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Posts

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 […]
Nov, 6

Automatic fitting of spiking neuron models to electrophysiological recordings

Spiking models can accurately predict the spike trains produced by cortical neurons in response to somatically injected currents. Since the specific characteristics of the model depend on the neuron, a computational method is required to fit models to electrophysiological recordings. The fitting procedure can be very time consuming both in terms of computer simulations and […]
Nov, 6

Optimization of linked list prefix computations on multithreaded GPUs using CUDA

We present a number of optimization techniques to compute prefix sums on linked lists and implement them on multithreaded GPUs using CUDA. Prefix computations on linked structures involve in general highly irregular fine grain memory accesses that are typical of many computations on linked lists, trees, and graphs. While the current generation of GPUs provides […]
Nov, 6

High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing

PMID: 20199097 Although molecular dynamics simulation methods are useful in the modeling of macromolecular systems, they remain computationally expensive, with production work requiring costly high-performance computing (HPC) resources. We review recent innovations in accelerating molecular dynamics on graphics processing units (GPUs), and we describe GPUGRID, a volunteer computing project that uses the GPU resources of […]
Nov, 6

A GPU implementation for LBG and SOM training

Vector quantization (VQ) is an effective technique applicable in a wide range of areas, such as image compression and pattern recognition. The most time-consuming procedure of VQ is codebook training, and two of the frequently used training algorithms are LBG and self-organizing map (SOM). Nowadays, desktop computers are usually equipped with programmable graphics processing units […]
Nov, 6

A matrix approach to tomographic reconstruction and its implementation on GPUs

Electron tomography allows elucidation of the molecular architecture of complex biological specimens. Weighted backprojection (WBP) is the standard reconstruction method in the field. In this work, three-dimensional reconstruction with WBP is addressed from a matrix perspective by formulating the problem as a set of sparse matrix-vector products, with the matrix being constant and shared by […]
Nov, 6

Exploring the multiple-GPU design space

Graphics Processing Units (GPUs) have been growing in popularity due to their impressive processing capabilities, and with general purpose programming languages such as NVIDIA’s CUDA interface, are becoming the platform of choice in the scientific computing community. Previous studies that used GPUs focused on obtaining significant performance gains from execution on a single GPU. These […]
Nov, 6

GPU Computing for Atmospheric Modeling

Much success has been achieved using GPUs to accelerate existing applications that are highly data parallel, or that are dominated by small, intense computational kernels. What are the prospects for porting existing large scientific models that do not fit this mold? We take an expensive routine from the CAM atmosphere model, and port it to […]
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