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Storage Systems for I/O-Intensive Applications in Computational Chemistry

  • Matthias Neuer
  • Christian Mosch
  • Jürgen Salk
  • Karsten Siegmund
  • Volodymyr Kushnarenko
  • Stefan Kombrink
  • Thomas Nau
  • Stefan Wesner

Abstract

Many programs in computational quantum chemistry need a fast storage system capable of serving more than 10,000 I/O operations per second while also being large enough to store the temporary files created by these applications. A good solution which fulfills both requirements is a hybrid approach consisting of a large network storage and small but very fast local SSDs. It was found that off-the-shelf SSD-based caching strategies did not perform satisfactorily for the applications investigated in this study. A better result can be achieved by concatenating the two storage systems via a RAID or even better via LVM. After taking care about the creation of the logical volume and the layout of the file system we could obtain 75 % of the performance gain of an SSD by using only 50 % SSD storage.

Notes

Acknowledgements

The authors would like to thank the Deutsche Forschungsgemeinschaft (DFG) and the Ministry for Science, Research and Arts Baden-Württemberg for funding the bwHPC project. Further more, the authors thank the bwHPC-C5 team Baden-Wrttemberg for fruitful and constructive discussions and are grateful to our project partner NEC for their support and cooperation.

References

  1. 1.
    Molpro quantum chemistry package. http://www.molpro.net. Accessed 2015
  2. 2.
    Gaussian, software for computational chemistry. http://www.gaussian.com. Accessed 2015
  3. 3.
    sysstat Package. http://sebastien.godard.pagesperso-orange.fr. Accessed 2015
  4. 4.
    sysstat, System Call Tracer. http://sourceforge.net/projects/strace. Accessed 2015
  5. 5.
    Flashcache. https://github.com/facebook/flashcache. Accessed 2015
  6. 6.
    bcache, block layer cache. http://bcache.evilpiepirate.org. Accessed 2015
  7. 7.
  8. 8.
    FIO, Flexible I/O Tester. https://github.com/axboe/fio. Accessed 2015
  9. 9.
    Sweeney, A., Doucette, D., Hu, W., Anderson, C., Nishimoto, M., Peck, G.: Scalability in the XFS file system. In: Proceedings of the USENIX 1996 Technical Conference, San Diego, CA, 1996, pp. 1–14Google Scholar
  10. 10.
    Mathur, A., Cao, M., Bhattacharya, S., Dilger, A., Tomas, A., Vivier, L.: The new ext4 filesystem: current status and future plans. In: Proceedings of the Linux Symposium, 2007Google Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Matthias Neuer
    • 1
  • Christian Mosch
    • 1
  • Jürgen Salk
    • 1
  • Karsten Siegmund
    • 1
  • Volodymyr Kushnarenko
    • 1
  • Stefan Kombrink
    • 1
  • Thomas Nau
    • 1
  • Stefan Wesner
    • 1
  1. 1.Ulm UniversityUlmGermany

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