high performance computing on graphics processing units: hgpu.org

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Petascale computations for Large-scale Atomic and Molecular collisions

Brendan M McLaughlin, Connor P Ballance

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Tags: BLAS, Computational Physics, Computer science, CUDA, Fortran, Molecular simulation, MPI, nVidia, Tesla K20

April 4, 2014 by hgpu

Molecular Simulations using CUDA

Gerhard Burger

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Tags: CUDA, Molecular dynamics, Molecular simulation, Monte Carlo simulation, nVidia, nVidia GeForce GT 520, nVidia GeForce GTX 480, nVidia GeForce GTX 580, Physics, Tesla C2075, Thesis

October 29, 2013 by hgpu

GALAMOST: GPU-accelerated large-scale molecular simulation toolkit

You-Liang Zhu, Hong Liu, Zhan-Wei Li, Hu-Jun Qian, Giuseppe Milano, Zhong-Yuan Lu

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Tags: Chemical Physics, Computational Physics, CUDA, Molecular simulation, nVidia, nVidia GeForce GTX 580, Phase transition, Physics, Soft Condensed Matter, Tesla K20

October 10, 2013 by hgpu

Hardware Accelerated Molecular Docking: A Survey

Imre Pechan, Bela Feher

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Tags: Bioinformatics, Biology, CUDA, FPGA, Molecular simulation, nVidia, Tesla C1060

February 6, 2013 by hgpu

Acceleration of Monte-Carlo Molecular Simulations on Hybrid Computing Architectures

Claus Braun, Stefan Holst, Hans-Joachim Wunderlich, Juan Manuel Castillo, Joachim Gross

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Tags: CUDA, Hybrid computing, Molecular simulation, nVidia, Physics, Tesla, Thermodynamics

November 5, 2012 by hgpu

Parboil: A Revised Benchmark Suite for Scientific and Commercial Throughput Computing

John A. Stratton, Christopher Rodrigues, I-Jui Sung, Nady Obeid, Li-Wen Chang, Nasser Anssari, Geng Daniel Liu, Wen-mei W. Hwu

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Source codes

Tags: Algorithms, Benchmarking, Computer science, CUDA, Molecular simulation, MPI, nVidia, nVidia GeForce GTX 480, Optimization, Package

April 25, 2012 by hgpu

RNA secondary structure prediction using dynamic programming algorithm – A review and proposed work

M.N. Osman, R. Abdullah, N. AbdulRashid

Tags: Biology, Macromolecule, Molecular simulation, Pharmaceuticals

June 2, 2011 by hgpu

Accelerating Two Algorithms for Large-Scale Compound Selection on GPUs

Quan Liao, Jibo Wang, Ian A. Watson

Tags: Algorithms, Chemistry, Molecular simulation, nVidia

May 24, 2011 by hgpu

Accelerating Molecular Dynamics Simulations with GPUs

John Paul Walters, Vidyananth Balu, Vipin Chaudhary, David Kofke, Andrew Schultz

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

February 28, 2011 by hgpu

HexServer: an FFT-based protein docking server powered by graphics processors

Gary Macindoe, Lazaros Mavridis, Vishwesh Venkatraman, Marie-Dominique Devignes, David W. Ritchie

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Tags: Bioinformatics, Biology, CUDA, FFT, Molecular simulation, nVidia, Tesla C1060

February 25, 2011 by hgpu

Probing biomolecular machines with graphics processors

James C. Phillips, John E. Stone

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Tags: Biology, Biomolecules, CUDA, GPU cluster, Molecular simulation, nVidia, OpenCL, Review, Tesla S1070

February 23, 2011 by hgpu

VolQD: Direct Volume Rendering of Multi-million Atom Quantum Dot Simulations

Wei Qiao, David S. Ebert, Alireza Entezari, Marek Korkusinski, Gerhard Klimeck

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Tags: Molecular simulation, nVidia, nVidia GeForce 6800 Ultra, OpenGL, Physics, Rendering, Visualization

February 8, 2011 by hgpu

Faial: finds bugs in CUDA kernels

Sound and Partially-Complete Static Analysis of Data-Races in GPU Programs

Effects of OpenCL-Based Parallelization Methods on Explicit Numerical Methods to Solve the Heat Equation

UVaFTLE: Lagrangian finite time Lyapunov exponent extraction for fluid dynamic applications

Challenging Portability Paradigms: FPGA Acceleration Using SYCL and OpenCL

HPCToolkit

Refining HPCToolkit for application performance analysis at exascale

Open Catalog of Best Practices for Modernization and Optimization

Optimizing the Weather Research and Forecasting Model with OpenMP Offload and Codee

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high performance computing on graphics processing units: hgpu.org

Petascale computations for Large-scale Atomic and Molecular collisions

Molecular Simulations using CUDA

GALAMOST: GPU-accelerated large-scale molecular simulation toolkit

Hardware Accelerated Molecular Docking: A Survey

Acceleration of Monte-Carlo Molecular Simulations on Hybrid Computing Architectures

Parboil: A Revised Benchmark Suite for Scientific and Commercial Throughput Computing

RNA secondary structure prediction using dynamic programming algorithm – A review and proposed work

Accelerating Two Algorithms for Large-Scale Compound Selection on GPUs

Accelerating Molecular Dynamics Simulations with GPUs

HexServer: an FFT-based protein docking server powered by graphics processors

Probing biomolecular machines with graphics processors

VolQD: Direct Volume Rendering of Multi-million Atom Quantum Dot Simulations

Recent source codes

Faial: finds bugs in CUDA kernels

Effects of OpenCL-Based Parallelization Methods on Explicit Numerical Methods to Solve the Heat Equation

Intel® SHMEM: Device initiated shared memory based communication library

miniLB: Lattice Botlzmann miniapp w/SYCL

AFOCL

2domination

MFC: Exascale simulation of multiphase/physics fluid dynamics

UVaFTLE: Lagrangian finite time Lyapunov exponent extraction for fluid dynamic applications

HPCToolkit

Open Catalog of Best Practices for Modernization and Optimization

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