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Molecular dynamics recipes for genome research

Tommaso Biagini, Giovanni Chillemi, Gianluigi Mazzoccoli, Alessandro Grottesi, Caterina Fusilli, Daniele Capocefalo, Stefano Castellana, Angelo Luigi Vescovi, Tommaso Mazza

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Tags: Benchmarking, Bioinformatics, Biology, Chemistry, CUDA, Genomics, Molecular dynamics, nVidia, OpenCL, Physics, Tesla C2070

December 19, 2017 by hgpu

Real-Time Rendering of Molecular Dynamics Simulation Data: A Tutorial

N.Alharbi, M. Chavent, RS. Laramee

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Tags: Computer science, Image generation, Intel HD 6100, Molecular dynamics, OpenCL, OpenGL, Package, Rendering, Tutorial

September 3, 2017 by hgpu

Dynamic Parallelism in GPU Optimized Barnes Hut Trees for Molecular Dynamics Simulations

Melisa Carranza Zuniga

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Tags: Algorithms, Biology, Biomolecules, Biophysics, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Physics, Thesis

August 26, 2017 by hgpu

OpenCL-Based Implementation of an FPGA Accelerator for Molecular Dynamics Simulation

Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara

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Tags: Chemistry, FPGA, Heterogeneous systems, Molecular dynamics, OpenCL

July 5, 2017 by hgpu

A Domain Specific Language for Performance Portable Molecular Dynamics Algorithms

William R. Saunders, James Grant, Eike H. Muller

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Tags: Algorithms, Biology, Chemistry, Code generation, Computer science, CUDA, Differential equations, DSL, Molecular dynamics, nVidia, Package, Partial differential equations, PDEs, Physics, Python, Tesla K20

April 15, 2017 by hgpu

Architectural Principles and Experimentation of Distributed High Performance Virtual Clusters

Andrew J. Younge

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Tags: Cloud, Computer science, CUDA, Distributed computing, Molecular dynamics, nVidia, OpenCL, Tesla C2075, Tesla K20, Thesis, Virtualization

March 9, 2017 by hgpu

LAMMPS’ PPPM Long-Range Solver for the Second Generation Xeon Phi

William McDoniel, Markus Hohnerbach, Rodrigo Canales, Ahmed E. Ismail, Paolo Bientinesi

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Tags: Chemistry, Computer science, Intel Xeon Phi, Molecular dynamics, Performance

February 18, 2017 by hgpu

An FPGA Accelerator for Molecular Dynamics Simulation Using OpenCL

Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara

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Tags: Chemistry, FPGA, Heterogeneous systems, Molecular dynamics, OpenCL, Performance, Physics

January 10, 2017 by hgpu

A hybrid algorithm for parallel molecular dynamics simulations

Chris M. Mangiardi, Ralf Meyer

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Tags: Condensed matter, Intel Xeon Phi, Materials Science, Molecular dynamics

November 3, 2016 by hgpu

Efficient molecular dynamics simulations with many-body potentials on graphics processing units

Zheyong Fan, Wei Chen, Ville Vierimaa, Ari Harju

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Tags: Computational Physics, CUDA, Materials Science, Molecular dynamics, nVidia, Physics, Tesla K40

October 15, 2016 by hgpu

GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing

Ye Fang, Yun Ding, Wei P. Feinstein, David M. Koppelman, Juana Moreno, Mark Jarrell, J. Ramanujam, Michal Brylinski

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Tags: Algorithms, Chemistry, CUDA, Heterogeneous systems, Intel Xeon Phi, Medicine, Molecular dynamics, nVidia, nVidia GeForce GTX 980, OpenMP, Package

July 16, 2016 by hgpu

GPU Accelerated Discrete Element Method (DEM) Molecular Dynamics for Conservative, Faceted Particle Simulations

Matthew Spellings, Ryan L. Marson, Joshua A. Anderson, Sharon C. Glotzer

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Tags: Computational Physics, CUDA, Molecular dynamics, nVidia, nVidia Quadro M 6000, Package, Particle simulation, Physics

July 13, 2016 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 recipes for genome research

Real-Time Rendering of Molecular Dynamics Simulation Data: A Tutorial

Dynamic Parallelism in GPU Optimized Barnes Hut Trees for Molecular Dynamics Simulations

OpenCL-Based Implementation of an FPGA Accelerator for Molecular Dynamics Simulation

A Domain Specific Language for Performance Portable Molecular Dynamics Algorithms

LAMMPS’ PPPM Long-Range Solver for the Second Generation Xeon Phi

An FPGA Accelerator for Molecular Dynamics Simulation Using OpenCL

A hybrid algorithm for parallel molecular dynamics simulations

Efficient molecular dynamics simulations with many-body potentials on graphics processing units

GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing

GPU Accelerated Discrete Element Method (DEM) Molecular Dynamics for Conservative, Faceted Particle Simulations

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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