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Exploring Chemical Structures using E-Science (ECSES)

Exploring Chemical Structures using E-Science (ECSES). Ken Meacham, IT Innovation Crystal Grid Workshop, 13-17 Sept 2004. Overview. Introduction Combinatorial Chemistry Comb-e-Chem ECSES objectives ECSES and Grid architecture Globus Web services ECSES migration into Comb-e-Chem.

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Exploring Chemical Structures using E-Science (ECSES)

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  1. Exploring Chemical Structures using E-Science(ECSES) Ken Meacham, IT Innovation Crystal Grid Workshop,13-17 Sept 2004

  2. Overview • Introduction • Combinatorial Chemistry • Comb-e-Chem • ECSES objectives • ECSES and Grid architecture • Globus • Web services • ECSES migration into Comb-e-Chem

  3. Combinatorial Chemistry • Parallel synthetic approach • create hundreds of materials • screen properties to find those that fit the bill • Typically requires several passes • find chemical structure of the best candidates • create new batches of similar materials for subsequent passes • Leads to explosive growth in: • volume of data generated • potential to exploit this data

  4. Comb-e-Chem VisionA Pervasive Grid-Based e-Science Environment Structure + Properties Knowledge + Prediction Structures DB Properties DB Simulation and calculation

  5. Chemistry: Specialist General users Computer Science: Implementation Research Comb-e-Chem Programme Proof of Concept Prototype Links to Computation Automation & Knowledge “ECSES” Dissemination Users Statistics: availability of modern techniques to Chemistry

  6. ECSES Objectives • Build an impressive e-Science demonstrator • for NeSc opening ceremony • for other early dissemination venues • Provide a proof-of-concept for Comb-e-Chem • prove that Comb-e-Chem can be built • proving ground for Comb-e-Chem requirements capture • Assess the use of Globus in Comb-e-Chem • Globus = leading Grid environment today • demo must be based on Globus

  7. ECSES Scope

  8. ECSES: A Proof of Concept Send sample material to NCS service Collaborate in e-Lab experiment and obtain structure Search materials database and predict properties using Grid computations Download full data on materials of interest

  9. ECSES Demo Scenario • Optically active materials design • application to sensor technology • needs high operating temperature • Researcher has found a candidate material • good optical properties, but • melting point is too low for operational use • Use e-Science structure-property queries • to find alternative candidate materials • to rank according to predicted melting points

  10. ECSES Demo Summary • Log into the X-Ray e-Laboratory • view experiment to determine crystal structure of new material • collaborate with crystallographers in lab (video conf.) • Search structures database (remote CCD) • retrieve structure from the experiment • find structurally similar compounds • compute predicted melting points • Visualise and inspect 2-3 top candidates • Design next combinatorial synthesis

  11. The Globus Project • Research • Combining parallel, multimedia, distributed, and collaborative computing • Globus Toolkit • The core services for grid-enabled applications • Testbeds • Multiple deployments to organisations for prototyping • Applications • Distributed projects, tele-immersion, etc.

  12. The Globus Architecture Applications Computation Collaboration Simulation Parameters Toolkit Condor-G Nimrod/G DUROC MPI globusrun Services HBM MDS Nexus GSI GASS GRAM Fabric Condor MPI UDP PBS TCP

  13. Authentication User • Private Key • Certificate • Grid ID Private key encodes a challenge string Server Decodes challenge with public key Mapfile Maps from Grid ID to Local ID CA Signs Users’ Certificates

  14. Globus Features / Issues • Authentication using Globus certificate • issued by Globus CA • poor sign-up process (basic checking of identity) • server “map file” for authentication of specific users • Scary execution model • allows user to upload (and run) any executable! • Has certain useful features • data staging (access to remote data by Globus-enabled programs) • Other problems • difficult (lengthy) to install, overweight • complex firewall configuration

  15. Compromise Globus / Web Services Approach • Globus used for • data staging • remote execution of melting point simulations • intermediate access to NCS lab “stepping stone” • Web services used for • access to NCS lab (from stepping stone) • pre-determined (restricted) services, e.g. • download x-ray images, and other raw data • send/receive messages to/from lab technician

  16. ECSES Architecture

  17. ECSES Network Config

  18. ECSES Architecture

  19. ECSES in Comb-e-Chem(original plans) • Plan to use ECSES as an initial test rig • extending Globus grid to include campus systems • Experiment by trying to extend ECSES • automatic transfer of experimental data to databases • adding multimedia to the experimental archive • greater range of property predictions • more sophisticated DOE for analysis service • Then isolate what works and re-implement • but this time using web services and not Globus

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