Parallel implementation of approximate atomistic models of the AMOEBA polarizable model

Omar Demerdash; Teresa Head-Gordon

doi:10.1016/j.cplett.2016.10.015

Parallel implementation of approximate atomistic models of the AMOEBA polarizable model

Omar Demerdash, Teresa Head-Gordon

Molecular Biophysics

Research output: Contribution to journal › Article › peer-review

Abstract

In this work we present a replicated data hybrid OpenMP/MPI implementation of a hierarchical progression of approximate classical polarizable models that yields speedups of up to ∼10 compared to the standard OpenMP implementation of the exact parent AMOEBA polarizable model. In addition, our parallel implementation exhibits reasonable weak and strong scaling. The resulting parallel software will prove useful for those who are interested in how molecular properties converge in the condensed phase with respect to the MBE, it provides a fruitful test bed for exploring different electrostatic embedding schemes, and offers an interesting possibility for future exascale computing paradigms.

Original language	English
Pages (from-to)	191-198
Number of pages	8
Journal	Chemical Physics Letters
Volume	664
DOIs	https://doi.org/10.1016/j.cplett.2016.10.015
State	Published - Nov 1 2016

Funding

We thank the National Science Foundation grant CHE-1265731 for the software developed in TINKER and CHE-1363320 for the MBE work. We thank the Edinburgh team: Weronika Filinger, Mario Antonioletti, Lorna Smith, Arno Proeme, and Neil Chue Hong, for their help during the last 3?years in regards parallelization.

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10.1016/j.cplett.2016.10.015

Cite this

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abstract = "In this work we present a replicated data hybrid OpenMP/MPI implementation of a hierarchical progression of approximate classical polarizable models that yields speedups of up to ∼10 compared to the standard OpenMP implementation of the exact parent AMOEBA polarizable model. In addition, our parallel implementation exhibits reasonable weak and strong scaling. The resulting parallel software will prove useful for those who are interested in how molecular properties converge in the condensed phase with respect to the MBE, it provides a fruitful test bed for exploring different electrostatic embedding schemes, and offers an interesting possibility for future exascale computing paradigms.",

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Parallel implementation of approximate atomistic models of the AMOEBA polarizable model

Abstract

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