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Implementation of the Particle Mesh Ewald method on a GPU
KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA.
2016 (English)Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesisAlternative title
Implementering av Particle Mesh Ewald metoden på en GPU (Swedish)
Abstract [en]

The Particle Mesh Ewald (PME) method is used for efficient long-range electrostatic calculations in molecular dynamics (MD).

In this project, PME is implemented for a single GPU alongside the existing CPU implementation, using the code base of an open source MD software GROMACS and NVIDIA CUDA toolkit. The performance of the PME GPU implementation is then studied.

The motivation for the project is examining the PME algorithm’s parallelism, and its potential benefit for performance scalability of MD simulations on various hardware.

Abstract [sv]

Particle Mesh Ewald (PME) metoden används inom molekyldynamiken (MD) för effektiva elektrostatiska beräkningar med långdistanspotentialer.

I detta projekt, PME implementeras för ett enda GPU tillsammans med en redan existerande CPU implementation. Här används koden av den fri tillgängliga MD mjukvaran GROMACS samt NVIDIA CUDA programmeringsomgivningen. Hädanefter, prestandan av PME GPU implementationen studeras.

Motivationen bakom projektet är att undersöka PME algoritmens parallelliserbarhet. Detta kan medföra en potentiell fördel för skalbarheten av prestandan för MD simulationer på olika hårdvaror.

Place, publisher, year, edition, pages
TRITA-MAT-E, 2016:43
National Category
Computational Mathematics
URN: urn:nbn:se:kth:diva-190048OAI: diva2:950752
Subject / course
Scientific Computing
Educational program
Master of Science - Computer Simulation for Science and Engineering
Available from: 2016-08-02 Created: 2016-08-02 Last updated: 2016-08-02Bibliographically approved

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