high performance computing on graphics processing units: hgpu.org

Applications

hgpu.org » Applications » Chemistry

Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation

Ivan S. Ufimtsev, Todd J. Martinez

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Tags: Chemistry, Computational chemistry, CUDA, Molecular modeling, nVidia, nVidia GeForce 8800 GTX

October 30, 2010 by hgpu

Accelerating Density Functional Calculations with Graphics Processing Unit

Koji Yasuda

Tags: Chemistry, Computational chemistry, Molecular modeling

October 30, 2010 by hgpu

Accelerating molecular modeling applications with graphics processors

John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, Klaus Schulten

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Tags: Chemistry, Computational chemistry, CUDA, Electrostatic potential, Molecular dynamics, Molecular modeling, Multilevel summation, nVidia, nVidia GeForce 8800 GTX

October 30, 2010 by hgpu

Accelerating molecular dynamic simulation on graphics processing units

Mark S. Friedrichs, Peter Eastman, Vishal Vaidyanathan, Mike Houston, Scott Legrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande

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Source codes

Tags: ATI, ATI Radeon HD 4870, ATI Stream, Biology, Brook, Chemistry, Computational chemistry, Molecular dynamics, nVidia, nVidia GeForce GTX 280, Package, Solvent effects

October 30, 2010 by hgpu

CUSA and CUDE: GPU-accelerated methods for estimating solvent accessible surface area and desolvation

David Dynerman, Erick Butzlaff, Julie C. Mitchell

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Tags: Bioinformatics, Biology, Biophysics, Chemistry, Computational biology, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 280, Solvent effects

October 29, 2010 by hgpu

Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced Poisson Boltzmann approach

Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Siegfried Hofinger

Tags: ASIC, Chemistry, Computational chemistry, MDGRAPE, Poisson Boltzmann, Solvent effects

October 29, 2010 by hgpu

GPU acceleration of cutoff pair potentials for molecular modeling applications

Christopher I. Rodrigues, David J. Hardy, John E. Stone, Klaus Schulten, Wen Mei

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Tags: Algorithms, Biology, Chemistry, CUDA, Medicine, Molecular dynamics, nVidia, Tesla C870

October 28, 2010 by hgpu

An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware

M. J. Harvey, G. De Fabritiis

Tags: Chemistry, Computational chemistry, Molecular dynamics, nVidia

October 28, 2010 by hgpu

GPU acceleration of a production molecular docking code

Bharat Sukhwani, Martin C. Herbordt

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Tags: Bioinformatics, Biophysics, Chemistry, FPGA, Molecular dynamics, nVidia, Tesla C1060

October 27, 2010 by hgpu

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

M. J. Harvey, G. Giupponi, G. De Fabritiis

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Tags: Biological Physics, Chemistry, Computational Physics, CUDA, GPU cluster, Molecular dynamics, nVidia, nVidia GeForce GTX 280, Package, Physics, Tesla C1060

October 27, 2010 by hgpu

Code generated HPC Kernels Using Llama-2-70b

Comparing Llama-2 and GPT-3 LLMs for HPC kernels generation

Scope is all you need: Transforming LLMs for HPC Code

pocl - Portable Computing Language

PoCL-R: An Open Standard Based Offloading Layer for Heterogeneous Multi-Access Edge Computing with Server Side Scalability

HPAC-Offload: Accelerating HPC Applications with Portable Approximate Computing on the GPU

openCLDispatcher

Novel insights on atomic synchronization for sort-based group-by on GPUs

CEED Benchmarks

Performant low-order matrix-free finite element kernels on GPU architectures

Sieve: Stratified GPU-Compute Workload Sampling

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high performance computing on graphics processing units: hgpu.org

Applications

Quantum Chemistry on Graphical Processing Units. 1. Strategies for Two-Electron Integral Evaluation

Accelerating Density Functional Calculations with Graphics Processing Unit

Accelerating molecular modeling applications with graphics processors

Accelerating molecular dynamic simulation on graphics processing units

CUSA and CUDE: GPU-accelerated methods for estimating solvent accessible surface area and desolvation

Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced Poisson Boltzmann approach

GPU acceleration of cutoff pair potentials for molecular modeling applications

An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware

GPU acceleration of a production molecular docking code

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

Recent source codes

Code generated HPC Kernels Using Llama-2-70b

Scope is all you need: Transforming LLMs for HPC Code

pocl - Portable Computing Language

HPAC-Offload: Accelerating HPC Applications with Portable Approximate Computing on the GPU

openCLDispatcher

CEED Benchmarks

Sieve: Stratified GPU-Compute Workload Sampling

EngineCL: Usability and Performance in Heterogeneous Computing

Ginkgo: high-performance linear algebra library for manycore systems

AlphaFold2

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