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Accelerating Molecular Dynamics Simulations with GPUs

John Paul Walters, Vidyananth Balu, Vipin Chaudhary, David Kofke, Andrew Schultz

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Tags: Chemistry, CUDA, Molecular dynamics, Molecular simulation, nVidia, nVidia GeForce 8800 GTX

February 28, 2011 by hgpu

Fast and Accurate Generalized Harmonic Analysis and Its Parallel Computation by GPU

Hisayori Noda, Akinori Nishihara

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Tags: Computer science, CUDA, FFT, nVidia

February 28, 2011 by hgpu

A Case Study for Petascale Applications in Astrophysics: Simulating Gamma-Ray Bursts

C. D. Ott, E. Schnetter, G. Allen, E. Seidel, J. Tao, B. Zink

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Tags: Astrophysics, CUDA, Instrumentation and Methods for Astrophysics, nVidia, nVidia Quadro FX 5600

February 28, 2011 by hgpu

A general relativistic evolution code on CUDA architectures

Burkhard Zink

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Tags: Astrophysics, CUDA, Finite difference, Instrumentation and Methods for Astrophysics, nVidia, nVidia Quadro FX 5600

February 28, 2011 by hgpu

HORIZON: Accelerated General Relativistic Magnetohydrodynamics

Burkhard Zink

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Tags: Computational Physics, CUDA, General Relativity and Quantum Cosmology, GPU cluster, Gravitation, Instrumentation and Methods for Astrophysics, Magnetohydrodynamics, MPI, nVidia, nVidia GeForce GTX 580, Tesla C2070

February 28, 2011 by hgpu

Calculation by articificial compressibility method and virtual flux method on GPU

I. Tanno, K. Morinishi, N. Satofuka, Y. Watanabe

Tags: CUDA, Fluid dynamics, nVidia

February 28, 2011 by hgpu

STOCHSIMGPU: Parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

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

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Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce 8800, Package, Stochastic simulation

February 28, 2011 by hgpu

Automatic data movement and computation mapping for multi-level parallel architectures with explicitly managed memories

Muthu Manikandan Baskaran, Uday Bondhugula, Sriram Krishnamoorthy, J. Ramanujam, Atanas Rountev, P. Sadayappan

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Tags: Algorithms, Code generation, Compilers, Computer science, CUDA, nVidia, nVidia GeForce 8800 GTX, Optimization, Performance

February 28, 2011 by hgpu

Data Mining and Machine Learning in Astronomy

Nicholas M. Ball, Robert J. Brunner

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Tags: Astrophysics, Cosmology and Extragalactic Astrophysics, CUDA, Data mining, Instrumentation and Methods for Astrophysics, nVidia, Review

February 27, 2011 by hgpu

A Method for Accelerating Bronchoscope Tracking Based on Image Registration by GPGPU

Takamasa Sugiura, Daisuke Deguchi, Takayuki Kitasaka, Kensaku Mori, Yasuhito Suenaga

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Tags: Computed tomography, CT, CUDA, Image registration, Medicine, nVidia, nVidia GeForce 8800 GTX

February 27, 2011 by hgpu

CUDAlign: using GPU to accelerate the comparison of megabase genomic sequences

Edans Flavius O. Sandes, Alba Cristina M.A. de Melo

Tags: Bioinformatics, Biology, CUDA, nVidia, nVidia GeForce GTX 280, Sequence alignment, Smith-Waterman algorithm

February 27, 2011 by hgpu

Size Matters: Space/Time Tradeoffs to Improve GPGPU Applications Performance

Abdullah Gharaibeh, Matei Ripeanu

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Tags: Bioinformatics, Biology, Computational biology, CUDA, nVidia, nVidia GeForce 8800 GTX, Package, Sequence alignment, Short read mapping, Suffix trees

February 27, 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

Accelerating Molecular Dynamics Simulations with GPUs

Fast and Accurate Generalized Harmonic Analysis and Its Parallel Computation by GPU

A Case Study for Petascale Applications in Astrophysics: Simulating Gamma-Ray Bursts

A general relativistic evolution code on CUDA architectures

HORIZON: Accelerated General Relativistic Magnetohydrodynamics

Calculation by articificial compressibility method and virtual flux method on GPU

STOCHSIMGPU: Parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

Automatic data movement and computation mapping for multi-level parallel architectures with explicitly managed memories

Data Mining and Machine Learning in Astronomy

A Method for Accelerating Bronchoscope Tracking Based on Image Registration by GPGPU

CUDAlign: using GPU to accelerate the comparison of megabase genomic sequences

Size Matters: Space/Time Tradeoffs to Improve GPGPU Applications Performance

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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