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Scalable Molecular Dynamics Simulation Using FPGAs and Multicore Processors

Ashfaquzzaman Khan

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Tags: Chemistry, FPGA, Molecular dynamics, nVidia, Review, Thesis

July 17, 2012 by hgpu

A hybrid Hermitian general eigenvalue solver

Raffaele Solca, Thomas C. Schulthess, Azzam Haidar, Stanimire Tomov, Ichitaro Yamazaki, Jack Dongarra

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Tags: Chemistry, Computer science, CUDA, Materials Science, Numerical Analysis, nVidia, Tesla M2090

July 10, 2012 by hgpu

Interactive Quantum Chemistry: A Divide-and-Conquer ASED-MO Method

Mael Bosson, Caroline Richard, Antoine Plet, Sergei Grudinin, Stephane Redon

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Tags: Algorithms, Chemistry, CUDA, nVidia, nVidia GeForce GTX 260

July 5, 2012 by hgpu

Solving Molecular Distance Geometry Problems in OpenCL

Istvan Lorentz, Razvan Andonie, Levente Fabry-Asztalos

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Tags: Chemistry, Computational chemistry, Molecular modeling, nVidia, nVidia GeForce GTX 560 Ti, OpenCL

June 27, 2012 by hgpu

Implementing density functional theory (DFT) methods on many-core GPGPU accelerators

Bishwajit Mohan Gosswami

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Tags: Chemistry, CUDA, Density-functional theory, nVidia, Tesla C2070, Thesis

June 19, 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

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

Andreas W. Gotz, Mark J. Williamson, Dong Xu, Duncan Poole, Scott Le Grand, Ross C. Walker

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Tags: Algorithms, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 580, Tesla C1060, Tesla C2070, Tesla M2090

May 26, 2012 by hgpu

Molecular Distance Geometry Optimization Using Geometric Build-up and Evolutionary Techniques on GPU

Levente Fabry-Asztalos, Istvan Lorentz, Razvan Andonie

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Tags: Chemistry, Molecular modeling, nVidia, nVidia GeForce GTX 560, OpenCL, Optimization

May 23, 2012 by hgpu

GPU Accelerated Molecular Surface Computing

Byungjoo Kim, Ku-Jin Kim, Joon-Kyung Seong

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Tags: Biochemistry, Chemistry, CUDA, KD-tree, Molecular surface, nVidia, nVidia GeForce GTX 590

February 26, 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

Parallelizing Kernel Polynomial Method Applying Graphics Processing Units

Shixun Zhang, Shinichi Yamagiwa, Masahiko Okumura, Seiji Yunoki

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Tags: Algorithms, Chemistry, Condensed matter, CUDA, nVidia, Physics, Tesla C2050

January 10, 2012 by hgpu

Fat versus Thin Threading Approach on GPUs: Application to Stochastic Simulation of Chemical Reactions

Guido Klingbeil, Radek Erban, Mike Giles, Philip K. Maini

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Tags: Algorithms, Chemistry, CUDA, nVidia, nVidia GeForce GTX 260, Stochastic simulation

January 7, 2012 by hgpu

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

Profile Util library: A quick and easy way to get MPI, OpenMP and GPU runtime information

MaC: Mamba CPU performance predictor

MambaCPU: Enhanced Correlation Mining with State Space Models for CPU Performance Prediction

Mixed-precision finite element kernels

Mixed-precision finite element kernels and assembly: Rounding error analysis and hardware acceleration

SHMT: The Simultaneous and Heterogenous Multithreading project

General-Purpose Computing on Tensor Processors

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

Online Energy Optimization in GPUs: A Multi-Armed Bandit Approach

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high performance computing on graphics processing units: hgpu.org

Scalable Molecular Dynamics Simulation Using FPGAs and Multicore Processors

A hybrid Hermitian general eigenvalue solver

Interactive Quantum Chemistry: A Divide-and-Conquer ASED-MO Method

Solving Molecular Distance Geometry Problems in OpenCL

Implementing density functional theory (DFT) methods on many-core GPGPU accelerators

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

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

Molecular Distance Geometry Optimization Using Geometric Build-up and Evolutionary Techniques on GPU

GPU Accelerated Molecular Surface Computing

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

Parallelizing Kernel Polynomial Method Applying Graphics Processing Units

Fat versus Thin Threading Approach on GPUs: Application to Stochastic Simulation of Chemical Reactions

Recent source codes

Kokkidio: Kokkos+Eigen - write fast, readable multi-platform code

LLaMA-Inference-Bench

MATAR

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

MaC: Mamba CPU performance predictor

Mixed-precision finite element kernels

SHMT: The Simultaneous and Heterogenous Multithreading project

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

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