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Discovery & Innovationvia Cyberinfrastructure
Russ MillerCyberinfrastructure Lab, SUNY-Buffalo
Hauptman-Woodward Med Res Inst
NSF, NIH, DOE, NIMA, NYS, HP www.cse.buffalo.edu/faculty/miller/CI/
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Academia in the 21st Century: High-Level View
Empower students to compete in knowledge-based economyEmbrace digital data-driven societyAccelerate discovery and comprehensionEnhance virtual organizationsProvide increased education, outreach, and trainingEnhance and expand relationships between academia and the corporate world
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Academia in the 21st Century: Medium-Level View
Create links between enabling technologists and disciplinary usersImprove efficiency of knowledge-driven applications in myriad disciplines
New TechniquesNew AlgorithmsNew Interactions (people & systems)
Support HPC infrastructure, research, and applications Deliver high-end cyberinfrastructure to enable efficient
Collection of data Management/Organization of dataDistribution of dataAnalysis of dataVisualization of data
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
NSF Integrated CI
NSF Integrated Cyberinfrastructure
NSF Director Arden L. Bement: “leadership in cyberinfrastructure may determine America's continued ability to innovate – and thus our ability to compete successfully in the global arena.”
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Academic Computing Initiative: Inverted Umbrella (Sample)
Departments, Colleges, Centers, Institutes, &User Support Staff: HPC, Viz, Interfaces, Data
Modeling Physical Multi-Systems &
Phenomena(“Simulation-
Based Eng Sci”)
Interactive Systems
Ubiquitous Computing
Environments
ComputationalDigital Art
High-Performance Systems, Networks, Storage, Visualization Sensors, Middleware, User-Interfaces, Staff
Engineering DesignEngineering DesignDisaster ManagementDisaster Management
Digital GovernmentDigital Government
Graphics, Haptics , SpeechGraphics, Haptics, Speech
Data Mining, FusionRecognition, LearningData Mining & Fusion
Multi -Scale ModelingMulti-Scale Modeling
Societal Challenges
(Knowledge & Discovery)
Parallel, Cluster, andGrid Computing
Multiprocessor Computing
Data/Computer SecurityData/Computer Security
CYBERINFRASTRUCTURE
Advanced MaterialsAdvanced MaterialsHealth CareHealth Care
Ontology and ReasoningOntology & Reasoning
EnvironmentalModeling
Environmental Modeling
Computational Sci & Eng
Middleware
Human-Computer Interaction Collaborative ComputingLearning & Recognition
Wireless ComputingWireless Technology
Strategy for E
xcellence (International P
rominence)
Initiatives
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
HPC/CI/CSE InitiativeMust be Pervasive Across the Entire UniversityMust Remove BarriersGroups Must Interact
Research GroupsSupport StaffStudentsDepartmentsColleges
IssuesTenure & PromotionUniversity vs Colleges vs Departments vs Faculty vsCenters/Institutes vs Degrees vs Courses
Details are University Dependent
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Center for Computational Research (CCR)
Founding Director (1998-2006)Facts & Figures
Top Academic HPC Center in World~25 TF of HPC~600 TB of High-End StorageSignificant VisualizationSpecial-Purpose Systems~30 FTEs Staff140 Projects Annually
EOT K-16, industry, communityNon-Traditional UsersVisualization Projects
ROI: $7M → ~$300M @ UBROI: ~$450M to WNY
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
CCR Highlights (1998-2006)Provide HE-CompProvide HE-Vis + AGNSpecial Purpose Systems
BioinformaticsData Warehouse / Mining
Support Local/National Efforts –Industry + AcadCreate jobs in WNYCertificate ProgramWorkshops + Tours
Campus, IndustryHigh-School
Urban Planning & DesignMTV VideosPeace Bridge, Med CampusOlmsted Parks, ThruwayNYS AgenciesElected OfficialsMagnet on CampusSignificant FundsNumerous AwardsSignificant Publicity
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
CCR Research & ProjectsArchaeologyBioinformatics/Protein FoldingComputational ChemistryComputational Fluid DynamicsData Mining/DatabaseEarthquake EngineeringEnviron Modeling & SimulationGrid ComputingMolecular Structure DeterminationPhysics
Videos: MTVUrban Simulation and Viz
StreetScenesI-90 Toll BarrierMedical CampusPeace Bridge
Accident ReconstructionScientific Viz
DentalSurgeryMRI/CT ScanConfocal MicroscopyCrystallization WellsCollaboratories
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Real-Time Visualization
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Accurate local landmarks: Bridges, Street Signs, Business, HomesCan be viewed from driver’s perspectiveReal-Time NavigationWorks with
CorsimSynchro
Generate AVI & MOVMultiple Simultaneous
Traffic LoadsSimulationVarying POV
StreetScenes: Real-Time3D Traffic Simulation
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Animation & Simulation
Rendered Scenes
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Visualization in Planning Studies
Bergmann Associates: Indian Street Bridge - Florida
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Peace Bridge Visualization:Animation & Simulation
International CrossingThe Problem
75 year old bridge3 lanes – poor capacityExisting US plaza: small and poor design
Proposed OptionsRelocate US plazaBuild a 3-lane companion span
& rehab existing bridgeBuild a six lane signature span
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Public Forum
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Song: I’m OK (I Promise)Band: Chemical Romance
Gaming Environment: Death Jr.MTV
IBC Digital & CCR
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Virtual Reality
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Networked art application for CAVEUsers from around the worldFirst performance 2001
Dance-floor environmentInhabited by life-size puppetsDance with each otherSynchro
Recording BoothUser enters boothUser dances System records dance from tracking
on head and handsDance mapped to Avatar
Alive on the Grid: PAAPAB
J. Anstey
Media Art
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Interactive virtual factoryCreates digital mock-up of
factoryDrag & place modular
machinesMathematical algorithms
for consistency checks
VR-Fact!
Kesh
Mechanical and Aerospace Engineering
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Western New York
Some Facts
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Buffalo, New YorkThe Queen City: 2nd Largest City in NYSCity of Lights
First U.S. city to have electric street lightsPan American Exposition (1901)
Pres. McKinley ShotArchitecture
Frederick Law Olmsted Frank Lloyd Wright
Underground RailroadSlaves escaped to freedom in Canada
Four straight Super Bowl appearancesCulinary Delights
Beef on Weck, Pizza, Fish Fries(Buffalo) Wings: Anchor Bar, 1964
Health ProblemsHeart Disease/StrokeMultiple Sclerosis
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Recent Biomedical Advances(Buffalo, NY)
PSA Test (screen for Prostate Cancer)Avonex: Interferon Treatment for Multiple SclerosisArtificial BloodNicorette GumFetal Viability TestEdible Vaccine for Hepatitis CTimed-Release Insulin TherapyAnti-Arrythmia Therapy
Tarantula venom
Direct Methods Structure Determination
Listed on “Top Ten Algorithms of the 20th
Century”VancomycinGramacidin AHigh Throughput Crystallization Method: PatentedNIH National Genomics Center: Northeast ConsortiumHoward Hughes Medical Institute: Center for Genomics & Proteomics
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Scientific Visualization
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Multiple Sclerosis Project
Collaboration with Buffalo Neuroimaging Analysis Center (BNAC)
Developers of Avonex, drug of choice for treatment of MS
MS Project examines patients and compares scans to healthy volunteers
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
3D Medical Visualization
Reads data output from a CT or MRI ScanCollaboration with Children’s HospitalVisualize multiple surfaces and volumesExport images, movies or CAD filePre-surgical planningRuns on a PC
M. Innus
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Positron emissiontomography (PET),shows sites activatedand deactivated as subjects decide whether asound is a target or not.
Current density maps ofbrain surface (1–700 ms after target) show dynamicpattern of brain activity during decision-makingprocess.
Mapping Brain ActivitySites Activated Sites Deactivated
A. Lockwood
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Science & Engineering
Small Subset of Projects
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Groundwater Flow Modeling
A. Rabideau, I. Jankovic, M. Becker
Regional scale modeling of groundwater flow and contaminant transport (Great Lakes)Ability to include all hydrogeologic features as independent objectsBased on Analytic Element MethodKey features:
Highly parallelObject-oriented programmingIntelligent user interface
Utilized 42 years of CPU timeon CCR computers in1 calendar year
Environmental Engineering
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Avalanches, Volcanic and Mud Flows
Flow models of Colima volcanoIn Mexico – courtesy Rupp et. al.’06
Modeling of Volcanic Flows, Mud flows (flash flooding), and avalanchesIntegrate information from several sources
Simulation resultsRemote sensingGIS data
Present information to decision makers using custom visualization tools local & remoteGRID enabled for remote accessKey Features
Parallel Adaptive ComputationIntegrated with GIS System for flowson natural terrain
A. Patra, B. Pitman, M. Sheridan, M. Jones
Geology, Engineering
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Literacy & Disability in CanadaExploring the relationship between illiteracy & disability across the Canadian landscapeSocial Systems GIS Lab in the Dept. of Anthropology is working with researchers from York University & the Canadian Abilities Foundation. Sponsored by The Adult Learning & Literacy Directorate of the Ministry of Human Resources & Social Development Canada.
E. Zubrow
Anthropology
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Wealth of new precision cosmological dataWMAP Cosmic Microwave Background MeasurementSloan Digital Sky Survey: 3-D map of a million galaxiesInterpret implications of data for models of the first trillionth of a second of the universe: inflationMonte Carlo Markov Chain data analysis: stochastic exploration of many-dimensional parameter spaces
W. Kinney
Cosmological Parameter EstimationCosmology
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
UB’s Structural Engineering and EarthquakeSimulation Laboratory (SEESL)
NEESWood: Development of a
Performance-Based Seismic Design for
WoodframeConstruction:
Reaction Wall
Strong Floor
2D-BearingsFast Actuator(100-200 ton)
5.0 m
2.75
m
6.2 m
SECTIONAL VIEW
PLAN
Shaking Frame on Strong Floor
Pile
α=2 or 3 deg.
Nevada Sand, Dr~45%
3.35
m
5.6 m
2-D Laminar Box (24 Laminates)
Ball Bearings
(EI)1
(EI)2>>(EI)1
See notes below 2-D Geotechnical Laminar Box Tests of Pile Foundations Subjected to Soil Liquefaction
Two-story Townhouse
on Twin Shake Tables
M. Bruneau, A. Reinhorn, G. Lee
Structural Engineering
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
r/D
Understanding CombustionFlame-wall interaction modeling for a non-premixed flame propelled by a vortex ring.In this figure different time instants are shown during the interaction. White line contours and color contours represent vortex ring and flame, respectively.Key Features:
Modeling of Detailed GRI3.Mechanism for MethaneCombustionParallel algorithm using mpi85-90% Parallel efficiency for upto 64 processors
FWI study is important to determineEngine DesignQuenching DistancesFlame StructureUnburned hydrocarbonMaximum Wall heat fluxes
C. Madnia
Computational Fluid Dynamics
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Computational Materials ScienceMolecular and mesoscale modeling used to understand the behavior of materialsExample application: ElectromigrationStrong electrical currents cause movement of atoms in metalResult is large defects that lead to failure of electrical connectionConsequences can be catastrophicInterdisciplinary experimental/ modeling studies leading to understanding of behavior
Photos of metal lines that have developed voids (above) and hillocks (below) due to electromigration. (source: www.nd.edu)
MV DV
MV DV
Simulation cells of solids with mono- and di-vacancies (light blue spheres), highlighting atoms neighboring the defects.D. Kofke
Chemical and Biological Engineering
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Shake-and-Bake
Molecular Structure Determinationfrom X-Ray Crystallographic Data
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Objective: Provide a 3-D mapping of the atoms in a crystal.Procedure:
1. Isolate a single crystal.2. Perform the X-Ray diffraction experiment.
3. Determine molecular structure that agrees with diffration data.
X-Ray Crystallography
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Experiment yields reflections and associated intensities.Underlying atomic arrangement is related to the reflections by a 3-D Fourier transform.Phase angles are lost in experiment.Phase Problem: Determine the set of phases corresponding to the reflections.
X-Ray Data Molecular Structure
FFT
FFT-1
X-Ray Data & Corresponding Molecular Structure
Reciprocal or “Phase” Space Real Space
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
FFTTrial
Phases
Solutions
?PhaseRefinement
DensityModification
(Peak Picking)
TangentFormula
Reciprocal Space Real Space
Conventional Direct Methods
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
FFTTrial
Phases
Solutions
?PhaseRefinement
TangentFormula
Reciprocal Space Real Space“Shake” “Bake”
PhaseRefinement
FFT-1ParameterShift
DensityModification
(Peak Picking)(LDE)
Trial Structures Shake-and-Bake
StructureFactors
Shake-and-Bake Method:Dual-Space Refinement
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Ph8755: SnB Histogram
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Number of Atoms in Structure0 100 1,000 10,000 100,000
Conventional Direct Methods
Shake-and-Bake
Multiple Isomorphous Replacement
Se-Met
Se-Met with Shake-and-Bake
Vancomycin
567 kDa (160 Se)
?
?
Phasing and Structure Size
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Grid Computing
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Grid Computing Overview
Coordinate Computing Resources, People, Instruments in Dynamic Geographically-Distributed Multi-Institutional EnvironmentTreat Computing Resources like Commodities
Compute cycles, data storage, instruments Human communication environments
No Central Control; No Trust
Imaging Instruments Large-Scale Databases
Data Acquisition AnalysisAdvanced Visualization
Computational ResourcesLHC
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Major Grid InitiativesTeraGrid (NSF)
Integrates High-End ResourcesHigh-Performance (Dedicated) Networks9 Sites (?); 250TF & 30PB (?)100+ Databases Available
OSG (DOE, NSF)High-Throughput Distributed FacilityOpen & HeterogeneousBiology, Computer Science, Astrophysics, LHC57 Compute Sites; 11 Storage Sites; 10K CPUS; 6PB
EGEE: Enabling Grids for E-SciencE (European Commision)Initial Focus on CERN (5PB of Data/Year)
High-Energy Physics and Life SciencesExpanded Focus Includes Virtually All Scientific Domains200 Institutions; 40 Countries20K+ CPUs; 5PB; 25,000 jobs per day!
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Miller’s Cyberinfrastructure Lab
CI sits at core of modern simulation & modelingCI allows for new methods of investigation to address previously unsolvable problemsFocus on development of algorithms, portals, interfaces, middlewareFree end-users to do disciplinary workFunding (2001-pres): NSF ITR, NSF CRI, NSF MRI, NYS, FedExperimental Equipment (Dell/Lenovo): 1.25 TF Clusters, 140 Cores (Intel/AMD), 4 TB Internal Storage, GigE, IB, Condor Flock (35 Intel/AMD), 22 TB Storage (2)Production Equipment (Dell): Workstations, 15 TB Storage, CCR equipment
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Evolution of CI Lab ProjectsACDC-Grid
Experimental Grid: Globus & CondorIntegrate Data & Compute, Monitor, Portal, Node Swapping, Predictive Scheduling/Resource ManagementGRASE VO: Structural Biology, Groundwater Modeling, Earthquake Eng, Comp Chemistry, GIS/BioHazardsBuffalo, Buffalo State, Canisius, Hauptman-Woodward
WNY GridHeterogeneous System: Hardware, Networking, UtilizationBuffalo, Geneseo, Hauptman-Woodward, Niagara
NYS GridExtension to Hardened Production-Level System State-WideAlbany, Binghamton, Buffalo, Geneseo, Canisius, Columbia, HWI, Niagara, [Cornell, NYU, RIT, Rochester, Syracuse, Marist], {Stony Brook, RPI, Iona}
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
NYS Grid ResourcesAlbany: 8 Dual-Processor Xeon NodesBinghamton: 15 Dual-Processor Xeon NodesBuffalo: 1050 Dual-Processor Xeon NodesCornell: 30 Dual-Processor Xeon NodesGeneseo State: Sun/AMD with 128 Compute CoresHauptman-Woodward Institute: 50 Dual-Core G5 NodesMarist: 9 P4 NodesNiagara University: 64 Dual-Processor Xeon NodesNYU: 58 Dual-Processor PowerPC NodesRIT: 4 Dual-Processor Xeon NodesSyracuse: 8 Dual-Processor Xeon Nodes
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
CI Lab CollaborationsHigh-Performance Networking InfrastructureGrid3+ CollaborationiVDGL Member
Only External MemberOpen Science Grid
GRASE VONYSGrid.org
NYS CI InitiativeExecutive DirectorVarious WGs
Grid-Lite: Campus GridHP Labs Collaboration
Innovative Laboratory PrototypeDell Collaboration
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CI Lab Grid Monitor: http://osg.ccr.buffalo.edu/
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CI Lab Operations Dashboard
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Structural BiologySnB and BnP for Molecular Structure Determination/Phasing
Groundwater ModelingOstrich: Optimization and Parameter Estimation ToolPOMGL: Princeton Ocean Model Great Lakes for Hydrodynamic CirculationSplit: Modeling Groundwater Flow with Analytic Element Method
Earthquake EngineeringEADR: Evolutionary Aseismic Design and Retrofit; Passive Energy Dissipation System for Designing Earthquake Resilient Structures
Computational ChemistryQ-Chem: Quantum Chemistry Package
Geographic Information Systems & BioHazardsTitan: Computational Modeling of Hazardous Geophysical Mass Flows
Grid-Enabling Application Templates (GATs)
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Grid Enabled SnB
Required Layered Grid ServicesGrid-enabled Application Layer
Shake – and – Bake applicationApache web serverMySQL database
High-level Service LayerGlobus, NWS, PHP, Fortran, and C
Core Service LayerMetacomputing Directory Service, Globus Security Interface,
GRAM, GASSLocal Service Layer
Condor, MPI, PBS, Maui, WINNT, IRIX, Solaris, RedHat Linux
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Startup Screen for CI Lab Grid Job Submission
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Instructions and Description for Running a Job on ACDC-Grid
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Software Package Selection
Full Structure / Substructure Template Selection
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Default Parameters Based on Template
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SnB Review (Grid job ID: 447)
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Graphical Representation of Intermediate Job Status
Histogram of Completed Trial Structures
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Status of Jobs
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User starts up – default image of structure.
Heterogeneous Back-End Interactive Collaboratory
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Molecule scaled, rotated, and labeled.
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
Acknowledgments
Mark GreenCathy RubyAmin GhadersohiNaimesh ShahSteve GalloJason RappleyeJon BednaszSam GuercioMartins InnusCynthia Cornelius
George DeTittaHerb HauptmanCharles WeeksSteve Potter
Alan RabideauIgor JanckovicMichael Sheridan Abani PatraMatt Jones
NSF ITRNSF CRINSF MRINYSCCR
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University at Buffalo The State University of New York CI LabCyberinfrastructure Laboratory
www.cse.buffalo.edu/faculty/miller