Abstract
Important components of molecular modeling applications are estimation and minimization of the internal energy of a molecule. For macromolecules such as proteins and amino acids, energy estimation is performed using empirical equations known as force fields. Over the past several decades, much effort has been directed towards improving the accuracy of these equations, and the resulting increased accuracy has come at the expense of greater computational complexity. For example, the interactions between a protein and surrounding water molecules have been modeled with improved accuracy using the generalized Born solvation model, which increases the computational complexity to \(O\left(n^3\right)\).
Fortunately, many force-field calculations are amenable to parallel execution. This paper describes the steps that were required to transform the Born calculation from a serial program into a parallel program suitable for parallel execution in both the OpenMP and MPI environments. Measurements of the parallel performance on a symmetric multiprocessor reveal that the Born calculation scales well for up to 144 processors, and that programmability and performance are better for the OpenMP implementation than for the MPI implementation.
This material is based upon work supported by DARPA under Contract No. NBCH3039002.
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Brown, R., Sharapov, I. (2008). Performance and Programmability Comparison Between OpenMP and MPI Implementations of a Molecular Modeling Application . In: Mueller, M.S., Chapman, B.M., de Supinski, B.R., Malony, A.D., Voss, M. (eds) OpenMP Shared Memory Parallel Programming. IWOMP 2005. Lecture Notes in Computer Science, vol 4315. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-68555-5_28
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DOI: https://doi.org/10.1007/978-3-540-68555-5_28
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