Multiple-Level MPI File Write-Back and Prefetching for Blue Gene Systems

  • Javier García Blas
  • Florin Isailă
  • J. Carretero
  • Robert Latham
  • Robert Ross
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5759)

Abstract

This paper presents the design and implementation of an asynchronous data-staging strategy for file accesses based on ROMIO, the most popular MPI-IO distribution, and ZeptoOS, an open source operating system solution for Blue Gene systems. We describe and evaluate a two-level file write-back implementation and a one-level prefetching solution. The experimental results demonstrate that both solutions achieve high performance through a high degree of overlap between computation, communication, and file I/O.

Keywords

MPI-IO Parallel I/O Parallel File Systems Supercomputers 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Top 500 list, http://www.top500.org
  2. 2.
    Isaila, F., Garcia Blas, J., Carretero, J., Latham, R., Lang, S., Ross, R.: Latency hiding file I/O for Blue Gene systems. In: CCGRID 2009 (2009)Google Scholar
  3. 3.
    Ma, X., Winslett, M., Lee, J., Yu, S.: Improving MPI-IO Output Performance with Active Buffering Plus Threads. In: IPDPS, pp. 22–26 (2003)Google Scholar
  4. 4.
    Liao, W.-k., Coloma, K., Choudhary, A.K., Ward, L.: Cooperative Write-Behind Data Buffering for MPI I/O. In: Di Martino, B., Kranzlmüller, D., Dongarra, J. (eds.) EuroPVM/MPI 2005. LNCS, vol. 3666, pp. 102–109. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  5. 5.
    Patterson, R.H., Gibson, G.A., Ginting, E., Stodolsky, D., Zelenka, J.: Informed prefetching and caching. SIGOPS Oper. Syst. Rev., 79–95 (1995)Google Scholar
  6. 6.
    Byna, S., Chen, Y., Sun, X.H., Thakur, R., Gropp, W.: Parallel I/O prefetching using MPI file caching and I/O signatures. In: SC 2008, pp. 1–12 (2008)Google Scholar
  7. 7.
    Chang, F., Gibson, G.: Automatic I/O Hint Generation Through Speculative Execution. In: Proceedings of OSDI (1999)Google Scholar
  8. 8.
    Chen, Y., Byna, S., Sun, X.H., Thakur, R., Gropp, W.: Hiding I/O latency with pre-execution prefetching for parallel applications. In: SC 2008, pp. 1–10 (2008)Google Scholar
  9. 9.
    Yu, W., Vetter, J.S., Canon, R.S.: OPAL: An Open-Source MPI-IO Library over Cray XT. In: SNAPI 2007, pp. 41–46 (2007)Google Scholar
  10. 10.
    Yu, W., Vetter, J.: ParColl: Partitioned Collective I/O on the Cray XT. In: ICPP, pp. 562–569 (2008)Google Scholar
  11. 11.
    Sahoo, Y.H., Howson, R., et al: High performance file I/O for the Blue Gene/L supercomputer. In: HPCA, pp. 187–196 (2006)Google Scholar
  12. 12.
    Moreira, J., et al.: Designing a highly-scalable operating system: the Blue Gene/L story. In: SC 2006, p. 118 (2006)Google Scholar
  13. 13.
    ZeptoOs Project (2008), http://wwwunix.mcs.anl.gov/zeptoos/
  14. 14.
    Iskra, K., Romein, J.W., Yoshii, K., Beckman, P.: ZOID: I/O-forwarding infrastructure for petascale architectures. In: PPoPP 2008, pp. 153–162 (2008)Google Scholar
  15. 15.
    Thakur, R., Gropp, W., Lusk, E.: On Implementing MPI-IO Portably and with High Performance. In: Proc. of IOPADS, May 1999, pp. 23–32 (1999)Google Scholar
  16. 16.
    Thakur, R., Lusk, E.: An Abstract-Device Interface for Implementing Portable Parallel-I/O Interfaces. In: Proc. of The 6th Symposium on the Frontiers of Massively Parallel Computation, pp. 180–187 (1996)Google Scholar
  17. 17.
    Blas, J.G., Isaila, F., Singh, D.E., Carretero, J.: View-Based Collective I/O for MPI-IO. In: CCGRID, pp. 409–416 (2008)Google Scholar
  18. 18.
    Wong, P., der Wijngaart, R.: NAS Parallel Benchmarks I/O Version 2.4. Technical report, NASA Ames Research Center (2003)Google Scholar
  19. 19.
    Isaila, F., Blas, J.G., Carretero, J., Liao, W.K., Choudhary, A.: AHPIOS: An MPI-based ad-hoc parallel I/O system. In: Proceedings of IEEE ICPADS (2008)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Javier García Blas
    • 1
  • Florin Isailă
    • 1
  • J. Carretero
    • 1
  • Robert Latham
    • 2
  • Robert Ross
    • 2
  1. 1.University Carlos IIISpain
  2. 2.Argonne National LaboratoryUSA

Personalised recommendations