high performance computing on graphics processing units: hgpu.org

Applications

hgpu.org » Applications » Chemistry

Multi-Level Ewald: A Hybrid Multigrid/Fast Fourier Transform Approach to the Electrostatic Particle-Mesh Problem

David S. Cerutti, David A. Case

Tags: Chemistry, Molecular dynamics, Molecular simulation

January 25, 2011 by hgpu

A Graphics Processing Unit Implementation of Coulomb Interaction in Molecular Dynamics

Prateek K. Jha, Rastko Sknepnek, Guillermo I. Guerrero-Garcia, Monica Olvera de la Cruz

Tags: Chemistry, Molecular dynamics

January 25, 2011 by hgpu

Fast Calculation of Electrostatic Potentials on the GPU or the ASIC MD-GRAPE-3

Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Francesco Zerbetto, Siegfried Hofinger

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Tags: Biomolecules, Biophysics, Chemistry, Molecular simulation, nVidia, nVidia GeForce GTX 280, Poisson Boltzmann

January 25, 2011 by hgpu

Implementing molecular dynamics on hybrid high performance computers – short range forces

W. Michael Brown, Peng Wang, Steven J. Plimpton, Arnold N. Tharrington

Tags: Chemistry, CUDA, GPU cluster, Molecular dynamics, nVidia, Physics

January 22, 2011 by hgpu

Gaussian split Ewald: A fast Ewald mesh method for molecular simulation

Yibing Shan, John L. Klepeis, Michael P. Eastwood, Ron O. Dror, David E. Shaw

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Tags: Algorithms, Chemistry, Molecular dynamics, Molecular modeling

January 20, 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

Source codes

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

January 16, 2011 by hgpu

Simulating Lattice Spin Models on Graphics Processing Units

Tal Levy, Guy Cohen, Eran Rabani

Tags: Chemistry, CUDA, Monte Carlo simulation, nVidia, Physics

January 13, 2011 by hgpu

Interactive Volume Rendering of Functional Representations in Quantum Chemistry

Yun Jang and Ugo Varetto

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Tags: Cg, Chemistry, Molecular modeling, nVidia, nVidia GeForce GTX 260, Rendering

January 11, 2011 by hgpu

SCELib3.0: The new revision of SCELib, the parallel computational library of molecular properties in the Single Center Approach

N. Sanna, I. Baccarelli, G. Morelli

Tags: Biology, Chemistry, CUDA, Molecular modeling, nVidia

January 11, 2011 by hgpu

Molecular Dynamics Simulations on Commodity GPUs with CUDA

Weiguo Liu, Bertil Schmidt, Gerrit Voss, Wolfgang Muller-Wittig

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Tags: Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce 8800 GTX

January 10, 2011 by hgpu

Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors

Joseph E. Davis, Adnan Ozsoy, Sandeep Patel, Michela Taufer

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Tags: Biology, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce 9800 GX2, nVidia GeForce GTX 280, nVidia Quadro FX 5600

January 3, 2011 by hgpu

FPGA-based acceleration of CHARMM-potential minimization

Bharat Sukhwani, Martin C. Herbordt

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Tags: Chemistry, FPGA, Molecular modeling, nVidia, Performance, Tesla C1060

January 3, 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

Multi-Level Ewald: A Hybrid Multigrid/Fast Fourier Transform Approach to the Electrostatic Particle-Mesh Problem

A Graphics Processing Unit Implementation of Coulomb Interaction in Molecular Dynamics

Fast Calculation of Electrostatic Potentials on the GPU or the ASIC MD-GRAPE-3

Implementing molecular dynamics on hybrid high performance computers – short range forces

Gaussian split Ewald: A fast Ewald mesh method for molecular simulation

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

Simulating Lattice Spin Models on Graphics Processing Units

Interactive Volume Rendering of Functional Representations in Quantum Chemistry

SCELib3.0: The new revision of SCELib, the parallel computational library of molecular properties in the Single Center Approach

Molecular Dynamics Simulations on Commodity GPUs with CUDA

Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors

FPGA-based acceleration of CHARMM-potential minimization

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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