Virtual Laboratory for eScience VLe Henri Bal Department
Virtual Laboratory for e-Science (VL-e) Henri Bal Department of Computer Science Vrije Universiteit Amsterdam bal@cs. vu. nl vrije Universiteit
e-Science • Web is about exchanging information • Grid is about sharing resources o Computers, data bases, instruments, services • e-Science supports experimental science by providing a virtual laboratory on top of Grids
Virtual Laboratories Distributed computing Application Specific Part Potential Generic Visualization & part Management collaboration of comm. & computing Knowledge Data & information Application Specific Part Potential Generic part Virtual Laboratory Management of comm. & services Application oriented computing Application Specific Part Potential Generic part Management of comm. & computing Grid Harness multi-domain distributed resources
Interactive PSE Adaptive information disclosure High-performance distributed computing User Interfaces & Virtual reality based visualization Security & Generic AAA Collaborative information Management Telescience Bio-Informatics Bio-diversity Medical diagnosis & imaging Food Informatics Data Intensive Science Virtual Laboratory for e-Science Virtual lab. & System integration Optical Networking
The VL-e project • 40 M€ (20 M€ BSIK funding) • 2004 - 2008 vrije Universiteit • 20 partners • Academic - Industrial
VL-e environments Application specific service Application Potential Generic service & Virtual Lab. services Grid & Network Services Telescience Medical Application Bio ASP Virtual Laboratory Virtual Lab. rapid prototyping (interactive simulation) Grid Middleware Additional Grid Services (OGSA services) Gigaport Network Service (lambda networking) VL-E Proof of concept Environment VL-E Experimental Environment
VL-e workshop A. I. D. High-performance distributed computing Jansen Visualization Security demo CIM Konijnenburg Telesc ience Bio-Inf Bio-div Medical imaging Marshall, Breit Virtual lab P 4: Scaling up i PSE Food Data Intensie Belleman Optical Networking Bouwhuis
Interactive Problem Solving Environments From Medical Image Acquisition to Interactive Virtual Visualization… MRI, PET Patient at MRI scanner MR image Segmentation Cave, Wall, PC, PDA Virtual Node navigation Bypass creation Simulated blood flow Shear stress, velocities ce (e. g. , Valencia) se (e. g. , Leiden) MD login and Grid Proxy creation Monolith, Cluster LB mesh generation Job submission ce (e. g. , Bratislava) Job monitoring ui (VRE) 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 Simulated Blood Flow
Visualization on the Grid
Visualization on the Grid
Visualization on the Grid
Visualization on the Grid
Visualization on the Grid
High-Performance Distributed Computing • Ibis: a Java-centric grid programming environment o Remote Method Invocation (RMI), group communication, divide&conquer parallelism, object migration (Pro. Active) • Written in pure Java, runs on heterogeneous grids o “Write once, run everywhere ” o Use bytecode rewriting for optimizations (e. g. serialization) o Use native code as special-case optimization (e. g. Myrinet)
Experiences with Ibis • Distributed supercomputing applications o Electromagnetic simulation (Jem 3 D) o Automated protein identification (AMOLF) o N-body simulations, SAT-solver, raytracer • Successful grid experiments o On DAS-2 (homogeneous Dutch grid) o On Grid. Lab (European grid) • Need co-allocation mechanisms More info + distribution at www. cs. vu. nl/ibis
Optical networking • Formally part of Giga. Port-NG BSIK project • Studies optical networking technology in a grid context (e. g. , bandwidth-on-demand) • Useful for many VL-e applications R CPU’s R CP U’ s o Data-intensive sciences, visualization, HPDC, etc. R U’s CP s U’ CP R R U’s CP NOC
Workshop program • 14: 15 - 14: 45 Workflow and data integration in e-bioscience: Some user requirements (Scot Marshall) • 14: 45 - 15: 15 The Knowledge Grid and Adaptive Information Disclosure (Machiel Jansen) • 15: 15 - 15: 45 Data management in the Proof-of-Concept environment of VL-e (Maurice Bouwhuis) • 15: 45 - 16: 00 Presentation of the Demos • 16: 00 - 16: 30 Break & Demo at the Light. House (SARA+Uv. A) • 16: 30 - 17: 00 Medical Application (Robert Belleman) • 17: 00 - 17: 30 Bioinformatics (Timo Breit) • 17: 30 - 18: 00 Dutch Tele-science Lab (Marco Konijnenburg)
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