high performance computing on graphics processing units: hgpu.org

hgpu.org » Biomolecules

Scalable Multi-GPU Simulation of Long-Range Molecular Dynamics

Marcos Novalbos, Jaime Gonzalez, Miguel A. Otaduy, Roberto Martinez Benito, Alberto Sanchez

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Tags: Algorithms, Biomolecules, Chemistry, CUDA, Electrostatic potential, Electrostatics, FFT, Molecular dynamics, Multilevel summation, N-body simulation, nVidia, nVidia GeForce GTX 580, nVidia GeForce GTX Titan

September 15, 2014 by hgpu

A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers

Christopher D. Cooper, Jaydeep P. Bardhan, L. A. Barba

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Tags: Biomolecules, Boltzmann equation, Computational Physics, CUDA, Electrostatics, Intel Phi, nVidia, Package, Physics, Poisson Boltzmann, Python, Tesla C2075

September 17, 2013 by hgpu

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

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

Performance of a GPU-based Direct Summation Algorithm for Computation of Small Angle Scattering Profile

Konstantin Berlin, Nail A. Gumerov, Ramani Duraiswami, David Fushman

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Tags: Algorithms, Biology, Biomolecules, Fast multipole method, Macromolecule, nVidia, nVidia GeForce GT 330 M, nVidia GeForce GTX 295, OpenCL, RNA

June 12, 2013 by hgpu

Improved Performance of CaFE and IRIS Model Fitting Using CUDA

Dylan Jackson

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Tags: Biology, Biomolecules, CUDA, nVidia, nVidia GeForce GTX 680, Sensing, Thesis

May 31, 2013 by hgpu

ClusCo: clustering and comparison of protein models

Jamroz Michal, Kolinski Andrzej

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Tags: Biology, Biomolecules, Clustering, Computational Engineering, CUDA, Finance, nVidia, nVidia GeForce GTX 470, Package

February 20, 2013 by hgpu

A Simplified and Accurate Model of Power-Performance Efficiency on Emergent GPU Architectures

Shuaiwen Song, Chunyi Su, Barry Rountree, Kirk W. Cameron

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Tags: Biomolecules, Computer science, CUDA, Electrostatics, Energy-efficient computing, GPU cluster, Heterogeneous systems, Machine learning, nVidia, Tesla C2075, Tesla M2090

February 18, 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-Optimized Molecular Dynamics Simulations

Tyson J. Lipscomb

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Tags: Biology, Biomolecules, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, nVidia GeForce GTX 580, Optimization, Pseudo-random number generators, Review, RNA, Tesla C2070, Thesis

July 8, 2012 by hgpu

Multi-dimensional characterization of electrostatic surface potential computation on graphics processors

Mayank Daga, Wu-chun Feng

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Tags: Algorithms, Biology, Biomolecules, Computational Complexity, CUDA, Electrostatics, Molecular modeling, nVidia, Optimization, Tesla C1060, Tesla C2050

May 12, 2012 by hgpu

Development and evaluation of a GPU-optimized N-body term for the simulation of biomolecules

Timo Strunk, Moritz Wolf, Wolfgang Wenzel

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Tags: ATI, ATI Radeon HD 5870, Benchmarking, Biology, Biomolecules, Monte Carlo simulation, N-body simulation, nVidia, nVidia GeForce GTX 285, OpenCL, Optimization

October 30, 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

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high performance computing on graphics processing units: hgpu.org

Scalable Multi-GPU Simulation of Long-Range Molecular Dynamics

A biomolecular electrostatics solver using Python, GPUs and boundary elements that can handle solvent-filled cavities and Stern layers

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

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

Performance of a GPU-based Direct Summation Algorithm for Computation of Small Angle Scattering Profile

Improved Performance of CaFE and IRIS Model Fitting Using CUDA

ClusCo: clustering and comparison of protein models

A Simplified and Accurate Model of Power-Performance Efficiency on Emergent GPU Architectures

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

GPU-Optimized Molecular Dynamics Simulations

Multi-dimensional characterization of electrostatic surface potential computation on graphics processors

Development and evaluation of a GPU-optimized N-body term for the simulation of biomolecules

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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