TR&D Project 4

Application Development

Michael Blinov Jeff Dutton Fei Gao Anuradha Lakshminaranaya Ye Li Frank Morgan Igor Novak Oliver Rübenacker Dan Vasilescu

Ion I. Moraru James C. Schaff

Summary1. Work that is presented in more

detail elsewhere– GUI “polishing” (better error

messages, more inline info, auto-complete, etc.)

– Enhanced geometry interface (segmentation support, primitives wizard, ROI goodies)

– New solver deployments– New external database links

(Pathway Commons)– New pathway search/import

functionality (SyBiL integration)– Enhanced metadata and

annotation support– Compute server upgrades– New backup and archival

infrastructure– VFRAP standalone application

2. Grid Initiative– Re-purposing older,

decommissioned cluster– UCHC OSG site operational– Production work since 9/09– VCell OSG layer prototype

design3. Enhanced VCell “Application”

– From global parameters to application parameters…

– Application-level output functions (simulation post-processing)

– New “pre-math” combined editor pane

– Reaction kinetics override– Application-level user-defined

functions– Application-level user-defined

equations

The Open Science Grid Initiative

• Site build ramped up in January of 2009

• 58 CPU cluster running Rocks Clusters operating system

• Theoretically 1,392 CPU hours available for production daily

• Only site known to us to have OSG Production Compute Element running on a Microsoft Active Directory integrated Linux cluster

• Site registered with OSG in February 2009

• Site name is UCHC_CBG

• Doing production in September 2009

• Our unique architecture has caused problems and brought us added attention from OSG resources to overcome these issues and to improve the OSG software stack

The Open Science Grid Initiative

Production – Job Counts

• More than 16 production users have run jobs

• Average about 228 hours of production per day

Production - Cumulative

• Average about 182 jobs per day

• More than 30,000 compute hours of production

• Engage (OSG generic VO) is biggest user

• SBGrid is ramping up and expected to be a heavy user

• New CompBioGrid user from Storrs will be prototyping a grid application on UCHC_CBG in the coming weeks

Mathematical Description(view-only, automaticallygenerated)

Mathematical Description(view-only, automaticallygenerated)

Mathematical Description(view-only, automaticallygenerated)

ResultsResultsResults

Applications

Structure mapping(topology to geometry)Initial ConditionsBoundary conditionsDiffusion constants (if spatial)Electrophysiology protocolsEnable/disable reactionsFast reactionsModel analysisStochastic rate conversion

Applications

Structure mapping(topology to geometry)Initial ConditionsBoundary conditionsDiffusion constants (if spatial)Electrophysiology protocolsEnable/disable reactionsFast reactionsModel analysisStochastic rate conversion

Applications

Structure mapping(topology to geometry)Initial ConditionsBoundary conditionsDiffusion constants (if spatial)Electrophysiology protocolsEnable/disable reactionsFast reactionsModel analysisStochastic rate conversion

Simulations

TimecourseTimestepMesh sizeSolver typeSolver settingsParameter changesParameter scansParameter sensitivity

Simulations

TimecourseTimestepMesh sizeSolver typeSolver settingsParameter changesParameter scansParameter sensitivity

Simulations

TimecourseTimestepMesh sizeSolver typeSolver settingsParameter changesParameter scansParameter sensitivity

Physiology

MoleculesStructures(topology)

ReactionsFluxes

Enhanced VCell Application