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

Content Provider	Springer Nature Link
Author	Brown, Russell Sharapov, Ilya
Copyright Year	2007
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 (n $^{3}$). 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. In some cases the OpenMP implementation scales better than the MPI implementation, but in other cases the MPI implementation scales better than the OpenMP implementation. However, in all cases the OpenMP implementation performs better than the MPI implementation, and requires less programming effort as well.
Starting Page	441
Ending Page	458
Page Count	18
File Format	PDF
ISSN	08857458
Journal	International Journal of Parallel Programming
Volume Number	35
Issue Number	5
e-ISSN	15737640
Language	English
Publisher	Springer US
Publisher Date	2007-07-20
Publisher Place	Boston
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Parallel programming OpenMP MPI Molecular modeling Software Engineering/Programming and Operating Systems Processor Architectures Theory of Computation
Content Type	Text
Resource Type	Article
Subject	Theoretical Computer Science Information Systems Software

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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