Advertisement

Journal of Grid Computing

, Volume 12, Issue 3, pp 485–497 | Cite as

User Interaction and Data Management for Large Scale Grid Applications

  • Alessandro Costantini
  • Osvaldo GervasiEmail author
  • Fabiana Zollo
  • Luca Caprini
Article

Abstract

In this paper we present a model that combines the X3DMMS application with the G3CPie execution framework, that enables the user to perform large scale computations on distributed computing environments. Such an approach facilitates the management and the preparation of the data required to define the input files for DL_POLY, a popular Molecular Dynamics (MD) package used for the study of molecular systems. The researcher can define in a intuitive way the initial configuration of the molecular system, making use of the X3DMMS virtual reality environment, and prepares the related MD package oriented input files. After having defined the initial conditions of the system, the researcher can carry out the required computations by using the G3CPie workflow environment, which controls the execution of the calculation on a distributed computing infrastructure. To test the validity of the developed model, implemented in the EGI infrastructure, we present the results carried out for a propane bulk system, where the solvation process of propane inside the bulk has been investigated. The presented approach provides a reusable example for other laboratories or groups interested both in acting through virtual representation of the molecular systems and porting their applications to distributed computing infrastructures.

Keywords

X3D X3DOM Molecular simulation DL_POLY X3DMMS 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Brutzman, D., Daly, L.: Extensible 3D Graphics for Web Authors. Morgan Kaufmann (2007)Google Scholar
  2. 2.
    Behr, J., Eschler, P., Jung, Y., Zöllner, M.: X3dom: a dom-based html5/x3d integration model. In: Proceedings of the 14th International Conference on 3D Web Technology, Web3D ’09, pp. 127–135. ACM, New York (2009)Google Scholar
  3. 3.
    Gervasi, O., Riganelli, A., Laganà, A.: Virtual reality applied to molecular sciences. In: Computational Science and Its Applications - ICCSA 2006, Volume 3044 of Lecture Notes in Computer Science, pp. 827–836. Springer, Berlin/Heidelberg (2004)Google Scholar
  4. 4.
    Gervasi, O., Riganelli, A., Pacifici, L., Laganà, A.: Vmslab-g: a virtual laboratory prototype for molecular science on the grid. Futur. Gener. Comput. Syst. 20(5), 717–726 (2004)CrossRefGoogle Scholar
  5. 5.
    Gervasi, O., Tasso, S., Laganà, A.: Immersive molecular virtual reality based on x3d and web services. In: Computational Science and Its Applications - ICCSA 2006, volume 3980 of Lecture Notes in Computer Science, pp. 212–221. Springer, Berlin/Heidelberg (2006)Google Scholar
  6. 6.
    Holdener III, A. T.: Ajax: The Definitive Guide. O’ Reilly Media (2008)Google Scholar
  7. 7.
    Protein data bank (pdb) web site. http://www.wwpdb.org/docs.html. Accessed 28 Dec 2012
  8. 8.
    Openbabel web site. http://openbabel.org. Accessed 28 Dec 2012
  9. 9.
    Smith, W., Forester, T. R.: DL_POLY2: a general purpose parallel molecular dynamics simulation package. J. Mol. Graph. 14(3), 136–141 (1996)CrossRefGoogle Scholar
  10. 10.
    Gervasi, O., Laganà, A.: Simbex: a portal for the a priori simulation of crossed beam experiments. Futur. Gener. Comput. Syst. 20(5), 703–715 (2004)CrossRefGoogle Scholar
  11. 11.
    Gervasi, O., Crocchianti, S., Pacifici, L., Skouteris, D., Laganà, A.: Towards the grid design of the dynamics engine of a molecular simulator. In: Proceedings of the International Conference of Computational Methods in Science and Engineering, ICCMSE 2006, pp. 1425–1428. CRC Press (2006)Google Scholar
  12. 12.
    Laganà, A., Costantini, A., Gervasi, O., Lago, N.F., Manuali, C., Rampino, S.: Compchem: progress towards gems a grid empowered molecular simulator and beyond. J. Grid. Comput. 8(4), 571–586 (2010)CrossRefGoogle Scholar
  13. 13.
    Laganà, A., Riganelli, A., Gervasi, O.: On the structuring of the computational chemistry virtual organization comp chem. In: Computational Science and Its Applications - ICCSA 2006, volume 3980 of Lecture Notes in Computer Science, pp. 665–674. Springer, Berlin Heidelberg. http://www.eu-egee.org/compchem (2006). Accessed 28 Dec 2012
  14. 14.
    European Grid Initiative. http://www.egi.eu. Accessed 28 Dec 2012
  15. 15.
    GC3Pie website. http://code.google.com/p/gc3pie/ Accessed 28 Dec 2012
  16. 16.
    Gc3 (grid computing competence center). http://www.gc3.uzh.ch/. Accessed 28 Dec 2012
  17. 17.
    Polys, N.F.: Stylesheet transformations for interactive visualization: towards a web3d chemistry curricula. In: Proceedings of the 8th International Conference on 3D Web Technology, Web3D ’03, pp. 85–ff. ACM, New York (2003)Google Scholar
  18. 18.
    Chemistry markup language (cml) web site: http://www.ch.ic.ac.uk/rzepa/cml/. Accessed 28 Dec 2012
  19. 19.
    Liu, F., Owen, S., Zhu, Y., Harrison, R., Weber, I.: Web based molecular visualization using procedural shaders in x3d. In: ACM SIGGRAPH 2005 Web Program,SIGGRAPH ’05. ACM, New York (2005)Google Scholar
  20. 20.
    Davies, R.A., John, N.W., MacDonald, J.N., Hughes, K.H.: Visualization of molecular quantum dynamics: a molecular visualization tool with integrated web3d and haptics. In: Proceedings of the 10th International Conference on 3D Web Technology, Web3D ’05, pp. 143–150. ACM, New York (2005)Google Scholar
  21. 21.
    Davies, R.A., Maskery, J.S., John, N.W.: Chemical education using feelable molecules. In: Proceedings of the 14th International Conference on 3D Web Technology, Web3D ’09, pp. 7–14. ACM, New York (2009)Google Scholar
  22. 22.
    Callieri, M., Andrei, R.M., Di Benedetto, M., Zoppè, M., Scopigno, R.: Visualization methods for molecular studies on the web platform. In: Proceedings of the 15th International Conference on Web 3D Technology, Web3D ’10, pp. 117–126. ACM, New York (2010)Google Scholar
  23. 23.
    Xj3d (x3d player) web site: http://www.xj3d.org/. Accessed 28 Dec 2012
  24. 24.
    Zollo, F., Caprini, L., Gervasi, O., Costantini, A.: X3dmms: an x3dom tool for molecular and material sciences. In: Proceedings of the 16th International Conference on 3D Web Technology, Web3D ’11, pp. 129–136. ACM, New York (2011)Google Scholar
  25. 25.
    Corey, R.B., Pauling, L.: Molecular models of amino acids, peptides, and proteins, Vol. 24 (1953)Google Scholar
  26. 26.
    Koltun, W.L.: Space filling atomic units and connectors for molecular models. http://www.freepatentsonline.com/3170246.html (1965). Accessed 28 Dec 2012
  27. 27.
    Rasmol cpk color scheme. http://life.nthu.edu.tw/fmhsu/rasframe/CPKCLRS.HTM. Accessed 28 Dec 2012
  28. 28.
    Costantini, A., Murri, R., Maffioletti, S., Laganà, A.: A grid execution model for computational chemistry applications using the gc3pie framework and the apppot vm environment. In: Computational Science and Its Applications - ICCSA 2012, volume 7333 of Lecture Notes in Computer Science, pp. 401–416. Springer, Berlin/Heidelberg(2012)Google Scholar
  29. 29.
    Skouteris, D., Castillo, J.F., Manolopoulos, D.E.: Abc: a quantum reactive scattering program. Comput. Phys. Commun. 133(1), 128–135 (2000)CrossRefzbMATHGoogle Scholar
  30. 30.
    Costantini, A., Laganà, A.: Investigation of propane and methane bulk properties structure using two different force fields. In: Computational Science and Its Applications - ICCSA 2008, volume 5072 of Lecture Notes in Computer Science, pp. 1052–1064. Springer, Berlin/Heidelberg (2008)Google Scholar
  31. 31.
    Jorgensen, W.L., Tirado-Rives, J.: The opls [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110(6), 1657–1666 (1988)CrossRefGoogle Scholar
  32. 32.
    Allen, M.P., Tildesley, D.J.: Computer Simulation of Liquids. Oxford Science Publications. Oxford University Press, USA (1989)Google Scholar
  33. 33.
  34. 34.
    Vella, F., Cefalà, R.M., Costantini, A., Gervasi, O.,Tanci, C.: Gpu computing in egi environment using a cloud approach. In: 2011 International Conference on Computational Science and Its Applications (ICCSA), pp. 150–155 (2011)Google Scholar
  35. 35.
    Bonifati, A., Cuzzocrea, A.: Efficient fragmentation of large XML documents. In: Wagner, R., Revell, N., Pernul, G. (eds.) Database and Expert Systems Applications, volume 4653 of Lecture Notes in Computer Science, pp. 539-550. Springer, Berlin Heidelberg (2007). doi: 10.1007/978-3-540-74469-6_53
  36. 36.
    Cuzzocrea, A., Serafino, P.: LCS-Hist: taming massive high-dimensional data cube compression. In: Proceedings of the 12th International Conference on Extending Database Technology: Advances in Database Technology, EDBT ’09, pp. 768–779. ACM, New York (2009). doi: 10.1145/1516360.1516448

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Alessandro Costantini
    • 1
    • 2
  • Osvaldo Gervasi
    • 2
    Email author
  • Fabiana Zollo
    • 3
  • Luca Caprini
    • 4
  1. 1.INFN — National Institute of Nuclear PhysicsRomeItaly
  2. 2.IGI — Italian Grid InfrastructureRomeItaly
  3. 3.Department of Mathematics and Computer ScienceUniversity of PerugiaPerugiaItaly
  4. 4.IMT Institute for Advanced StudiesLuccaItaly

Personalised recommendations