high performance computing on graphics processing units: hgpu.org

hgpu.org » Molecular surface

Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes

Tao Liao, Yongjie Zhang, Peter M. Kekenes-Huskey, Yuhui Cheng, Anushka Michailova, Andrew D. McCulloch, Michael Holst, J. Andrew McCammon

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Tags: Algorithms, Bioinformatics, Biology, Biomolecules, CUDA, KD-tree, Molecular surface, nVidia, nVidia GeForce GTX 680

August 9, 2013 by hgpu

A GPU-accelerated Direct-sum Boundary Integral Poisson-Boltzmann Solver

Weihua Geng, Ferosh Jacob

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Tags: Biomolecules, CUDA, Electrostatics, Linear Algebra, Mathematics, Molecular surface, Numerical Analysis, nVidia, Poisson Boltzmann, Tesla M2070

January 25, 2013 by hgpu

GPU Accelerated Molecular Surface Computing

Byungjoo Kim, Ku-Jin Kim, Joon-Kyung Seong

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Tags: Biochemistry, Chemistry, CUDA, KD-tree, Molecular surface, nVidia, nVidia GeForce GTX 590

February 26, 2012 by hgpu

Parallel Contour-Buildup Algorithm for the Molecular Surface

Michael Krone, Sebastian Grottel, Thomas Ertl

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Tags: Algorithms, Chemistry, CUDA, Molecular dynamics, Molecular surface, nVidia, nVidia GeForce GTX 580, Optimization, Pharmaceuticals, Visualization

December 20, 2011 by hgpu

Interactive Visualization of Molecular Surface Dynamics

Michael Krone, Katrin Bidmon, Thomas Ertl

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

June 18, 2011 by hgpu

GPU-based triangulation of the van der Waals surface

S. Dias, A. Gomes

Tags: Biology, Chemistry, Molecular modeling, Molecular surface

May 14, 2011 by hgpu

Parallel, stochastic measurement of molecular surface area

D. Juba, A. Varshney

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Tags: Chemistry, Computational chemistry, CUDA, Molecular modeling, Molecular surface, nVidia, nVidia GeForce 8800 GTX

November 3, 2010 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

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high performance computing on graphics processing units: hgpu.org

Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes

A GPU-accelerated Direct-sum Boundary Integral Poisson-Boltzmann Solver

GPU Accelerated Molecular Surface Computing

Parallel Contour-Buildup Algorithm for the Molecular Surface

Interactive Visualization of Molecular Surface Dynamics

GPU-based triangulation of the van der Waals surface

Parallel, stochastic measurement of molecular surface area

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

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