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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

Simulations of Large Particle Systems in Real Time

Witold Alda, Krzysztof Boryczko

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Tags: Algorithms, Computer science, CUDA, Molecular dynamics, nVidia, OpenCL, Particle simulation, Visualization

November 16, 2011 by hgpu

Exploring Fine-Grained Task-based Execution on Multi-GPU Systems

Long Chen, Oreste Villa, Guang R. Gao

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Tags: Computer science, CUDA, GPU cluster, Molecular dynamics, nVidia, Tesla C1060

November 1, 2011 by hgpu

Accelerated MD Program Using CUDA Technology

Hoang Van Hue, Nguyen Thi Thanh Ha, Pham Khac Hung

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Tags: CUDA, Materials Science, Molecular dynamics, nVidia, nVidia GeForce GTS 250, Physics

October 26, 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

Numerical Accuracy Analysis Based on the Discrete Stochastic Arithmetic on Multiprocessor Platforms

Christian Motzing

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Tags: Computer science, CUDA, Molecular dynamics, Numerical Analysis, nVidia, nVidia GeForce GTX 480, Review, Software Engineering, Thesis

October 17, 2011 by hgpu

Molecular dynamics simulation of UO2 nanocrystals melting

A.S. Boyarchenkov, S.I. Potashnikov, K.A. Nekrasov, A.Ya. Kupryazhkin

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Tags: CUDA, Molecular dynamics, Physics

October 9, 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

Two-Level Approach to Efficient Visualization of Protein Dynamics

Ove Daae Lampe, I. Viola, N. Reuter, H. Hauser

Tags: Bioinformatics, Biology, Molecular dynamics, Rendering, Visualization

August 31, 2011 by hgpu

Fine-grain Parallelism using Multi-core, Cell/BE, and GPU Systems

Frederico Pratas, Pedro Trancoso, Leonel Sousa, Alexandros Stamatakis, Guochun Shi, Volodymyr Kindratenko

Tags: Bioinformatics, Biology, Cell processor, CUDA, Molecular dynamics, nVidia

August 25, 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

SimSYCL: Synchronous, single-threaded, library-only SYCL implementation for debugging and verification

SimSYCL: A SYCL Implementation Targeting Development, Debugging, Simulation and Conformance

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

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

94% on CIFAR-10 in 3.29 Seconds on a Single GPU

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

See all packages

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high performance computing on graphics processing units: hgpu.org

Molecular Dynamics Simulation Based on Hadoop MapReduce

Simulations of Large Particle Systems in Real Time

Exploring Fine-Grained Task-based Execution on Multi-GPU Systems

Accelerated MD Program Using CUDA Technology

Characterization of FPGA-based High Performance Computers

Numerical Accuracy Analysis Based on the Discrete Stochastic Arithmetic on Multiprocessor Platforms

Molecular dynamics simulation of UO2 nanocrystals melting

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

Two-Level Approach to Efficient Visualization of Protein Dynamics

Fine-grain Parallelism using Multi-core, Cell/BE, and GPU Systems

Efficient Calculation of Pairwise Nonbonded Forces

The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations

Recent source codes

SimSYCL: Synchronous, single-threaded, library-only SYCL implementation for debugging and verification

GPU plugin for PySCF

QArray

Celerity: High-level C++ for Accelerator Clusters

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

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

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

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