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Solving Molecular Distance Geometry Problems in OpenCL

Istvan Lorentz, Razvan Andonie, Levente Fabry-Asztalos

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Tags: Chemistry, Computational chemistry, Molecular modeling, nVidia, nVidia GeForce GTX 560 Ti, OpenCL

June 27, 2012 by hgpu

Implementing density functional theory (DFT) methods on many-core GPGPU accelerators

Bishwajit Mohan Gosswami

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Tags: Chemistry, CUDA, Density-functional theory, nVidia, Tesla C2070, Thesis

June 19, 2012 by hgpu

GPUmotif: An Ultra-Fast and Energy-Efficient Motif Analysis Program Using Graphics Processing Units

Pooya Zandevakili, Ming Hu, Zhaohui Qin

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Tags: Algorithms, Biochemistry, Biology, Chemistry, Computational biology, Computer science, CUDA, Genetics, nVidia, nVidia GeForce GTX 260, nVidia GeForce GTX 480, Package

June 17, 2012 by hgpu

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

Andreas W. Gotz, Mark J. Williamson, Dong Xu, Duncan Poole, Scott Le Grand, Ross C. Walker

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Tags: Algorithms, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 580, Tesla C1060, Tesla C2070, Tesla M2090

May 26, 2012 by hgpu

Molecular Distance Geometry Optimization Using Geometric Build-up and Evolutionary Techniques on GPU

Levente Fabry-Asztalos, Istvan Lorentz, Razvan Andonie

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Tags: Chemistry, Molecular modeling, nVidia, nVidia GeForce GTX 560, OpenCL, Optimization

May 23, 2012 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

Implementing Molecular Dynamics on Hybrid High Performance Computers – Particle-Particle Particle-Mesh

W. Michael Brown, Axel Kohlmeyer, Steven J. Plimpton, Arnold N. Tharrington

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Tags: Algorithms, Chemistry, CUDA, Electrostatics, GPU cluster, Heterogeneous systems, Molecular dynamics, nVidia, OpenCL, OpenMPI, Package, Physics, Tesla M2070

February 10, 2012 by hgpu

Parallelizing Kernel Polynomial Method Applying Graphics Processing Units

Shixun Zhang, Shinichi Yamagiwa, Masahiko Okumura, Seiji Yunoki

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Tags: Algorithms, Chemistry, Condensed matter, CUDA, nVidia, Physics, Tesla C2050

January 10, 2012 by hgpu

Fat versus Thin Threading Approach on GPUs: Application to Stochastic Simulation of Chemical Reactions

Guido Klingbeil, Radek Erban, Mike Giles, Philip K. Maini

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Tags: Algorithms, Chemistry, CUDA, nVidia, nVidia GeForce GTX 260, Stochastic simulation

January 7, 2012 by hgpu

Parallel computing system for the efficient calculation of molecular similarity based on negative electrostatic potential

Raul Ernesto Torres Carvajal

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Tags: Algorithms, Chemistry, Cluster analysis, CUDA, Electrostatic potential, Electrostatics, nVidia, nVidia GeForce GT 240, Pattern recognition, Thesis

December 29, 2011 by hgpu

GPU-accelerated Chemical Similarity Assessment for Large Scale Databases

Marco Maggioni, Marco Domenico Santambrogio, Jie Liang

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Tags: Algorithms, Chemistry, CUDA, Databases, nVidia, nVidia GeForce 9400 M, nVidia GeForce GTX 460, Optimization

December 27, 2011 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

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

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high performance computing on graphics processing units: hgpu.org

Solving Molecular Distance Geometry Problems in OpenCL

Implementing density functional theory (DFT) methods on many-core GPGPU accelerators

GPUmotif: An Ultra-Fast and Energy-Efficient Motif Analysis Program Using Graphics Processing Units

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

Molecular Distance Geometry Optimization Using Geometric Build-up and Evolutionary Techniques on GPU

GPU Accelerated Molecular Surface Computing

Implementing Molecular Dynamics on Hybrid High Performance Computers – Particle-Particle Particle-Mesh

Parallelizing Kernel Polynomial Method Applying Graphics Processing Units

Fat versus Thin Threading Approach on GPUs: Application to Stochastic Simulation of Chemical Reactions

Parallel computing system for the efficient calculation of molecular similarity based on negative electrostatic potential

GPU-accelerated Chemical Similarity Assessment for Large Scale Databases

Parallel Contour-Buildup Algorithm for the Molecular Surface

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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