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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

Scaling Soft Matter Physics to Thousands of GPUs in Parallel

Alan Gray, Alistair Hart, Oliver Henrich, Kevin Stratford

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Tags: CUDA, Fluid dynamics, Lattice Boltzmann model, Molecular dynamics, nVidia, Physics, Tesla K20

October 15, 2013 by hgpu

Measurements of performance of hardware and general purpose classical molecular dynamics simulation software

Jose O. Sotero-Esteva

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Tags: CUDA, Molecular dynamics, nVidia, Physics, Tesla C2075

October 5, 2013 by hgpu

Kokkos: Enabling performance portability across manycore architectures

H. Carter Edwards, Christian R. Trott

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Source codes

Tags: Code generation, Computer science, CUDA, Intel Phi, Molecular dynamics, nVidia, Package, Tesla K20

September 17, 2013 by hgpu

On the Use of Graphics Processing Units (GPUs) for Molecular Dynamics Simulation of Spherical Particles

R.C. Hidalgo, T. Kanzaki, F. Alonso-Marroquin, S. Luding

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Tags: CUDA, Molecular dynamics, nVidia, nVidia GeForce GT 430, Physics

August 28, 2013 by hgpu

The development and expansion of HOOMD-blue through six years of GPU proliferation

Joshua A. Anderson, Sharon C. Glotzer

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Tags: Computational Physics, CUDA, Molecular dynamics, nVidia, nVidia GeForce 9800 GTX, nVidia GeForce GTX 580, nVidia GeForce GTX Titan, Package, Physics, Python, Software Engineering, Tesla S1070

August 27, 2013 by hgpu

Tight Binding Molecular Dynamics on CPU and GPU clusters

Dimitar Pashov

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Tags: Algorithms, CUDA, Electrostatics, Fortran, GPU cluster, Linear Algebra, Molecular dynamics, MPI, nVidia, Physics, Tesla K20

August 23, 2013 by hgpu

Implementing Molecular Dynamics on Hybrid High Performance Computers – Three-Body Potentials

W. Michael Brown, Masako Yamada

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Tags: Algorithms, Chemistry, CUDA, Molecular dynamics, nVidia, Package, Physics, Tesla K20

August 20, 2013 by hgpu

A GPU implementation for improved granular simulations with LAMMPS

Emmanuel N. Millan, Christian Ringl, Carlos S. Bederian, Maria Fabiana Piccoli, Carlos Garcia Garino, Herbert M. Urbassek, Eduardo M. Bringa

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Tags: CUDA, Molecular dynamics, nVidia, Performance, Physics, Tesla C2050, Tesla C2075, Tesla M2090

August 18, 2013 by hgpu

Molecular Dynamics Simulation of Multi-Scale Flows on GPUs

S. Mulla, S. Ivekovic, J.M. Reese

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Tags: Biology, Chemistry, CUDA, Molecular dynamics, nVidia, OpenCL, Tesla M2075

August 12, 2013 by hgpu

Hybrid Acceleration of a Molecular Dynamics Simulation Using Short-Ranged Potentials

Julian Hornich

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Tags: Algorithms, Chemistry, CUDA, Molecular dynamics, nVidia, Tesla M2090, Thesis

July 5, 2013 by hgpu

GPU-Optimized Hybrid Neighbor/Cell List Algorithm for Coarse-Grained Molecular Dynamics Simulations

Andrew J. Proctor

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Tags: Algorithms, Biomolecules, Computer science, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Tesla C2070, Thesis

June 16, 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

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high performance computing on graphics processing units: hgpu.org

Molecular Simulations using CUDA

Scaling Soft Matter Physics to Thousands of GPUs in Parallel

Measurements of performance of hardware and general purpose classical molecular dynamics simulation software

Kokkos: Enabling performance portability across manycore architectures

On the Use of Graphics Processing Units (GPUs) for Molecular Dynamics Simulation of Spherical Particles

The development and expansion of HOOMD-blue through six years of GPU proliferation

Tight Binding Molecular Dynamics on CPU and GPU clusters

Implementing Molecular Dynamics on Hybrid High Performance Computers – Three-Body Potentials

A GPU implementation for improved granular simulations with LAMMPS

Molecular Dynamics Simulation of Multi-Scale Flows on GPUs

Hybrid Acceleration of a Molecular Dynamics Simulation Using Short-Ranged Potentials

GPU-Optimized Hybrid Neighbor/Cell List Algorithm for Coarse-Grained 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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