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Online Web-Based Science Gateway for Nanotechnology Research

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Building a National Distributed e-Infrastructure–PL-Grid

Abstract

The main objective of Science Gateways is to give users remote access to supercomputers and large-scale computing environments in an interactive, web-based and graphical manner. We present a tool, called Vine Toolkit, that has been successfully used as a core web platform for various Science Gateways. Vine Toolkit is a modular, extensible and easy-to-use tool as well as a high-level Application Programming Interface (API) for various applications, visualization components and building blocks. In a nutshell, it allows interoperability between many different HPC and grid technologies within the service layer. As a result, Vine Toolkit provides an ability to build a portal upon different HPC technologies working together to deliver a complete solution to the users. In this article, we briefly describe our most complex and feature-rich project – the Nanotechnology Gateway, as well as a set of tools relevant to advanced scientific portals, development of which was driven by various requirements defined by scientists and gathered in scope of the PL-Grid project.

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References

  1. Russell, M., Dziubecki, P., Grabowski, P., Krysinśki, M., Kuczyński, T., Szjenfeld, D., Tarnawczyk, D., Wolniewicz, G., Nabrzyski, J.: 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 

  2. 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 

  3. 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 Workshop on Science Gateways (IWSG 2010). Consorzio COMETA, Catania (2010)

    Google Scholar 

  4. 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) ISSN 0167-739X, doi:10.1016/j.future.2010.11.015

    Article  Google Scholar 

  5. 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 

  6. 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 

  7. gLite 3, http://glite.cern.ch/introduction

  8. GRIA 5.3, http://www.gria.org/about-gria/overview

  9. 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 

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

    Google Scholar 

  11. 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 

  12. 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 

  13. 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

  14. 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

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

  16. Microsoft’s Active Directory, http://www.microsoft.com/windowsserver2008/en/us/active-directory.aspx

  17. 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 

  18. P-GRADE, http://www.p-grade.hu/

  19. EnginFrame, http://www.nice-software.com/web/nice/products/enginframe

  20. SAGA, http://saga.cct.lsu.edu/

  21. 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 

  22. myExperiment, http://www.myexperiment.org/

  23. Guim, F., Rodero, I., Corbalan, J., Labarta, J., Oleksiak, A., Kuczynski, T., Szejnfeld, D., Nabrzyski, J.: Uniform job monitoring in the HPC-Europa project: data model, API and services. International Journal of Web and Grid Services 3(3), 333–353 (2007)

    Article  Google Scholar 

  24. 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 

  25. 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 

  26. Adobe, Flex/BlazeDs, http://www.adobe.com/products/flex/

  27. Kokalj, A.: Computer graphics and graphical user interfaces as tools in simulations of matter at the atomic scale. Comp. Mat. Sci. 28, 155–168 (2003)

    Article  Google Scholar 

  28. GoVASP, http://www.govasp.com/

  29. 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 

  30. Vine-users mailing list, http://gforge.man.poznan.pl/mailman/listinfo/vine-users

  31. Kocot, J., Szepieniec, T., Noga, K., Harężlak, D., Sterzel, M.: InSilicoLab – Managing Complexity of Chemistry Computations. In: Bubak, M., Szepieniec, T., Wiatr, K. (eds.) PL-Grid 2011. LNCS, vol. 7136, pp. 265–275. Springer, Heidelberg (2012)

    Google Scholar 

  32. Ciepiela, E., Nowakowski, P., Kocot, J., Harężlak, D., Gubała, T., Meizner, J., Kasztelnik, M., Bartyński, T., Malawski, M., Bubak, M.: Managing Entire Lifecycles of e-Science Applications in the GridSpace2 Virtual Laboratory – from Motivation through Idea to Operable Web-Accessible Environment Built on Top of PL-Grid e-Infrastructure. In: Bubak, M., Szepieniec, T., Wiatr, K. (eds.) PL-Grid 2011. LNCS, vol. 7136, pp. 228–239. Springer, Heidelberg (2012)

    Google Scholar 

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Marian Bubak Tomasz Szepieniec Kazimierz Wiatr

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Dziubecki, P. et al. (2012). Online Web-Based Science Gateway for Nanotechnology Research. In: Bubak, M., Szepieniec, T., Wiatr, K. (eds) Building a National Distributed e-Infrastructure–PL-Grid. Lecture Notes in Computer Science, vol 7136. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-28267-6_16

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  • DOI: https://doi.org/10.1007/978-3-642-28267-6_16

  • Publisher Name: Springer, Berlin, Heidelberg

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