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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

Molecular Dynamics Simulation of Multi-Scale Flows on GPUs

S. Mulla, S. Ivekovic, J.M. Reese

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Tags: Biology, Chemistry, CUDA, Molecular dynamics, nVidia, OpenCL, Tesla M2075

August 12, 2013 by hgpu

Hybrid Acceleration of a Molecular Dynamics Simulation Using Short-Ranged Potentials

Julian Hornich

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Tags: Algorithms, Chemistry, CUDA, Molecular dynamics, nVidia, Tesla M2090, Thesis

July 5, 2013 by hgpu

Modernizing the core quantum chemistry algorithms

Andrey Asadchev

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Tags: Algorithms, Chemistry, Computational chemistry, CUDA, nVidia, Programming techniques, Tesla C2050, Thesis

June 8, 2013 by hgpu

Implementing Continuous Integration Software in an Established Computational Chemistry Software Package

Robin M. Betz, Ross C. Walker

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Tags: Benchmarking, Chemistry, Computational chemistry, CUDA, Molecular dynamics, nVidia, Software Engineering, Tesla M2090

May 21, 2013 by hgpu

Accelerating Population Balance Model-based particulate process simulations via parallel computing

Anuj Varghese Prakash

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Tags: Biochemistry, Chemistry, Computer science, CUDA, Distributed computing, nVidia, nVidia GeForce GTX 280, Thesis

April 26, 2013 by hgpu

GPU-SD and DPD Parallelization for Gromacs tools for molecular dynamics simulations

Nicolae Goga, Siewert Marrink, Ruxandra Cioromela, Florica Moldoveanu

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Tags: Algorithms, Bioinformatics, Biology, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce 9600 GT

April 21, 2013 by hgpu

Scaling up scientific computations by using map-reduce-like control flow on NUMA architectures

Vlad Slavici

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Tags: Algorithms, Chemistry, Computational chemistry, CUDA, MapReduce, Matrix multiplication, nVidia, Tesla M2090, Thesis

April 3, 2013 by hgpu

An application of graphical numerical accelerators in simulations of ion-transport through biological membranes

A. Gorecki

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Tags: Chemistry, CUDA, Differential equations, Electrochemistry, nVidia, ODEs, Ordinary differential equations, Tesla C870

March 26, 2013 by hgpu

Parallelization with Different API on Multicore Architecture

Georg Rempfer

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Tags: Chemistry, CUDA, Liquid crystals, nVidia, nVidia GeForce GTX 680, Physics, Statistical Mechanics, Thesis

March 18, 2013 by hgpu

Acceleration of Coarse Grain Molecular Dynamics on GPU Architectures

Ardita Shkurti, Mario Orsi, Enrico Macii, Elisa Ficarra, Andrea Acquaviva

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Tags: Algorithms, Chemistry, CUDA, Molecular dynamics, nVidia, nVidia GeForce GTX 480

March 2, 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

CATO: automatic source transformation to apply HPC frameworks with minimal user interaction

Compiler-assisted distribution of OpenMP code for improved scalability

ADIOS2.jl: a Julia interface to ADIOS2

Julia as a unifying end-to-end workflow language on the Frontier exascale system

Code generated HPC Kernels Using Llama-2-70b

Comparing Llama-2 and GPT-3 LLMs for HPC kernels generation

Scope is all you need: Transforming LLMs for HPC Code

pocl - Portable Computing Language

PoCL-R: An Open Standard Based Offloading Layer for Heterogeneous Multi-Access Edge Computing with Server Side Scalability

HPAC-Offload: Accelerating HPC Applications with Portable Approximate Computing on the GPU

openCLDispatcher

Novel insights on atomic synchronization for sort-based group-by on GPUs

CEED Benchmarks

Performant low-order matrix-free finite element kernels on GPU architectures

Sieve: Stratified GPU-Compute Workload Sampling

EngineCL: Usability and Performance in Heterogeneous Computing

Mashing load balancing algorithm to boost hybrid kernels in molecular dynamics simulations

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

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

Molecular Dynamics Simulation of Multi-Scale Flows on GPUs

Hybrid Acceleration of a Molecular Dynamics Simulation Using Short-Ranged Potentials

Modernizing the core quantum chemistry algorithms

Implementing Continuous Integration Software in an Established Computational Chemistry Software Package

Accelerating Population Balance Model-based particulate process simulations via parallel computing

GPU-SD and DPD Parallelization for Gromacs tools for molecular dynamics simulations

Scaling up scientific computations by using map-reduce-like control flow on NUMA architectures

An application of graphical numerical accelerators in simulations of ion-transport through biological membranes

Parallelization with Different API on Multicore Architecture

Acceleration of Coarse Grain Molecular Dynamics on GPU Architectures

Acceleration of the MMFF94 routines within OpenBabel using Eigen and OpenCL

Recent source codes

CATO: automatic source transformation to apply HPC frameworks with minimal user interaction

ADIOS2.jl: a Julia interface to ADIOS2

Code generated HPC Kernels Using Llama-2-70b

Scope is all you need: Transforming LLMs for HPC Code

pocl - Portable Computing Language

HPAC-Offload: Accelerating HPC Applications with Portable Approximate Computing on the GPU

openCLDispatcher

CEED Benchmarks

Sieve: Stratified GPU-Compute Workload Sampling

EngineCL: Usability and Performance in Heterogeneous Computing

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