Parallel Molecular Dynamics with Irregular Domain Decomposition

The spatial domain of Molecular Dynamics simulations is usually a regular box that can be easily divided in subdomains for parallel processing.Recent efforts aimed at simulating complex biological systems,like the blood flow inside arteries,require the execution of Parallel Molecular Dynamics(PMD)in vessels that have,by nature,an irregular shape.In those cases,the geometry of the domain becomes an additional input parameter that directly influences the outcome of the simulation.In this paper we discuss the problems due to the parallelization of MD in complex geometries and show an efficient and general method to perform MD in irregular domains.

High efficient parallel numerical surface wave model based on an irregular quasi-rectangular domain decomposition scheme

To achieve high parallel efficiency for the global MASNUM surface wave model, the algorithm of an irregular quasirectangular domain decomposition and related serializing of calculating points and data exchanging schemes are developed and conducted, based on the environment of Message Passing Interface(MPI). The new parallel version of the surface wave model is tested for parallel computing on the platform of the Sunway BlueLight supercomputer in the National Supercomputing Center in Jinan. The testing involves four horizontal resolutions, which are 1°×1°,(1/2)°×(1/2)°,(1/4)°×(1/4)°, and(1/8)°×(1/8)°. These tests are performed without data Input/Output(IO) and the maximum amount of processors used in these tests reaches to 131072. The testing results show that the computing speeds of the model with different resolutions are all increased with the increasing of numbers of processors. When the number of processors is four times that of the base processor number, the parallel efficiencies of all resolutions are greater than 80%. When the number of processors is eight times that of the base processor number, the parallel efficiency of tests with resolutions of 1°×1°,(1/2)°×(1/2)° and(1/4)°×(1/4)° is greater than 80%, and it is 62% for the test with a resolution of(1/8)°×(1/8)° using 131072 processors, which is the nearly all processors of Sunway BlueLight. When the processor's number is 24 times that of the base processor number, the parallel efficiencies for tests with resolutions of 1°×1°,(1/2)°×(1/2)°, and(1/4)°×(1/4)° are 72%, 62%, and 38%, respectively. The speedup and parallel efficiency indicate that the irregular quasi-rectangular domain decomposition and serialization schemes lead to high parallel efficiency and good scalability for a global numerical wave model.