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Multiprocessor molecular dynamics using the Brenner potential: parallelization of an implicit multibody
 

Summary: Multi­processor molecular dynamics using the Brenner
potential: parallelization of an implicit multi­body
potential
Irina Rosenblum a;b , Joan Adler a \Lambda and Simon Brandon b
a Department of Physics, Technion­IIT, 32000, Haifa, Israel.
b Department of Chemical Engineering, Technion­IIT, 32000, Haifa, Israel.
Abstract
We present computational aspects of Molecular Dynamics calculations of thermal properties
of diamond using the Brenner potential. Parallelization was essential in order to carry out
these calculations on samples of suitable sizes. Our implementation uses MPI on a multi­
processor machine such as the IBM SP2. Three aspects of parallelization of the Brenner potential
are discussed in depth. These are its long­range nature, the need for different parallelization
algorithms for forces and neighbours, and the relative expense of force calculations compared
to that of data communication. The efficiency of parallelization is presented as a function of
different approaches to these issues as well as of cell size and number of processors employed in
the calculation. Superlinear speedup was achieved for 4 processors with 512 atom samples, and
5ps long trajectories were calculated (for 5120 atom samples) in 53 hours using 16 processors;
514 hours would have been needed to complete this calculation using a serial program. Finally,
we discuss and make available a set of routines that enable MPI­based codes such as ours to be
debugged on scalar machines.

  

Source: Adler, Joan - Physics Department, Technion, Israel Institute of Technology

 

Collections: Physics