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Easy Development and Integration of Science Gateways with Vine Toolkit

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eScience on Distributed Computing Infrastructure

Abstract

Science Gateway is a set of tools for scientists to facilitate access to their computational resources in a comprehensive, efficient and easy manner. The most common instance of Science Gateway comes in the form of a web portal. It provides space for communities, collaboration, data sharing and visualization along with the possibility of defining, running and managing computational tasks. The main objective of such a portal is to allow users to access the computational resources, to process and analyze their data and to obtain results in a uniform and user friendly way. In this publication we briefly describe solutions for Nanomechanics, Quantum Chemistry and Molecular Physics fields with the use of Vine Toolkit and QosCosGrid tools and different domain-specific applications.

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References

  1. Dziubecki, P., Grabowski, P., Krysiński, M., Kuczyński, T., Kurowski, K., Piontek, T., Szejnfeld, D.: Online Web-Based Science Gateway for Nanotechnology Research. In: Bubak, M., Szepieniec, T., Wiatr, K. (eds.) PL-Grid 2011. LNCS, vol. 7136, pp. 205–216. Springer, Heidelberg (2012)

    Chapter  Google Scholar 

  2. Russell, M., et al.: The Vine Toolkit: A Java Framework for Developing Grid Applications. In: Wyrzykowski, R., Dongarra, J., Karczewski, K., Wasniewski, J. (eds.) PPAM 2007. LNCS, vol. 4967, pp. 331–340. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

  3. Szejnfeld, D., Dziubecki, P., Kopta, P., Krysinski, M., Kuczynski, T., Kurowski, K., Ludwiczak, B., Piontek, T., Tarnawczyk, D., Wolniewicz, M., Domagalski, P., Nabrzyski, J., Witkowski, K.: Vine Toolkit – Towards Portal Based Production Solutions for Scientific and Engineering Communities with Grid-Enabled Resources Support. Scalable Computing: Practice and Experience 11(2), 161–172 (2011)

    Google Scholar 

  4. Dziubecki, P., Grabowski, P., Krysinski, M., Kuczynski, T., Kurowski, K., Szejnfeld, D.: Nano-Science Gateway development with Vine Toolkit and Adobe Flex. In: Barbera, R., Andronico, G., La Rocca, G. (eds.) Proceedings of the International Worshop on Science Gateways (IWSG 2010). Consorzio COMETA, Catania (2010)

    Google Scholar 

  5. Agullo, E., Coti, C., Herault, T., Langou, J., Peyronnet, S., Rezmerita, A., Cappello, F., Dongarra, J.: QCG-OMPI: MPI applications on grids. Future Generation Computer Systems 27(4), 357–369 (2011), doi:10.1016/j.future.2010.11.015, ISSN 0167-739X

    Article  Google Scholar 

  6. Kurowski, K., Piontek, T., Kopta, P., Mamoński, M., Bosak, B.: Parallel Large Scale Simulations in the PL-Grid Environment. Computational Methods in Science and Technology Special Issue, 47–56 (2010)

    Google Scholar 

  7. Kurowski, K., de Back, W., Dubitzky, W., Gulyás, L., Kampis, G., Mamonski, M., Szemes, G., Swain, M.: Complex System Simulations with QosCosGrid. In: Allen, G., Nabrzyski, J., Seidel, E., van Albada, G.D., Dongarra, J., Sloot, P.M.A. (eds.) ICCS 2009, Part I. LNCS, vol. 5544, pp. 387–396. Springer, Heidelberg (2009), doi:10.1007/978-3-642-01970-8_38

    Chapter  Google Scholar 

  8. Streit, A., Bala, P., Beck-Ratzka, A., Benedyczak, K., Bergmann, S., Breu, R., Daivandy, J.M., Demuth, B., Eifer, A., Giesler, A., Hagemeier, B., Holl, S., Huber, V., Lamla, N., Mallmann, D., Memon, A.S., Memon, M.S., Rambadt, M., Riedel, M., Romberg, M., Schuller, B., Schlauch, T., Schreiber, A., Soddemann, T., Ziegler, W.: UNICORE 6 – Recent and Future Advancements. JUEL-4319 (2010) ISSN 0944-2952

    Google Scholar 

  9. gLite 3, http://glite.cern.ch/introduction (accessed April 10, 2014)

  10. GRIA 5.3, http://www.gria.org/about-gria/overview (accessed April 10, 2014)

  11. Foster, I.: Globus Toolkit Version 4: Software for Service-Oriented Systems. In: Jin, H., Reed, D., Jiang, W. (eds.) NPC 2005. LNCS, vol. 3779, pp. 2–13. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  12. Moor, R.: Towards a Theory of Digital Preservation. The International Journal of Digital Curation 1(3) (2008)

    Google Scholar 

  13. Rajasekar, A., Wan, M., Moore, R., Schroeder, W., Kremenek, G., Jagatheesan, A., Cowart, C., Zhu, B., Chen, S., Olschanowsky, R.: Storage Resource Broker – Managing Distributed Data in a Grid. Computer Society of India Journal, Special Issue on SAN 33(4), 42–54 (2003)

    Google Scholar 

  14. Antonioletti, M., Atkinson, M.P., Baxter, R., Borley, A., Chue Hong, N.P., Collins, B., Hardman, N., Hume, A., Knox, A., Jackson, M., Krause, A., Laws, S., Magowan, J., Paton, N.W., Pearson, D., Sugden, T., Watson, P., Westhead, M.: The Design and Implementation of Grid Database Services in OGSA-DAI. Concurrency and Computation: Practice and Experience 17(2-4), 357–376 (2005)

    Article  Google Scholar 

  15. Foster, I., Grimshaw, A., Lane, P., Lee, W., Morgan, M., Newhouse, S., Pickles, S., Pulsipher, D., Smith, C., Theimer, M.: Open Grid Services Architecture Basic Execution Service, Version 1.0, GFD-R.108 (2008), http://www.ggf.org/documents/GFD.108.pdf

  16. Anjomshoaa, A., Brisard, F., Drescher, M., Fellows, D., Ly, A., McGough, S., Pulsipher, D., Savva, A.: Job Submission Description Language (JSDL) Specification, Version 1.0, GFD-R.056 (2005), http://www.ggf.org/documents/GFD.56.pdf

  17. OGSA Resource Usage Service, http://forge.ggf.org/sf/projects/rus-wg

  18. Microsoft’s Active Directory, http://www.microsoft.com/windowsserver2008/en/us/active-directory.aspx (accessed April 10, 2014)

  19. Oleksiak, A., Tullo, A., Graham, P., Kuczynski, T., Nabrzyski, J., Szejnfeld, D., Sloan, T.: HPC-Europa single point of access as a framework for building science gateways: Research Articles. Concurrency and Computation: Practice & Experience 19(6), 851–866 (2007)

    Article  Google Scholar 

  20. Bubak, M., Szepieniec, T., Wiatr, K. (eds.): PL-Grid 2011. LNCS, vol. 7136. Springer, Heidelberg (2012)

    Google Scholar 

  21. PLGrid Plus project web site, http://www.plgrid.pl/en/projects/plus (accessed April 10, 2014)

  22. P-GRADE, http://www.p-grade.hu/ (accessed April 10, 2014)

  23. EnginFrame, http://www.nice-software.com/web/nice/products/enginframe (accessed April 10, 2014)

  24. Goodale, T., Jha, S., Kaiser, H., Kielmann, T., Kleijer, P., von Laszewski, G., Lee, C., Merzky, A., Rajic, H., Shalf, J.: SAGA: A Simple API for Grid applications, High-Level Application Programming on the Grid. Computational Methods in Science and Technology 12(1) (2006)

    Google Scholar 

  25. Klimeck, G., McLennan, M., Brophy, S.P., Adams III, G.B., Lundstrom, M.S.: nanoHUB.org: Advancing Education and Research in Nanotechnology. Computing in Science and Engineering 10(5), 17–23 (2008), doi:10.1109/MCSE.2008.120

    Article  Google Scholar 

  26. Dooley, R., et al.: Software-as-a-Service: The iPlant Foundation API. In: 5th IEEE Workshop on Many-Task Computing on Grids and Supercomputers (MTAGS). IEEE (2012)

    Google Scholar 

  27. myExperiment, http://www.myexperiment.org/ (accessed April 10, 2014)

  28. EGI Applications Database, https://appdb.egi.eu/store/software/ (accessed April 10, 2014)

  29. XSEDE Science Gateways Listing, https://www.xsede.org/gateways-listing (accessed April 10, 2014)

  30. Microsoft Silverlight, http://www.silverlight.net/ (accessed April 10, 2014)

  31. Gridsphere, http://gridlab.org/Resources/Deliverables/B4.pdf (accessed April 10, 2014)

  32. Liferay, http://www.liferay.com/ (accessed April 10, 2014)

  33. JSR-168, http://jcp.org/en/jsr/detail?id=168 (accessed April 10, 2014)

  34. JSR-286, http://jcp.org/en/jsr/detail?id=286 (accessed April 10, 2014)

  35. LAMMPS Molecular Dynamics Simulator, http://lammps.sandia.gov/ (accessed April 10, 2014)

  36. Bialoskorski, M., Rybicki, J.: Mechanical properties of the carbon nanotubes: simulation program and exemplary results. In: Proc. of the 8th Workshop of PTSK Gdańsk-Sobieszewo, p. 8 (2001)

    Google Scholar 

  37. Laskowski, R.: Pakiet SIMPL – metody geometrii stochastycznej w analizie strukturalnej. In: Sympozjum Symulacje MD w Polsce, Gdańsk (2000) (in Polish)

    Google Scholar 

  38. Bergmanski, G., Rybicki, J.: Pakiet ANELLI – analiza uporządkowania średniego zasięgu w strukturach symulowanych numerycznie. In: Sympozjum Symulacje MD w Polsce, Gdańsk (2000) (in Polish)

    Google Scholar 

  39. Adobe, Flex/BlazeDs, http://www.adobe.com/products/flex/ (accessed April 10, 2014)

  40. Gonze, X., Amadon, B., Anglade, P.-M., Beuken, J.-M., Bottin, F., Boulanger, P., Bruneval, F., Caliste, D., Caracas, R., Cote, M., Deutsch, T., Genovese, L., Ghosez, P., Giantomassi, M., Goedecker, S., Hamann, D.R., Hermet, P., Jollet, F., Jomard, G., Leroux, S., Mancini, M., Mazevet, S., Oliveira, M.J.T., Onida, G., Pouillon, Y., Rangel, T., Rignanese, G.-M., Sangalli, D., Shaltaf, R., Torrent, M., Verstraete, M.J., Zerah, G., Zwanziger, J.W.: ABINIT: First-principles approach of materials and nanosystem properties. Computer Phys. Commun. 180, 2582–2615 (2009)

    Article  Google Scholar 

  41. Gonze, X., Rignanese, G.-M., Verstraete, M., Beuken, J.-M., Pouillon, Y., Caracas, R., Jollet, F., Torrent, M., Zerah, G., Mikami, M., Ghosez, P., Veithen, M., Raty, J.-Y., Olevano, V., Bruneval, F., Reining, L., Godby, R., Onida, G., Hamann, D.R., Allan, D.C.: A brief introduction to the ABINIT software package. Zeit. Kristallogr. 220, 558–562 (2005)

    Google Scholar 

  42. Ludascher, B., Altintas, I., Berkley, C., Higgins, D., Jaeger-Frank, E., Jones, M., Lee, E., Tao, J., Zhao, Y.: Scientific Workflow Management and the Kepler System. Concurrency and Computation: Practice & Experience 18(10), 1039–1065 (2005)

    Article  Google Scholar 

  43. Radecki, M., Szymocha, T., Piontek, T., Bosak, B., Mamoński, M., Wolniewicz, P., Benedyczak, K., Kluszczyński, R.: Reservations for Compute Resources in Federated e-Infrastructure. In: Bubak, M., Kitowski, J., Wiatr, K. (eds.) PLGrid Plus. LNCS, vol. 8500, pp. 80–93. Springer, Heidelberg (2014)

    Google Scholar 

  44. Bosak, B., Kopta, P., Kurowski, K., Piontek, T., Mamoński, M.: New QosCosGrid Middleware Capabilities and Its Integration with European e-Infrastructure. In: Bubak, M., Kitowski, J., Wiatr, K. (eds.) PLGrid Plus. LNCS, vol. 8500, pp. 34–53. Springer, Heidelberg (2014)

    Google Scholar 

  45. Karanastasis, E., Varvarigou, T., Grabowski, P.: Portals for Service Oriented Infrastructures. In: Dimitrakos, T., Martrat, J., Wesner, S. (eds.) Service Oriented Infrastructures and Cloud Service Platforms for the Enterprise, pp. 159–177. Springer, Heidelberg (2010) ISBN 978-3-642-04085-6

    Chapter  Google Scholar 

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Kurowski, K., Dziubecki, P., Grabowski, P., Krysiński, M., Piontek, T., Szejnfeld, D. (2014). Easy Development and Integration of Science Gateways with Vine Toolkit. In: Bubak, M., Kitowski, J., Wiatr, K. (eds) eScience on Distributed Computing Infrastructure. Lecture Notes in Computer Science, vol 8500. Springer, Cham. https://doi.org/10.1007/978-3-319-10894-0_11

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  • DOI: https://doi.org/10.1007/978-3-319-10894-0_11

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