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  Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC.

Kutzner, C., Apostolov, R., Hess, B., & Grubmüller, H. (2014). Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC. In M. Bader, A. Bode, & H. J. Bungartz (Eds.), Parallel Computing: Accelerating Computational Science and Engineering (CSE) (pp. 722-730). Amsterdam: IOS Press.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0019-DB41-8 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-CDB3-A
Genre: Book Chapter

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2037317.pdf (Publisher version), 177KB
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 Creators:
Kutzner, C.1, Author              
Apostolov, R., Author
Hess, B., Author
Grubmüller, H.1, Author              
Affiliations:
1Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society, ou_578631              

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Free keywords: GROMACS, molecular dynamics, SuperMUC, benchmark, biomolecular simulation
 Abstract: Here we report on the performance of GROMACS 4.6 on the SuperMUC cluster at the Leibniz Rechenzentrum in Garching. We carried out benchmarks with three biomolecular systems consisting of eighty thousand to twelve million atoms in a strong scaling test each. The twelve million atom simulation system reached a performance of 49 nanoseconds per day on 32,768 cores.

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Language(s): eng - English
 Dates: 2014-03-31
 Publication Status: Published in print
 Pages: -
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 Rev. Method: Peer
 Identifiers: DOI: 10.3233/978-1-61499-381-0-722
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Title: Parallel Computing: Accelerating Computational Science and Engineering (CSE)
Source Genre: Book
 Creator(s):
Bader, M., Editor
Bode, A., Editor
Bungartz, H. J., Editor
Affiliations:
-
Publ. Info: Amsterdam : IOS Press
Pages: XIX, 846 Volume / Issue: - Sequence Number: - Start / End Page: 722 - 730 Identifier: ISBN: 978-1-61499-380-3

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Title: Advances in parallel computing
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Pages: - Volume / Issue: 25 Sequence Number: - Start / End Page: - Identifier: -

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Title: International Conference on Parallel Programming, ParCo. Garching, 2013.09.10-13
Source Genre: Proceedings
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