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Different Simulations (different + simulation)

Distribution by Scientific Domains

Engineering	50%

Selected Abstracts

Implementation and evaluation of MPI-based parallel MD program

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 1 2001
R. Trobec
Abstract The message-passing interface (MPI)-based object-oriented particle,particle interactions (PPI) library is implemented and evaluated. The library can be used in the n -particle simulation algorithm designed for a ring of p interconnected processors. The parallel simulation is scalable with the number of processors, and has the time requirement proportional to n2/p if n/p is large enough, which guarantees optimal speedup. In a certain range of problem sizes, the speedup becomes superlinear because enough cache memory is available in the system. The library is used in a simple way by any potential user, even with no deep programming knowledge. Different simulations using particles can be implemented on a wide spectrum of different computer platforms. The main purpose of this article is to test the PPI library on well-known methods, e.g., the parallel molecular dynamics (MD) simulation of the monoatomic system by the second-order leapfrog Verlet algorithm. The performances of the parallel simulation program implemented with the proposed library are competitive with a custom-designed simulation code. Also, the implementation of the split integration symplectic method, based on the analytical calculation of the harmonic part of the particle interactions, is shown, and its expected performances are predicted. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 84: 23,31, 2001 [source]

SIMDE: An educational simulator of ILP architectures with dynamic and static scheduling

COMPUTER APPLICATIONS IN ENGINEERING EDUCATION, Issue 3 2007
I. Castilla
Abstract This article presents SIMDE, a cycle-by-cycle simulator to support teaching of Instruction-Level Parallelism (ILP) architectures. The simulator covers dynamic and static instruction scheduling by using a shared structure for both approaches. Dynamic scheduling is illustrated by means of a simple superscalar processor based on Tomasulo's algorithm. A basic Very Long Instruction Word (VLIW) processor has been designed for static scheduling. The simulator is intended as an aid-tool for teaching theoretical contents in Computer Architecture and Organization courses. The students are provided with an easy-to-use common environment to perform different simulations and comparisons between superscalar and VLIW processors. Furthermore, the simulator has been tested by students in a Computer Architecture course in order to assess its real usefulness. © 2007 Wiley Periodicals, Inc. Comput Appl Eng Educ 14: 226,239, 2007; Published online in Wiley InterScience (www.interscience.wiley.com); DOI 10.1002/cae.20154 [source]

Estimating haplotype relative risks in complex disease from unphased SNPs data in families using a likelihood adjusted for ascertainment

GENETIC EPIDEMIOLOGY, Issue 8 2006
J. Carayol
Abstract The understanding of complex diseases and insights to improve their medical management may be achieved through the deduction of how specific haplotypes may play a joint effect to change relative risk information. In this paper we describe an ascertainment adjusted likelihood-based method to estimate haplotype relative risks using pooled family data coming from association and/or linkage studies that were used to identify specific haplotypes. Haplotype-based analysis tends to require a large amount of parameters to capture all the information that leads to efficiency problems. An adaptation of the Stochastic Expectation Maximization algorithm is used for haplotypes inference from genotypic data and to reduce the number of nuisance parameters for risk estimation. Using different simulations, we show that this method provides unbiased relative risk estimates even in case of departure from Hardy-Weinberg equilibrium. Genet. Epidemiol. 2006. © 2006 Wiley-Liss, Inc. [source]

Contrasting Lumped and Distributed Hydrology Models for Estimating Climate Change Impacts on California Watersheds,

JOURNAL OF THE AMERICAN WATER RESOURCES ASSOCIATION, Issue 5 2010
Edwin P. Maurer
Maurer, Edwin P., Levi D. Brekke, and Tom Pruitt, 2010. Contrasting Lumped and Distributed Hydrology Models for Estimating Climate Change Impacts on California Watersheds. Journal of the American Water Resources Association (JAWRA) 46(5):1024,1035. DOI: 10.1111/j.1752-1688.2010.00473.x Abstract:, We compare the projected changes to streamflows for three Sierra Nevada rivers using statistically downscaled output from 22 global climate projections. The downscaled meteorological data are used to drive two hydrology models: the Sacramento Soil Moisture Accounting model and the variable infiltration capacity model. These two models differ in their spatial resolution, computational time step, and degree and objective of calibration, thus producing significantly different simulations of current and future streamflow. However, the projected percentage changes in monthly streamflows through mid-21st Century generally did not differ, with the exceptions of streamflow during low flow months, and extreme low flows. These findings suggest that for physically based hydrology models applied to snow-dominated basins in Mediterranean climate regimes like the Sierra Nevada, California, model formulation, resolution, and calibration are secondary factors for estimating projected changes in extreme flows (seasonal or daily). For low flows, hydrology model selection and calibration can be significant factors in assessing impacts of projected climate change. [source]