Related papers: A flexible algorithm for calculating pair interact…
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…
The simulation of large ensembles of particles is usually parallelized by partitioning the domain spatially and using message passing to communicate between the processes handling neighboring subdomains. The particles are represented as…
The problem of counting collisions or interactions is common in areas as computer graphics and scientific simulations. Since it is a major bottleneck in applications of these areas, a lot of research has been carried out on such subject,…
Calculating the correlation in a sliding window is a common method of statistical evaluation of the interconnect between two sets of data. And although the calculation of a single correlation coefficient is not resource-intensive and…
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…
The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its…
In this paper, we propose a new algorithm based on radial symmetry center method to track colloidal particles close to contact, where the optical images of the particles start to overlap in digital video microscopy. This overlapping effect…
We present an algorithm for cluster dynamics to efficiently simulate large systems on MIMD parallel computers with large numbers of processors. The method divides physical space into rectangular cells which are assigned to processors and…
Particle-In-Cell (PIC) codes are broadly applied to the kinetic simulation of plasmas, from laser-matter interaction to astrophysics. Their heavy simulation cost can be mitigated by using the Single Instruction Multiple Data (SIMD)…
In this work, we design, analyze, and optimize sequential and shared-memory parallel algorithms for partitioned local depths (PaLD). Given a set of data points and pairwise distances, PaLD is a method for identifying strength of pairwise…
In current computer architectures, data movement (from die to network) is by far the most energy consuming part of an algorithm (10pJ/word on-die to 10,000pJ/word on the network). To increase memory locality at the hardware level and reduce…
This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…
The Simplex tableau has been broadly used and investigated in the industry and academia. With the advent of the big data era, ever larger problems are posed to be solved in ever larger machines whose architecture type did not exist in the…
Particle-in-cell merging algorithms aim to resample dynamically the six-dimensional phase space occupied by particles without distorting substantially the physical description of the system. Whereas various approaches have been proposed in…
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…
The Particle-In-Cell (PIC) method for plasma simulation tracks particle phase space information using particle and grid data structures. High computational costs in 2D and 3D device-scale PIC simulations necessitate parallelization, with…
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…
Particle tracking in large-scale numerical simulations of turbulent flows presents one of the major bottlenecks in parallel performance and scaling efficiency. Here, we describe a particle tracking algorithm for large-scale parallel…
This paper presents novel approaches to parallelizing particle interactions on a GPU when there are few particles per cell and the interactions are limited by a cutoff distance. The paper surveys classical algorithms and then introduces two…
Computational intensity and sequential nature of estimation techniques for Bayesian methods in statistics and machine learning, combined with their increasing applications for big data analytics, necessitate both the identification of…