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Fine-grained parallelization of the Car-Parrinello ab initio molecular dynamics method on the IBM Blue Gene/L supercomputer

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IBM JOURNAL OF RESEARCH AND DEVELOPMENT 2008年第1-2期52卷 159-175页

作者： Bohm, E. Bhatele, A. Kale, L. V. Tuckerman, M. E. Kumar, S. Gunnels, J. A. Martyna, G. J. Univ Illinois Dept Comp Sci Thomas M Siebel Ctr Urbana IL 61801 USA NYU Dept Chem New York NY 10003 USA NYU Courant Inst Math Sci New York NY 10003 USA IBM Corp Div Res Thomas J Watson Res Ctr Yorktown Hts NY 10598 USA IBM Corp Div Phys Sci TJ Watson Res Ctr Yorktown Hts NY 10598 USA

Important scientific problems can be treated via ab initio-based molecular modeling approaches, wherein atomic forces are derived from an energy function that explicitly considers the electrons. The Car-Parrinello ab initio molecular dynamics (CPAIMD) method is widely used to study small systems containing on the order of 10 to 103 atoms. However, the impact of CPAIMD has been limited until recently because of difficulties inherent to scaling the technique beyond processor numbers about equal to the number of electronic states. CPAIMD computations involve a large number of interdependent phases with high interprocessor communication overhead. These phases require the evaluation of various transforms and non-square matrix multiplications that require large interprocessor data movement when efficiently parallelized. Using the Charm++ parallel programming language and runtime system, the phases are discretized into a large number of virtual processors, which are, in turn, mapped flexibly onto physical processors, thereby allowing interleaving of work. Algorithmic and IBM Blue Gene/L (TM) system-specfic optimizations are employed to scale the CPAIMD method to at least 30 times the number of electronic states in small systems consisting of 24 to 768 atoms (32 to 1,024 electronic states) in order to demonstrate fine-grained parallelism. The largest systems studied scaled well across the entire machine (20,480 nodes).

关键词： MOLECULAR dynamics ELECTRONIC systems PARALLEL processing (Electronic computers) PARALLEL programming (Computer science) object-oriented programming languages INTERNATIONAL Business Machines Corp.

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On the prediction of Java object lifetimes

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IEEE TRANSACTIONS ON COMPUTERS 2006年第7期55卷 880-892页

作者： Inoue, Hajime Stefanovic, Darko Forrest, Stephanie Carleton Univ Sch Comp Sci Ottawa ON K1S 5B6 Canada Univ New Mexico Dept Comp Sci Albuquerque NM 87131 USA

Accurately predicting object lifetimes is important for improving memory management systems. Current garbage collectors make relatively coarse-grained predictions ( e. g., "short-lived" versus "long-lived") and rely on application- independent heuristics related to the local characteristics of an allocation. This paper introduces a prediction method which is fully precise and makes its predictions based on application- specific training rather than application- independent heuristics. By "fully precise" we mean that the granularity of predictions is equal to the smallest unit of allocation. The method described here is the first to combine high precision and efficiency in a single lifetime predictor. Fully precise prediction enables us, for the first time, to study zero-lifetime objects. The paper reports results showing that zero-lifetime objects comprise a significant fraction of object allocations in benchmark programs for the Java programming language and that they are correlated with their allocation context ( the call stack and allocation site). Beyond zero-lifetime objects, the paper reports results on predicting longer lived objects, where, in some cases, it is possible to predict the lifetime of objects based on their allocation context ( the call stack and allocation site) well. For the SPEC benchmark programs, the number of dynamically allocated objects whose call sites have accurate predictors ranges from 0.2 percent to 61 percent. This method could potentially improve the performance of garbage collectors. The paper proposes a death- ordered collector (DOC) and analyzes its implementation overheads and its best possible performance. The study shows how memory performance could be enhanced using the extra information provided by fully precise prediction.

关键词： object lifetimes workload characterization pretenuring object-oriented programming languages garbage collection program behavior

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MultiJava: Design rationale, compiler implementation, and applications

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ACM TRANSACTIONS ON programming languages AND SYSTEMS 2006年第3期28卷 517-575页

作者： Clifton, Curtis Millstein, Todd Leavens, Gary T. Chambers, Craig Rose Hulman Inst Technol Dept Comp Sci & Software Engn Terre Haute IN 47803 USA Univ Calif Los Angeles Dept Comp Sci Los Angeles CA 90095 USA Iowa State Univ Dept Comp Sci Ames IA 50011 USA Univ Washington Dept Comp Sci & Engn Seattle WA 98195 USA

MultiJava is a conservative extension of the Java programming language that adds symmetric multiple dispatch and open classes. Among other benefits, multiple dispatch provides a solution to the binary method problem. Open classes provide a solution to the extensibility problem of object-oriented programming languages, allowing the modular addition of both new types and new operations to an existing type hierarchy. This article illustrates and motivates the design of MultiJava and describes its modular static typechecking and modular compilation strategies. Although MultiJava extends Java, the key ideas of the language design are applicable to other object-oriented languages, such as C# and C++, and even, with some modifications, to functional languages such as ML. This article also discusses the variety of application domains in which MultiJava has been successfully used by others, including pervasive computing, graphical user interfaces, and compilers. MultiJava allows users to express desired programming idioms in a way that is declarative and supports static typechecking, in contrast to the tedious and type-unsafe workarounds required in Java. MultiJava also provides opportunities for new kinds of extensibility that are not easily available in Java.

关键词： open objects extensible classes extensible external methods external methods multimethods method families generic functions object-oriented programming languages single dispatch multiple dispatch encapsulation modularity static type-checking subtyping inheritance Java language MultiJava language separate compilation expression problem binary method problem augmenting method problem

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Scalable extensibility via nested inheritance

Scalable extensibility via nested inheritance

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19th Conference on object-oriented programming, Systems, languages, and Applications

作者： Nystrom, N Chong, S Myers, AC Cornell Univ Dept Comp Sci Ithaca NY 14853 USA

Inheritance is a useful mechanism for factoring and reusing code. However, it has limitations for building extensible systems. We describe nested inheritance, a mechanism that addresses some of the limitations of ordinary inheritance and other code reuse mechanisms. Using our experience with an extensible compiler framework, we show how nested inheritance can be used to construct highly extensible software frameworks. The essential aspects of nested inheritance are formalized in a simple object-oriented language with an operational semantics and type system. The type system of this language is sound, so no run-time type checking is required to implement it and no run-time type errors can occur. We describe our implementation of nested inheritance as an unobtrusive extension of the Java language, called Jx. Our prototype implementation translates Jx code to ordinary Java code, without duplicating inherited code.

关键词： object-oriented programming languages inheritance nested classes virtual classes

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Scalable extensibility via nested inheritance 04

Scalable extensibility via nested inheritance

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Proceedings of the 19th annual ACM SIGPLAN conference on object-oriented programming, systems, languages, and applications

作者： Nathaniel Nystrom Stephen Chong Andrew C. Myers Cornell University

ISBN: (纸本)9781581138313

Inheritance is a useful mechanism for factoring and reusing code. However, it has limitations for building extensible systems. We describe nested inheritance, a mechanism that addresses some of the limitations of ordinary inheritance and other code reuse mechanisms. Using our experience with an extensible compiler framework, we show how nested inheritance can be used to construct highly extensible software frameworks. The essential aspects of nested inheritance are formalized in a simple object-oriented language with an operational semantics and type system. The type system of this language is sound, so no run-time type checking is required to implement it and no run-time type errors can occur. We describe our implementation of nested inheritance as an unobtrusive extension of the Java language, called Jx. Our prototype implementation translates Jx code to ordinary Java code, without duplicating inherited code.

关键词： virtual classes object-oriented programming languages nested classes inheritance

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Characterization and automatic identification of type infeasible call chains

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INFORMATION AND SOFTWARE TECHNOLOGY 2002年第13期44卷 721-732页

作者： Souter, AL Pollock, LL Univ Delaware Newark DE 19716 USA

Many software engineering applications utilize static program analyses to gain information about programs. Some applications perform static analysis over the whole program's call graph, while others are more interested in specific call chains within a program's call graph. A particular static call chain for an object-oriented program may in fact be impossible to execute, or infeasible, such that there is no input for which the chain will be taken. Identifying infeasible static call chains can save time and resources with respect to the targeted software development tool. This paper examines type infeasibility of call chains, which may be caused by inherently polymorphic call sites and are sometimes due to imprecision in call graphs. The problem of determining whether a call chain is type infeasible is defined and exemplified, and a key property characterizing type infeasible call chains is described. An empirical study was performed on a set of Java programs, and results from examining the call graphs of these programs are presented. Finally, an algorithm that automatically determines the type infeasibility of a call chain due to object parameters is presented. (C) 2002 Elsevier Science B.V. All rights reserved.

关键词： object-oriented programming languages static program analysis call chains

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Analyzing exception flow in Java programs 7

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Proceedings of the 7th European software engineering conference held jointly with the 7th ACM SIGSOFT international symposium on Foundations of software engineering

作者： Martin P. Robillard Gail C. Murphy Univ. of British Columbia Vancouver B.C. Canada

ISBN: (纸本)9783540665380

Exception handling mechanisms provided by programming languages are intended to ease the difficulty of developing robust software systems. Using these mechanisms, a software developer can describe the exceptional conditions a module might raise, and the response of the module to exceptional conditions that may occur as it is executing. Creating a robust system from such a localized view requires a developer to reason about the flow of exceptions across modules. The use of unchecked exceptions, and in object-oriented languages, subsumption, makes it difficult for a software developer to perform this reasoning manually. In this paper, we describe a tool called Jex that analyzes the flow of exceptions in Java code to produce views of the exception structure. We demonstrate how Jex can help a developer identify program points where exceptions are caught accidentally, where there is an opportunity to add finer-grained recovery code, and where error-handling policies are not being followed.

关键词： software analysis software engineering tools object-oriented programming languages exception handling

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An overview of object-oriented simulation

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SIMULATION 1998年第6期70卷 359-368页

作者： Roberts, CA Dessouky, YM Arizona State Univ Dept Ind & Management Syst Engn Tempe AZ 85287 USA San Jose State Univ Dept Comp Informat & Syst Engn San Jose CA 95192 USA

With an immense increase in research, development, and application of object-oriented simulation (OOS) over the past decade, there is evidence that this technology is becoming the choice for modeling large, complex, and/or distributed systems. This paper discusses the features of OOS that dispose it to modeling these types of systems and compares the OOS approach with traditional simulation approaches. A review of OOS languages and environments is followed by a discussion of current issues pertaining to object-oriented simulation.

关键词： OOS object-oriented object-oriented programming languages simulation environments

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High performance sets

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International Conference and Exhibition on High-Performance Computing and Networking

作者： Kosch, H Böszörményi, L Univ Klagenfurt Dept Informat Technol A-9020 Klagenfurt Austria

ISBN: (纸本)3540644431

This short paper presents a system offering parallel persistent and polymorphic sets of objects, on the level of ari existing general purpose object-oriented programming language, like Modula-3 and JAVA. The user of such a system gets distribution, and persistence ill the same natural way, as users of tradition systems get volatile arrays of numbers, of objects. In addition, advantages are taken from sophisticated optimization techniques.

关键词： parallel persistent and polymorphic sets of object object-oriented programming languages query optimization

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REFLECTIONS ON METAprogramming

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IEEE TRANSACTIONS ON SOFTWARE ENGINEERING 1995年第11期21卷 883-893页

作者： LEE, AH ZACHARY, JL UNIV UTAH DEPT COMP SCISALT LAKE CITYUT 84112

By encapsulating aspects of language semantics within a set of default classes and allowing the programmer to derive new versions, object-oriented languages whose semantics can be tailored to the needs of individual programmers have been provided, The degree to which such languages are simultaneously flexible and efficient is an open question, We describe our experience with using this technique to incorporate transparent support for persistence into the Common Lisp object System via its' metaobject protocol, an open implementation based on reflection, For many aspects of our implementation the metaobject protocol was perfectly suitable, In other cases we had to choose among extending the protocol, requiring the application programmer to employ special idioms, and tolerating a large performance penalty. Based on our experience we evaluate the metaobject protocol, propose some improvements and extensions, and present performance measurements that reveal the need for improved language implementation techniques.

关键词： CLOS METAobject PROTOCOL object-oriented programming languages object PERSISTENCE OPEN IMPLEMENTATION

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