high performance computing on graphics processing units: hgpu.org

In this paper we explore the possibility of using commodity graphics processing units (GPUs) to speedup standard schedulability analysis algorithms. Our long-term goal is to exploit GPUs to accelerate common electronic design automation algorithms, most of which tend to be computationally expensive. Our main contribution in this paper is a reformulation of a standard demand […]

The method of molecular dynamics (MD) is widely used to study static and dynamic properties of the condensed matter [1]. In particular an approach to study the relaxation of metastable states is developed [2]. These states play essential role in the impulse loading processes such as shock compression, laser ablation, etc. Herewith we report on […]

Graphics Processing Units (GPUs) were originally designed to manipulate images, but due to their intrinsic parallel nature, they turned into a powerful tool for scientific applications. In this article, we evaluated GPU performance in an implementation of a traditional stochastic simulation – the correlated Brownian motion. This movement can be described by the Generalized Langevin […]

We report on simulation technique and benchmarks for molecular dynamics simulations of the relaxation processes in solids and liquids using the graphics processing units (GPUs). The implementation of a many-body potential such as the embedded atom method (EAM) on GPU is discussed. The benchmarks obtained by LAMMPS and HOOMD packages for simple Lennard-Jones liquids and […]

We present a scalable spatial decomposition coloring approach to implement molecular dynamics simulations with embedded atom method (EAM) on multi-core architectures. It effectively solves parallelization of reduction operations on irregular arrays in molecular dynamics simulations. In OpenMP program model, our methodology avoids that the same memory location is simultaneously modified by more than one thread […]

We report a GPU implementation in HOOMD Blue of long-range electrostatic interactions based on the orientation-averaged Ewald sum scheme, introduced by Yakub and Ronchi (J. Chem. Phys. 2003, 119, 11556). The performance of the method is compared to an optimized CPU version of the traditional Ewald sum available in LAMMPS, in the molecular dynamics of […]

We present a new method for decomposing the one convolution required by standard Particle-Particle Particle-Mesh (P3M) electrostatic methods into a series of convolutions over slab-shaped subregions of the original simulation cell. Most of the convolutions derive data from separate regions of the cell and can thus be computed independently via FFTs, in some cases with […]

The scaling of serial algorithms cannot rely on the improvement of CPUs anymore. The performance of classical Support Vector Machine (SVM) implementations has reached its limit and the arrival of the multi core era requires these algorithms to adapt to a new parallel scenario. Graphics Processing Units (GPU) have arisen as high performance platforms to […]

Electrostatic potentials (ESPs) are frequently used in structural biology for the characterization of biomolecules. Here we study the potential employment of hardware accelerators like the graphics processing unit or the application-specific integrated circuit MD-GRAPE-3 for the purpose of efficient computation of ESPs. An algorithm closely coupled to the general description of molecular surfaces is ported […]

Recent advances in graphics processing units (GPUs) technology open a new era in high performance computing. Applications of GPUs to scientific computations are attracting a lot of attention due to their low cost in conjunction with their inherently remarkable performance features and the recently enhanced computational precision and improved programming tools. Domain decomposition methods (DDM) […]

This paper proposes novel methods for visualizing specifically the large power-law graphs that arise in sociology and the sciences. In such cases a large portion of edges can be shown to be less important and removed while preserving component connectedness and other features (e.g. cliques) to more clearly reveal the networkpsilas underlying connection pathways. This […]

A novel technique that uses the Moving Least Squares (MLS) method to interpolate sparse constraints over mesh surfaces is introduced in this paper. Given a set of constraints, the proposed technique constructs, directly on the surface, a smooth scalar field that interpolates or approximates the constraints. Three types of constraints: point-value, point-gradient and iso-contour, are […]