Memory access optimization of molecular dynamics simulation software Crystal-MD on Sunway Taihulight
نویسندگان
چکیده
منابع مشابه
Comments on the parallelization efficiency of the Sunway TaihuLight supercomputer
In the world of supercomputers, the large number of processors requires to minimize the inefficiencies of parallelization, which appear as a sequential part of the program from the point of view of Amdahl’s law. The recently suggested new figure of merit is applied to the recently presented supercomputer, and the timeline of ”Top 500” supercomputers is scrutinized using the metric. It is demons...
متن کاملMemory-Access Optimization of Parallel Molecular Dynamics Simulation via Dynamic Data Reordering
Dynamic irregular applications such as molecular dynamics (MD) simulation often suffer considerable performance deterioration during execution. To address this problem, an optimal data-reordering schedule has been developed for runtime memory-access optimization of MD simulations on parallel computers. Analysis of the memory-access penalty during MD simulations shows that the performance improv...
متن کاملPipelining Computation and Optimization Strategies for Scaling GROMACS on the Sunway Many-Core Processor
The increasing gap between plentiful computing elements and limited memory bandwidth makes it increasingly difficult and sometimes even infeasible for HPC community to port more applications onto many-core processor archi‐ tectures. The Sunway many-core processor SW26010 used to build the Sunway TaihuLight System contains a total of 260 heterogeneous cores. All these cores can be divided into 4...
متن کاملInvestigation of Melting by Molecular Dynamics Simulation
The melting of a 64 ion microcrystal of KCI was studied by means of a molecular dynamics computer simulation. We used a central pair interaction with an inverse power law repulsion. The thermodynamics, kinetic and structural properties such as melting temperature, latent heat, mean square displacement, diffusion constant, radial distribution function and bond angle distribution are calculated. ...
متن کاملScalable coupling of Molecular Dynamics (MD) and Direct Numerical Simulation
The objective of this project was the development and performance optimisation of a coupling application. The coupler library is intended for interfacing massively-parallel algorithms for multi-physics simulations. The development of the coupler library adopted the same philosophy of the Message Passing Interface (MPI) library: The coupler was engineered as a set of libraries that are accessibl...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Tsinghua Science and Technology
سال: 2021
ISSN: 1007-0214
DOI: 10.26599/tst.2019.9010074