high performance computing on graphics processing units: hgpu.org

hgpu.org » Molecular dynamics

Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs)

Narayan Ganesan, Brad A. Bauer, Timothy R. Lucas, Sandeep Patel, Michela Taufer

Tags: Algorithms, Chemistry, Computational chemistry, Electrostatic potential, Electrostatics, Molecular dynamics

August 8, 2011 by hgpu

Hardware accelerators for biocomputing: A survey

Souradip Sarkar, Turbo Majumder, Ananth Kalyanaraman, Partha Pratim Pande

View

Download (PDF)

Tags: Biology, Cell processor, CUDA, FPGA, Molecular dynamics, nVidia, nVidia GeForce 7800 GTX, Performance, Review, Sequence alignment

August 7, 2011 by hgpu

Molecular Dynamics Simulations Using Graphics Processing Units

John A. Baker, Jonathan D. Hirst

Tags: Biomolecules, Chemistry, Molecular dynamics, Molecular modeling

July 22, 2011 by hgpu

Coming Soon: Research in a Cloud

Pam Frost Gorder

View

Download (PDF)

Source codes

Tags: Chemistry, Cloud, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 280, Package

June 18, 2011 by hgpu

Interactive Visualization of Molecular Surface Dynamics

Michael Krone, Katrin Bidmon, Thomas Ertl

View

Download (PDF)

Tags: Chemistry, GLSL, Molecular dynamics, Molecular surface, nVidia, nVidia GeForce GTX 280, OpenGL, Rendering, Visualization

June 18, 2011 by hgpu

Brownian dynamics simulations on CPU and GPU with BD_BOX

Maciej Dlugosz, Pawel Zielinski, Joanna Trylska

Source codes

Tags: Chemistry, CUDA, Molecular dynamics, MPI, nVidia, OpenMP, Package

June 16, 2011 by hgpu

Loose capacity-constrained representatives for the qualitative visual analysis in molecular dynamics

Steffen Frey, Thomas Schlomer, Sebastian Grottel, Carsten Dachsbacher, Oliver Deussen, Thomas Ertl

View

Download (PDF)

Tags: Computer science, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Visualization, Voronoi diagram

June 15, 2011 by hgpu

Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit

Li Liu, Xiaofeng Liu, Jiayu Gong, Hualiang Jiang, Honglin Li

Tags: Biology, Chemistry, CUDA, Macromolecule, Molecular dynamics, nVidia, Pharmaceuticals

June 2, 2011 by hgpu

Acceleration of the GAMESS-UK electronic structure package on graphical processing units

Karl A. Wilkinson, Paul Sherwood, Martyn F. Guest, Kevin J. Naidoo

Tags: Chemistry, Fortran, Molecular dynamics, Molecular modeling, nVidia

May 21, 2011 by hgpu

Improving numerical reproducibility and stability in large-scale numerical simulations on GPUs

Michela Taufer, Omar Padron, Philip Saponaro, Sandeep Patel

View

Download (PDF)

Tags: Chemistry, CUDA, Floating point error, Molecular dynamics, nVidia, Tesla S1070

April 25, 2011 by hgpu

The development of Mellanox/NVIDIA GPUDirect over InfiniBand-a new model for GPU to GPU communications

Gilad Shainer, Ali Ayoub, Pak Lui, Tong Liu, Michael Kagan, Christian Trott, Greg Scantlen, Paul Crozier

Tags: Computer science, Memory model, Molecular dynamics, Network communications, Networks, nVidia, Tesla

April 15, 2011 by hgpu

GPGPU supported cooperative acceleration in molecular dynamics

Gang Chen, Guobo Li, Songwen Pei, Baifeng Wu

Tags: ATI, Brook, Chemistry, Molecular dynamics

April 5, 2011 by hgpu

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

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

Optical flow algorithms for SYCL

SYCL in the edge: performance and energy evaluation for heterogeneous acceleration

OpenMP5-Offload-OpenMC-Intel-PVC

Distributed OpenMP Offloading of OpenMC on Intel GPU MAX Accelerators

See all packages

* * *

high performance computing on graphics processing units: hgpu.org

Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs)

Hardware accelerators for biocomputing: A survey

Molecular Dynamics Simulations Using Graphics Processing Units

Interactive Visualization of Molecular Surface Dynamics

Brownian dynamics simulations on CPU and GPU with BD_BOX

Loose capacity-constrained representatives for the qualitative visual analysis in molecular dynamics

Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit

Acceleration of the GAMESS-UK electronic structure package on graphical processing units

Improving numerical reproducibility and stability in large-scale numerical simulations on GPUs

The development of Mellanox/NVIDIA GPUDirect over InfiniBand-a new model for GPU to GPU communications

GPGPU supported cooperative acceleration in molecular dynamics

Recent source codes

QArray

Celerity: High-level C++ for Accelerator Clusters

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

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

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

Optical flow algorithms for SYCL

OpenMP5-Offload-OpenMC-Intel-PVC

Most viewed papers (last 30 days)