High-Scalability Parallelization of a Molecular Modeling Application: Performance and Productivity Comparison Between OpenMP and MPI Implementations

@article{Brown2007HighScalabilityPO,
  title={High-Scalability Parallelization of a Molecular Modeling Application: Performance and Productivity Comparison Between OpenMP and MPI Implementations},
  author={Russell Brown and Ilya Sharapov},
  journal={International Journal of Parallel Programming},
  year={2007},
  volume={35},
  pages={441-458}
}
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… CONTINUE READING
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References

Publications referenced by this paper.
Showing 1-10 of 22 references

NAB, a language for molecular manipulation

  • T. Macke
  • PhD Thesis, the Scripps Research Institute
  • 1996
Highly Influential
10 Excerpts

Validity of the single-processor approach to achieving large scale computing capabilities

  • G. M. Amdahl
  • AFIPS Conference Proceedings, AFIPS Press, pp…
  • 2007
2 Excerpts

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