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