Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Empirical potential structure refinement (EPSR) is a neutron scattering data analysis algorithm and a software package. It was developed by the British spallation neutron source (ISIS) Disordered Materials Group in 1980s, and aims to construct the most-probable atomic structures of disordered liquids. It has been extensively used during the past decades, and has generated reliable results. However, it is programmed in Fortran and implements a shared-memory architecture with OpenMP. With the extensive construction of supercomputer clusters and the widespread use of graphics processing unit (GPU) acceleration technology, it is now necessary to rebuild the EPSR with these techniques in the effort to improve its calculation speed. In this study, an open source framework NeuDATool is proposed. It is programmed in the object-oriented language C++, can be paralleled across nodes within a computer cluster, and supports GPU acceleration. The performance of NeuDATool has been tested with water and amorphous silica neutron scattering data. The test shows that the software could reconstruct the correct microstructure of the samples, and the calculation speed with GPU acceleration could increase by more than 400 times compared with CPU serial algorithm at a simulation box consists about 100 thousand atoms. NeuDATool provides another choice for scientists who are familiar with C++ programming and want to define specific models and algorithms for their analyses.

pdf/epsr-an-open-source-empirical-potential-structure-refinement-xhdohd4hqf.pdf

EPSR++: An Open Source Empirical Potential Structure Refinement Neutron Data Analysis Framework Supporting Parallel Across Computer Cluster Nodes and GPU Hardware Acceleration

The invention relates to the field of neutron scattering data analysis technology, and particularly to a neutron scattering data analysis system which uses C++ kind inheriting, MPI distributed memoryframework paralleling and GPU acceleration and is based on an empirical potential refinement algorithm, and a method thereof. The system comprises a user-defined atom or molecule re-compiling programmodule, an analog system initializing module, a parallel mode selecting module, a reference potential Monte Carlo simulation module, an empirical Monte Carlo simulation module and an analog data accumulation module. The system is used for researching operation of neutron scattering data analysis. A C++ language kind inhibiting mechanism facilitates self-defined analysis of molecule type and motionmode of the system by a user. MPI over-node paralleling and GPU hardware acceleration are used for improving operation speed of software. The system can be installed and operates on a personal computer, a computer server and a computer cluster with a Linum operating system. The system has relatively high applicability. The software system has capability of analyzing an atom simulating system withscale which exceeds 10 millions.

Neutron scattering data analysis system based on empirical potential refinement algorithm

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EPSR++: An Open Source Empirical Potential Structure Refinement Neutron Data Analysis Framework Supporting Parallel Across Computer Cluster Nodes and GPU Hardware Acceleration

Neutron scattering data analysis system based on empirical potential refinement algorithm