high performance computing on graphics processing units: hgpu.org

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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

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

Using Graphics Processors to Facilitate Explicit Digital Electrochemical Simulation: Theory of Elliptical Disc Electrodes

Ian Cutress, Richard Compton

Tags: Chemistry, Electrochemistry

November 19, 2010 by hgpu

Direct numerical simulation of sub-grid structures in gas-solid flow — GPU implementation of macro-scale pseudo-particle modeling

Qingang Xiong, Bo Li, Feiguo Chen, Jingsen Ma, Wei Ge, Jinghai Li

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Tags: Chemistry, Fluid dynamics, Navier-Stokes equations, NSEs, nVidia

November 17, 2010 by hgpu

Code Generation for Cryptographic Kernels using Multi-word Modular Arithmetic on GPU

GSParLib

GSParLib: A multi-level programming interface unifying OpenCL and CUDA for expressing stream and data parallelism

Keras Sig: Efficient Path Signature Computation on GPU in Keras 3

KSig: GPU-accelerated computation of popular time series kernels

A User’s Guide to KSig: GPU-Accelerated Computation of the Signature Kernel

IterApp: Iterative Application Skeleton

Boosting Performance of Iterative Applications on GPUs: Kernel Batching with CUDA Graphs

SCALE-Ahead-Of-Time Compilation of CUDA for AMD GPUs

LeetDecoding: A PyTorch Library for Exponentially Decaying Causal Linear Attention with CUDA Implementations

Anari-visionaray

Data Parallel Visualization and Rendering on the RAMSES Supercomputer with ANARI

PROM: an open-source software framework to enhance the robustness and performance of predictive models against such changes during deployment

Enhancing Deployment-Time Predictive Model Robustness for Code Analysis and Optimization

DeepSpeed: a deep learning optimization library that makes distributed training and inference easy, efficient, and effective

Scalable Access-Pattern Aware I/O Acceleration and Multi-Tiered Data Management for HPC and AI Workloads

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

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

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

Using Graphics Processors to Facilitate Explicit Digital Electrochemical Simulation: Theory of Elliptical Disc Electrodes

Direct numerical simulation of sub-grid structures in gas-solid flow — GPU implementation of macro-scale pseudo-particle modeling

Recent source codes

Code Generation for Cryptographic Kernels using Multi-word Modular Arithmetic on GPU

GSParLib

Keras Sig: Efficient Path Signature Computation on GPU in Keras 3

KSig: GPU-accelerated computation of popular time series kernels

IterApp: Iterative Application Skeleton

SCALE-Ahead-Of-Time Compilation of CUDA for AMD GPUs

LeetDecoding: A PyTorch Library for Exponentially Decaying Causal Linear Attention with CUDA Implementations

Anari-visionaray

PROM: an open-source software framework to enhance the robustness and performance of predictive models against such changes during deployment

DeepSpeed: a deep learning optimization library that makes distributed training and inference easy, efficient, and effective

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