high performance computing on graphics processing units: hgpu.org

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Accelerating Drug Discovery in AutoDock-GPU with Tensor Cores

Gabin Schieffer, Ivy Peng

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Tags: Chemistry, Computer science, CUDA, Macromolecule, molecular docking, nVidia, nVidia A100, nVidia V100, Physics, Tesla T4

October 20, 2024 by hgpu

Accelerating AutoDock4 with GPUs and Gradient-Based Local Search

Diogo Santos-Martins, Leonardo Solis-Vasquez, Andreas Koch, and Stefano Forli

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Tags: Algorithms, Chemistry, Macromolecule, molecular docking, OpenCL, Package, Physics

February 28, 2021 by hgpu

Accelerating Molecular Docking by Parallelized Heterogeneous Computing – A Case Study of Performance, Quality of Results, and Energy-Efficiency using CPUs, GPUs, and FPGAs

Leonardo Solis Vasquez

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Tags: AMD Radeon RX Vega 56, ATI, Computer science, FPGA, Heterogeneous systems, Macromolecule, nVidia, OpenCL, Package, Physics, Tesla V100, Thesis

December 29, 2019 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

gEMpicker: A Highly Parallel GPU-Accelerated Particle Picking Tool for Cryo-Electron Microscopy

Thai V. Hoang, Xavier Cavin, Patrick Schultz, David W. Ritchie

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Tags: Algorithms, Biology, Cryo-EM, CUDA, Electron microscopy, FFT, Macromolecule, Microscopy, nVidia, Tesla C1060, Tesla C2075

October 24, 2013 by hgpu

gEMfitter: A Highly Parallel FFT-Based 3D Density Fitting Tool With GPU Texture Memory Acceleration

Thai V. Hoang, Xavier Cavin, David W. Ritchie

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Tags: Biology, Cryo-EM, CUDA, Electron microscopy, FFT, Macromolecule, Microscopy, nVidia, Tesla C2075

September 28, 2013 by hgpu

Performance of a GPU-based Direct Summation Algorithm for Computation of Small Angle Scattering Profile

Konstantin Berlin, Nail A. Gumerov, Ramani Duraiswami, David Fushman

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Tags: Algorithms, Biology, Biomolecules, Fast multipole method, Macromolecule, nVidia, nVidia GeForce GT 330 M, nVidia GeForce GTX 295, OpenCL, RNA

June 12, 2013 by hgpu

GPU-based Steady-State Solution of the Chemical Master Equation

Marco Maggioni, Tanya Berger-Wolf, Jie Liang

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Tags: Biology, CUDA, Macromolecule, nVidia, nVidia GeForce GTX 580, Probability, Sparse matrix

May 1, 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

GPU-based Cloud Computing for Comparing the Structure of Protein Binding Sites

Matthias Leinweber, Lars Baumgartner, Marco Mernberger, Thomas Fober, Eyke Hullermeier, Gerhard Klebe, Bernd Freisleben

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Tags: Biology, Java, Macromolecule, nVidia, nVidia GeForce GTX 580, OpenCL, Tesla M2050

June 26, 2012 by hgpu

GPU-accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks, and hyperboloids

Matthieu Chavent, Antoine Vanel, Alex Tek, Bruno Levy, Sophie Robert, Bruno Raffin, Marc Baaden

Tags: Algorithms, Chemistry, Macromolecule, Molecular modeling, Visualization

July 23, 2011 by hgpu

Accelerating the Nussinov RNA folding algorithm with CUDA/GPU

Dar-Jen Chang, C. Kimmer, Ming Ouyang

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Tags: Biology, CUDA, Macromolecule, nVidia, Tesla C1060, Tesla C2050, Tesla C870

July 12, 2011 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

Accelerating Drug Discovery in AutoDock-GPU with Tensor Cores

Accelerating AutoDock4 with GPUs and Gradient-Based Local Search

Accelerating Molecular Docking by Parallelized Heterogeneous Computing – A Case Study of Performance, Quality of Results, and Energy-Efficiency using CPUs, GPUs, and FPGAs

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

gEMpicker: A Highly Parallel GPU-Accelerated Particle Picking Tool for Cryo-Electron Microscopy

gEMfitter: A Highly Parallel FFT-Based 3D Density Fitting Tool With GPU Texture Memory Acceleration

Performance of a GPU-based Direct Summation Algorithm for Computation of Small Angle Scattering Profile

GPU-based Steady-State Solution of the Chemical Master Equation

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

GPU-based Cloud Computing for Comparing the Structure of Protein Binding Sites

GPU-accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks, and hyperboloids

Accelerating the Nussinov RNA folding algorithm with CUDA/GPU

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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