Nov, 1

High-throughput sequence alignment using Graphics Processing Units

BACKGROUND:The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated for several purposes, including genotyping, genome resequencing, metagenomics, and de novo genome assembly projects. Sequence alignment programs such as MUMmer have proven essential for […]
Oct, 30

Bio-sequence database scanning on a GPU

Protein sequences with unknown functionality are often compared to a set of known sequences to detect functional similarities. Efficient dynamic programming algorithms exist for this problem, however current solutions still require significant scan times. These scan time requirements are likely to become even more severe due to the rapid growth in the size of these […]
Oct, 30

Graphics Processing Units and High-Dimensional Optimization

This paper discusses the potential of graphics processing units (GPUs) in high-dimensional optimization problems. A single GPU card with hundreds of arithmetic cores can be inserted in a personal computer and dramatically accelerates many statistical algorithms. To exploit these devices fully, optimization algorithms should reduce to multiple parallel tasks, each accessing a limited amount of […]
Oct, 30

How GPUs Work

GPUs have moved away from the traditional fixed-function 3D graphics pipeline toward a flexible general-purpose computational engine. Today, GPUs can implement many parallel algorithms directly using graphics hardware. Well-suited algorithms that leverage all the underlying computational horsepower often achieve tremendous speedups. Truly, the GPU is the first widely deployed commodity desktop parallel computer
Oct, 30

GPUs: A Closer Look

A gamer wanders through a virtual world rendered in near- cinematic detail. Seconds later, the screen fills with a 3D explosion, the result of unseen enemies hiding in physically accurate shadows. Disappointed, the user exits the game and returns to a computer desktop that exhibits the stylish 3D look-and-feel of a modern window manager. Both […]
Oct, 30

Mapping computational concepts to GPUs

Recently, graphics processors have emerged as a powerful computational platform. A variety of encouraging results, mostly from researchers using GPUs to accelerate scientific computing and visualization applications, have shown that significant speedups can be achieved by applying GPUs to data-parallel computational problems. However, attaining these speedups requires knowledge of GPU programming and architecture.The preceding chapters […]
Oct, 30

Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation

Modern videogames place increasing demands on the computational and graphical hardware, leading to novel architectures that have great potential in the context of high performance computing and molecular simulation. We demonstrate that Graphical Processing Units (GPUs) can be used very efficiently to calculate two-electron repulsion integrals over Gaussian basis functionsthe first step in most quantum […]
Oct, 30

A Memory Model for Scientific Algorithms on Graphics Processors

We present a memory model to analyze and improve the performance of scientific algorithms on graphics processing units (GPUs). Our memory model is based on texturing hardware, which uses a 2D block-based array representation to perform the underlying computations. We incorporate many characteristics of GPU architectures including smaller cache sizes, 2D block representations, and use […]
Oct, 30

Accelerating Density Functional Calculations with Graphics Processing Unit

An algorithm is presented for graphics processing units (GPUs), which execute single-precision arithmetic much faster than commodity microprocessors (CPUs), to calculate the exchange-correlation term in ab initio density functional calculations. The algorithm was implemented and applied to two molecules, taxol and valinomycin. The errors in the total energies were about 10−5 a.u., which is accurate […]
Oct, 30

A hardware redundancy and recovery mechanism for reliable scientific computation on graphics processors

General purpose computation on graphics processors (GPGPU) has rapidly evolved since the introduction of commodity programmable graphics hardware. With the appearance of GPGPU computation-oriented APIs such as AMD’s Close to the Metal (CTM) and NVIDIA’s Compute Unified Device Architecture (CUDA), we begin to see GPU vendors putting financial stakes into this non-graphics, one-time niche market. […]
Oct, 30

Performance enhancement of MAGIC FDTD-PIC plasma-wave simulations using GPU processing

Summary form only given. Present day computers equipped with powerful graphics processing units (GPUs) show considerable promise of increased performance for the electromagnetic (EM) modeler. In order to determine the degree of performance gain achievable for electro-energetic physics computations, the MAGIC EM finite difference-time domain (FDTD) particle-in-cell (PIC) plasma code is undergoing testing for parallel […]
Oct, 30

Optimizing data intensive GPGPU computations for DNA sequence alignment

MUMmerGPU uses highly-parallel commodity graphics processing units (GPU) to accelerate the data-intensive computation of aligning next generation DNA sequence data to a reference sequence for use in diverse applications such as disease genotyping and personal genomics. MUMmerGPU 2.0 features a new stackless depth-first-search print kernel and is 13× faster than the serial CPU version of […]
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