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

Overview IntroductionIntroduction –Combinatorial Chemistry –Comb-e-Chem ECSES objectivesECSES objectives ECSES and Grid architectureECSES and Grid architecture –Globus –Web services ECSES migration into Comb-e-ChemECSES migration into Comb-e-Chem

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

Comb-e-Chem Vision A Pervasive Grid-Based e-Science Environment Structures DB Properties DB Simulation and calculation Structure + PropertiesKnowledge + Prediction

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

ECSES Objectives Build an impressive e-Science demonstratorBuild an impressive e-Science demonstrator –for NeSc opening ceremony –for other early dissemination venues Provide a proof-of-concept for Comb-e-ChemProvide 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-ChemAssess the use of Globus in Comb-e-Chem –Globus = leading Grid environment today –demo must be based on Globus

ECSES Scope

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

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

ECSES Demo Summary Log into the X-Ray e-LaboratoryLog 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)Search structures database (remote CCD) –retrieve structure from the experiment –find structurally similar compounds –compute predicted melting points Visualise and inspect 2-3 top candidatesVisualise and inspect 2-3 top candidates Design next combinatorial synthesisDesign next combinatorial synthesis

The Globus Project ResearchResearch –Combining parallel, multimedia, distributed, and collaborative computing Globus ToolkitGlobus Toolkit –The core services for grid-enabled applications TestbedsTestbeds –Multiple deployments to organisations for prototyping ApplicationsApplications –Distributed projects, tele-immersion, etc.

The Globus Architecture Applications Fabric Services Toolkit ParametersSimulationCollaborationComputation TCPPBSUDPMPICondor GRAMGASSGSINexus globusrunMPIDUROC MDSHBM Nimrod/GCondor-G

Authentication User Private KeyPrivate Key CertificateCertificate Grid IDGrid ID CA Signs Users’ Certificates Private key encodes a challenge string Server Decodes challenge with public key Mapfile Maps from Grid ID to Local ID

Globus Features / Issues Authentication using Globus certificateAuthentication 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 modelScary execution model –allows user to upload (and run) any executable! Has certain useful featuresHas certain useful features –data staging (access to remote data by Globus-enabled programs) Other problemsOther problems –difficult (lengthy) to install, overweight –complex firewall configuration

Compromise Globus / Web Services Approach Globus used forGlobus used for –data staging –remote execution of melting point simulations –intermediate access to NCS lab “stepping stone” Web services used forWeb 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

ECSES Architecture

ECSES Network Config

ECSES Architecture

ECSES in Comb-e-Chem (original plans) Plan to use ECSES as an initial test rigPlan to use ECSES as an initial test rig –extending Globus grid to include campus systems Experiment by trying to extend ECSESExperiment 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-implementThen isolate what works and re-implement –but this time using web services and not Globus