high performance computing on graphics processing units: hgpu.org

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A massively multicore parallelization of the Kohn-Sham energy gradients

Philip Brown, Christopher J. Woods, Simon McIntosh-Smith, Frederick R. Manby

Tags: Chemistry, Computational chemistry, Molecular modeling

December 16, 2010 by hgpu

Two-electron integral evaluation on the graphics processor unit

Koji Yasuda

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

December 12, 2010 by hgpu

Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA

W. Liu, B. Schmidt, G. Voss, W. Mullerwittig

Tags: Chemistry, CUDA, Molecular dynamics, nVidia

December 11, 2010 by hgpu

The impact of accelerator processors for high-throughput molecular modeling and simulation

G. Giupponi, M. Harvey, G. Defabritiis

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Tags: Bioinformatics, Cell processor, Chemistry, Medicine, Molecular modeling, nVidia, Review

December 11, 2010 by hgpu

Graphical Processing Units for Quantum Chemistry

I. S. Ufimtsev, T. J. Martinez

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

December 10, 2010 by hgpu

Simulation of Coarse-Grained Protein-Protein Interactions with Graphics Processing Units

Ian Tunbridge, Robert B. Best, James Gain, Michelle M. Kuttel

Tags: Chemistry, Molecular dynamics

December 7, 2010 by hgpu

Efficient Parallelization of Stochastic Simulation Algorithm for Chemically Reacting Systems on the Graphics Processing Unit

Linda Petzold, Hong Li

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Tags: Chemistry, Stochastic simulation

November 27, 2010 by hgpu

Molecular dynamics simulation of complex multiphase flow on a computer cluster with GPUs

Feiguo Chen, Wei Ge, Jinghai Li

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Tags: Chemistry, CUDA, GPU cluster, Molecular dynamics, MPI, nVidia, Tesla C870

November 27, 2010 by hgpu

Density functional theory calculation on many-cores hybrid central processing unit-graphic processing unit architectures

Luigi Genovese, Matthieu Ospici, Thierry Deutsch, Jean F. Méhaut, Alexey Neelov, Stefan Goedecker

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Tags: Chemistry, CUDA, Density-functional theory, Molecular modeling, nVidia, Physics, Tesla S1070

November 25, 2010 by hgpu

Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics

Ivan S. Ufimtsev, Todd J. Martinez

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Tags: Chemistry, Computational chemistry, CUDA, Molecular dynamics, Molecular modeling, nVidia, nVidia GeForce GTX 295

November 25, 2010 by hgpu

GPU-accelerated molecular modeling coming of age

John E. Stone, David J. Hardy, Ivan S. Ufimtsev, Klaus Schulten

Tags: Chemistry, Molecular dynamics, Molecular modeling

November 22, 2010 by hgpu

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

ParaCodex: A Profiling-Guided Autonomous Coding Agent for Reliable Parallel Code Generation and Translation

SeedFold: Scaling Biomolecular Structure Prediction

Tilus: A Tile-Level GPU Kernel Programming Language

Tilus: A Tile-Level GPGPU Programming Language for Low-Precision Computation

Memory-Efficient Acceleration of Block Low-Rank Foundation Models on Resource Constrained GPUs

CUDA-L2: Surpassing cuBLAS Performance for Matrix Multiplication through Reinforcement Learning

BoltzGen:Toward Universal Binder Design

cuPilot: A Strategy-Coordinated Multi-agent Framework for CUDA Kernel Evolution

MATLAB Tensor Core models

Accurate Models of NVIDIA Tensor Cores

TritonForge: Transform PyTorch Operations into Optimized GPU Kernels with LLMs

TritonForge: Profiling-Guided Framework for Automated Triton Kernel Optimization

RLTune: Hybrid Learning and Optimization-Based Dynamic Scheduling for DL Workloads on Heterogeneous GPU Clusters

Hybrid Learning and Optimization-Based Dynamic Scheduling for DL Workloads on Heterogeneous GPU Clusters

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high performance computing on graphics processing units: hgpu.org

A massively multicore parallelization of the Kohn-Sham energy gradients

Two-electron integral evaluation on the graphics processor unit

Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA

The impact of accelerator processors for high-throughput molecular modeling and simulation

Graphical Processing Units for Quantum Chemistry

Simulation of Coarse-Grained Protein-Protein Interactions with Graphics Processing Units

Efficient Parallelization of Stochastic Simulation Algorithm for Chemically Reacting Systems on the Graphics Processing Unit

Molecular dynamics simulation of complex multiphase flow on a computer cluster with GPUs

Density functional theory calculation on many-cores hybrid central processing unit-graphic processing unit architectures

Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics

GPU-accelerated molecular modeling coming of age

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

Recent source codes

ParaCodex: A Profiling-Guided Autonomous Coding Agent for Reliable Parallel Code Generation and Translation

SeedFold: Scaling Biomolecular Structure Prediction

Tilus: A Tile-Level GPU Kernel Programming Language

Memory-Efficient Acceleration of Block Low-Rank Foundation Models on Resource Constrained GPUs

CUDA-L2: Surpassing cuBLAS Performance for Matrix Multiplication through Reinforcement Learning

BoltzGen:Toward Universal Binder Design

cuPilot: A Strategy-Coordinated Multi-agent Framework for CUDA Kernel Evolution

MATLAB Tensor Core models

TritonForge: Transform PyTorch Operations into Optimized GPU Kernels with LLMs

RLTune: Hybrid Learning and Optimization-Based Dynamic Scheduling for DL Workloads on Heterogeneous GPU Clusters

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