In order to improve the scalability and reduce the pause time, an on-the-fly generational garbage collector called Yama is proposed for multiprocessor systems. This uses the on-the-fly deferred reference counting in the young generation and the DLG (Doligez Leroy Gonthier) on-the-fly mark and sweep garbage collector in the old generation. We have proposed and experimented with two novel variations of the on-the-fly deferred reference counting called Chitragupt1 and Chitragupt2 in the young generation. Yama does not pause all the application threads simultaneously. An adaptive tenuring policy based on object reference count and survival rate is also proposed. Yama has been implemented in the IBM Jikes RVM (Research virtual machine). The above claims are supported with experimental results for standard benchmark programs. The results show that Yama has an extremely low pause time in both the young and the old generation. The pause time reduction results in better response times for the user programs.

关键词： garbage collection memory management java programming languages java virtual machine on-the-fly garbage collection

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Platform independent dynamic java virtual machine analysis: the java Grande Forum benchmark suite

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CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE 2003年第3-5期15卷 459-484页

作者： Gregg, D Power, J Waldron, J Univ Dublin Trinity Coll Dept Comp Sci Dublin 2 Ireland Natl Univ Ireland Dept Comp Sci Maynooth Kildare Ireland

In this paper we present a platform independent analysis of the dynamic profiles of java programs when executing on the java virtual machine. The java programs selected are taken from the java Grande Forum benchmark suite and five different java-to-bytecode compilers are analysed. The results presented describe the dynamic instruction usage frequencies. as well as the sizes of the local variable, parameter and operand stacks during execution on the JVM. These results, presenting a picture of the actual (rather than presumed) behaviour of the JVM, have implications both for the coverage aspects of the java Grande benchmark suites, for the performance of the java-to-bytecode compilers and for the design of the JVM. Copyright (C) 2003 John Wiley Sons, Ltd.

关键词： java virtual machine java Grande instruction frequency method profiling

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ILJc: Porting *** IL (intermediate language) to java

ILJc: Porting *** IL (intermediate language) to Java

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International Conference on Industrial and Information Systems

作者： Siddique, S. Sheriff, S. D. Wijesuriya, H. Wickramaratne, C. Makalanda, J. IT Depratment Sri Lanka Institute of Information Technology Sri Lanka

ISBN: (纸本)9781424403219

ILJc (Intermediate Language to java compiler) would map IL (Intermediate Language) of the *** framework to java based applications. ILJc would be the middle-base in compiling and translating the IL code which ports out of Microsoft Visual *** into the equivalent java byte code. Thus, ILJc would simply transform Visual *** into relative java applications. ILJc does its best to map *** entities to java equivalents, furthermore ILJc must deal with the exceptions too. For an instance, in the case of exceptions, java provides one exception class, but *** provides three;ILJc is forced to map all three *** exceptions to the single java exception. The task is no easy to fix, but simply have to write around this many-to-one mapping. Although all *** exceptions are derived from the *** class, not all java exceptions are derived from ***;some generated by the JVM (java virtual machine) are derived from the *** class. This incongruence shows up in *** code that tries to catch all exceptions, when translated into java, exceptions derived from *** is taken for granted and slip off. As a proof of concept of how that system could be, we started sometime ago to implement ILJc, featuring a modular, flexible architecture. In this paper we show its structure, how it can be used, and how it can be further extended.

关键词： java exception handling network operating systems program compilers visual languages java based application java compiler java virtual machine Microsoft Visual intermediate language exception handling Intermediate Language java compiler java virtual machine (JVM) compilers Network operating systems visual languages EXCEPTIONS

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Accurate, efficient, and adaptive calling context profiling

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ACM SIGPLAN NOTICES 2006年第6期41卷 263-271页

作者： Zhuang, Xiaotong Serrano, Mauricio J. Cain, Harold W. Choi, Jong-Deok Georgia Inst Technol Atlanta GA 30332 USA IBM Corp TJ Watson Res Ctr San Diego CA USA

Calling context profiles are used in many inter-procedural code optimizations and in overall program understanding. Unfortunately, the collection of profile information is highly intrusive due to the high frequency of method calls in most applications. Previously proposed calling-context profiling mechanisms consequently suffer from either low accuracy, high overhead, or both. We have developed a new approach for building the calling context tree at runtime, called adaptive bursting. By selectively inhibiting redundant profiling, this approach dramatically reduces overhead while preserving profile accuracy. We first demonstrate the drawbacks of previously proposed calling context profiling mechanisms. We show that a low-overhead solution using sampled stack-walking alone is less than 50% accurate, based on degree of overlap with a complete calling-context tree. We also show that a static bursting approach collects a highly accurate profile, but causes an unacceptable application slowdown. Our adaptive solution achieves 85% degree of overlap and provides an 88% hot-edge coverage when using a 0.1 hot-edge threshold, while dramatically reducing overhead compared to the static bursting approach.

关键词： algorithms measurement performance profiling call graph calling context calling context tree adaptive java virtual machine

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Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor

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BMC BIOINFORMATICS 2006年第1期7卷 474-474页

作者： Kohany, Oleksiy Gentles, Andrew J. Hankus, Lukasz Jurka, Jerzy Genet Informat Res Inst Mountain View CA 94043 USA Stanford Univ Sch Med Stanford CA 94301 USA

Background: Repbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations. Updating and maintenance of the database requires specialized tools, which we have created and made available for use with Repbase, and which may be useful as a template for other curated databases. Results: We describe the software tools RepbaseSubmitter and Censor, which are designed to facilitate updating and screening the content of Repbase. RepbaseSubmitter is a java-based interface for formatting and annotating Repbase entries. It eliminates many common formatting errors, and automates actions such as calculation of sequence lengths and composition, thus facilitating curation of Repbase sequences. In addition, it has several features for predicting protein coding regions in sequences;searching and including Pubmed references in Repbase entries;and searching the NCBI taxonomy database for correct inclusion of species information and taxonomic position. Censor is a tool to rapidly identify repetitive elements by comparison to known repeats. It uses WU-BLAST for speed and sensitivity, and can conduct DNA-DNA, DNA-protein, or translated DNA- translated DNA searches of genomic sequence. Defragmented output includes a map of repeats present in the query sequence, with the options to report masked query sequence( s), repeat sequences found in the query, and alignments. Conclusion: Censor and RepbaseSubmitter are available as both web-based services and downloadable versions. They can be found at http://***/repbase/*** ( RepbaseSubmitter) and http://***/censor/*** ( Censor).

关键词： Transposable Element Query Sequence Repetitive Element Simple Repeat java virtual machine

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HotSwap for bioinformatics: A STRAP tutorial

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BMC BIOINFORMATICS 2006年第1期7卷 64-64页

作者： Gille, C Robinson, PN Humboldt Univ Charite Univ Hosp Inst Biochem Berlin Germany Humboldt Univ Charite Univ Hosp Inst Med Genet Berlin Germany

Background: Bioinformatics applications are now routinely used to analyze large amounts of data. Application development often requires many cycles of optimization, compiling, and testing. Repeatedly loading large datasets can significantly slow down the development process. We have incorporated HotSwap functionality into the protein workbench STRAP, allowing developers to create plugins using the java HotSwap technique. Results: Users can load multiple protein sequences or structures into the main STRAP user interface, and simultaneously develop plugins using an editor of their choice such as Emacs. Saving changes to the java file causes STRAP to recompile the plugin and automatically update its user interface without requiring recompilation of STRAP or reloading of protein data. This article presents a tutorial on how to develop HotSwap plugins. STRAP is available at http://*** and http://***/bioinf/strap. Conclusion: HotSwap is a useful and time-saving technique for bioinformatics developers. HotSwap can be used to efficiently develop bioinformatics applications that require loading large amounts of data into memory.

关键词： Coiled Coil FASTA File java virtual machine User Code Coiled Coil Region

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Design and performance analysis of a distributed java virtual machine

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IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS 2002年第6期13卷 611-627页

作者： Surdeanu, M Moldovan, D Language Comp Corp Dallas TX 75206 USA Univ Texas Dept Comp Sci Richardson TX 75083 USA

This paper introduces DISK, a distributed java virtual machine for networks of heterogenous workstations. Several research issues are addressed. A novelty of the system is its object-based, multiple-writer memory consistency protocol (OMW). The correctness of the protocol and its java compliance is demonstrated by comparing the nonoperational definitions of Release Consistency, the consistency model implemented by OMW, with the java virtual machine memory consistency model (JVMC), as defined in the java virtual machine Specification, An analytical performance model was developed to study and compare the design trade-offs between OMW and the lazy invalidate Release Consistency (LI) protocols as a function of the number of processors, network characteristics, and application types. The DISK system has been implemented and running on a network of 16 Pentium III computers interconnected by a 100 Mbps Ethernet network. Experiments performed with two applications: parallel matrix multiplication and traveling salesman problem confirm the analytical model.

关键词： object-oriented distributed shared memory java virtual machine performance analysis memory consistency protocols consistency models

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JVM Bytecode Verification Without Dataflow Analysis

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ELECTRONIC NOTES IN THEORETICAL COMPUTER SCIENCE 2005年第1期141卷 203-220页

作者： Bayley, Ian Shiel, Sam Oxford Brookes Univ Dept Comp Oxford OX33 1HX England

Bytecode verification algorithms are traditionally based on dataflow analysis. We present an alternative algorithm that first restructures the bytecode and then infers a type signature for each method in a manner typical of functional programming languages. We also give an operational semantics to an algebra of structured bytecode and thereby prove both that restructuring preserves semantics and that our type inference is sound.

关键词： program transformation bytecode verification java virtual machine

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A method-level comparison of the java Grande and SPEC JVM98 benchmark suites

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CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE 2005年第7-8期17卷 757-773页

作者： Gregg, D Power, J Waldron, J Natl Univ Ireland Dept Comp Sci Maynooth Kildare Ireland Univ Dublin Trinity Coll Dept Comp Sci Dublin 2 Ireland

In this paper we seek to provide a foundation for the study of the level of use of object-oriented techniques in java programs in general, and scientific applications in particular. Specifically, we investigate the profiles of java programs from a number of perspectives, including the use of class library methods, the size of methods called, the mode of invoke instruction used and the polymorphicity of call sites. We also present a categorization of the nature of small methods used in java programs. We compare the java Grande and SPEC JVM98 benchmark suites, and note a significant difference in the nature and composition of these suites, with the programs from the java Grande suite demonstrating a less object-oriented approach. Copyright (c) 2005 John Wiley & Sons, Ltd.

关键词： benchmark suites java virtual machine dynamic profiling

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