A high-extensibility molecular dynamics simulation parallel computing system

Abstract

The application discloses a high-scalability molecular dynamics simulation parallel computing system and relates to the field of particle motion, comprising a domain decomposition module, a collective communication abstraction layer module, a short-range interaction calculation module and a long-range interaction calculation module; the domain decomposition module is used for uniformly dividing a global periodic simulation box into a plurality of subdomains; the collective communication abstraction layer module is used for shielding the back-end differences of different GPU special communication libraries and providing a standardized collective communication interface; the short-range interaction calculation module performs short-range force calculation and global mean force correction based on a random batch table method; and the long-range interaction calculation module performs long-range force calculation by synchronously generating consistent sampling vector sequences locally on each computing node based on a random batch Ewald method. The system can realize the high-efficiency communication abstraction and the random algorithm cooperative parallel molecular dynamics simulation system and method on the basis of maintaining the compatibility of the existing parallel computing ecology.

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