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Accelerating electrostatic surface potential calculation with multi-scale approximation on graphics processing units

Ramu Anandakrishnan, Tom R. W. Scogland, Andrew T. Fenley, John C. Gordon, Wu-chun Feng, Alexey V. Onufriev

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Tags: ATI, ATI CAL, ATI Radeon HD 4870, Brook, Chemistry, Molecular modeling, Solvent effects

November 22, 2010 by hgpu

Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation

Ivan S. Ufimtsev, Todd J. Martinez

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Tags: Chemistry, Computational chemistry, CUDA, Molecular modeling, nVidia, nVidia GeForce 8800 GTX, nVidia GeForce GTX 280

November 21, 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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Source codes

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

November 7, 2010 by hgpu

Parallel, stochastic measurement of molecular surface area

D. Juba, A. Varshney

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

November 3, 2010 by hgpu

Accelerating Resolution-of-the-Identity Second-Order Moller-Plesset Quantum Chemistry Calculations with Graphical Processing Units

Leslie Vogt, Roberto Olivares-Amaya, Sean Kermes, Yihan Shao, Carlos Amador-Bedolla, Alan Aspuru-Guzik

Tags: Chemistry, Computational chemistry, CUBLAS, CUDA, Molecular modeling, nVidia, nVidia Quadro FX 5600

November 2, 2010 by hgpu

Multilevel summation of electrostatic potentials using graphics processing units

David J. Hardy, John E. Stone, Klaus Schulten

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Tags: Chemistry, CUDA, Electrostatics, Molecular dynamics, Molecular modeling, Multilevel summation, nVidia, nVidia GeForce GTX 280, Physics, Tesla C870, Tesla D870

November 2, 2010 by hgpu

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

Efficient GPU Implementation of Multi-Precision Integer Division

ParEval: A Parallel Code Evaluation Benchmark

ParEval-Repo: A Benchmark Suite for Evaluating LLMs with Repository-level HPC Translation Tasks

FlashSparse: Minimizing Computation Redundancy for Fast Sparse Matrix Multiplications on Tensor Cores

Libra: Synergizing CUDA and Tensor Cores for High-Performance Sparse Matrix Multiplication

exa-AMD: Exascale Accelerated Materials Discovery

Accelerated discovery and design of Fe-Co-Zr magnets with tunable magnetic anisotropy through machine learning and parallel computing

WiLLM: An Open Wireless LLM Communication System

Vcc: the Vulkan Clang Compiler

No More Shading Languages: Compiling C++ to Vulkan Shaders

hpcbench: A set of benchmarking utilities for biomolecular simulation tools

Engineering Supercomputing Platforms for Biomolecular Applications

HPCTransCompile: An AI Compiler Generated Dataset for High-Performance CUDA Transpilation and LLM Preliminary Exploration

chemtrain: Training Molecular Dynamics Potentials in JAX

chemtrain-deploy: A parallel and scalable framework for machine learning potentials in million-atom MD simulations

microSYCL: SYCL micro-benchmarks repository

Exploring SYCL as a Portability Layer for High-Performance Computing on CPUs

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high performance computing on graphics processing units: hgpu.org

Accelerating electrostatic surface potential calculation with multi-scale approximation on graphics processing units

Quantum Chemistry on Graphical Processing Units. 2. Direct Self-Consistent-Field Implementation

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

Parallel, stochastic measurement of molecular surface area

Accelerating Resolution-of-the-Identity Second-Order Moller-Plesset Quantum Chemistry Calculations with Graphical Processing Units

Multilevel summation of electrostatic potentials using graphics processing units

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

Recent source codes

Efficient GPU Implementation of Multi-Precision Integer Division

ParEval: A Parallel Code Evaluation Benchmark

FlashSparse: Minimizing Computation Redundancy for Fast Sparse Matrix Multiplications on Tensor Cores

exa-AMD: Exascale Accelerated Materials Discovery

WiLLM: An Open Wireless LLM Communication System

Vcc: the Vulkan Clang Compiler

hpcbench: A set of benchmarking utilities for biomolecular simulation tools

HPCTransCompile: An AI Compiler Generated Dataset for High-Performance CUDA Transpilation and LLM Preliminary Exploration

chemtrain: Training Molecular Dynamics Potentials in JAX

microSYCL: SYCL micro-benchmarks repository

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