high performance computing on graphics processing units: hgpu.org

hgpu.org » Molecular modeling

Architecture-Aware Mapping and Optimization on Heterogeneous Computing Systems

Mayank Daga

View

Tags: ATI, ATI Radeon HD 5870, Computer science, CUDA, Heterogeneous systems, Molecular modeling, nVidia, nVidia GeForce GTX 280, OpenCL, Optimization, Tesla C2050, Thesis

September 30, 2011 by hgpu

Energy-aware metrics for benchmarking heterogeneous systems

Simon McIntosh-Smith, Terry Wilson, Jon Crisp, Amaurys Avila Ibarra, Richard B. Sessions

View

Download (PDF)

Tags: Benchmarking, Computer science, Energy-efficient computing, Heterogeneous systems, Molecular modeling, nVidia, nVidia GeForce GTX 280, OpenCL, Tesla C2050

August 18, 2011 by hgpu

FPGA acceleration of rigid-molecule docking codes

Bharat Sukhwani, Martin C. Herbordt

View

Download (PDF)

Tags: Biology, Biomolecules, CUDA, FPGA, Molecular modeling, nVidia, Performance, Tesla C1060

August 15, 2011 by hgpu

Ambient Occlusion and Edge Cueing for Enhancing Real Time Molecular Visualization

Marco Tarini, Paolo Cignoni, Claudio Montani

View

Download (PDF)

Source codes

Tags: ATI, ATI Radeon X1600, Computer science, Molecular modeling, Package, Real-time graphics, Rendering, Visualization

August 7, 2011 by hgpu

GPU-accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks, and hyperboloids

Matthieu Chavent, Antoine Vanel, Alex Tek, Bruno Levy, Sophie Robert, Bruno Raffin, Marc Baaden

Tags: Algorithms, Chemistry, Macromolecule, Molecular modeling, Visualization

July 23, 2011 by hgpu

Molecular Dynamics Simulations Using Graphics Processing Units

John A. Baker, Jonathan D. Hirst

Tags: Biomolecules, Chemistry, Molecular dynamics, Molecular modeling

July 22, 2011 by hgpu

Acceleration of the GAMESS-UK electronic structure package on graphical processing units

Karl A. Wilkinson, Paul Sherwood, Martyn F. Guest, Kevin J. Naidoo

Tags: Chemistry, Fortran, Molecular dynamics, Molecular modeling, nVidia

May 21, 2011 by hgpu

GPU-based triangulation of the van der Waals surface

S. Dias, A. Gomes

Tags: Biology, Chemistry, Molecular modeling, Molecular surface

May 14, 2011 by hgpu

Towards accelerating molecular modeling via multi-scale approximation on a GPU

M. Daga, Wu-chun Feng, T. Scogland

Tags: Algorithms, Biomolecules, Electrostatic potential, Medicine, Molecular modeling

May 5, 2011 by hgpu

GPU-Based Implementations of the Noniterative Regularized-CCSD(T) Corrections: Applications to Strongly Correlated Systems

Wenjing Ma, Sriram Krishnamoorthy, Oreste Villa, Karol Kowalski

Tags: Chemistry, Molecular modeling

April 15, 2011 by hgpu

Poster: GPU-accelerated rigid body fitting of atomic structures into electron density maps

Edward W. Lowe Jr., Nils Woetzel, Jens Meiler

View

Download (PDF)

Source codes

Tags: ATI, ATI Radeon HD 5970, Biology, Cryo-EM, Molecular modeling, nVidia, nVidia GeForce GTX 470, OpenCL, Package, Poster, Tesla C1060, Tesla C2050

April 1, 2011 by hgpu

Accelerating Molecular Docking Calculations Using Graphics Processing Units

Oliver Korb, Thomas Stutzle, Thomas E. Exner

Tags: Algorithms, Chemistry, Molecular modeling

March 28, 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

See all packages

* * *

high performance computing on graphics processing units: hgpu.org

Architecture-Aware Mapping and Optimization on Heterogeneous Computing Systems

Energy-aware metrics for benchmarking heterogeneous systems

FPGA acceleration of rigid-molecule docking codes

Ambient Occlusion and Edge Cueing for Enhancing Real Time Molecular Visualization

GPU-accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks, and hyperboloids

Molecular Dynamics Simulations Using Graphics Processing Units

Acceleration of the GAMESS-UK electronic structure package on graphical processing units

GPU-based triangulation of the van der Waals surface

Towards accelerating molecular modeling via multi-scale approximation on a GPU

GPU-Based Implementations of the Noniterative Regularized-CCSD(T) Corrections: Applications to Strongly Correlated Systems

Poster: GPU-accelerated rigid body fitting of atomic structures into electron density maps

Accelerating Molecular Docking Calculations Using Graphics Processing Units

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

Most viewed papers (last 30 days)