Abstract
Molecular Dynamics (MD) codes predict the fundamental properties of matter by following the trajectories of a collection of interacting model particles. To exploit diverse modern manycore hardware, efficient codes must use all available parallelism. At the same time they need to be portable and easily extendible by the domain specialist (physicist/chemist) without detailed knowledge of this hardware. To address this challenge, we recently described a new Domain Specific Language (DSL) for the development of performance portable MD codes based on a "Separation of Concerns": a Python framework automatically generates efficient parallel code for a range of target architectures. Electrostatic interactions between charged particles are important in many physical systems and often dominate the runtime. Here we discuss the inclusion of long-range interaction algorithms in our code generation framework. These algorithms require global communications and careful consideration has to be given to any impact on parallel scalability. We implemented an Ewald summation algorithm for electrostatic forces, present scaling comparisons for different system sizes and compare to the performance of existing codes. We also report on further performance optimisations delivered with OpenMP shared memory parallelism.
Original language | English |
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Title of host publication | Parallel Computing is Everywhere |
Subtitle of host publication | Proceedings of the ParCo2017 Parallel Computing Conference |
Editors | Sanzio Bassini, Marco Danelutto, Patrizio Dazzi, Gerhard R. Joubert, Frans Peters |
Publisher | IOS Press |
Pages | 37 - 46 |
Number of pages | 9 |
Volume | 32 |
ISBN (Electronic) | 978-1-61499-843-3 |
ISBN (Print) | 978-1-61499-842-6 |
DOIs | |
Publication status | Published - Mar 2018 |
Event | ParCo 2017 Parallel Computing Conference - Bologna, Italy Duration: 12 Sept 2017 → 15 Sept 2017 |
Publication series
Name | Advances in Parallel Computing |
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Publisher | IOS Press |
Volume | 32 |
Conference
Conference | ParCo 2017 Parallel Computing Conference |
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Country/Territory | Italy |
City | Bologna |
Period | 12/09/17 → 15/09/17 |
Keywords
- Domain Specific Language
- Electrostatic
- Ewald Summation
- Molecular Dynamics
- Parallel Computing
ASJC Scopus subject areas
- General Computer Science
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Balena High Performance Computing (HPC) System
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High Performance Computing (HPC) Facility
Chapman, S. (Manager)
University of BathFacility/equipment: Facility