high performance computing on graphics processing units: hgpu.org

Applications

Enhanced molecular dynamics performance with a programmable graphics processor

D. C. Rapaport

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Tags: Chemistry, Computational chemistry, Computational Physics, CUDA, Molecular dynamics, nVidia, nVidia Quadro FX 770 M, Physics

November 13, 2010 by hgpu

Sop-GPU: Accelerating biomolecular simulations in the centisecond timescale using graphics processors

A. Zhmurov, R. I. Dima, Y. Kholodov, V. Barsegov

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Tags: Bioinformatics, Biomolecular assemblies, Chemistry, CUDA, Dynamic force spectroscopy, Langevin dynamics, Molecular dynamics, nVidia, nVidia GeForce GTX 295

November 9, 2010 by hgpu

A molecular docking system using CUDA

Youngtae Roh, Jun Lee, Sungjun Park, Jee I. Kim

Tags: Bioinformatics, Biology, Biophysics, Chemistry, Molecular dynamics

November 9, 2010 by hgpu

SIML: A Fast SIMD Algorithm for Calculating LINGO Chemical Similarities on GPUs and CPUs

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

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Source codes

Tags: Chemistry, CUDA, nVidia, nVidia GeForce GTS 250, OpenMP, Package, Tesla T10

November 9, 2010 by hgpu

Theory of square, rectangular, and microband electrodes through explicit GPU simulation

Ian Cutress, Richard Compton

Tags: Chemistry, Electrochemistry, Finite difference

November 8, 2010 by hgpu

Large-scale mixer simulations using massively parallel GPU architectures

Charles A. Radeke, Benjamin J. Glasser, Johannes G. Khinast

Tags: Chemistry, CUDA, nVidia, Pharmaceuticals, Powder processing

November 8, 2010 by hgpu

Biomolecular electrostatics simulation with a parallel FMM-based BEM, using up to 512 GPUs

Rio Yokota, Jaydeep P. Bardhan, Matthew G. Knepley, L. A. Barba, Tsuyoshi Hamada

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Tags: Chemistry, CUDA, GPU cluster, Molecular modeling, nVidia, nVidia GeForce GTX 295, Package

November 7, 2010 by hgpu

Efficient nonbonded interactions for molecular dynamics on a graphics processing unit

P. Eastman, V. S. Pande

Tags: Chemistry, Computational chemistry, Molecular dynamics, Solvent effects

November 7, 2010 by hgpu

MDLab: A molecular dynamics simulation prototyping environment

Trevor Cickovski, Santanu Chatterjee, Jacob Wenger, Christopher R. Sweet, Jesus A. Izaguirre

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Source codes

Tags: Chemistry, Computational chemistry, CUDA, Molecular dynamics, nVidia, Package, Python

November 6, 2010 by hgpu

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

I. Buch, M. J. Harvey, T. Giorgino, D. P. Anderson, G. De Fabritiis

Tags: Biochemistry, Chemistry, Molecular dynamics, Thermodynamics

November 6, 2010 by hgpu

Iterative induced dipoles computation for molecular mechanics on GPUs

Frederico Pratas,Ricardo A. Mata,Leonel Sousa

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Tags: Chemistry, Computational chemistry, Computer science, CUDA, Molecular dynamics, nVidia, nVidia GeForce 8800 GT, nVidia GeForce GTX 285

November 5, 2010 by hgpu

Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1-39)

Vincent A. Voelz, Gregory R. Bowman, Kyle Beauchamp, Vijay S. Pande

Tags: Bioinformatics, Biology, Chemistry, Molecular dynamics

November 4, 2010 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

Applications

Enhanced molecular dynamics performance with a programmable graphics processor

Sop-GPU: Accelerating biomolecular simulations in the centisecond timescale using graphics processors

A molecular docking system using CUDA

SIML: A Fast SIMD Algorithm for Calculating LINGO Chemical Similarities on GPUs and CPUs

Theory of square, rectangular, and microband electrodes through explicit GPU simulation

Large-scale mixer simulations using massively parallel GPU architectures

Biomolecular electrostatics simulation with a parallel FMM-based BEM, using up to 512 GPUs

Efficient nonbonded interactions for molecular dynamics on a graphics processing unit

MDLab: A molecular dynamics simulation prototyping environment

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

Iterative induced dipoles computation for molecular mechanics on GPUs

Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1-39)

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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