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Using Compiler Directives for Performance Portability in Scientific Computing: Kernels from Molecular Simulation

Ada Sedova, Andreas Tillack, Arnold Tharrington

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Tags: Chemistry, Molecular dynamics, Molecular simulation, nVidia, OpenACC, performance portability, Physics, Tesla K20

March 3, 2019 by hgpu

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

IPMACC: a framework for translating OpenACC for C API to CUDA, OpenCL, and Intel ISPC

Loop Perforation in OpenACC

multiQueryStream: Concurrent query processing in a GPU-based database system

Concurrent query processing in a GPU-based database system

SYCL-DNN: The SYCL-DNN neural network acceleration library

Accelerated Neural Networks on OpenCL Devices Using SYCL-DNN

OpenCL vs: Accelerated Finite-Difference Digital Synthesis

SYCL-BLAS: An implementation of BLAS using the SYCL open standard for acceleration on OpenCL devices

Cross-Platform Performance Portability Using Highly Parametrized SYCL Kernels

High Performance Monte Carlo Simulation of Ising Model on TPU Clusters

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Larnaca, Cyprus

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

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

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Rome, Italy

International Conference on Frontiers of Artificial Intelligence and Machine Learning (FAIML), 2019

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high performance computing on graphics processing units: hgpu.org

Applications

Using Compiler Directives for Performance Portability in Scientific Computing: Kernels from Molecular Simulation

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

Recent source codes

IPMACC: a framework for translating OpenACC for C API to CUDA, OpenCL, and Intel ISPC

multiQueryStream: Concurrent query processing in a GPU-based database system

SYCL-DNN: The SYCL-DNN neural network acceleration library

OpenCL vs: Accelerated Finite-Difference Digital Synthesis

SYCL-BLAS: An implementation of BLAS using the SYCL open standard for acceleration on OpenCL devices

High Performance Monte Carlo Simulation of Ising Model on TPU Clusters

The Study of the OpenCL Processing Models for the FPGA Device

TonY: a framework to natively run deep learning frameworks on Apache Hadoop

fairseq: Facebook AI Research Sequence-to-Sequence Toolkit written in Python

mARGOt: Dynamic Application Autotuning for Self-Aware Approximate Computing

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Featured events

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

International Conference on Frontiers of Artificial Intelligence and Machine Learning (FAIML), 2019