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A Case Study in Using OpenCL on FPGAs: Creating an Open-Source Accelerator of the AutoDock Molecular Docking Software

Leonardo Solis-Vasquez, Andreas Koch

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Tags: Chemistry, FPGA, Molecular dynamics, OpenCL, Package

August 11, 2018 by hgpu

Chebyshev Filter Diagonalization on Modern Manycore Processors and GPGPUs

Moritz Kreutzer, Georg Hager, Dominik Ernst, Holger Fehske, Alan R. Bishop, Gerhard Wellein

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Tags: Chemistry, Computational Physics, Computer science, CUDA, Intel Xeon Phi, nVidia, OpenMP, Package, Performance, Physics, Quantum Physics, Tesla P100

March 10, 2018 by hgpu

GAMER-2: a GPU-accelerated adaptive mesh refinement code — accuracy, performance, and scalability

Hsi-Yu Schive, John A. ZuHone, Nathan J. Goldbaum, Matthew J. Turk, Massimo Gaspari, Chin-Yu Cheng

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Tags: ARM, Astrophysics, Chemistry, CUDA, Instrumentation and Methods for Astrophysics, Magnetohydrodynamics, MPI, nVidia, OpenMP, Package, Tesla K20, Tesla P100

December 24, 2017 by hgpu

Molecular dynamics recipes for genome research

Tommaso Biagini, Giovanni Chillemi, Gianluigi Mazzoccoli, Alessandro Grottesi, Caterina Fusilli, Daniele Capocefalo, Stefano Castellana, Angelo Luigi Vescovi, Tommaso Mazza

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Tags: Benchmarking, Bioinformatics, Biology, Chemistry, CUDA, Genomics, Molecular dynamics, nVidia, OpenCL, Physics, Tesla C2070

December 19, 2017 by hgpu

Dynamic Parallelism in GPU Optimized Barnes Hut Trees for Molecular Dynamics Simulations

Melisa Carranza Zuniga

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Tags: Algorithms, Biology, Biomolecules, Biophysics, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480, Physics, Thesis

August 26, 2017 by hgpu

An efficient MPI/OpenMP parallelization of the Hartree-Fock method for the second generation of Intel Xeon Phi processor

Vladimir Mironov, Yuri Alexeev, Kristopher Keipert, Michael D'mello, Alexander Moskovsky, Mark S. Gordon

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Tags: Algorithms, Benchmarking, Chemistry, Computer science, Intel Xeon Phi, MPI, OpenMP, Physics

August 8, 2017 by hgpu

OpenCL-Based Implementation of an FPGA Accelerator for Molecular Dynamics Simulation

Hasitha Muthumala Waidyasooriya, Masanori Hariyama, Kota Kasahara

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Tags: Chemistry, FPGA, Heterogeneous systems, Molecular dynamics, OpenCL

July 5, 2017 by hgpu

MEDINA: MECCA Development in Accelerators – KPP Fortran to CUDA source-to-source Preprocessor

Michail Alvanos, Theodoros Christoudias

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Tags: Chemistry, Compilers, Computer science, CUDA, Fortran, nVidia, Package, Python

May 22, 2017 by hgpu

GPU accelerated atmospheric chemical kinetics in the ECHAM/MESSy (EMAC) Earth system model

Michail Alvanos, Theodoros Christoudias

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Tags: Chemistry, Code generation, CUDA, Earth and Space Sciences, Fortran, nVidia, Package, Tesla M2070

May 2, 2017 by hgpu

A Domain Specific Language for Performance Portable Molecular Dynamics Algorithms

William R. Saunders, James Grant, Eike H. Muller

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Tags: Algorithms, Biology, Chemistry, Code generation, Computer science, CUDA, Differential equations, DSL, Molecular dynamics, nVidia, Package, Partial differential equations, PDEs, Physics, Python, Tesla K20

April 15, 2017 by hgpu

Exploiting Multi-level Parallelism on a Many-core System for the Application of Hyperheuristics to a Molecular Docking Problem

Jose M. Cecilia, Jose-Matias, Cutillas-Lozano, Domingo Gimenez, Baldomero Imbernon

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Tags: Bioinformatics, Biology, Chemistry, Intel Xeon Phi, Metaheuristics, molecular docking

March 20, 2017 by hgpu

LAMMPS’ PPPM Long-Range Solver for the Second Generation Xeon Phi

William McDoniel, Markus Hohnerbach, Rodrigo Canales, Ahmed E. Ismail, Paolo Bientinesi

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Tags: Chemistry, Computer science, Intel Xeon Phi, Molecular dynamics, Performance

February 18, 2017 by hgpu

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OCLADock - OpenCL Accelerated Molecular Docking

A Case Study in Using OpenCL on FPGAs: Creating an Open-Source Accelerator of the AutoDock Molecular Docking Software

sentiment-discovery: Unsupervised Language Modeling at scale for robust sentiment classification

Large Scale Language Modeling: Converging on 40GB of Text in Four Hours

Parallax: A Tool for Automatic Parallelization of Deep Learning Training in Distributed Multi-GPU Environments

Parallax: Automatic Data-Parallel Training of Deep Neural Networks

OpenCLIPER: an OpenCL-based C++ Framework for Overhead-Reduced Medical Image processing and Reconstruction on heterogeneous Devices

OpenCLIPER: an OpenCL-based C++ Framework for Overhead-Reduced Medical Image Processing and Reconstruction on Heterogeneous Devices

Spatial: Specify Parameterized Accelerators Through Inordinately Abstract Language

Spatial: A Language and Compiler for Application Accelerators

cuPentBatch: A batched pentadiagonal solver for NVIDIA GPUs

cuPentBatch – A batched pentadiagonal solver for NVIDIA GPUs

LeFlow: Enabling Flexible FPGA High-Level Synthesis of Tensorflow Deep Neural Networks

CloudCL: Single-Paradigm Distributed Heterogeneous Computing for Cloud Infrastructures

Calamari: OCR Engine based on OCRopy and Kraken

Calamari – A High-Performance Tensorflow-based Deep Learning Package for Optical Character Recognition

FluidFFT: efficient and easy Fast Fourier Transform for Python

FluidFFT: common API (C++ and Python) for Fast Fourier Transform HPC libraries

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Academic Exchange Center in Ocean University of China, Qingdao, China

The 4th International Conference on Communication and Information Processing (ICCIP), 2018

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27-30

Hida Takayama, Japan

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Nagoya University, Japan

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MediaCityUK, Salford Quays, Greater Manchester, England

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high performance computing on graphics processing units: hgpu.org

Applications

A Case Study in Using OpenCL on FPGAs: Creating an Open-Source Accelerator of the AutoDock Molecular Docking Software

Chebyshev Filter Diagonalization on Modern Manycore Processors and GPGPUs

GAMER-2: a GPU-accelerated adaptive mesh refinement code — accuracy, performance, and scalability

Molecular dynamics recipes for genome research

Dynamic Parallelism in GPU Optimized Barnes Hut Trees for Molecular Dynamics Simulations

An efficient MPI/OpenMP parallelization of the Hartree-Fock method for the second generation of Intel Xeon Phi processor

OpenCL-Based Implementation of an FPGA Accelerator for Molecular Dynamics Simulation

MEDINA: MECCA Development in Accelerators – KPP Fortran to CUDA source-to-source Preprocessor

GPU accelerated atmospheric chemical kinetics in the ECHAM/MESSy (EMAC) Earth system model

A Domain Specific Language for Performance Portable Molecular Dynamics Algorithms

Exploiting Multi-level Parallelism on a Many-core System for the Application of Hyperheuristics to a Molecular Docking Problem

LAMMPS’ PPPM Long-Range Solver for the Second Generation Xeon Phi

Recent source codes

OCLADock - OpenCL Accelerated Molecular Docking

sentiment-discovery: Unsupervised Language Modeling at scale for robust sentiment classification

Parallax: A Tool for Automatic Parallelization of Deep Learning Training in Distributed Multi-GPU Environments

OpenCLIPER: an OpenCL-based C++ Framework for Overhead-Reduced Medical Image processing and Reconstruction on heterogeneous Devices

Spatial: Specify Parameterized Accelerators Through Inordinately Abstract Language

cuPentBatch: A batched pentadiagonal solver for NVIDIA GPUs

LeFlow: Enabling Flexible FPGA High-Level Synthesis of Tensorflow Deep Neural Networks

CloudCL: Single-Paradigm Distributed Heterogeneous Computing for Cloud Infrastructures

Calamari: OCR Engine based on OCRopy and Kraken

FluidFFT: efficient and easy Fast Fourier Transform for Python

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Featured events

The 3rd International Conference on Computer Systems and Communication Technology (ICCSCT), 2018

The 4th International Conference on Communication and Information Processing (ICCIP), 2018

The Third International Workshop on GPU Computing and AI (GCA), 2018

The 5th International Conference on Power and Energy Systems Engineering (CPESE), 2018

The 10th International Conference on Information Management and Engineering (ICIME), 2018