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Accelerating Molecular Docking by Parallelized Heterogeneous Computing – A Case Study of Performance, Quality of Results, and Energy-Efficiency using CPUs, GPUs, and FPGAs

Leonardo Solis Vasquez

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Tags: AMD Radeon RX Vega 56, ATI, Computer science, FPGA, Heterogeneous systems, Macromolecule, nVidia, OpenCL, Package, Physics, Tesla V100, Thesis

December 29, 2019 by hgpu

JAX, M.D.: End-to-End Differentiable, Hardware Accelerated, Molecular Dynamics in Pure Python

Samuel S. Schoenholz, Ekin D. Cubuk

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Tags: Biochemistry, Chemistry, Computational Physics, CUDA, Fortran, Machine learning, Materials Science, Molecular dynamics, Neural networks, nVidia, Package, Physics, Python

December 15, 2019 by hgpu

Accelerating Stochastic Simulations on GPUs Using OpenCL

Pilsung Kang

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Tags: Heterogeneous systems, nVidia, nVidia GeForce GTX 1080 Ti, OpenCL, Physics, Stochastic simulation

November 10, 2019 by hgpu

waLBerla: A block-structured high-performance framework for multiphysics simulations

Martin Bauer, Sebastian Eibl, Christian Godenschwager, Nils Kohl, Michael Kuron, Christoph Rettinger, Florian Schornbaum, Christoph Schwarzmeier, Dominik Thönnes, Harald Köstler, Ulrich Rüde

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Tags: Code generation, CUDA, Heterogeneous systems, Lattice Boltzmann model, MPI, nVidia, Package, Particle simulation, performance portability, Physics, Tesla P100

October 6, 2019 by hgpu

Efficient Simulation of Fluid Flow and Transport in Heterogeneous Media Using Graphics Processing Units (GPUs)

Hassan Dashtian, Muhammad Sahimi

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Tags: Computational Physics, CUDA, Heterogeneous systems, nVidia, nVidia GeForce GTX 880, Physics

August 18, 2019 by hgpu

PANNA: Properties from Artificial Neural Network Architectures

Ruggero Lot, Franco Pellegrini, Yusuf Shaidu, Emine Kucukbenli

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Tags: Deep learning, Machine learning, Molecular dynamics, Neural networks, Package, Physics, TensorFlow

July 10, 2019 by hgpu

PIConGPU: Predictive Simulations of Laser-Particle Accelerators with Manycore Hardware

Axel Hübl

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Tags: CUDA, HPC, nVidia, Package, Particle-in-cell methods, Physics, Tesla P100, Thesis

July 4, 2019 by hgpu

Classify QCD phase transition with deep learning

Long-Gang Pang, Kai Zhou, Nan Su, Hannah Petersen, Horst Stoecker, Xin-Nian Wang

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Tags: Deep learning, HEP, Machine learning, Neural networks, OpenCL, Package, Pattern recognition, Phase transition, Physics, QCD

June 2, 2019 by hgpu

FPGA-based acceleration of a particle simulation High Performance Computing application

Aldo Conte

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Tags: FPGA, Molecular dynamics, OpenCL, Particle simulation, Physics, Thesis

May 8, 2019 by hgpu

TensorNetwork: A Library for Physics and Machine Learning

Chase Roberts, Ashley Milsted, Martin Ganahl, Adam Zalcman, Bruce Fontaine, Yijian Zou, Jack Hidary, Guifre Vidal, Stefan Leichenauer

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Tags: Machine learning, Package, Physics, TensorFlow

May 8, 2019 by hgpu

OpenCL vs: Accelerated Finite-Difference Digital Synthesis

Harri Renney, Benedict R. Gaster, Tom Mitchell

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Tags: AMD Radeon 530, ATI, FDTD, Finite-difference time-domain, OpenCL, OpenGL, Package, Physics

April 14, 2019 by hgpu

High Performance Monte Carlo Simulation of Ising Model on TPU Clusters

Kun Yang, Yi-Fan Chen, Georgios Roumpos, Chris Colby, John Anderson

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Tags: Cloud, CUDA, Ising model, Machine learning, Monte Carlo simulation, Neural networks, nVidia, Package, Physics, Tesla V100, TPU

April 7, 2019 by hgpu

SolidTextureNets

On Demand Solid Texture Synthesis Using Deep 3D Networks

md_poly: A Performance-Portable Polyhedral Compiler Based on Multi-Dimensional Homomorphisms

deepnetts: Deep Netts Pure Java Deep Learning Engine

Towards High Performance Java-based Deep Learning Frameworks

PASTA: A Parallel Sparse Tensor Algorithm Benchmark Suite

A Parallel Sparse Tensor Benchmark Suite on CPUs and GPUs

TACO: The Tensor Algebra Compiler (taco) computes sparse tensor expressions on CPUs and GPUs

A Unified Iteration Space Transformation Framework for Sparse and Dense Tensor Algebra

OpenCL-FPGA-LLVM: LLVM-based automation of memory decoupling for OpenCL applications on FPGAs

LLVM-based automation of memory decoupling for OpenCL applications on FPGAs

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13-15

Boston, USA

7th International Workshop on OpenCL, 2019

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Boston, MA, USA

Distributed Heterogeneous Programming in C/C++ (DHPCC++), 2019

2019

May

Larnaca, Cyprus

3rd International Workshop on Theoretical Approaches to Performance Evaluation, Modeling and Simulation (TAPEMS), 2019

2019

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26-28

Rome, Italy

International Conference on Frontiers of Neural Networks (ICFNN), 2019

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high performance computing on graphics processing units: hgpu.org

Accelerating Molecular Docking by Parallelized Heterogeneous Computing – A Case Study of Performance, Quality of Results, and Energy-Efficiency using CPUs, GPUs, and FPGAs

JAX, M.D.: End-to-End Differentiable, Hardware Accelerated, Molecular Dynamics in Pure Python

Accelerating Stochastic Simulations on GPUs Using OpenCL

waLBerla: A block-structured high-performance framework for multiphysics simulations

Efficient Simulation of Fluid Flow and Transport in Heterogeneous Media Using Graphics Processing Units (GPUs)

PANNA: Properties from Artificial Neural Network Architectures

PIConGPU: Predictive Simulations of Laser-Particle Accelerators with Manycore Hardware

Classify QCD phase transition with deep learning

FPGA-based acceleration of a particle simulation High Performance Computing application

TensorNetwork: A Library for Physics and Machine Learning

OpenCL vs: Accelerated Finite-Difference Digital Synthesis

Recent source codes

SolidTextureNets

md_poly: A Performance-Portable Polyhedral Compiler Based on Multi-Dimensional Homomorphisms

deepnetts: Deep Netts Pure Java Deep Learning Engine

PASTA: A Parallel Sparse Tensor Algorithm Benchmark Suite

TACO: The Tensor Algebra Compiler (taco) computes sparse tensor expressions on CPUs and GPUs

OpenCL-FPGA-LLVM: LLVM-based automation of memory decoupling for OpenCL applications on FPGAs

CUDAnative.jl: Julia support for native CUDA programming

GPU explicit-state model checking

OCLADock: OpenCL Accelerated Molecular Docking

jax-md: Differentiable, Hardware Accelerated, Molecular Dynamics

Most viewed papers (last 30 days)

Featured events

8th International Workshop on OpenCL, including SYCLCon, 2019

7th International Workshop on OpenCL, 2019

Distributed Heterogeneous Programming in C/C++ (DHPCC++), 2019

3rd International Workshop on Theoretical Approaches to Performance Evaluation, Modeling and Simulation (TAPEMS), 2019

International Conference on Frontiers of Neural Networks (ICFNN), 2019