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Two Level Approach to Efficient Visualization of Protein Dynamics

Ove Daae Lampe, Ivan Viola, Nathalie Reuter, Helwig Hauser

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Tags: Biology, Molecular dynamics, nVidia, nVidia GeForce 8800 GTX, OpenGL, Visualization

February 4, 2011 by hgpu

Molecular dynamics simulation of the supercooled Al melt on GPUs

Roman Bystryi, Andrey Kazennov, Igor Morozov, Vasily Pisarev, Vladimir Stegailov

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Tags: Molecular dynamics, nVidia, nVidia GeForce GTX 260, Physics

January 25, 2011 by hgpu

Molecular dynamics simulations of the relaxation processes in the condensed matter on GPUs

I. V. Morozov, A. M. Kazennov, R. G. Bystryi, G. E. Norman, V. V. Pisarev, V. V. Stegailov

Tags: Molecular dynamics, nVidia, nVidia GeForce GTX 260, Physics

January 25, 2011 by hgpu

Efficient Parallel Implementation of Molecular Dynamics with Embedded Atom Method on Multi-core Platforms

Changjun Hu, Yali Liu, Jianjiang Li

Tags: Chemistry, Molecular dynamics, Molecular simulation, OpenMP

January 25, 2011 by hgpu

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

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

Energy efficient biomolecular simulations with FPGA-based reconfigurable computing

Ananth Nallamuthu, Melissa C. Smith, Scott Hampton, Pratul K. Agarwal, Sadaf R. Alam

Tags: Bioinformatics, Biology, FPGA, Molecular dynamics

January 19, 2011 by hgpu

Towards microsecond biological molecular dynamics simulations on hybrid processors

Scott Hampton, Pratul K. Agarwal, Sadaf R. Alam, Paul S. Crozier

Tags: Bioinformatics, Biology, CUDA, Molecular dynamics, nVidia, Tesla C1060, Tesla C2050

January 19, 2011 by hgpu

Optimal Utilization of Heterogeneous Resources for Biomolecular Simulations

Scott S. Hampton, Sadaf R. Alam, Paul S. Crozier, Pratul K. Agarwal

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Tags: Bioinformatics, Biology, CUDA, Molecular dynamics, nVidia, Tesla C1060, Tesla C2050

January 19, 2011 by hgpu

Using generalized ensemble simulations and Markov state models to identify conformational states

Gregory R. Bowman, Xuhui Huang, Vijay S. Pande

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Tags: CUDA, Molecular dynamics, Molecular modeling, nVidia, Package, Physics, Thermodynamics

January 16, 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

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high performance computing on graphics processing units: hgpu.org

Two Level Approach to Efficient Visualization of Protein Dynamics

Molecular dynamics simulation of the supercooled Al melt on GPUs

Molecular dynamics simulations of the relaxation processes in the condensed matter on GPUs

Efficient Parallel Implementation of Molecular Dynamics with Embedded Atom Method on Multi-core Platforms

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

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

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

Energy efficient biomolecular simulations with FPGA-based reconfigurable computing

Towards microsecond biological molecular dynamics simulations on hybrid processors

Optimal Utilization of Heterogeneous Resources for Biomolecular Simulations

Using generalized ensemble simulations and Markov state models to identify conformational states

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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