high performance computing on graphics processing units: hgpu.org

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Acceleration of Coarse Grain Molecular Dynamics on GPU Architectures

Ardita Shkurti, Mario Orsi, Enrico Macii, Elisa Ficarra, Andrea Acquaviva

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Tags: Algorithms, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480

March 2, 2013 by hgpu

Developing Performance-Portable Molecular Dynamics Kernels in OpenCL

S. J. Pennycook, S. A. Jarvis

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Tags: ATI, ATI FirePro V7800, ATI Radeon HD 6550, Benchmarking, Computer science, Molecular dynamics, nVidia, nVidia GeForce GTX 680, OpenCL, Package, Performance, Tesla C1060, Tesla C2050

February 14, 2013 by hgpu

Exploring SIMD for Molecular Dynamics, Using Intel Xeon Processors and Intel Xeon Phi Coprocessors

S. J. Pennycook, C. J. Hughes, M. Smelyanskiy, S. A. Jarvis

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Tags: Algorithms, Benchmarking, Computer science, Intel, Intel Phi, Molecular dynamics

February 14, 2013 by hgpu

Bouncing Behavior of Microscopic Dust Aggregates

Alexander Seizinger, Wilhelm Kley

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Tags: Astrophysics, Earth and Planetary Astrophysics, Molecular dynamics, nVidia, nVidia GeForce GTX 460, nVidia GeForce GTX 570, Tesla C2070

January 17, 2013 by hgpu

GPU-Optimized Coarse-Grained MD Simulations of Protein and RNA Folding and Assembly

Andrew J. Proctor, Tyson J. Lipscomb, Anqi Zou, Joshua A. Anderson, Samuel S. Cho

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Tags: Bioinformatics, Biology, CUDA, Macromolecule, Molecular dynamics, nVidia, RNA, Tesla C2070

January 8, 2013 by hgpu

Long Timestep Molecular Dynamics on the Graphical Processing Unit

James C. Sweet, Ronald J. Nowling, Trevor Cickovski, Christopher R. Sweet, Vijay S. Pande, Jesus A. Izaguirre

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Tags: Biology, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 580, OpenCL, Package

January 4, 2013 by hgpu

Molecular dynamics simulations with many-body potentials on multiple GPUs – the implementation, package and performance

Qing Hou, Min Li, Yulu Zhou, Jiechao Cui, Zhenguo Cui, Jun Wang

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Tags: Computational Physics, CUDA, GPU cluster, Materials Science, Molecular dynamics, nVidia, Physics, Tesla C2050

January 2, 2013 by hgpu

Molecular dynamics for long-range interacting systems on Graphic Processing Units

Tarcisio M. Rocha Filho

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Tags: Algorithms, Computational Physics, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 690, Physics, Statistical Mechanics

December 4, 2012 by hgpu

Accelerated molecular dynamics force evaluation on graphics processing units for thermal conductivity calculations

Zheyong Fan, Topi Siro, Ari Harju

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Tags: Computational Physics, Condensed matter, CUDA, Materials Science, Molecular dynamics, nVidia, Physics, Tesla M2070

November 19, 2012 by hgpu

Parallel execution of a parameter sweep for molecular dynamics simulations in a hybrid GPU/CPU environment

Emmanuel N. Millan, Carlos Garcia Garino, Eduardo M. Bringa

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Tags: Chemistry, CUDA, Molecular dynamics, nVidia, OpenMPI, Package, Ruby, Tesla C2050

November 10, 2012 by hgpu

Computational Physics on Graphics Processing Units

Ari Harju, Topi Siro, Filippo Federici-Canova, Samuli Hakala, Teemu Rantalaiho

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Tags: Computational Physics, High Energy Physics - Lattice, Molecular dynamics, Physics, Review

October 31, 2012 by hgpu

Performance Analysis Cluster and GPU Computing Environment on Molecular Dynamic Simulation of BRV-1 and REM2 with GROMACS

Heru Suhartanto, Arry Yanuar, Ari Wibisono

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Tags: Cluster computing, Computer science, CUDA, GPU cluster, Molecular dynamics, nVidia, nVidia GeForce GTS 250, nVidia GeForce GTX 465, nVidia GeForce GTX 470, nVidia Quadro FX 4000

October 17, 2012 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

Acceleration of Coarse Grain Molecular Dynamics on GPU Architectures

Developing Performance-Portable Molecular Dynamics Kernels in OpenCL

Exploring SIMD for Molecular Dynamics, Using Intel Xeon Processors and Intel Xeon Phi Coprocessors

Bouncing Behavior of Microscopic Dust Aggregates

GPU-Optimized Coarse-Grained MD Simulations of Protein and RNA Folding and Assembly

Long Timestep Molecular Dynamics on the Graphical Processing Unit

Molecular dynamics simulations with many-body potentials on multiple GPUs – the implementation, package and performance

Molecular dynamics for long-range interacting systems on Graphic Processing Units

Accelerated molecular dynamics force evaluation on graphics processing units for thermal conductivity calculations

Parallel execution of a parameter sweep for molecular dynamics simulations in a hybrid GPU/CPU environment

Computational Physics on Graphics Processing Units

Performance Analysis Cluster and GPU Computing Environment on Molecular Dynamic Simulation of BRV-1 and REM2 with GROMACS

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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