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Virtual Laboratory for e-Science (VL-e)

vrije Universiteit. Virtual Laboratory for e-Science (VL-e). Henri Bal Department of Computer Science Vrije Universiteit Amsterdam bal@cs.vu.nl. e-Science. Web is about exchanging information Grid is about sharing resources Computers, data bases, instruments, services

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Virtual Laboratory for e-Science (VL-e)

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  1. vrije Universiteit Virtual Laboratory fore-Science (VL-e) Henri Bal Department of Computer ScienceVrije Universiteit Amsterdam bal@cs.vu.nl

  2. e-Science • Web is about exchanging information • Grid is about sharing resources • Computers, data bases, instruments, services • e-Science supports experimental science by providing a virtual laboratory on top of Grids

  3. Grid Harness multi-domain distributed resources Virtual Laboratories Distributed computing Application Specific Part Application Specific Part Application Specific Part Visualization & collaboration Potential Generic part Potential Generic part Potential Generic part Management of comm. & computing Virtual Laboratory Application oriented services Management of comm. & computing Management of comm. & computing Knowledge Data & information

  4. User Interfaces & Virtual reality based visualization Virtual Laboratory for e-Science Bio-diversity Telescience Food Informatics Bio-Informatics Data Intensive Science Medical diagnosis & imaging Interactive PSE Adaptive information disclosure Virtual lab. & System integration Collaborative information Management High-performancedistributed computing Security & Generic AAA Optical Networking

  5. vrije Universiteit The VL-e project • 20 partners • Academic - Industrial • 40 M€ (20 M€ BSIK funding) • 2004 - 2008

  6. VL-e environments Application specific service Medical Application Telescience Bio ASP Application Potential Generic service & Virtual Lab. services Virtual Lab. rapid prototyping (interactive simulation) Virtual Laboratory Additional Grid Services (OGSA services) Grid Middleware Grid & Network Services Network Service (lambda networking) Gigaport Rapid Prototyping environment Proof of Concept environment Source: Prof. Bob Hertzberger (University of Amsterdam)

  7. Outline • Infrastructure for the Rapid Prototyping group • Based on DAS (Distributed ASCI Supercomputer) • SURFnet-6 optical network (Gigaport-NG) & DAS-3 • Distributed supercomputing (Ibis) • Visualization • Interactive problem solving environments • Management of optical networks (StarPlane)

  8. DAS-1 (1997 - 2002) • Geographically distributed cluster-based system • 4 clusters with 200 nodes in total • Homogeneous system:same processors, network, OS • Eases collaboration, software exchange,systems management, experimentation • Shared test bed of the ASCI research school • For experimental Computer Science research,not for production use

  9. DAS-1 VU (128) Amsterdam (24) Configuration 200 MHz Pentium Pro Myrinet LAN Redhat Linux 6 Mb/s ATM Leiden (24) Delft (24)

  10. DAS-2 (2002) Node configuration two 1 GHz Pentium-3s >= 1 GB memory 20-80 GB disk Myrinet LAN Redhat Enterprise Linux Globus 3.2, SGE VU (72) Amsterdam (32) SURFnet1 Gb/s Leiden (32) Delft (32) Utrecht (32)

  11. Some DAS highlights • 200 users in total • Used for over 20 Ph.D. theses • Used for many publications, including 11 in ACM/IEEE journals and 1 in Nature • Used to solve Awari(3500-year old game)

  12. DAS-3 • Next generation grid in the Netherlands (2006) • Partners: • NWO & NCF (Dutch science foundation) • ASCI • Gigaport-NG/SURFnet: DWDM computer backplane (dedicated optical group of up to 8 lambdas) • VL-e and MultimediaN BSIK projects

  13. CPU’s R CPU’s R CPU’s R NOC CPU’s R CPU’s R DAS-3

  14. Outline • Infrastructure for the Rapid Prototyping group • Based on DAS (Distributed ASCI Supercomputer) • SURFnet-6 optical network (Gigaport-NG) & DAS-3 • Distributed supercomputing (Ibis) • Visualization • Interactive problem solving environments • Management of optical networks (StarPlane)

  15. Distributed supercomputing (parallel computing on grids)

  16. HPC on a grid? • Can grids be used for High-Performance Computing applications that are not trivially parallel? • Key: grids usually are hierarchical • Collections of clusters, supercomputers • Fast local links, slow wide-area links • Can optimize algorithms to exploit this hierarchy • Message combining + latency hiding on wide-area links • Optimized collective communication operations (broadcast etc.) • Often gives latency-insensitive, throughput-bound algorithms

  17. Ibis: a Java-centric grid programming environment • Written in pure Java, runs on heterogeneous grids • “Write once, run everywhere ” • Many applications: • Automated protein identification (VL-e, AMOLF) • Grammar learning (VL-e, UvA) • Cellular automaton (VL-e, UvA) • N-body simulations • SAT-solver • Raytracer • Jem3D Electromagnetic simulation (with ProActive) Available from www.cs.vu.nl/ibis

  18. Performance on wide-area DAS-2

  19. GridLab • Latencies: • 9-200 ms (daytime),9-66 ms (night) • Bandwidths: • 9-4000 KB/s • Machines come and go • Succeeded in doingreal experimentswith real speedups

  20. Configuration

  21. Visualization on the Grid

  22. Visualization on the Grid

  23. Visualization on the Grid

  24. Visualization on the Grid

  25. Visualization on the Grid

  26. ui (VRE) MRI, PET Monolith, Cluster Cave, Wall, PC, PDA From Medical Image Acquisition to Interactive Virtual Visualization… Simulated blood flow MR image Patient at MRI scanner MR image Segmentation Shear stress, velocities GVK LB Solver Medical Data MD login and Grid Proxy creation Bypass creation LB mesh generation Job submission ce (e.g., Bratislava) ce (e.g., Valencia) se (e.g., Leiden) • P.M.A. Sloot, A.G. Hoekstra, R.G. Belleman, A. Tirado-Ramos, E.V. Zudilova, D.P. Shamonin, R.M. Shulakov, A.M. Artoli , L. Abrahamyan Interactive Problem Solving Environments Virtual Node navigation Job monitoring Simulated Blood Flow VRE

  27. StarPlane project • Application-specific management of optical networks • Future applications can: • dynamically allocate light paths, of 10 Gbit/sec each • control topology through the Network Operations Center • Gives flexible, dynamic, high-bandwidth links • Research questions: • How to provide this flexibility (across domains)? • How to integrate optical networks with applications? • Joint project with Cees de Laat (Univ. of Amsterdam), funded by NWO

  28. CPU’s R CPU’s R CPU’s R NOC CPU’s R CPU’s R DAS-3

  29. Summary • VL-e (Virtual Laboratory for e-Science) studies entire e-Science chain, including applications, middleware and grids • Organized into 2 environments: • Proof of Concept (for applications) • Rapid Prototyping (computer science research) • New state-of-the-art Grid infrastructure planned for 2006 using optical networking More information: http://www.vl-e.nl

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