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Outline

NBCR Science Gateway: Transparent Access to Remote Resources Through Rich Desktop Clients Luca Clementi clem@sdsc.edu. Outline. NBCR/PRAGMA NBCR SOA infrastructure Opal Overview Opal Toolkit GUI Opal Integration into Existing Tools Access to Multiple Resources (TG, PRAGMA).

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Outline

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  1. NBCR Science Gateway: Transparent Access to Remote Resources Through Rich Desktop ClientsLuca Clementiclem@sdsc.edu

  2. Outline • NBCR/PRAGMA • NBCR SOA infrastructure • Opal Overview • Opal Toolkit GUI • Opal Integration into Existing Tools • Access to Multiple Resources (TG, PRAGMA)

  3. National Biomedical Computational Resource • Funded by NIH (NCRR) • Its mission is to conduct, catalyze, and enable biomedical research by harnessing, developing, and deploying forefront computational, information and grid technologies • Develop and deploy advanced computational, data and visualization tools. • Integrate them in an advanced grid framework. • Deliver and support this grid/Cyber-infrastructure • Training (Summer Institute)

  4. National Biomedical Computational Resource • Funded by NIH (NCRR) • Its mission is to conduct, catalyze, and enable biomedical research by harnessing, developing, and deploying forefront computational, information and grid technologies • Develop and deploy advanced computational, data and visualization tools. • Integrate them in an advanced grid framework. • Deliver and support this grid/Cyber-infrastructure • Training (Summer Institute)

  5. Pacific Rim Application and Grid Middleware Assembly (PRAGMA) A Practical Collaborative Framework In the Pacific Rim and Globally 29 institutions Strengthen Existing and Establish New Sustainable Collaborations Work with Science Teams to Advance Grid Technologies and Improve the Underlying Infrastructure • Collaborations • Integration of existing applications • Deployment of a Grid infrastructure http://www.pragma-grid.net

  6. Motivation • Integration of different tools (client side application, workflow tools, web portals, etc.) • Several user interfaces • Seamless access to computational resources • Easy from the scientific user perspective

  7. Big Picture Web server PMV/Vision Kepler State Mgmt Application Services Security Services (GAMA) Globus Globus Globus PBS Cluster Condor pool SGE Cluster

  8. Opal Toolkit Opal allows application developers to publish command-line applications using Web services Minimal deployment effort: no coding, only a simple configuration file plain web service, SOAP Common interface: every application uses the same WSDL (same stubs on the client side) Simple APIs (Launch job, Query job status, Get job outputs, Get output as Base64, Destroy job, etc.)

  9. Opal Toolkit • Every application exposed with its own URL http://ws.nbcr.net/opal/services/Pdb2pqrService • It takes care of data staging • It supports submission via: • Fork • Globus GRAM • DRMAA • CSF4 (experimental) • Run all the applications under a single user account • Used in NBCR, CAMERA, GLEON, among other

  10. Opal Toolkit / Client Side Several clients APIs available: Java, Python, PERL. Command line generic client: # java edu.sdsc.nbcr.opal.GenericServiceClient -l http://localhost:8080/axis/services/PDB2PQRServicePort -r launchJob -a "-ipdb sample.pdb -h -opdb output.pdb“ -f etc/sample.pdb • Too complex for beginner users • Graphical User Interfaces

  11. User User clients Browser Vision getAppMetadata Kepler PDB2PQR launchJob getOutput … getAppMetadata MEME launchJob getOutput … … Opal server

  12. Opal GUI Main characteristics: Working out of the box (no configuration) Multiplatform -> Web interface Shipped with Opal Key features: Access Statistics List of services Simple submission form Advanced submission form

  13. Access Statistics Go to http://ws.nbcr.net NBCR production server

  14. List of Services

  15. Simple Submission Form User has to input command line! Too error prone. Submission form should be customized on command line arguments

  16. Advanced Submission Form When deploying a scientific application there is an optional part to describe input and output of the application It is a command line syntax description language

  17. PDB2PQR Advanced Submission Form Exclusive group Input file Group 1 String Group 2 Exclusive enumeration Group 3 Flag Group 4

  18. Vision Opal Node

  19. Kepler Opal Web Services Actor

  20. Autodock Tools

  21. PBD2PQR Web Site

  22. Access to Multiple Resources

  23. CSF4 • Community Scheduler Framework: • Open Source project and can be accessed at http://sourceforge.net/projects/gcsf • Developed by Lab. of Distributed Computing and System Architecture, Jilin University, China • It is a metascheduler framework hosted as an Execution Component in GT4 container • It uses WSRF compliant services • It can submit jobs to Globus

  24. CSF4 Typical Deployment • GT2 (gatekeeper) • GT4 (WS-GRAM)

  25. CSF4 New Feature Users want to run applications • Application based scheduling: • CSF4 keeps a table of available applications

  26. CSF4 New Feature Users want to run applications • Application based scheduling: • CSF4 keeps a table of available applications Avian Flu Grid

  27. Opal CSF4 Integration • Opal plug-in for submission to CSF4 • Deployment architecture:

  28. Opal Enable Clients WS/SOAP App A App B App C Opal Server WSRF App A App B App C CSF4 (Pre/WS)-GRAM Globus GRAM Globus GRAM ClusterB appA appC ClusterA appA appB …

  29. Future Directions • Opal 2.0 will be released soon • Improved architecture (plug-in model) • URL support for input and output files • Embedded database (Hibernate) • Support for other metascheduler (Gridway) • Opal GUI for Gridsphere (Portlet)

  30. Acknowledgments • Wilfred Li, Peter Arzberg (NBCR vision) • Sriram Krishnan (Opal) • Xiaohui Wei (CFS4) • Many other NBCR developers... • More information, downloads, documentation: • http://nbcr.net • http://nbcr.net/software/opal/

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