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Parallel Architectures (parallel + architecture)
Selected AbstractsReal-time primer design for DNA chipsCONCURRENCY AND COMPUTATION: PRACTICE & EXPERIENCE, Issue 9 2004H. Simmler Abstract The design of PCR or DNA chip experiments is a time-consuming process where bioinformatics is extensively used. The selection of the primers, which are immobilized on the DNA chip, requires a complex algorithm. Based on several parameters an optimized set of primers is automatically determined for a given gene sequence. This paper describes a parallel architecture which performs the optimization of the primer selection on a hardware accelerator. In contrast to the pure software approach, the parallel architecture gains a speedup of factor 500 using a PCI-based hardware accelerator. This approach allows an optimization of a specified primer set in real time. Copyright © 2004 John Wiley & Sons, Ltd. [source] Simulation of two-dimensional turbulent flows in a rotating annulusINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, Issue 3 2004Brian D. Storey Abstract Rotating water tank experiments have been used to study fundamental processes of atmospheric and geophysical turbulence in a controlled laboratory setting. When these tanks are undergoing strong rotation the forced turbulent flow becomes highly two dimensional along the axis of rotation. An efficient numerical method has been developed for simulating the forced quasi-geostrophic equations in an annular geometry to model current laboratory experiments. The algorithm employs a spectral method with Fourier series and Chebyshev polynomials as basis functions. The algorithm has been implemented on a parallel architecture to allow modelling of a wide range of spatial scales over long integration times. This paper describes the derivation of the model equations, numerical method, testing and performance of the algorithm. Results provide reasonable agreement with the experimental data, indicating that such computations can be used as a predictive tool to design future experiments. Copyright © 2004 John Wiley & Sons, Ltd. [source] Exploring the performance of massively multithreaded architecturesCONCURRENCY AND COMPUTATION: PRACTICE & EXPERIENCE, Issue 5 2010Shahid Bokhari Abstract We present a new scheme for evaluating the performance of multithreaded computers and demonstrate its application to the Cray MTA-2 and XMT supercomputers. Our scheme is based on the concept of clock cycles per element, , plotted against both problem size and the number of processors. This scheme clearly shows if an implementation has achieved its asymptotic efficiency and is more general than (but includes) the commonly used speedup metric. It permits the discovery of any imperfections in both the software as well as the hardware, and is expected to permit a unified comparison of many different parallel architectures. Measurements on a number of well-known parallel algorithms, ranging from matrix multiply to quicksort, are presented for the MTA-2 and XMT and highlight some interesting differences between these machines. The performance of sequence alignment using dynamic programming is evaluated on the MTA-2, XMT, IBM x3755 and SGI Altix 350 and provides a useful comparison of the capabilities of the Cray machines with more conventional shared memory architectures. Copyright © 2009 John Wiley & Sons, Ltd. [source] Object comparison using PDE-based wave metric on cellular neural networksINTERNATIONAL JOURNAL OF CIRCUIT THEORY AND APPLICATIONS, Issue 4 2006István Szatmári Abstract The paper investigates PDE-based dynamic phenomena for comparing objects and introduces a spatio-temporal non-linear wave metric. This metric is capable of comparing both binary and grey-scale object pairs in a parallel way. Spatio-temporal waves are initialized and controlled to explore the quantitative properties of objects. In addition to spatial data, even ,hidden', time-related information is also extracted and used for evaluating differences and similarities. The detailed analysis of the proposed metric shows that this wave-based approach can outperform well-known metrics such as Hausdorff and Hamming metrics in selectivity and sensitivity. The approach in question can be efficiently implemented on massively parallel architectures, e.g. on Cellular Neural/Non-linear Networks (CNN), providing solutions either for real time applications. Copyright © 2006 John Wiley & Sons, Ltd. [source] CHARMM: The biomolecular simulation programJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2009B. R. Brooks Abstract CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983. © 2009 Wiley Periodicals, Inc.J Comput Chem, 2009. [source] Retrieval of spectral and dynamic properties from two-dimensional infrared pump-probe experimentsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2008Riccardo Chelli Abstract We have developed a fitting algorithm able to extract spectral and dynamic properties of a three level oscillator from a two-dimensional infrared spectrum (2D-IR) detected in time resolved nonlinear experiments. Such properties go from the frequencies of the ground-to-first and first-to-second vibrational transitions (and hence anharmonicity) to the frequency-fluctuation correlation function. This last is represented through a general expression that allows one to approach the various strategies of modeling proposed in the literature. The model is based on the Kubo picture of stochastic fluctuations of the transition frequency as a result of perturbations by a fluctuating surrounding. To account for the line-shape broadening due to pump pulse spectral width in double-resonance measurements, we supply the fitting algorithm with the option to perform the convolution of the spectral signal with a Lorentzian function in the pump-frequency dimension. The algorithm is tested here on 2D-IR pump-probe spectra of a Gly-Ala dipeptide recorded at various pump-probe delay times. Speedup benchmarks have been performed on a small Beowulf cluster. The program is written in FORTRAN language for both serial and parallel architectures and is available free of charge to the interested reader. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] | ||||||||||