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LAMMPS’ PPPM Long-Range Solver for the Second Generation Xeon Phi

William McDoniel, Markus Hohnerbach, Rodrigo Canales, Ahmed E. Ismail, Paolo Bientinesi

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Tags: Chemistry, Computer science, Intel Xeon Phi, Molecular dynamics, Performance

February 18, 2017 by hgpu

An FPGA Accelerator for Molecular Dynamics Simulation Using OpenCL

Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara

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Tags: Chemistry, FPGA, Heterogeneous systems, Molecular dynamics, OpenCL, Performance, Physics

January 10, 2017 by hgpu

A hybrid algorithm for parallel molecular dynamics simulations

Chris M. Mangiardi, Ralf Meyer

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Tags: Condensed matter, Intel Xeon Phi, Materials Science, Molecular dynamics

November 3, 2016 by hgpu

Efficient molecular dynamics simulations with many-body potentials on graphics processing units

Zheyong Fan, Wei Chen, Ville Vierimaa, Ari Harju

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Tags: Computational Physics, CUDA, Materials Science, Molecular dynamics, nVidia, Physics, Tesla K40

October 15, 2016 by hgpu

GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing

Ye Fang, Yun Ding, Wei P. Feinstein, David M. Koppelman, Juana Moreno, Mark Jarrell, J. Ramanujam, Michal Brylinski

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Tags: Algorithms, Chemistry, CUDA, Heterogeneous systems, Intel Xeon Phi, Medicine, Molecular dynamics, nVidia, nVidia GeForce GTX 980, OpenMP, Package

July 16, 2016 by hgpu

GPU Accelerated Discrete Element Method (DEM) Molecular Dynamics for Conservative, Faceted Particle Simulations

Matthew Spellings, Ryan L. Marson, Joshua A. Anderson, Sharon C. Glotzer

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Tags: Computational Physics, CUDA, Molecular dynamics, nVidia, nVidia Quadro M 6000, Package, Particle simulation, Physics

July 13, 2016 by hgpu

The Vectorization of the Tersoff Multi-Body Potential: An Exercise in Performance Portability

Markus Hohnerbach, Ahmed E. Ismail, Paolo Bientinesi

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Tags: Chemistry, Computational chemistry, Computer science, CUDA, Intel Xeon Phi, Materials Science, Molecular dynamics, MPI, nVidia, Package, performance portability, Tesla K20, Tesla K40

July 13, 2016 by hgpu

Optimization of Molecular Dynamics Simulation Code and Applications to Biomolecular Systems

David M. Bowman

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Tags: Biochemistry, Biomolecules, Chemistry, CUDA, Molecular dynamics, MPI, nVidia, OpenCL, OpenMP, Thesis

March 1, 2016 by hgpu

Study of low density nuclear matter with quantum molecular dynamics: the role of the symmetry energy

Rana Nandi, Stefan Schramm

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Tags: AMD FirePro S10000, ATI, Molecular dynamics, Nuclear Theory, OpenCL, Physics

January 12, 2016 by hgpu

Experimentation Procedure for Offloaded Mini-Apps Executed on Cluster Architectures with Xeon Phi Accelerators

Gary Lawson, Vaibhav Sundriyal, Masha Sosonkina, Yuzhong Shen

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Tags: Computer science, Heterogeneous systems, Intel Xeon Phi, Molecular dynamics

September 9, 2015 by hgpu

A parallel algorithm for implicit depletant simulations

Jens Glaser, Andrew S. Karas, Sharon C. Glotzer

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Tags: Condensed matter, CUDA, Molecular dynamics, nVidia, Package, Physics, Soft Condensed Matter, Tesla K20, Tesla K80

August 31, 2015 by hgpu

Best bang for your buck: GPU nodes for GROMACS biomolecular simulations

Carsten Kutzner, Szilard Pall, Martin Fechner, Ansgar Esztermann, Bert L. de Groot, Helmut Grubmuller

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Tags: Benchmarking, Biological Physics, Biomolecules, Computational Physics, Computer science, Molecular dynamics, Molecular simulation, MPI, nVidia, Package, Performance, Tesla K20, Tesla K40

July 6, 2015 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

LAMMPS’ PPPM Long-Range Solver for the Second Generation Xeon Phi

An FPGA Accelerator for Molecular Dynamics Simulation Using OpenCL

A hybrid algorithm for parallel molecular dynamics simulations

Efficient molecular dynamics simulations with many-body potentials on graphics processing units

GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing

GPU Accelerated Discrete Element Method (DEM) Molecular Dynamics for Conservative, Faceted Particle Simulations

The Vectorization of the Tersoff Multi-Body Potential: An Exercise in Performance Portability

Optimization of Molecular Dynamics Simulation Code and Applications to Biomolecular Systems

Study of low density nuclear matter with quantum molecular dynamics: the role of the symmetry energy

Experimentation Procedure for Offloaded Mini-Apps Executed on Cluster Architectures with Xeon Phi Accelerators

A parallel algorithm for implicit depletant simulations

Best bang for your buck: GPU nodes for GROMACS biomolecular 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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