high performance computing on graphics processing units: hgpu.org

Applications

hgpu.org » Applications » Chemistry

Fat versus Thin Threading Approach on GPUs: Application to Stochastic Simulation of Chemical Reactions

Guido Klingbeil, Radek Erban, Mike Giles, Philip K. Maini

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Tags: Algorithms, Chemistry, CUDA, nVidia, nVidia GeForce GTX 260, Stochastic simulation

January 7, 2012 by hgpu

Parallel computing system for the efficient calculation of molecular similarity based on negative electrostatic potential

Raul Ernesto Torres Carvajal

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Tags: Algorithms, Chemistry, Cluster analysis, CUDA, Electrostatic potential, Electrostatics, nVidia, nVidia GeForce GT 240, Pattern recognition, Thesis

December 29, 2011 by hgpu

GPU-accelerated Chemical Similarity Assessment for Large Scale Databases

Marco Maggioni, Marco Domenico Santambrogio, Jie Liang

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Tags: Algorithms, Chemistry, CUDA, Databases, nVidia, nVidia GeForce 9400 M, nVidia GeForce GTX 460, Optimization

December 27, 2011 by hgpu

Parallel Contour-Buildup Algorithm for the Molecular Surface

Michael Krone, Sebastian Grottel, Thomas Ertl

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Tags: Algorithms, Chemistry, CUDA, Molecular dynamics, Molecular surface, nVidia, nVidia GeForce GTX 580, Optimization, Pharmaceuticals, Visualization

December 20, 2011 by hgpu

GPU Accelerated Dissipative Particle Dynamics with Parallel Cell-list Updating

Hao Wu, Junbo Xu, Shengfei Zhang, Hao Wen

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Tags: Algorithms, Benchmarking, Chemistry, CUDA, Fluid dynamics, nVidia, nVidia GeForce GTX 285, Optimization

November 30, 2011 by hgpu

Acceleration of computational quantum chemistry by heterogeneous computer architectures

Yuki Furukawa, Ryota Koga, Koji Yasuda

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Tags: Algorithms, Chemistry, Computational chemistry, CUDA, Heterogeneous systems, Molecular modeling, nVidia, nVidia GeForce GTX 580

November 30, 2011 by hgpu

Molecular Dynamics Simulation Based on Hadoop MapReduce

Chen He

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Tags: Chemistry, Cluster computing, CUDA, MapReduce, Molecular dynamics, nVidia, nVidia GeForce 9400 GT, Physics, Thesis

November 28, 2011 by hgpu

Many-body quantum chemistry on graphics processing units

A. Eugene DePrince III, Jeff R. Hammond, Stephen K. Gray

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Tags: Algorithms, Chemistry, Computational chemistry, CUDA, Heterogeneous systems, Matrix multiplication, Molecular modeling, nVidia, Tesla C2050

November 11, 2011 by hgpu

Development of a Flow Solver with Complex Kinetics on the Graphic Processing Units

Hai P. Le, Jean-Luc Cambier

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Tags: Chemistry, Computational Physics, CUDA, Finite volume method, Fluid dynamics, nVidia, Tesla C2050, Tesla C2070

October 25, 2011 by hgpu

Characterization of FPGA-based High Performance Computers

Karl Savio Pimenta Pereira

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Tags: Algorithms, Benchmarking, Chemistry, Computer science, CUDA, DSP, FFT, FPGA, Molecular dynamics, nVidia, nVidia GeForce GTX 280, OpenCL, Tesla C2050, Thesis

October 18, 2011 by hgpu

The Anatomy of High-Performance 2D Similarity Calculations

Imran S. Haque, Vijay S. Pande, W. Patrick Walters

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Source codes

Tags: Algorithms, Biochemistry, Chemistry, Clustering, CUDA, nVidia, nVidia GeForce GTX 260, nVidia GeForce GTX 480, Package

October 16, 2011 by hgpu

Fast analysis of molecular dynamics trajectories with graphics processing units-Radial distribution function histogramming

Benjamin G. Levine, John E. Stone, Axel Kohlmeyer

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Tags: Algorithms, Chemistry, CUDA, GPU cluster, Heterogeneous systems, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Visualization

September 21, 2011 by hgpu

CLUEstering: a high-performance density-based clustering library for scientific computing

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high performance computing on graphics processing units: hgpu.org

Applications

Fat versus Thin Threading Approach on GPUs: Application to Stochastic Simulation of Chemical Reactions

Parallel computing system for the efficient calculation of molecular similarity based on negative electrostatic potential

GPU-accelerated Chemical Similarity Assessment for Large Scale Databases

Parallel Contour-Buildup Algorithm for the Molecular Surface

GPU Accelerated Dissipative Particle Dynamics with Parallel Cell-list Updating

Acceleration of computational quantum chemistry by heterogeneous computer architectures

Molecular Dynamics Simulation Based on Hadoop MapReduce

Many-body quantum chemistry on graphics processing units

Development of a Flow Solver with Complex Kinetics on the Graphic Processing Units

Characterization of FPGA-based High Performance Computers

The Anatomy of High-Performance 2D Similarity Calculations

Fast analysis of molecular dynamics trajectories with graphics processing units-Radial distribution function histogramming

Recent source codes

CLUEstering: a high-performance density-based clustering library for scientific computing

PyOMP: OpenMP for Python in Numba

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Gaia AVU-GSR

Kokkidio: Kokkos+Eigen - write fast, readable multi-platform code

LLaMA-Inference-Bench

MATAR

Over-synchronization in GPU Programs

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