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Programming Paradigm (programming + paradigm)

Distribution by Scientific Domains

Information Science and Computing	50%

Selected Abstracts

OpenMP-oriented applications for distributed shared memory architectures

CONCURRENCY AND COMPUTATION: PRACTICE & EXPERIENCE, Issue 4 2004
Ami Marowka
Abstract The rapid rise of OpenMP as the preferred parallel programming paradigm for small-to-medium scale parallelism could slow unless OpenMP can show capabilities for becoming the model-of-choice for large scale high-performance parallel computing in the coming decade. The main stumbling block for the adaptation of OpenMP to distributed shared memory (DSM) machines, which are based on architectures like cc-NUMA, stems from the lack of capabilities for data placement among processors and threads for achieving data locality. The absence of such a mechanism causes remote memory accesses and inefficient cache memory use, both of which lead to poor performance. This paper presents a simple software programming approach called copy-inside,copy-back (CC) that exploits the data privatization mechanism of OpenMP for data placement and replacement. This technique enables one to distribute data manually without taking away control and flexibility from the programmer and is thus an alternative to the automat and implicit approaches. Moreover, the CC approach improves on the OpenMP-SPMD style of programming that makes the development process of an OpenMP application more structured and simpler. The CC technique was tested and analyzed using the NAS Parallel Benchmarks on SGI Origin 2000 multiprocessor machines. This study shows that OpenMP improves performance of coarse-grained parallelism, although a fast copy mechanism is essential. Copyright © 2004 John Wiley & Sons, Ltd. [source]

A Parallel PCG Solver for MODFLOW

GROUND WATER, Issue 6 2009
Yanhui Dong
In order to simulate large-scale ground water flow problems more efficiently with MODFLOW, the OpenMP programming paradigm was used to parallelize the preconditioned conjugate-gradient (PCG) solver with in this study. Incremental parallelization, the significant advantage supported by OpenMP on a shared-memory computer, made the solver transit to a parallel program smoothly one block of code at a time. The parallel PCG solver, suitable for both MODFLOW-2000 and MODFLOW-2005, is verified using an 8-processor computer. Both the impact of compilers and different model domain sizes were considered in the numerical experiments. Based on the timing results, execution times using the parallel PCG solver are typically about 1.40 to 5.31 times faster than those using the serial one. In addition, the simulation results are the exact same as the original PCG solver, because the majority of serial codes were not changed. It is worth noting that this parallelizing approach reduces cost in terms of software maintenance because only a single source PCG solver code needs to be maintained in the MODFLOW source tree. [source]

An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2004
Robert M. Dirks
Abstract Given a nucleic acid sequence, a recent algorithm allows the calculation of the partition function over secondary structure space including a class of physically relevant pseudoknots. Here, we present a method for computing base-pairing probabilities starting from the output of this partition function algorithm. The approach relies on the calculation of recursion probabilities that are computed by backtracking through the partition function algorithm, applying a particular transformation at each step. This transformation is applicable to any partition function algorithm that follows the same basic dynamic programming paradigm. Base-pairing probabilities are useful for analyzing the equilibrium ensemble properties of natural and engineered nucleic acids, as demonstrated for a human telomerase RNA and a synthetic DNA nanostructure. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1295,1304, 2004 [source]

A programming environment for behavioural animation

COMPUTER ANIMATION AND VIRTUAL WORLDS (PREV: JNL OF VISUALISATION & COMPUTER ANIMATION), Issue 5 2002
Frédéric Devillers
Abstract Behavioural models offer the ability to simulate autonomous agents like organisms and living beings. Psychological studies have shown that human behaviour can be described by a perception,decision,action loop, in which the decisional process should integrate several programming paradigms such as real time, concurrency and hierarchy. Building such systems for interactive simulation requires the design of a reactive system treating flows of data to and from the environment, and involving task control and preemption. Since a complete mental model based on vision and image processing cannot be constructed in real time using purely geometrical information, higher levels of information are needed in a model of the virtual environment. For example, the autonomous actors of a virtual world would exploit the knowledge of the environment topology to navigate through it. Accordingly, in this paper we present our programming environment for real-time behavioural animation which is compounded of a general animation and simulation platform, a behavioural modelling language and a scenario-authoring tool. Those tools has been used for different applications such as pedestrian and car driver interaction in urban environments, or a virtual museum populated by a group of visitors. Copyright © 2002 John Wiley & Sons, Ltd. [source]