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A flexible algorithm for calculating pair interactions on SIMD architectures

Szilard Pall, Berk Hess

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Tags: Algorithms, Computational Physics, CUDA, Molecular dynamics, nVidia, Physics

June 10, 2013 by hgpu

Implementing Continuous Integration Software in an Established Computational Chemistry Software Package

Robin M. Betz, Ross C. Walker

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Tags: Benchmarking, Chemistry, Computational chemistry, CUDA, Molecular dynamics, nVidia, Software Engineering, Tesla M2090

May 21, 2013 by hgpu

Programming for scientific computing on peta-scale heterogeneous parallel systems

Yang Can-qun, Wu Qiang, Tang Tao, Wang Feng, Xue Jing-ling

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Tags: Computer science, CUDA, Heterogeneous systems, Molecular dynamics, nVidia, Tesla M2050

May 13, 2013 by hgpu

GPU-SD and DPD Parallelization for Gromacs tools for molecular dynamics simulations

Nicolae Goga, Siewert Marrink, Ruxandra Cioromela, Florica Moldoveanu

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Tags: Algorithms, Bioinformatics, Biology, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce 9600 GT

April 21, 2013 by hgpu

Simulation of a flowing snow avalanche using molecular dynamics

Denizhan Gucer, Halil Bulent Ozguc

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Tags: Algorithms, Collision detection, Computer science, CUDA, Molecular dynamics, nVidia, nVidia GeForce 8800 GT, Rendering

March 14, 2013 by hgpu

Large-scale ferrofluid simulations on graphics processing units

A.Yu. Polyakov, T.V. Lyutyy, S. Denisov, V.V. Reva, P. Hanggi

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Tags: CUDA, Fluid simulation, Molecular dynamics, Numerical simulation, nVidia, Physics, Tesla M2050

March 2, 2013 by hgpu

Acceleration of Coarse Grain Molecular Dynamics on GPU Architectures

Ardita Shkurti, Mario Orsi, Enrico Macii, Elisa Ficarra, Andrea Acquaviva

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Tags: Algorithms, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480

March 2, 2013 by hgpu

Developing Performance-Portable Molecular Dynamics Kernels in OpenCL

S. J. Pennycook, S. A. Jarvis

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Source codes

Tags: ATI, ATI FirePro V7800, ATI Radeon HD 6550, Benchmarking, Computer science, Molecular dynamics, nVidia, nVidia GeForce GTX 680, OpenCL, Package, Performance, Tesla C1060, Tesla C2050

February 14, 2013 by hgpu

Exploring SIMD for Molecular Dynamics, Using Intel Xeon Processors and Intel Xeon Phi Coprocessors

S. J. Pennycook, C. J. Hughes, M. Smelyanskiy, S. A. Jarvis

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Tags: Algorithms, Benchmarking, Computer science, Intel, Intel Phi, Molecular dynamics

February 14, 2013 by hgpu

Bouncing Behavior of Microscopic Dust Aggregates

Alexander Seizinger, Wilhelm Kley

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Tags: Astrophysics, Earth and Planetary Astrophysics, Molecular dynamics, nVidia, nVidia GeForce GTX 460, nVidia GeForce GTX 570, Tesla C2070

January 17, 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

Long Timestep Molecular Dynamics on the Graphical Processing Unit

James C. Sweet, Ronald J. Nowling, Trevor Cickovski, Christopher R. Sweet, Vijay S. Pande, Jesus A. Izaguirre

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Tags: Biology, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 580, OpenCL, Package

January 4, 2013 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

A flexible algorithm for calculating pair interactions on SIMD architectures

Implementing Continuous Integration Software in an Established Computational Chemistry Software Package

Programming for scientific computing on peta-scale heterogeneous parallel systems

GPU-SD and DPD Parallelization for Gromacs tools for molecular dynamics simulations

Simulation of a flowing snow avalanche using molecular dynamics

Large-scale ferrofluid simulations on graphics processing units

Acceleration of Coarse Grain Molecular Dynamics on GPU Architectures

Developing Performance-Portable Molecular Dynamics Kernels in OpenCL

Exploring SIMD for Molecular Dynamics, Using Intel Xeon Processors and Intel Xeon Phi Coprocessors

Bouncing Behavior of Microscopic Dust Aggregates

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

Long Timestep Molecular Dynamics on the Graphical Processing Unit

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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