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hgpu.org » Applications » Chemistry

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

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

Molecular Activity Prediction using Deep Learning Software Library

Yoshiki Kato, Shinji Hamada, Hitoshi Goto

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Tags: Bioinformatics, Chemistry, Computer science, CUDA, Deep learning, nVidia, Package, Python, Tesla K20

November 5, 2016 by hgpu

GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing

Ye Fang, Yun Ding, Wei P. Feinstein, David M. Koppelman, Juana Moreno, Mark Jarrell, J. Ramanujam, Michal Brylinski

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Tags: Algorithms, Chemistry, CUDA, Heterogeneous systems, Intel Xeon Phi, Medicine, Molecular dynamics, nVidia, nVidia GeForce GTX 980, OpenMP, Package

July 16, 2016 by hgpu

The Vectorization of the Tersoff Multi-Body Potential: An Exercise in Performance Portability

Markus Hohnerbach, Ahmed E. Ismail, Paolo Bientinesi

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Tags: Chemistry, Computational chemistry, Computer science, CUDA, Intel Xeon Phi, Materials Science, Molecular dynamics, MPI, nVidia, Package, performance portability, Tesla K20, Tesla K40

July 13, 2016 by hgpu

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

Mark James Abraham, Teemu Murtola, Roland Schulz, Szilard Pall, Jeremy C. Smith, Berk Hess, Erik Lindahl

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Tags: Algorithms, Biomolecules, Chemistry, CUDA, Heterogeneous systems, Molecular simulation, nVidia, nVidia GeForce GTX 980, OpenCL, Package, Tesla K40

July 20, 2015 by hgpu

A Highly Extensible Framework for Molecule Dynamic Simulation on GPUs

Xiao Zhang, Wan Guo, Xiao Qin, Xiaonan Zhao

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Tags: Chemistry, CUDA, Molecular dynamics, nVidia, Package, Tesla C2070, Tesla M2070, Tesla S1070

December 8, 2013 by hgpu

Implementing Molecular Dynamics on Hybrid High Performance Computers – Three-Body Potentials

W. Michael Brown, Masako Yamada

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Tags: Algorithms, Chemistry, CUDA, Molecular dynamics, nVidia, Package, Physics, Tesla K20

August 20, 2013 by hgpu

Acceleration of the MMFF94 routines within OpenBabel using Eigen and OpenCL

Omar Valerio Minero

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Tags: Chemistry, Molecular modeling, OpenCL, Package, Thesis

February 28, 2013 by hgpu

Long Timestep Molecular Dynamics on the Graphical Processing Unit

James C. Sweet, Ronald J. Nowling, Trevor Cickovski, Christopher R. Sweet, Vijay S. Pande, Jesus A. Izaguirre

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Tags: Biology, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 580, OpenCL, Package

January 4, 2013 by hgpu

HPCTransCompile: An AI Compiler Generated Dataset for High-Performance CUDA Transpilation and LLM Preliminary Exploration

Efficient Graph Embedding at Scale: Optimizing CPU-GPU-SSD Integration

Can Large Language Models Predict Parallel Code Performance?

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high performance computing on graphics processing units: hgpu.org

Applications

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

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

Molecular Activity Prediction using Deep Learning Software Library

GeauxDock: Accelerating Structure-Based Virtual Screening with Heterogeneous Computing

The Vectorization of the Tersoff Multi-Body Potential: An Exercise in Performance Portability

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

A Highly Extensible Framework for Molecule Dynamic Simulation on GPUs

Implementing Molecular Dynamics on Hybrid High Performance Computers – Three-Body Potentials

Acceleration of the MMFF94 routines within OpenBabel using Eigen and OpenCL

Long Timestep Molecular Dynamics on the Graphical Processing Unit

Recent source codes

HPCTransCompile: An AI Compiler Generated Dataset for High-Performance CUDA Transpilation and LLM Preliminary Exploration

chemtrain: Training Molecular Dynamics Potentials in JAX

microSYCL: SYCL micro-benchmarks repository

XaaS containers

SYCL Container

CASS: Cuda-Amd aSSembly

Cluser of smartphones for edge computing application using TensorFlow

CFAL-bench

Efficient Graph Embedding at Scale: Optimizing CPU-GPU-SSD Integration

Can Large Language Models Predict Parallel Code Performance?

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