Related papers: A hybrid algorithm for parallel molecular dynamics…
Numerous algorithms and parallelisations have been developed for short-range particle simulations; however, none are optimally performant for all scenarios. Such a concept led to the prior development of the particle simulation library…
For computational fluid dynamics (CFD) applications with a large number of grid points/cells, parallel computing is a common efficient strategy to reduce the computational time. How to achieve the best performance in the modern…
Although event-driven algorithms have been shown to be far more efficient than time-driven methods such as conventional molecular dynamics, they have not become as popular. The main obstacle seems to be the difficulty of parallelizing…
We examine the Xeon Phi, which is based on Intel's Many Integrated Cores architecture, for its suitability to run the FDK algorithm--the most commonly used algorithm to perform the 3D image reconstruction in cone-beam computed tomography.…
Writing efficient hybrid parallel code is tedious, error-prone, and requires good knowledge of both parallel programming and multithreading such as MPI and OpenMP, resp. Therefore, we present a framework which is based on a job model that…
This paper presents implementation details and empirical results for a hybrid message passing and shared memory paralleliziation of the adaptive integral method (AIM). AIM is implemented on a (near) petaflop supercomputing cluster of…
In this paper I describe some results on the use of virtual processors technology for parallelize some SPMD computational programs. The tested technology is the INTEL Hyper Threading on real processors, and the programs are MATLAB scripts…
Due to decelerating gains in single-core CPU performance, computationally expensive simulations are increasingly executed on highly parallel hardware platforms. Agent-based simulations, where simulated entities act with a certain degree of…
Molecular dynamics models materials by simulating each individual particle's trajectory. Many-body potentials lead to a more accurate trajectory simulation, and are used in materials science and computational chemistry. We present…
Many robot planning tasks require satisfaction of one or more constraints throughout the entire trajectory. For geometric constraints, manifold-constrained motion planning algorithms are capable of planning collision-free path between start…
Computation of a signal's estimated covariance matrix is an important building block in signal processing, e.g., for spectral estimation. Each matrix element is a sum of products of elements in the input matrix taken over a sliding window.…
Serial and parallel algorithms for simulation of tandem queueing systems with infinite buffers are presented, and their performance is examined. It is shown that the algorithms which are based on a simple computational procedure involve low…
This paper proposes a parallel numerical algorithm to simulate the flow and the transport in a discrete fracture network taking into account the mass exchanges with the surrounding matrix. The discretization of the Darcy fluxes is based on…
Many applications in Bayesian statistics are extremely computationally intensive. However, they are often inherently parallel, making them prime targets for modern massively parallel processors. Multi-core and distributed computing is…
Numerical studies of shock waves in large scale systems via kinetic simulations with millions of particles are too computationally demanding to be processed in serial. In this work we focus on optimizing the parallel performance of a…
In this paper we solve on GPUs massive problems with large amount of data, which are not appropriate for solution with the SIMD technology. For the given problem we consider a three-level parallelization. The multithreading of CPU is used…
In this tutorial paper, we will firstly review some basic simulation concepts and then introduce the parallel and distributed simulation techniques in view of some new challenges of today and tomorrow. More in particular, in the last years…
Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this…
In this work, we have developed a multiscale computational algorithm to couple finite element method with an open source molecular dynamics code --- the Large scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) --- to perform…
To prepare images for better segmentation, we need preprocessing applications, such as smoothing, to reduce noise. In this paper, we present an enhanced computation method for smoothing 2D object in binary case. Unlike existing approaches,…