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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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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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Class-level Non-Interference

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NEW GENERATION COMPUTING 2012年第2-3期30卷 241-270页

作者： Zanardini, Damiano Univ Politecn Madrid Dept Inteligencia Artificial Fac Informat E-28660 Madrid Spain

The Information-Flow property of Non-Interference was recently relaxed into Abstract Non-Interference (ANI), a weakened version where attackers can only observe properties of data, rather than their exact value. ANI was originally defined on integers, where a property models the set of numbers satisfying it. The present work proposes an object-oriented, Java-based formulation of an instance of ANI where data take the form of objects, and the observed property comes to be their type. The execution of a program is taken to be the invocation of some method by an external user: a class is secure if, for all its (non-private) methods, the type of their low-security data after the execution does not depend on the initial type of its high-security data (i.e., there are no illicit flows). The relation to ANI theory (in its abstract version) can be seen in the representation of abstract domains in terms of class hierarchies: an upper closure operator map an object into the smallest class it is an instance of. An analyzer for a non-trivial subset of Java is illustrated. A sketch of a soundness proof is provided: a program is never misclassified as secure, i.e., it is rejected whenever the absence of illicit ows cannot be guaranteed.

关键词： Information Flow Non-Interference Language-based Security Abstract Interpretation object-oriented programming languages

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objects and session types

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INFORMATION AND COMPUTATION 2009年第5期207卷 595-641页

作者： Dezani-Ciancaglini, Mariangiola Drossopoulou, Sophia Mostrous, Dimitris Yoshida, Nobuko Univ Turin Dipartimento Informat IT-10149 Turin Italy Univ London Imperial Coll Sci Technol & Med Dept Comp London SW7 2AZ England

A session takes place between two parties;after establishing a connection, each party interleaves local computations and communications (sending or receiving) with the other. Session types characterise such sessions in terms of the types of values communicated and the shape of protocols, and have been developed for the pi-calculus, CORBA interfaces, and functional languages. We study-the incorporation of session types into object-oriented languages through MOOSE, a multi-threaded language with session types, thread spawning, iterative, and higher-order sessions. Our design aims to consistently integrate the object-oriented programming style and sessions, and to be able to treat various case studies from the literature. We describe the design of MOOSE, its syntax, operational semantics, and type system, and develop a type inference system. After proving subject reduction, we establish the progress property: once a communication has been established, well-typed programs will never starve at communication points. (C) 2009 Elsevier Inc. All rights reserved.

关键词： COMMUNICATION & technology COMPUTER network protocols CORBA (Computer architecture) FUNCTIONAL analysis object-oriented programming languages ITERATIVE methods (Mathematics)

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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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MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory

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BIOINFORMATICS 2015年第8期31卷 1328-1330页

作者： Marchetti, Luca Manca, Vincenzo Univ Verona Dept Comp Sci I-37134 Verona Italy Univ Verona Ctr BioMed Comp I-37134 Verona Italy Microsoft Res Univ Trento Ctr Computat & Syst Biol COSBI I-38068 Rovereto TN Italy

MpTheory Java library is an open-source project collecting a set of objects and algorithms for modeling observed dynamics by means of the Metabolic P (MP) theory, that is, a mathematical theory introduced in 2004 for modeling biological dynamics. By means of the library, it is possible to model biological systems both at continuous and at discrete time. Moreover, the library comprises a set of regression algorithms for inferring MP models starting from time series of observations. To enhance the modeling experience, beside a pure Java usage, the library can be directly used within the most popular computing environments, such as MATLAB, GNU Octave, Mathematica and R.

关键词： SYSTEMS biology RESEARCH COMPUTATIONAL biology BIOINFORMATICS JAVA (Computer program language) object-oriented programming languages

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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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An object-oriented parallel programming language for distributed-memory parallel computing platforms

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SCIENCE OF COMPUTER programming 2014年第parta期80卷 65-90页

作者： Pinho, Eduardo Gurgel de Carvalho Junior, Francisco Heron Univ Fed Ceara Fortaleza Ceara Brazil

In object-oriented programming (OOP) languages, the ability to encapsulate software concerns of the dominant decomposition in objects is the key to reaching high modularity and loss of complexity in large scale designs. However, distributed-memory parallelism tends to break modularity, encapsulation, and the functional independence of objects, since parallel computations cannot be encapsulated in individual objects, which reside in a single address space. For reconciling object-orientation and distributed-memory parallelism, this paper introduces OOPP (object-oriented Parallel programming), a style of OOP where objects are distributed by default. As an extension of C++, a widespread language in HPC, the PObC++ language has been designed and prototyped, incorporating the ideas of OOPP. (C) 2013 Elsevier B.V. All rights reserved.

关键词： object-oriented programming languages Parallel programming languages Parallel programming techniques High performance computing

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Learning Swift 1

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丛书名： Community experience distilled

2015年

作者： Andrew J Wagner

If you are looking to build iOS or OS X apps using the most modern technology, this book is ideal for you. You will find this book especially useful if you are new to programming or if you have yet to develop for iOS ... 详细信息

ISBN: (数字)9781784399627

ISBN: (纸本)9781784392505

关键词： Application software -- Development iOS (Electronic resource) Macintosh (Computer) -- programming object-oriented programming languages

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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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