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An OpenCL 3D FFT for Molecular Dynamics Simulations on Multiple FPGAs

Lawrence C. Stewart, Carlo Pasoe, Brian W. Sherman, Martin Herbordt, Vipin Sachdeva

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Tags: Computer science, Electrostatics, FFT, FPGA, Molecular dynamics, OpenCL

October 4, 2020 by hgpu

Acceleration of Linear Finite-Difference Poisson-Boltzmann Methods on Graphics Processing Units

Ruxi Qi, Wesley M. Botello-Smith, Ray Luo

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Tags: Biomolecules, Biophysics, Boltzmann equation, Computational Physics, CUBLAS, CUDA, Electrostatics, Molecular simulation, nVidia, nVidia GeForce GTX 980 Ti, Physics, Poisson Boltzmann

April 11, 2017 by hgpu

Challenges Adapting CUDA PIC Codes to multiple GPUs

Olav Emil Eiksund

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Tags: Benchmarking, CUDA, Electrostatics, FFT, nVidia, nVidia GeForce GTX 980, OpenMP, Particle simulation, Particle-in-cell methods, Physics, Plasma physics, Tesla K20, Thesis

December 19, 2015 by hgpu

Poisson-Boltzmann model for protein-surface electrostatic interactions and grid-convergence study using the PyGBe code

Christopher D. Cooper, Lorena A. Barba

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Tags: Biomolecules, Boltzmann equation, Computational Physics, CUDA, Electrostatics, nVidia, Package, Physics, Poisson Boltzmann, Python, Tesla C2075

June 14, 2015 by hgpu

Scalable Multi-GPU Simulation of Long-Range Molecular Dynamics

Marcos Novalbos, Jaime Gonzalez, Miguel A. Otaduy, Roberto Martinez Benito, Alberto Sanchez

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Tags: Algorithms, Biomolecules, Chemistry, CUDA, Electrostatic potential, Electrostatics, FFT, Molecular dynamics, Multilevel summation, N-body simulation, nVidia, nVidia GeForce GTX 580, nVidia GeForce GTX Titan

September 15, 2014 by hgpu

Parallel Computation of Non-Bonded Interactions in Drug Discovery: Nvidia GPUs vs. Intel Xeon Phi

Jianbin Fang, Ana Lucia Varbanescu, Baldomero Imbernon, Jose M. Cecilia, Horacio Perez-Sanchez

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Tags: Bioinformatics, Biology, CUDA, Electrostatics, Intel Xeon Phi, nVidia, Performance, Pharmaceuticals, Tesla K20

September 13, 2014 by hgpu

Cell Charge Approximation for Accelerating Molecular Simulation on CUDA-Enabled GPU

Shyam Mohan K T, Jayaraj P B

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Tags: Chemistry, CUDA, Electrostatics, Molecular dynamics, Molecular simulation, nVidia, Programming techniques

August 7, 2014 by hgpu

A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation

Jose Colmenares, Antonella Galizia, Jesus Ortiz, Andrea Clematis, Walter Rocchia

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Tags: Algorithms, Biology, Boltzmann equation, CUDA, Electrostatic potential, Electrostatics, Heterogeneous systems, Macromolecule, MPI, nVidia, nVidia GeForce GTX 580, Poisson Boltzmann, Tesla C2075

May 21, 2014 by hgpu

High Performance Poisson Equation Solver for Hybrid CPU/GPU Systems

Stoyan Markov, Peicho Petkov, Damyan Grancharov, Georgi Georgiev

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Tags: Computer science, Electrostatics, Laplace and Poisson equation, nVidia, nVidia GeForce GTX 580, Poisson equation

December 11, 2013 by hgpu

A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers

Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba

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Tags: Biomolecules, Boltzmann equation, Computational Physics, CUDA, Electrostatics, Intel Phi, nVidia, Package, Physics, Poisson Boltzmann, Python, Tesla C2075

September 17, 2013 by hgpu

Tight Binding Molecular Dynamics on CPU and GPU clusters

Dimitar Pashov

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Tags: Algorithms, CUDA, Electrostatics, Fortran, GPU cluster, Linear Algebra, Molecular dynamics, MPI, nVidia, Physics, Tesla K20

August 23, 2013 by hgpu

Plasma Visualization in Parallel using Particle Systems on Graphical Processing Units

Timothy S. Lyes, K. A. Hawick

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Tags: Computer science, CUDA, Electrostatics, nVidia, nVidia GeForce GTX 680, nVidia Quadro FX 4000, Plasma physics, Rendering, Visualization

June 4, 2013 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

See all packages

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high performance computing on graphics processing units: hgpu.org

An OpenCL 3D FFT for Molecular Dynamics Simulations on Multiple FPGAs

Acceleration of Linear Finite-Difference Poisson-Boltzmann Methods on Graphics Processing Units

Challenges Adapting CUDA PIC Codes to multiple GPUs

Poisson-Boltzmann model for protein-surface electrostatic interactions and grid-convergence study using the PyGBe code

Scalable Multi-GPU Simulation of Long-Range Molecular Dynamics

Parallel Computation of Non-Bonded Interactions in Drug Discovery: Nvidia GPUs vs. Intel Xeon Phi

Cell Charge Approximation for Accelerating Molecular Simulation on CUDA-Enabled GPU

A combined MPI-CUDA parallel solution of linear and nonlinear Poisson-Boltzmann equation

High Performance Poisson Equation Solver for Hybrid CPU/GPU Systems

A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers

Tight Binding Molecular Dynamics on CPU and GPU clusters

Plasma Visualization in Parallel using Particle Systems on Graphical Processing Units

Recent source codes

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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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