Posts
Oct, 27
Fast parallel GPU-sorting using a hybrid algorithm
This paper presents an algorithm for fast sorting of large lists using modern GPUs. The method achieves high speed by efficiently utilizing the parallelism of the GPU throughout the whole algorithm. Initially, GPU -based bucketsort or quicksort splits the list into enough sublists then to be sorted in parallel using merge-sort. The algorithm is of […]
Oct, 27
GPU-based spatial interaction force simulation
This paper presents a study of performance in spatial interaction force simulation. Both CPU-based and GPU-based simulations are examined using a realistic scalable data set. Performance is analyzed for various stages of execution and simulation/optimization parameters.
Oct, 27
Techniques for efficient DCT/IDCT implementation on generic GPU
The emergence of programmable graphics processing units (GPU) has led to increasing interest in off-loading numerically intensive computations on to graphics hardware. DCT/IDCT is widely adopted in modern image/video compression standards and is usually one of the most computationally expensive parts. We present several techniques for efficient implementation of DCT/IDCT on generic programmable GPU, using […]
Oct, 27
GPU acceleration of a production molecular docking code
Modeling the interactions of biological molecules, or docking , is critical to both understanding basic life processes and to designing new drugs. Here we describe the GPU-based acceleration of a recently developed, complex, production docking code. We show how the various functions can be mapped to the GPU and present numerous optimizations. We find which […]
Oct, 27
GPU accelerated molecular dynamics simulation of thermal conductivities
Molecular dynamics (MD) simulations have become a powerful tool for elucidating complex physical phenomena. However, MD method is very time-consuming. This paper presents a method to accelerate computation of MD simulation. The acceleration is achieved by take advantage of modern graphics processing units (GPU). As an example, the thermal conductivities of solid argon were calculated […]
Oct, 27
ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale
The high arithmetic performance and intrinsic parallelism of recent graphical processing units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is a production-class biomolecular dynamics (MD) engine supporting CHARMM and AMBER force fields. Designed specifically for GPUs it is able to achieve supercomputing scale performance of 40 ns/day for all-atom protein systems […]
Oct, 27
Monte Carlo simulations on Graphics Processing Units
Implementation of basic local Monte-Carlo algorithms on ATI Graphics Processing Units (GPU) is investigated. The Ising model and pure SU(2) gluodynamics simulations are realized with the Compute Abstraction Layer (CAL) of ATI Stream environment using the Metropolis and the heat-bath algorithms, respectively. We present an analysis of both CAL programming model and the efficiency of […]
Oct, 27
GPU Cluster for High Performance Computing
Inspired by the attractive Flops/dollar ratio and the incredible growth in the speed of modern graphics processing units (GPUs), we propose to use a cluster of GPUs for high performance scientific computing. As an example application, we have developed a parallel flow simulation using the lattice Boltzmann model (LBM) on a GPU cluster and have […]
Oct, 27
GPU Gems 3
The GPU Gems series features a collection of the most essential algorithms required by Next-Generation 3D Engines.” -Martin Mittring, Lead Graphics Programmer, Crytek This third volume of the best-selling GPU Gems series provides a snapshot of today’s latest Graphics Processing Unit (GPU) programming techniques. The programmability of modern GPUs allows developers to not only distinguish […]
Oct, 27
Fast fluid dynamics simulation on the GPU
This chapter describes a method for fast, stable fluid simulation that runs entirely on the GPU. It introduces fluid dynamics and the associated mathematics, and it describes in detail the techniques to perform the simulation on the GPU. After reading this chapter, you should have a basic understanding of fluid dynamics and know how to […]
Oct, 27
Simulating spin models on GPU
Over the last couple of years it has been realized that the vast computational power of graphics processing units (GPUs) could be harvested for purposes other than the video game industry. This power, which at least nominally exceeds that of current CPUs by large factors, results from the relative simplicity of the GPU architectures as […]
Oct, 27
Getting Started with GPU Programming
This tutorial describes a step-by-step procedure for programming a Macintosh Nvidia GPU. General scientific programmers with some C knowledge can get started in parallel processing application development with relative ease.
