high performance computing on graphics processing units: hgpu.org

hgpu.org » Molecular simulation

Petascale computations for Large-scale Atomic and Molecular collisions

Brendan M McLaughlin, Connor P Ballance

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Tags: BLAS, Computational Physics, Computer science, CUDA, Fortran, Molecular simulation, MPI, nVidia, Tesla K20

April 4, 2014 by hgpu

Molecular Simulations using CUDA

Gerhard Burger

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Tags: CUDA, Molecular dynamics, Molecular simulation, Monte Carlo simulation, nVidia, nVidia GeForce GT 520, nVidia GeForce GTX 480, nVidia GeForce GTX 580, Physics, Tesla C2075, Thesis

October 29, 2013 by hgpu

GALAMOST: GPU-accelerated large-scale molecular simulation toolkit

You-Liang Zhu, Hong Liu, Zhan-Wei Li, Hu-Jun Qian, Giuseppe Milano, Zhong-Yuan Lu

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Tags: Chemical Physics, Computational Physics, CUDA, Molecular simulation, nVidia, nVidia GeForce GTX 580, Phase transition, Physics, Soft Condensed Matter, Tesla K20

October 10, 2013 by hgpu

Hardware Accelerated Molecular Docking: A Survey

Imre Pechan, Bela Feher

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Tags: Bioinformatics, Biology, CUDA, FPGA, Molecular simulation, nVidia, Tesla C1060

February 6, 2013 by hgpu

Acceleration of Monte-Carlo Molecular Simulations on Hybrid Computing Architectures

Claus Braun, Stefan Holst, Hans-Joachim Wunderlich, Juan Manuel Castillo, Joachim Gross

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Tags: CUDA, Hybrid computing, Molecular simulation, nVidia, Physics, Tesla, Thermodynamics

November 5, 2012 by hgpu

Parboil: A Revised Benchmark Suite for Scientific and Commercial Throughput Computing

John A. Stratton, Christopher Rodrigues, I-Jui Sung, Nady Obeid, Li-Wen Chang, Nasser Anssari, Geng Daniel Liu, Wen-mei W. Hwu

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Source codes

Tags: Algorithms, Benchmarking, Computer science, CUDA, Molecular simulation, MPI, nVidia, nVidia GeForce GTX 480, Optimization, Package

April 25, 2012 by hgpu

RNA secondary structure prediction using dynamic programming algorithm – A review and proposed work

M.N. Osman, R. Abdullah, N. AbdulRashid

Tags: Biology, Macromolecule, Molecular simulation, Pharmaceuticals

June 2, 2011 by hgpu

Accelerating Two Algorithms for Large-Scale Compound Selection on GPUs

Quan Liao, Jibo Wang, Ian A. Watson

Tags: Algorithms, Chemistry, Molecular simulation, nVidia

May 24, 2011 by hgpu

Accelerating Molecular Dynamics Simulations with GPUs

John Paul Walters, Vidyananth Balu, Vipin Chaudhary, David Kofke, Andrew Schultz

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Tags: Chemistry, CUDA, Molecular dynamics, Molecular simulation, nVidia, nVidia GeForce 8800 GTX

February 28, 2011 by hgpu

HexServer: an FFT-based protein docking server powered by graphics processors

Gary Macindoe, Lazaros Mavridis, Vishwesh Venkatraman, Marie-Dominique Devignes, David W. Ritchie

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Tags: Bioinformatics, Biology, CUDA, FFT, Molecular simulation, nVidia, Tesla C1060

February 25, 2011 by hgpu

Probing biomolecular machines with graphics processors

James C. Phillips, John E. Stone

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Tags: Biology, Biomolecules, CUDA, GPU cluster, Molecular simulation, nVidia, OpenCL, Review, Tesla S1070

February 23, 2011 by hgpu

VolQD: Direct Volume Rendering of Multi-million Atom Quantum Dot Simulations

Wei Qiao, David S. Ebert, Alireza Entezari, Marek Korkusinski, Gerhard Klimeck

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Tags: Molecular simulation, nVidia, nVidia GeForce 6800 Ultra, OpenGL, Physics, Rendering, Visualization

February 8, 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

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high performance computing on graphics processing units: hgpu.org

Petascale computations for Large-scale Atomic and Molecular collisions

Molecular Simulations using CUDA

GALAMOST: GPU-accelerated large-scale molecular simulation toolkit

Hardware Accelerated Molecular Docking: A Survey

Acceleration of Monte-Carlo Molecular Simulations on Hybrid Computing Architectures

Parboil: A Revised Benchmark Suite for Scientific and Commercial Throughput Computing

RNA secondary structure prediction using dynamic programming algorithm – A review and proposed work

Accelerating Two Algorithms for Large-Scale Compound Selection on GPUs

Accelerating Molecular Dynamics Simulations with GPUs

HexServer: an FFT-based protein docking server powered by graphics processors

Probing biomolecular machines with graphics processors

VolQD: Direct Volume Rendering of Multi-million Atom Quantum Dot Simulations

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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