exploring chemical structures using e-science (ecses) ken meacham, it innovation crystal grid...
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Exploring Chemical Structures Exploring Chemical Structures using E-Scienceusing E-Science
(ECSES)(ECSES)Ken Meacham, IT InnovationKen Meacham, IT Innovation
Crystal Grid Workshop,Crystal Grid Workshop,13-17 Sept 200413-17 Sept 2004
OverviewOverview
• IntroductionIntroduction– Combinatorial ChemistryCombinatorial Chemistry– Comb-e-ChemComb-e-Chem
• ECSES objectivesECSES objectives• ECSES and Grid architectureECSES and Grid architecture
– GlobusGlobus– Web servicesWeb services
• ECSES migration into Comb-e-ChemECSES migration into Comb-e-Chem
Combinatorial ChemistryCombinatorial Chemistry• Parallel synthetic approachParallel synthetic approach
– create hundreds of materialscreate hundreds of materials– screen properties to find those screen properties to find those
that fit the billthat fit the bill
• Typically requires several Typically requires several passespasses– find chemical structure of the find chemical structure of the
best candidatesbest candidates– create new batches of similar create new batches of similar
materials for subsequent passesmaterials for subsequent passes
• Leads to explosive growth in:Leads to explosive growth in:– volume of data generatedvolume of data generated– potential to exploit this datapotential to exploit this data
Comb-Comb-ee-Chem Vision-Chem VisionA Pervasive Grid-Based e-Science EnvironmentA Pervasive Grid-Based e-Science Environment
Structures DB
Properties DB
Simulation andcalculation
Structure + Properties Knowledge + Prediction
Comb-Comb-ee-Chem Programme-Chem Programme
Proof of Concept
Prototype Links to Computation
Automation & Knowledge
Dissemination
Chemistry: Specialist General users
Computer Science: Implementation Research
Statistics: availability of modern techniques to Chemistry
User
s
““ECSES”ECSES”
ECSES ObjectivesECSES Objectives
• Build an impressive e-Science demonstratorBuild an impressive e-Science demonstrator– for NeSc opening ceremonyfor NeSc opening ceremony– for other early dissemination venuesfor 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 builtprove that Comb-e-Chem can be built– proving ground for Comb-e-Chem requirements proving ground for Comb-e-Chem requirements
capturecapture
• Assess the use of Globus in Comb-e-ChemAssess the use of Globus in Comb-e-Chem– Globus = leading Grid environment todayGlobus = leading Grid environment today– demo demo mustmust be based on Globus be based on Globus
ECSES ScopeECSES Scope
Grid Infrastructure:
PropertiesPrediction
E-Lab:X-Ray
Crystallography
LaboratoryProcesses
StructuresDB
PropertiesDB
Visualisation
ECSES: A Proof of ConceptECSES: A Proof of Concept
X-Ray e-LaboratoryStructuresDatabase
ComputationService
Send sample Send sample material to material to
NCS serviceNCS service
Search materials database Search materials database and predict properties using and predict properties using
Grid computationsGrid computations
Download full Download full data on materials data on materials
of interestof interest
Collaborate in e-Lab Collaborate in e-Lab experiment and experiment and obtain structureobtain structure
ECSES Demo ScenarioECSES Demo Scenario
• Optically active materials designOptically active materials design– application to sensor technologyapplication to sensor technology– needs high operating temperatureneeds high operating temperature
• Researcher has found a candidate materialResearcher has found a candidate material– good optical properties, butgood optical properties, but– melting point is too low for operational usemelting point is too low for operational use
• Use e-Science structure-property queriesUse e-Science structure-property queries– to find alternative candidate materialsto find alternative candidate materials– to rank according to predicted melting pointsto rank according to predicted melting points
ECSES Demo SummaryECSES Demo Summary
• Log into the X-Ray e-LaboratoryLog into the X-Ray e-Laboratory– view experiment to determine crystal structure of view experiment to determine crystal structure of
new materialnew material– collaborate with crystallographers in lab (video collaborate with crystallographers in lab (video
conf.)conf.)
• Search structures database (remote CCD)Search structures database (remote CCD)– retrieve structure from the experimentretrieve structure from the experiment– find structurally similar compoundsfind structurally similar compounds– compute predicted melting pointscompute 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 ProjectThe Globus Project
• ResearchResearch– Combining parallel, multimedia, distributed, and Combining parallel, multimedia, distributed, and
collaborative computingcollaborative computing
• Globus ToolkitGlobus Toolkit– The core services for grid-enabled applicationsThe core services for grid-enabled applications
• TestbedsTestbeds– Multiple deployments to organisations for Multiple deployments to organisations for
prototypingprototyping
• ApplicationsApplications– Distributed projects, tele-immersion, etc.Distributed projects, tele-immersion, etc.
The Globus ArchitectureThe Globus Architecture
ApplicationsApplications
FabricFabric
ServicesServices
ToolkitToolkit
ParametersSimulationCollaborationComputation
TCPPBSUDPMPICondor
GRAMGASSGSINexus
globusrunMPIDUROC
MDSHBM
Nimrod/GCondor-G
AuthenticationAuthentication
UserUser
•Private KeyPrivate Key
•CertificateCertificate
•Grid IDGrid ID
CACA
Signs Users’ CertificatesSigns Users’ Certificates
Private key encodes a Private key encodes a challenge stringchallenge string
ServerServer
Decodes challenge with Decodes challenge with public keypublic key
MapfileMapfile
Maps from Grid ID to Maps from Grid ID to Local IDLocal ID
Globus Features / IssuesGlobus Features / Issues
• Authentication using Globus certificateAuthentication using Globus certificate– issued by Globus CAissued by Globus CA– poor sign-up process (basic checking of identity)poor sign-up process (basic checking of identity)– server “map file” for authentication of specific usersserver “map file” for authentication of specific users
• Scary execution modelScary execution model– allows user to upload (and run) any executable!allows user to upload (and run) any executable!
• Has certain useful featuresHas certain useful features– data staging (access to remote data by Globus-enabled data staging (access to remote data by Globus-enabled
programs)programs)
• Other problemsOther problems– difficult (lengthy) to install, overweightdifficult (lengthy) to install, overweight– complex firewall configurationcomplex firewall configuration
Compromise Globus / Web Compromise Globus / Web Services ApproachServices Approach
• Globus used forGlobus used for– data stagingdata staging– remote execution of melting point simulationsremote execution of melting point simulations– intermediate access to NCS lab “stepping stone”intermediate access to NCS lab “stepping stone”
• Web services used forWeb services used for– access to NCS lab (from stepping stone)access to NCS lab (from stepping stone)– pre-determined (restricted) services, e.g.pre-determined (restricted) services, e.g.
– download x-ray images, and other raw datadownload x-ray images, and other raw data– send/receive messages to/from lab techniciansend/receive messages to/from lab technician
ECSES ArchitectureECSES Architecture
So
uth
amp
ton
Cam
pu
s F
IRE
WA
LL
ComputationService
NC
S L
abo
rato
ry F
IRE
WA
LL
Globus 1.1.4 GRID SOAP/HTTPS/PGP
SOAP/HTTPS/PGP
NCSGATEWAYSERVER
GASSGrid DataService
X-Ray e-Laboratory
StructuresDatabase
ECSES Network ConfigECSES Network Config
SU
CS
Fire
wa
ll
IT Innovation Firewall
New NCS Firewall
IT Innovation DMZ Firewall
Globus 1.1.4Network
Soap/HTTPTransactions
Unregulated (Internal) Network Traffic
Globus "DemoClient"
Globus"Stepping
Stone"
Lab SoapServer
ExperimentController
NCS OfficeW/S
Globus"Compute
Nodes"
ECSES ArchitectureECSES Architecture
Laboratory Experiment Controller(Linux box)
ExperimentData
GridInformation
Service
Conquest -Python
eScience Proxy - Java, Java MediaFramework, CoGKit (including GRAM
Client Library)
Schedules
Demo Site (Linux)
Query Resources
Melting PointPrediction
Code
Properties Database
IT Innovation (SGI)
GRAM
ResourceInformation
Melting Point calcs and results
Lab Portal Layer- limits user access to areas in filesystem and data stores,
handles encryption and decryption
ScheduleQuerying
CDDC Mediator -handlesuser specific interactionswith DB and CIF export
ExperimentVisualisation
CCDC
CambridgeCrystalographic
Database
SouthamptonCrystalographic
Database
Lab Portal Machine (Linux)
GARA
Computation Time Reservation
Portal SteppingStone
GASS -providesaccess to
structure files
Structure File Cache
GRAMLab Globus Gateway (Linux)
SOAP Messaging(Wraps queries, query results
and structures. Messagesare encrypted and signed using PGP)
GASS URLs + Structure Files
Visualisation Streams(RMI)
XML Messaging(Wraps queries and results,
encryption through GSI)
Portal Layer Webservice(accessed through single URL)
ECSES in Comb-e-ChemECSES in Comb-e-Chem(original plans)(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 systemsextending Globus grid to include campus systems
• Experiment by trying to extend ECSESExperiment by trying to extend ECSES– automatic transfer of experimental data to automatic transfer of experimental data to
databasesdatabases– adding multimedia to the experimental archiveadding multimedia to the experimental archive– greater range of property predictionsgreater range of property predictions– more sophisticated DOE for analysis servicemore 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 Globusbut this time using web services and not Globus