GPU implementation of atomic fluid MD simulation

Dawid, Aleksander

doi:10.17466/tq2022/26.1/b

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Tytuł artykułu

GPU implementation of atomic fluid MD simulation

Autorzy

Dawid Aleksander

Treść / Zawartość

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DOI

10.17466/tq2022/26.1/b

Warianty tytułu

Języki publikacji

Abstrakty

A computer simulation of an atomic fluid on a GPU was implemented using the CUDA architecture. It was shown that the programming model for efficient numerical computing applications was changing with the development of the CUDA architecture. The introduction of the L2 cache decreased the latency between the global GPU memory and the registers. The performed MD simulation using the global memory and registers showed that the average acceleration relative to the CPU reached 80 times for single-precision calculations. Usually, the shared block memory gives much be4er results for this kind of calculation. We have found that using the shared memory gives acceleration over 116 times in comparison to the CPU. It is about 49% faster than using the global memory and registers. It is shown here that the performance of generally available graphics cards for double-precision calculations is significantly lower than for single-precision calculations. The recorded double-precision acceleration relative to the CPU in our experiment averaged 6 and 7 times for the global and shared memory, respectively. We performed these calculations on two different CUDA enable device systems.

Słowa kluczowe

MD simulation GPU atomic fluid MD parallel algorithm

symulacja MD GPU płyn atomowy algorytm równoległy MD

Wydawca

Politechnika Gdańska

Czasopismo

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

Rocznik

2022

Tom

Vol. 26, No 1

Strony

25--37

Opis fizyczny

Bibliogr. 29 poz., rys., tab.

Twórcy

autor

Dawid Aleksander

Department of Transport and Computer Science, The University of Dąbrowa Górnicza, 1c Cieplaka St., 41-300 Dąbrowa Górnicza, Poland

Bibliografia

1. Huang B, Li Z, Liu Z, Zhou G, Hao S, Wu J, Gu B L, Duan W 2008 Adsorption of Gas Molecules on Graphene Nanoribbons and Its Implication for Nanoscale Molecule Sensor J. Phys. Chem. C. 112pp. 13442-13446
2. Zhang F, Yang F, Huang J, Sumpter B G and Qiao R 2016 Thermodynamics and Kinetics of Gas Storage in Porous Liquids J Phys. Chem B 120 pp. 7195-7200
3. Dawid A, Raczyński P and Gburski Z 2014 Depolarised Rayleigh light scattering in argon layer confined between graphite plains: MD simulation Mol. Phys. pp. 1-6
4. Dawid A and Gburski Z 1997 Dynamical properties of the argon-krypton clusters: molecular dynamics calculations J Mol. Struct. 410 pp. 507-511
5. Blaisten-Barojas E and D. Levesque 1986 Molecular-dynamics simulation of silicon clusters Phys Rev. B. 34 pp. 3910-3916
6. Dawid A and Gburski Z 1998 Interaction-induced absorption in argon-krypton mixture clusters: Molecular-dynamics study Phys Rev. A. 58 pp. 740-743
7. Sokol M, Dawid A, Dendzik Z and Gburski Z 2004 Structure and dynamics of water - molecular dynamics study J Mol. Struct. 704 pp. 341-345.
8. Akbarzadeh H, Abroshan H, Taherkhani F, Izanloo C and Parsafar G 2011 A Size dependence and effect of potential parameters on properties of nano-cavities in liquid xenon using molecular dynamics simulation Chem Phys. 381 pp. 44-48
9. Devarajan D, Liang L, Gu B, Brooks S C, Parks J M and Smith J C 2022 Molecular Dynamics Simulation of the Structures, Dynamics, and Aggregation of Dissolved Organic Matter Environ Sci. Technol. 54pp. 13527-13537
10. Dawid A and Gburski 2017 Z Molecular dynamics simulation of collision-induced absorption spectra of neon-krypton mixture thin layer confined between graphite walls J Mol. Liq 2017 245 pp. 85-90
11. Dawid A and Gburski Z 2017 Interaction-induced light scattering in thin neon film confined between graphite slabs: MD study J Mol. Liq 245 pp. 71-75
12. Dawid A and Gburski Z 2017 Structural and Dynamical Properties of Argon-Krypton Binary Mixture Confined Between Graphite Slabs: Molecular Dynamics Simulation Interface Stud. Appl 195
13. Piatek A, Dawid A and Gburski Z 2006 Theexistence of a plastic phase and a solid–liquid dynamical bistability region in small fullerene cluster (C60)7: molecular dynamics simulation J Phys. Condens. Matter 18 pp. 8471.
14. Dawid A and Gburski 2007 Z Dielectric relaxation of 4-cyano-4-n-pentylbiphenyl (5CB) thin layer adsorbed on carbon nanotube - MD simulationJ Non-Cryst. Solids 353 pp. 4339-4343.
15. Dawid A and Gwizdała W 2009 Dynamical and structural properties of 4-cyano-4-n-pentylbiphenyl (5CB) molecules adsorbed on carbon nanotubes of different chiralities: Computer simulation J Non-Cryst. Solids 355 pp. 1302-1306.
16. Raczyński P, Dawid A, Piętek A and Gburski Z 2006 Reorienatational dynamics of cholesterol molecules in thin film surrounded carbon nanotube: Molecular dynamics simulations J Mol. Struct. 792pp. 216-220.
17. Raczyński P, Dawid A, Sokoł M and Gburski Z 2007 The influence of the carbon nanotube on the structural and dynamical properties of cholesterol cluster Biomol Eng. 24 pp. 572-576.
18. Dawid A, Piątek A, Sokoł M and Gburski Z 2008 Dynamical properties of potassium ion K+ trapped in a fullerene C60 cage: An MD simulation J Non-Cryst. Solids 354 pp. 4296-4299.
19. Dawid A and Gorny K 2007 Dynamics of Endohedral Fullerene K+@C60 inside single walled carbon nanotube: MD simulation10
20. Dawid A, Gorny K and Gburski Z 2011 The structural studies of fullerenol C60(OH)24 and nitric oxide mixture in water solvent – MD simulation Nitric Oxide 25 pp. 373-380.
21. Liu W, Schmidt B, Voss G and Muller-Wittig W 2008 Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA Comput Phys. Commun. 179 pp. 634-641.
22. Kondratyuk N, Nikolskiy V, Pavlov D and Stegailov V 2021 GPU-accelerated molecular dynamics: State-of-art software performance and porting from Nvidia CUDA to AMD HIP Int J. High Perform. Comput. Appl. 35 pp. 312-324.
23. Dawid A 2019 GPU-Based Parallel Algorithm of Interaction Induced Light Scattering Simulations in Fluids TASK Q. 23 5-17
24. Dawid A 2020 GPU Implementation of the Parallel Ising Model Algorithm Using Object-Oriented Programming Springer International Publishing
25. NVIDIA 2013 CUDA Toolkit
26. Rapaport D C 2004 The Art of Molecular Dynamics Simulation Cambridge University Press
27. Frenkel D and Smit B 2001 Understanding Molecular Simulation From Algorithms to Applications Elsevier
28. Cuda C++ Best Practices Guide http://docs.nvidia.com/cuda/cuda-c-best-practices-guide/index.html. 2021
29. TechPowerUp Nvidia GeForce Gtx 960m Specshttps://www.techpowerup.com/gpu-specs/geforce-gtx-960m.c2635

Typ dokumentu

Bibliografia

Identyfikator YADDA

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