high performance computing on graphics processing units: hgpu.org

hgpu.org » Biomolecules

FPGA acceleration of rigid-molecule docking codes

Bharat Sukhwani, Martin C. Herbordt

View

Download (PDF)

Tags: Biology, Biomolecules, CUDA, FPGA, Molecular modeling, nVidia, Performance, Tesla C1060

August 15, 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

Massively parallelized replica-exchange simulations of polymers on GPUs

Jonathan Gross, Wolfhard Janke, Michael Bachmann

View

Download (PDF)

Tags: Biomolecules, Computational Physics, Condensed matter, CUDA, Monte Carlo simulation, nVidia, nVidia GeForce GTX 285, nVidia GeForce GTX 480, Physics, Polymer Systems, Tesla C1060

July 19, 2011 by hgpu

Towards accelerating molecular modeling via multi-scale approximation on a GPU

M. Daga, Wu-chun Feng, T. Scogland

Tags: Algorithms, Biomolecules, Electrostatic potential, Medicine, Molecular modeling

May 5, 2011 by hgpu

Probing biomolecular machines with graphics processors

James C. Phillips, John E. Stone

View

Download (PDF)

Tags: Biology, Biomolecules, CUDA, GPU cluster, Molecular simulation, nVidia, OpenCL, Review, Tesla S1070

February 23, 2011 by hgpu

Fast Calculation of Electrostatic Potentials on the GPU or the ASIC MD-GRAPE-3

Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Francesco Zerbetto, Siegfried Hofinger

View

Download (PDF)

Tags: Biomolecules, Biophysics, Chemistry, Molecular simulation, nVidia, nVidia GeForce GTX 280, Poisson Boltzmann

January 25, 2011 by hgpu

Langevin dynamics simulations of biomolecules on graphics processors

A. Zhmurov, R. I. Dima, Y. Kholodov, V. Barsegov

View

Download (PDF)

Tags: Biological Physics, Biomolecules, Condensed matter, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 295, Physics, Soft Condensed Matter

November 12, 2010 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

* * *

high performance computing on graphics processing units: hgpu.org

FPGA acceleration of rigid-molecule docking codes

Molecular Dynamics Simulations Using Graphics Processing Units

Massively parallelized replica-exchange simulations of polymers on GPUs

Towards accelerating molecular modeling via multi-scale approximation on a GPU

Probing biomolecular machines with graphics processors

Fast Calculation of Electrostatic Potentials on the GPU or the ASIC MD-GRAPE-3

Langevin dynamics simulations of biomolecules on graphics processors

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

Most viewed papers (last 30 days)