high performance computing on graphics processing units: hgpu.org

hgpu.org » Molecular dynamics

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

Data analysis and 3D evolution in High Energy Physics using graphic processor

Alexandru Jipa, Ciprian-Mihai Mitu, Mihai Niculescu, Sorin-Ion Zgura

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Tags: CUDA, Molecular dynamics, Nuclear physics, nVidia, nVidia GeForce 9600 GT, Physics, Visualization

December 11, 2011 by hgpu

Directives Based Programming of GPU Accelerated Systems

Saif Mulla

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Tags: Computer science, CUDA, Molecular dynamics, nVidia, Programming techniques, Tesla C2050, Thesis

November 29, 2011 by hgpu

Solving Dense Generalized Eigenproblems on Multi-threaded Architectures

Jose I. Aliaga, Paolo Bientinesi, Davor Davidovic, Edoardo Di Napoli, Francisco D. Igual, Enrique S. Quintana-Orti

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Tags: Computer science, CUDA, Linear Algebra, Mathematical Software, Molecular dynamics, nVidia, Performance, Tesla C2050

November 29, 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

Simulations of Large Particle Systems in Real Time

Witold Alda, Krzysztof Boryczko

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Tags: Algorithms, Computer science, CUDA, Molecular dynamics, nVidia, OpenCL, Particle simulation, Visualization

November 16, 2011 by hgpu

Exploring Fine-Grained Task-based Execution on Multi-GPU Systems

Long Chen, Oreste Villa, Guang R. Gao

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Tags: Computer science, CUDA, GPU cluster, Molecular dynamics, nVidia, Tesla C1060

November 1, 2011 by hgpu

Accelerated MD Program Using CUDA Technology

Hoang Van Hue, Nguyen Thi Thanh Ha, Pham Khac Hung

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Tags: CUDA, Materials Science, Molecular dynamics, nVidia, nVidia GeForce GTS 250, Physics

October 26, 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

Numerical Accuracy Analysis Based on the Discrete Stochastic Arithmetic on Multiprocessor Platforms

Christian Motzing

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Tags: Computer science, CUDA, Molecular dynamics, Numerical Analysis, nVidia, nVidia GeForce GTX 480, Review, Software Engineering, Thesis

October 17, 2011 by hgpu

Molecular dynamics simulation of UO2 nanocrystals melting

A.S. Boyarchenkov, S.I. Potashnikov, K.A. Nekrasov, A.Ya. Kupryazhkin

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Tags: CUDA, Molecular dynamics, Physics

October 9, 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

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

Profile Util library: A quick and easy way to get MPI, OpenMP and GPU runtime information

MaC: Mamba CPU performance predictor

MambaCPU: Enhanced Correlation Mining with State Space Models for CPU Performance Prediction

Mixed-precision finite element kernels

Mixed-precision finite element kernels and assembly: Rounding error analysis and hardware acceleration

SHMT: The Simultaneous and Heterogenous Multithreading project

General-Purpose Computing on Tensor Processors

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

Online Energy Optimization in GPUs: A Multi-Armed Bandit Approach

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high performance computing on graphics processing units: hgpu.org

Parallel Contour-Buildup Algorithm for the Molecular Surface

Data analysis and 3D evolution in High Energy Physics using graphic processor

Directives Based Programming of GPU Accelerated Systems

Solving Dense Generalized Eigenproblems on Multi-threaded Architectures

Molecular Dynamics Simulation Based on Hadoop MapReduce

Simulations of Large Particle Systems in Real Time

Exploring Fine-Grained Task-based Execution on Multi-GPU Systems

Accelerated MD Program Using CUDA Technology

Characterization of FPGA-based High Performance Computers

Numerical Accuracy Analysis Based on the Discrete Stochastic Arithmetic on Multiprocessor Platforms

Molecular dynamics simulation of UO2 nanocrystals melting

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

Recent source codes

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

LLaMA-Inference-Bench

MATAR

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

MaC: Mamba CPU performance predictor

Mixed-precision finite element kernels

SHMT: The Simultaneous and Heterogenous Multithreading project

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

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