Research On Parallel Acceleration Technology For AMBER:a Molecular Dynamic Simulation Software On TianHe-2 Supercomputer

Molecular dynamics(MD)is a computer simulation of physical movements of atoms and molecules.With the continuous improvement and perfection in methods,molecular dynamics simulation is becoming more and more flexible with more function in different application area,and the simulation scale is also expanding.However,the molecular dynamics simulation for system with billions of atomic in microsecond scale requires a large amount of computing resources and time,while the current existing server and molecular dynamics simulation algorithm can't deal with such a large scale dynamic simulation task.The research subject is aimed at the above problems,according to the large scale CPU-MIC micro heterogeneous system structure of the TianHe-2 supercomputer system,achieving the goal to accelerate Assisted Model Building with Energy Refinement(AMBER)on parallel.Under the premise of ensuring the correct results,we carry out some parallel optimization in different levels and scales for AMBER,the main research work is as follows:First of all,a fine grained parallel optimization is conducted in the CPU for the sander program of the AMBER software package.As the simulator of AMBER software package,sander is the core of molecular dynamics simulation.By removing the cycle dependent and improving the data structure,and so on,we can finally achieve the parallel acceleration of the molecular dynamics simulation program AMBER-sander in fine grain based on OpenMP programming.As the MIC(Integrated Cores Many)Co processor is provided with a strong computing power,MIC will be used to Accelerate the sander program.We port the hot area of the AMBER-sander to the MIC,for the first time,parallel acceleration of molecular dynamics simulation program AMBER-sander based on MIC transplantation is finished.Ultimately we obtained the acceleration of 3 to 4 times,comparing with the origin program.Secondly,in order to make full use of the computing resources of CPU and MIC,we design and implement a parallel optimization algorithm for the molecular dynamics simulation of the CPU/MIC micro heterogeneous cooperative in TianHe-2 supercomputer.Through the parallel optimization methods including memory management optimization,data transmission optimization,the communication latency hiding,vectorization and load balancing,we achieved 5-6 times acceleration compared with the origin program on a single node,and program sander-mic extended from single CPU and single MIC co parallel speedup to multi CPU and multi MIC Card.Finally,through the analysis of the scalability of AMBER-sander,it is carried out in the multi node layer in parallel.For molecular dynamics simulation algorithm,the data reduction and data distribution are needed in every iteration.However as the number of iterations is large,Communication overhead becomes a bottleneck for multi node parallel optimization.But as long as ensuring that the calculation results are within a certain error,some optimizations are applied to the algorithm,for example,changing the frequent of data reduction.The communication overhead can be greatly reduced,and the parallel scalability of the program can be improved,which make the program can be run efficiently in TianHe-2.In a word,based on TianHe-2,the parallel optimization of molecular dynamics simulation software AMBER-sander is carried out at three levels.From the single CPU on the fine grained OpenMP parallel,single node CPU/MIC parallel optimization,to multi node and multi node multi MIC card,the highest speedup of 5X-6X is achieved,compared to the original program has a different degree of acceleration.