Abstract
This article analyzes the impact of different solutions of I/O performance problem on Molecular Dynamics (MD) simulation. MD accesses data in a non-contiguous way, with unpredictable patterns that change as the simulation progresses. Such application drastically affect the performance of Parallel File Systems. We show that there is a strong relation between the distribution of the atoms on the simulation space and MD I/O performance. We propose a variant of data sieving approach that uses the symmetry of the MD’s access pattern to minimize the number of I/O operations, and behaves considerably better than other tested solutions.
This work has been supported by the Spanish Ministry of Science under the TIN2004-02156 contract.
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© 2005 Springer-Verlag Berlin Heidelberg
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Ibáñez, M.B., García, F., Carretero, J. (2005). Symmetrical Data Sieving for Noncontiguous I/O Accesses in Molecular Dynamics Simulations. In: Di Martino, B., Kranzlmüller, D., Dongarra, J. (eds) Recent Advances in Parallel Virtual Machine and Message Passing Interface. EuroPVM/MPI 2005. Lecture Notes in Computer Science, vol 3666. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11557265_56
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DOI: https://doi.org/10.1007/11557265_56
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-29009-4
Online ISBN: 978-3-540-31943-6
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