high performance computing on graphics processing units: hgpu.org

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hgpu.org » Applications » Chemistry

GPU Accelerated Dissipative Particle Dynamics with Parallel Cell-list Updating

Hao Wu, Junbo Xu, Shengfei Zhang, Hao Wen

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Tags: Algorithms, Benchmarking, Chemistry, CUDA, Fluid dynamics, nVidia, nVidia GeForce GTX 285, Optimization

November 30, 2011 by hgpu

Acceleration of computational quantum chemistry by heterogeneous computer architectures

Yuki Furukawa, Ryota Koga, Koji Yasuda

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Tags: Algorithms, Chemistry, Computational chemistry, CUDA, Heterogeneous systems, Molecular modeling, nVidia, nVidia GeForce GTX 580

November 30, 2011 by hgpu

Molecular Dynamics Simulation Based on Hadoop MapReduce

Chen He

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Tags: Chemistry, Cluster computing, CUDA, MapReduce, Molecular dynamics, nVidia, nVidia GeForce 9400 GT, Physics, Thesis

November 28, 2011 by hgpu

Many-body quantum chemistry on graphics processing units

A. Eugene DePrince III, Jeff R. Hammond, Stephen K. Gray

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Tags: Algorithms, Chemistry, Computational chemistry, CUDA, Heterogeneous systems, Matrix multiplication, Molecular modeling, nVidia, Tesla C2050

November 11, 2011 by hgpu

Development of a Flow Solver with Complex Kinetics on the Graphic Processing Units

Hai P. Le, Jean-Luc Cambier

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Tags: Chemistry, Computational Physics, CUDA, Finite volume method, Fluid dynamics, nVidia, Tesla C2050, Tesla C2070

October 25, 2011 by hgpu

Characterization of FPGA-based High Performance Computers

Karl Savio Pimenta Pereira

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Tags: Algorithms, Benchmarking, Chemistry, Computer science, CUDA, DSP, FFT, FPGA, Molecular dynamics, nVidia, nVidia GeForce GTX 280, OpenCL, Tesla C2050, Thesis

October 18, 2011 by hgpu

The Anatomy of High-Performance 2D Similarity Calculations

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

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Source codes

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

October 16, 2011 by hgpu

Fast analysis of molecular dynamics trajectories with graphics processing units-Radial distribution function histogramming

Benjamin G. Levine, John E. Stone, Axel Kohlmeyer

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Tags: Algorithms, Chemistry, CUDA, GPU cluster, Heterogeneous systems, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Visualization

September 21, 2011 by hgpu

High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs

John E. Stone, Jan Saam, David J. Hardy, Kirby L. Vandivort, Wen-mei W. Hwu, Klaus Schulten

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Tags: Algorithms, Chemistry, CUDA, nVidia, nVidia GeForce 8800 GTX, nVidia GeForce GTX 280, Performance, Programming techniques, Rendering, Visualization

September 7, 2011 by hgpu

Efficient Calculation of Pairwise Nonbonded Forces

Matt Chiu, Md. Ashfaquzzaman Khan, Martin C. Herbordt

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Tags: Chemistry, Electrostatics, FPGA, Molecular dynamics, Optimization, Performance

August 15, 2011 by hgpu

The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations

Urban Borstnik, Benjamin T. Miller, Bernard R. Brooks, Dusanka Janezic

Tags: Algorithms, Chemistry, Computational chemistry, Molecular dynamics, Performance

August 8, 2011 by hgpu

Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs)

Narayan Ganesan, Brad A. Bauer, Timothy R. Lucas, Sandeep Patel, Michela Taufer

Tags: Algorithms, Chemistry, Computational chemistry, Electrostatic potential, Electrostatics, Molecular dynamics

August 8, 2011 by hgpu

gpu_tracker: Context manager and CLI that tracks the computational-resource-usage of a code block or shell command, particularly the GPU usage

gpu_tracker: Python package for tracking and profiling GPU utilization in both desktop and high-performance computing environments

LOOPer: a polyhedral compiler for expressing fast and portable data parallel algorithms

LOOPer: A Learned Automatic Code Optimizer For Polyhedral Compilers

OpenMC Monte Carlo Code

Performance Portable Monte Carlo Particle Transport on Intel, NVIDIA, and AMD GPUs

Polygeist: C/C++ frontend for MLIR

Retargeting and Respecializing GPU Workloads for Performance Portability

Parallel Gaussian process with kernel approximation in CUDA

Optical flow algorithms for SYCL

SYCL in the edge: performance and energy evaluation for heterogeneous acceleration

OpenMP5-Offload-OpenMC-Intel-PVC

Distributed OpenMP Offloading of OpenMC on Intel GPU MAX Accelerators

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

GPU Accelerated Dissipative Particle Dynamics with Parallel Cell-list Updating

Acceleration of computational quantum chemistry by heterogeneous computer architectures

Molecular Dynamics Simulation Based on Hadoop MapReduce

Many-body quantum chemistry on graphics processing units

Development of a Flow Solver with Complex Kinetics on the Graphic Processing Units

Characterization of FPGA-based High Performance Computers

The Anatomy of High-Performance 2D Similarity Calculations

Fast analysis of molecular dynamics trajectories with graphics processing units-Radial distribution function histogramming

High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs

Efficient Calculation of Pairwise Nonbonded Forces

The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations

Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs)

Recent source codes

QArray

Celerity: High-level C++ for Accelerator Clusters

CIFAR-10 Airbench: 94% on CIFAR-10 in 3.29 second

gpu_tracker: Context manager and CLI that tracks the computational-resource-usage of a code block or shell command, particularly the GPU usage

LOOPer: a polyhedral compiler for expressing fast and portable data parallel algorithms

OpenMC Monte Carlo Code

Polygeist: C/C++ frontend for MLIR

Parallel Gaussian process with kernel approximation in CUDA

Optical flow algorithms for SYCL

OpenMP5-Offload-OpenMC-Intel-PVC

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