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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

Deep Learning for Computational Chemistry

Garrett B. Goh, Nathan O. Hodas, Abhinav Vishnu

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Tags: Algorithms, Chemistry, Computational chemistry, Computer science, Deep learning, Machine learning, Neural networks, Review

January 19, 2017 by hgpu

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HLS4ML

Fast inference of deep neural networks in FPGAs for particle physics

cytonRL: reinforcement learning, deep Q-network, double DQN, dueling DQN, prioritized experience replay

CytonRL: an Efficient Reinforcement Learning Open-source Toolkit Implemented in C++

DLL: Deep Learning Library (DLL) for C++ (ANNs, CNNs, RBMs, DBNs...)

DLL: A Blazing Fast Deep Neural Network Library

HCC: Open Source, Optimizing C++ Compiler for Heterogeneous Compute for the ROCm GPU Computing Platform

Evaluating Performance Tradeoffs on the Radeon Open Compute Platform

pynufft: Python non-uniform fast Fourier transform (NUFFT)

Python Non-Uniform Fast Fourier Transform (PyNUFFT): An Accelerated Non-Cartesian MRI Package on a Heterogeneous Platform (CPU/GPU)

MALBEC: a new CUDA-C ray-tracer in General Relativity

Volna-OP2: OP2 port of the original Volna code

The VOLNA-OP2 Tsunami Code (Version 1.0)

CuLDA_CGS: Solving Large-scale LDA Problems on GPUs

MeterPU: Generic Portable Measurement Framework for Multicore CPU and Multi-GPU Systems

Programming Abstractions and Optimization Techniques for GPU-based Heterogeneous Systems

GHOST: General, Hybrid and Optimized Sparse Toolkit

Chebyshev Filter Diagonalization on Modern Manycore Processors and GPGPUs

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high performance computing on graphics processing units: hgpu.org

Applications

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

Deep Learning for Computational Chemistry

Recent source codes

HLS4ML

cytonRL: reinforcement learning, deep Q-network, double DQN, dueling DQN, prioritized experience replay

DLL: Deep Learning Library (DLL) for C++ (ANNs, CNNs, RBMs, DBNs...)

HCC: Open Source, Optimizing C++ Compiler for Heterogeneous Compute for the ROCm GPU Computing Platform

pynufft: Python non-uniform fast Fourier transform (NUFFT)

MALBEC: a new CUDA-C ray-tracer in General Relativity

Volna-OP2: OP2 port of the original Volna code

CuLDA_CGS: Solving Large-scale LDA Problems on GPUs

MeterPU: Generic Portable Measurement Framework for Multicore CPU and Multi-GPU Systems

GHOST: General, Hybrid and Optimized Sparse Toolkit

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International Conference on Biomedicine & Pharmacotherapy, 2018

8th International Workshop on Computer Science and Engineering (WCSE’18), 2018

International Conference on Robotics, Artificial Intelligence, Automation and Mechatronics, 2018

The 3rd IEEE International Conference on Image, Vision and Computing (ICIVC), 2018

The 2th International Conference on Robotics and Automation Sciences (ICRAS), 2018