ﻻ يوجد ملخص باللغة العربية
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.
Developers of Molecular Dynamics (MD) codes face significant challenges when adapting existing simulation packages to new hardware. In a continuously diversifying hardware landscape it becomes increasingly difficult for scientists to be experts both
Searching for geometric objects that are close in space is a fundamental component of many applications. The performance of search algorithms comes to the forefront as the size of a problem increases both in terms of total object count as well as in
Programming current supercomputers efficiently is a challenging task. Multiple levels of parallelism on the core, on the compute node, and between nodes need to be exploited to make full use of the system. Heterogeneous hardware architectures with ac
The performance of biomolecular molecular dynamics simulations has steadily increased on modern high performance computing resources but acceleration of the analysis of the output trajectories has lagged behind so that analyzing simulations is becomi
Inspired by one--dimensional light--particle systems, the dynamics of a non-Hamiltonian system with long--range forces is investigated. While the molecular dynamics does not reach an equilibrium state, it may be approximated in the thermodynamic limi