high performance computing on graphics processing units: hgpu.org

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Molecular dynamics simulation of UO2 nanocrystals melting

A.S. Boyarchenkov, S.I. Potashnikov, K.A. Nekrasov, A.Ya. Kupryazhkin

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Tags: CUDA, Molecular dynamics, Physics

October 9, 2011 by hgpu

Fast analysis of molecular dynamics trajectories with graphics processing units-Radial distribution function histogramming

Benjamin G. Levine, John E. Stone, Axel Kohlmeyer

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Tags: Algorithms, Chemistry, CUDA, GPU cluster, Heterogeneous systems, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Visualization

September 21, 2011 by hgpu

Two-Level Approach to Efficient Visualization of Protein Dynamics

Ove Daae Lampe, I. Viola, N. Reuter, H. Hauser

Tags: Bioinformatics, Biology, Molecular dynamics, Rendering, Visualization

August 31, 2011 by hgpu

Fine-grain Parallelism using Multi-core, Cell/BE, and GPU Systems

Frederico Pratas, Pedro Trancoso, Leonel Sousa, Alexandros Stamatakis, Guochun Shi, Volodymyr Kindratenko

Tags: Bioinformatics, Biology, Cell processor, CUDA, Molecular dynamics, nVidia

August 25, 2011 by hgpu

Efficient Calculation of Pairwise Nonbonded Forces

Matt Chiu, Md. Ashfaquzzaman Khan, Martin C. Herbordt

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Tags: Chemistry, Electrostatics, FPGA, Molecular dynamics, Optimization, Performance

August 15, 2011 by hgpu

The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations

Urban Borstnik, Benjamin T. Miller, Bernard R. Brooks, Dusanka Janezic

Tags: Algorithms, Chemistry, Computational chemistry, Molecular dynamics, Performance

August 8, 2011 by hgpu

Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs)

Narayan Ganesan, Brad A. Bauer, Timothy R. Lucas, Sandeep Patel, Michela Taufer

Tags: Algorithms, Chemistry, Computational chemistry, Electrostatic potential, Electrostatics, Molecular dynamics

August 8, 2011 by hgpu

Hardware accelerators for biocomputing: A survey

Souradip Sarkar, Turbo Majumder, Ananth Kalyanaraman, Partha Pratim Pande

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Tags: Biology, Cell processor, CUDA, FPGA, Molecular dynamics, nVidia, nVidia GeForce 7800 GTX, Performance, Review, Sequence alignment

August 7, 2011 by hgpu

Molecular Dynamics Simulations Using Graphics Processing Units

John A. Baker, Jonathan D. Hirst

Tags: Biomolecules, Chemistry, Molecular dynamics, Molecular modeling

July 22, 2011 by hgpu

Coming Soon: Research in a Cloud

Pam Frost Gorder

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Source codes

Tags: Chemistry, Cloud, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 280, Package

June 18, 2011 by hgpu

Interactive Visualization of Molecular Surface Dynamics

Michael Krone, Katrin Bidmon, Thomas Ertl

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Tags: Chemistry, GLSL, Molecular dynamics, Molecular surface, nVidia, nVidia GeForce GTX 280, OpenGL, Rendering, Visualization

June 18, 2011 by hgpu

Brownian dynamics simulations on CPU and GPU with BD_BOX

Maciej Dlugosz, Pawel Zielinski, Joanna Trylska

Source codes

Tags: Chemistry, CUDA, Molecular dynamics, MPI, nVidia, OpenMP, Package

June 16, 2011 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

Molecular dynamics simulation of UO2 nanocrystals melting

Fast analysis of molecular dynamics trajectories with graphics processing units-Radial distribution function histogramming

Two-Level Approach to Efficient Visualization of Protein Dynamics

Fine-grain Parallelism using Multi-core, Cell/BE, and GPU Systems

Efficient Calculation of Pairwise Nonbonded Forces

The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations

Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs)

Hardware accelerators for biocomputing: A survey

Molecular Dynamics Simulations Using Graphics Processing Units

Interactive Visualization of Molecular Surface Dynamics

Brownian dynamics simulations on CPU and GPU with BD_BOX

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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