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Posts

Nov, 7

GPU-based Acceleration of System-level Design Tasks

Many system-level design tasks (e.g., high-level timing analysis, hardware/software partitioning and design space exploration) involve computational kernels that are intractable (usually NP-hard). As a result, they involve high running times even for mid-sized problems. In this paper we explore the possibility of using commodity graphics processing units (GPUs) to accelerate such tasks that commonly arise […]
Nov, 7

Evolution of thread-level parallelism in desktop applications

As the effective limits of frequency and instruction level parallelism have been reached, the strategy of microprocessor vendors has changed to increase the number of processing cores on a single chip each generation. The implicit expectation is that software developers will write their applications with concurrency in mind to take advantage of this sudden change […]
Nov, 7

GPU-accelerated molecular dynamics simulation for study of liquid crystalline flows

We have developed a GPU-based molecular dynamics simulation for the study of flows of fluids with anisotropic molecules such as liquid crystals. An application of the simulation to the study of macroscopic flow (backflow) generation by molecular reorientation in a nematic liquid crystal under the application of an electric field is presented. The computations of […]
Nov, 7

Data-intensive document clustering on GPU clusters

Document clustering is a central method to mine massive amounts of data. Due to the explosion of raw documents generated on the Internet and the necessity to analyze them efficiently in various intelligent information systems, clustering techniques have reached their limitations on single processors. Instead of single processors, general-purpose multi-core chips are increasingly deployed in […]
Nov, 7

Accelerating epistasis analysis in human genetics with consumer graphics hardware

BACKGROUND:Human geneticists are now capable of measuring more than one million DNA sequence variations from across the human genome. The new challenge is to develop computationally feasible methods capable of analyzing these data for associations with common human disease, particularly in the context of epistasis. Epistasis describes the situation where multiple genes interact in a […]
Nov, 7

Real-time 3D registration using GPU

3D registration is a computer vision technique of aligning multi-view range images with respect to a reference coordinate system. Aligning range images is an important but time-consuming task for complete 3D reconstruction. In this paper, we propose a real-time 3D registration technique by employing the computing power of graphic processing unit (GPU). A point-to-plane 3D […]
Nov, 7

GPU accelerated simulations of bluff body flows using vortex particle methods

We present a GPU accelerated solver for simulations of bluff body flows in 2D using a remeshed vortex particle method and the vorticity formulation of the Brinkman penalization technique to enforce boundary conditions. The efficiency of the method relies on fast and accurate particle-grid interpolations on GPUs for the remeshing of the particles and the […]
Nov, 7

Biomolecular electrostatics simulation with a parallel FMM-based BEM, using up to 512 GPUs

We present teraflop-scale simulations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a boundary element method (BEM) formulation of the continuum electrostatic model, as well as the BIBEE approximation to BEM. The hardware acceleration is achieved through […]
Nov, 7

Efficient nonbonded interactions for molecular dynamics on a graphics processing unit

We describe an algorithm for computing nonbonded interactions with cutoffs on a graphics processing unit. We have incorporated it into OpenMM, a library for performing molecular simulations on high-performance computer architectures. We benchmark it on a variety of systems including boxes of water molecules, proteins in explicit solvent, a lipid bilayer, and proteins with implicit […]
Nov, 6

MDLab: A molecular dynamics simulation prototyping environment

Molecular dynamics (MD) simulation involves solving Newton’s equations of motion for a system of atoms, by calculating forces and updating atomic positions and velocities over a timestep Deltat. Despite the large amount of computing power currently available, the timescale of MD simulations is limited by both the small timestep required for propagation, and the expensive […]
Nov, 6

CUDASW++ 2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions

BACKGROUND:Due to its high sensitivity, the Smith-Waterman algorithm is widely used for biological database searches. Unfortunately, the quadratic time complexity of this algorithm makes it highly time-consuming. The exponential growth of biological databases further deteriorates the situation. To accelerate this algorithm, many efforts have been made to develop techniques in high performance architectures, especially the […]
Nov, 6

Parallel GPU-based data-dependent triangulations

In this paper we introduce a new technique for data-dependent triangulation which is suitable for implementation on a GPU. Our solution is based on a new parallel version of the well known Lawson’s optimization process and is fully compatible with restrictions of the GPU hardware. We test and compare the quality of our solution in […]
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