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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

GPUmotif: An Ultra-Fast and Energy-Efficient Motif Analysis Program Using Graphics Processing Units

Pooya Zandevakili, Ming Hu, Zhaohui Qin

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Tags: Algorithms, Biochemistry, Biology, Chemistry, Computational biology, Computer science, CUDA, Genetics, nVidia, nVidia GeForce GTX 260, nVidia GeForce GTX 480, Package

June 17, 2012 by hgpu

Implementing Molecular Dynamics on Hybrid High Performance Computers – Particle-Particle Particle-Mesh

W. Michael Brown, Axel Kohlmeyer, Steven J. Plimpton, Arnold N. Tharrington

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Tags: Algorithms, Chemistry, CUDA, Electrostatics, GPU cluster, Heterogeneous systems, Molecular dynamics, nVidia, OpenCL, OpenMPI, Package, Physics, Tesla M2070

February 10, 2012 by hgpu

The Anatomy of High-Performance 2D Similarity Calculations

Imran S. Haque, Vijay S. Pande, W. Patrick Walters

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Tags: Algorithms, Biochemistry, Chemistry, Clustering, CUDA, nVidia, nVidia GeForce GTX 260, nVidia GeForce GTX 480, Package

October 16, 2011 by hgpu

Coming Soon: Research in a Cloud

Pam Frost Gorder

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

June 18, 2011 by hgpu

Brownian dynamics simulations on CPU and GPU with BD_BOX

Maciej Dlugosz, Pawel Zielinski, Joanna Trylska

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

June 16, 2011 by hgpu

Daubechies wavelets for high performance electronic structure calculations: The BigDFT project

Luigi Genovese, Brice Videau, Matthieu Ospici, Thierry Deutsch, Stefan Goedecker, Jean-Francois Mehaut

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Tags: Chemistry, Molecular modeling, OpenCL, Package, Physics

January 16, 2011 by hgpu

OpenMM: A Hardware-Independent Framework for Molecular Simulations

Peter Eastman, Vijay Pande

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Tags: Chemistry, Computational chemistry, Molecular modeling, Package

December 16, 2010 by hgpu

SIML: A Fast SIMD Algorithm for Calculating LINGO Chemical Similarities on GPUs and CPUs

Imran S. Haque, Vijay S. Pande, W. Patrick Walters

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Tags: Chemistry, CUDA, nVidia, nVidia GeForce GTS 250, OpenMP, Package, Tesla T10

November 9, 2010 by hgpu

Biomolecular electrostatics simulation with a parallel FMM-based BEM, using up to 512 GPUs

Rio Yokota, Jaydeep P. Bardhan, Matthew G. Knepley, L. A. Barba, Tsuyoshi Hamada

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Tags: Chemistry, CUDA, GPU cluster, Molecular modeling, nVidia, nVidia GeForce GTX 295, Package

November 7, 2010 by hgpu

MDLab: A molecular dynamics simulation prototyping environment

Trevor Cickovski, Santanu Chatterjee, Jacob Wenger, Christopher R. Sweet, Jesus A. Izaguirre

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Tags: Chemistry, Computational chemistry, CUDA, Molecular dynamics, nVidia, Package, Python

November 6, 2010 by hgpu

PAPER – Accelerating parallel evaluations of ROCS

Imran S. Haque, Vijay S. Pande

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Tags: Chemistry, Computational chemistry, CUDA, Molecular overlay, nVidia, nVidia GeForce 8600 GT, nVidia GeForce 8800 GTX, nVidia GeForce GTX 280, Package, ROCS, Shape comparison

November 3, 2010 by hgpu

HPCTransCompile: An AI Compiler Generated Dataset for High-Performance CUDA Transpilation and LLM Preliminary Exploration

Efficient Graph Embedding at Scale: Optimizing CPU-GPU-SSD Integration

Can Large Language Models Predict Parallel Code Performance?

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high performance computing on graphics processing units: hgpu.org

Applications

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

GPUmotif: An Ultra-Fast and Energy-Efficient Motif Analysis Program Using Graphics Processing Units

Implementing Molecular Dynamics on Hybrid High Performance Computers – Particle-Particle Particle-Mesh

The Anatomy of High-Performance 2D Similarity Calculations

Brownian dynamics simulations on CPU and GPU with BD_BOX

Daubechies wavelets for high performance electronic structure calculations: The BigDFT project

OpenMM: A Hardware-Independent Framework for Molecular Simulations

SIML: A Fast SIMD Algorithm for Calculating LINGO Chemical Similarities on GPUs and CPUs

Biomolecular electrostatics simulation with a parallel FMM-based BEM, using up to 512 GPUs

MDLab: A molecular dynamics simulation prototyping environment

PAPER – Accelerating parallel evaluations of ROCS

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