Related papers: Implementation of parallel algorithms for 2D vorte…
The parallel simulation of Spiking Neural P systems is mainly based on a matrix representation, where the graph inherent to the neural model is encoded in an adjacency matrix. The simulation algorithm is based on a matrix-vector…
This paper reports large-scale direct numerical simulations of homogeneous-isotropic fluid turbulence, achieving sustained performance of 1.08 petaflop/s on gpu hardware using single precision. The simulations use a vortex particle method…
Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of simulated models and morphologies have exceeded the capacity of any…
The effectiveness of a new algorithm, parallel tempering, is studied for numerical simulations of biological molecules. These molecules suffer from a rough energy landscape. The resulting slowing down in numerical simulations is overcome by…
Furthering our understanding of many of today's interesting problems in plasma physics---including plasma based acceleration and magnetic reconnection with pair production due to quantum electrodynamic effects---requires large-scale kinetic…
Optimal multiple sequence alignment by dynamic programming, like many highly dimensional scientific computing problems, has failed to benefit from the improvements in computing performance brought about by multi-processor systems, due to…
The implicit 2D3V particle-in-cell (PIC) code developed to study the interaction of ultrashort pulse lasers with matter [G. M. Petrov and J. Davis, Computer Phys. Comm. 179, 868 (2008); Phys. Plasmas 18, 073102 (2011)] has been parallelized…
In this thesis, we focus on some of the NP-hard problems in control theory. Thanks to the converse Lyapunov theory, these problems can often be modeled as optimization over polynomials. To avoid the problem of intractability, we establish a…
For the last thirty years, several Dynamic Memory Managers (DMMs) have been proposed. Such DMMs include first fit, best fit, segregated fit and buddy systems. Since the performance, memory usage and energy consumption of each DMM differs,…
Data-intensive, graph-based computations are pervasive in several scientific applications, and are known to to be quite challenging to implement on distributed memory systems. In this work, we explore the design space of parallel algorithms…
Sequential computation is well understood but does not scale well with current technology. Within the next decade, systems will contain large numbers of processors with potentially thousands of processors per chip. Despite this, many…
Distributed Computation has been a recent trend in engineering research. Parallel Computation is widely used in different areas of Data Mining, Image Processing, Simulating Models, Aerodynamics and so forth. One of the major usage of…
We describe, study, and experiment with an algorithm for finding all solutions of systems of polynomial equations using homotopy continuation and monodromy. This algorithm follows a framework developed in previous work and can operate in…
In this paper we consider the problem of identifying intersections between two sets of d-dimensional axis-parallel rectangles. This is a common problem that arises in many agent-based simulation studies, and is of central importance in the…
Metastability is a common obstacle to performing long molecular dynamics simulations. Many numerical methods have been proposed to overcome it. One method is parallel replica dynamics, which relies on the rapid convergence of the underlying…
We give an overview of the theoretical results for matrix block-recursive algorithms in commutative domains and present the results of experiments that we conducted with new parallel programs based on these algorithms on a supercomputer…
We develop a parallel rejection algorithm to tackle the problem of low acceptance in Monte Carlo methods, and apply it to the simulation of the hopping conduction in Coulomb glasses using Graphics Processing Units, for which we also…
This paper discusses opportunities to parallelize graph based path planning algorithms in a time varying environment. Parallel architectures have become commonplace, requiring algorithm to be parallelized for efficient execution. An…
This article presents the parallel implementation of the coupled harmonic oscillator. From the analytical solution of the coupled harmonic oscillator, the design parameters are obtained. After that, a numerical integration of the system…
The problem of identifying intersections between two sets of d-dimensional axis-parallel rectangles appears frequently in the context of agent-based simulation studies. For this reason, the High Level Architecture (HLA) specification -- a…