Mark L' Green, Ph'D'

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GRASE VO Science and Engineering Applicationson
Open Science Grid

• Mark L. Green, Ph.D.
• Grid Computational Scientist, CCR

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Outline
Outline

• Center for Computational Research
• Advanced Computational Data Center Grid
  (ACDC-Grid) System Architecture
• Molecular Structure Determination
• Quantum Chemistry
• Earthquake Engineering
• Princeton Ocean Model and Biohazards
• Geophysical Mass Flows
• Numerical Methods
• ACDC Grid Dashboards

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Major Compute/Storage Resources

• SGI Altix3700 (0.4TF peak)
• 64 Processors (1.3GHz ITF2)
• 256 GB RAM
• 2.5 TB Disk
• Apex Bioinformatics System
• Sun V880 (3), Sun 6800
• Sun 280R (2)
• Intel PIIIs
• Sun 3960 7 TB Disk Storage
• HP/Compaq SAN
• 75 TB Disk 190 TB Tape
• 64 Alpha Processors (400 MHz)
• 32 GB RAM 400 GB Disk

• Dell Linux Cluster (10TF peak)
• 1600 Xeon EM64T Processors (3.2 GHz)
• 2 TB RAM 65 TB Disk
• Myrinet / Force10
• 30 TB EMC SAN
• Dell Linux Cluster (2.9TF peak)
• 600 P4 Processors (2.4 GHz)
• 600 GB RAM 40 TB Disk Myrinet
• Dell Linux Cluster (6TF peak)
• 4036 Processors (PIII 1.2 GHz)
• 2TB RAM 160TB Disk 16TB SAN
• IBM BladeCenter Cluster (3TF peak)
• 532 P4 Processors (2.8 GHz)
• 5TB SAN
• SGI Intel Linux Cluster (0.1TF peak)
• 150 PIII Processors (1 GHz)
• Myrinet

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ACDC-Grid System Architecture
Grid Portal Applications and Administration
Grid Collaborations
Campus Grid Infrastructure
Data Grid Infrastructure
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ACDC-Grid System Architecture
Grid Collaborations
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Grid-enabled Data Mining Infrastructure
ACDC-Grid Computational Resources
Grid Portal Workflow Job Manager
Molecular Structure Database
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Grid-enabling Application Template (GAT)
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Grid-enabling Application Template (GAT)
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ACDC Data Grid Database Schema
ACDC-Grid Data Grid
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SnB GAT

• SnB is a computer program based on Shake-and-Bake
  where
• A dual-space direct-methods procedure for
  determining molecular crystal structures from
  X-ray diffraction data is used.
• As many as 2000 unique non-H atom difficult
  molecular structures have been solved in a
  routine fashion.
• SnB has been routinely applied to jump-start the
  solution of large proteins, increasing the number
  of selenium atoms determined in Se-Met molecules
  from dozens to several hundred.
• SnB is expected to play a vital role in the study
  of ribosomes and large macromolecular assemblies
  containing many different protein molecules and
  hundreds of heavy-atom sites.

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SnB GAT
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SnB GAT
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SnB GAT
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SnB GAT
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Q-Chem GAT

• Quantum Chemistry Software (Q-Chem)
• ab initio electronic structure program
• capable of performing first principles
  calculations on both the ground and excited
  states of molecules
• the Q-Chem program exploits the latest
  developments in computer science, having adopted
  an Object Oriented approach to program design
• allows developers to rapidly implement new
  methodologies with ease and reduce program code
  redundancy

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Q-Chem GAT

• Features
• Ground State Self-Consistent Field Methods
• Hartree-Fock Methods Density Functional Theory
  Linear Scaling Methods AOINTS Package for Two
  Electron Integrals SCF Improvement Features
• Wave Function Based Treatments of Electron
  Correlation
• Møller-Plesset Perturbation Theory Local MP2
  Methods Coupled Cluster Methods Optimized
  Orbital Coupled-Cluster Methods
• Excited State Methods
• Supported Calculation Types CIS Methods
  Time-Dependent DFT Coupled-Cluster Excited
  State Methods Attachment-Detachment Analysis
• Properties Analysis
• Automated Geometry and Transition Structure
  Optimization Vibrational Spectroscopy NMR
  Shielding Tensors Natural Bond Orbital Analysis
  Stewart Atoms Momentum Densities Intracules
  Atoms in Molecules Solvation Modeling
  Relativistic Energy Corrections Diagonal
  Adiabatic Correction
• Basis Sets
• Gaussian Basis Sets Pseudopotential Basis Sets
• Correction for Basis Set Superposition Error

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Q-Chem GAT
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Q-Chem GAT
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Q-Chem GAT
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Earthquake Engineering
EADR GAT

• Evolutionary Aseismic Design Retrofit (EADR)
• In our effort to develop disaster-resilient
  communities, there is a need to model,
  understand, and ultimately direct the behavior of
  a wide variety of complex multi-scale systems,
  including the many engineering systems that shape
  our physical environment.
• Two aspects of the structural system needs
• a multi-scale evaluation tools of progressive
  collapse of structures and
• use of such evaluation tools in a new general
  framework for aseismic design and retrofit, based
  upon evolutionary methodologies.

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EADR GAT

• Multidisciplinary Center for Earthquake
  Engineering (MCEER)
• MCEER is a national center of excellence that
  applies knowledge and advanced technologies to
  reduce earthquake losses.
• Network for Earthquake Engineering Simulation
  (NEES)
• NEES is a national, networked, simulation
  resource that includes geographically-distributed,
  shared-use, next-generation experimental
  equipment sites.
• Department of Civil, Structural, and
  Environmental Engineering (CSEE)
• CSEE faculty support eight research centers,
  programs, institutes, and laboratories providing
  synergistic collaborative activities.

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Earthquake Engineering
EADR GAT
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EADR GAT
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EADR GAT
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POM GAT

• Monitoring and Event Response for Harmful Algal
  Blooms
• Development of a transport model capable of
  predicting the movement of harmful algal blooms
  in a lake is currently underway.
• Developed for each of the three main lakes in the
  Monitoring and Event Response for Harmful Algal
  Blooms (MERHAB) study Ontario, Erie and
  Champlain.
• To accomplish the goal of predicting bloom
  movement, it is necessary to maintain a near
  real-time database for water velocity fields in
  the lakes and to provide short-term predictions
  of lake circulations.
• This requires a combination of hydrodynamic and
  transport modeling, along with linkages to
  various data sources, including regional weather
  stations, water monitoring stations, and
  satellite data.

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POM GAT
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POM GAT
Assessment of the Regional Great Lakes Watershed
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POM GAT
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POM GAT
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Geophysical Mass Flows
Titan GAT

• Titan2d Mass-Flow Model
• The risk of potential volcanic eruptions and
  associated mass flows is a problem that public
  safety authorities throughout the world face
  several times a year.
• Flow models are useful to forecast the movement
  of volcanic materials on or above the surface.
• Applications of such models include
• pre-crisis understanding of hazards and
  developing risk maps,
• real-time crisis assistance and management and
• post-crisis reconstruction and distribution of
  aid.

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Geophysical Mass Flows
Titan GAT
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Geophysical Mass Flows
Titan GAT
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Geophysical Mass Flows
Titan GAT
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Geophysical Mass Flows
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OSTRICH GAT

• Ostrich Optimization Software Tool
• OSTRICH implements numerous model-independent
  optimization and calibration (parameter
  estimation) algorithms including
• Particle Swarm Optimization,
• Genetic Algorithm,
• Simulated Annealing,
• Levenberg-Marquardt least-squares regression and
• several zero- and 1st-order numerical techniques.
• OSTRICH can be used for optimizing many of the
  existing ACDC-Grid grid-enabled applications.

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OSTRICH GAT
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OSTRICH GAT
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OSTRICH GAT
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OSTRICH GAT
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ACDC Grid Dashboards
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Acknowledgments

• GAT Team Leaders
• Russ Miller (SnB)
• Tom Furlani (Q-Chem)
• Gary Dargush (EADR)
• Joseph Atkinson (POM)
• Abani Patra (Titan)
• Alan Rabideau (OSTRICH)
• ACDC-Grid Portal
• Steve Gallo
• Jon Bednasz
• ACDC-Grid Research
• Naimesh Shah
• Cathy Ruby
• Amin Ghadersohi

• Center Personnel
• Jason Rappleye
• Sam Guercio
• Tony Kew
• Dori Macchioni
• Martins Innus
• Adam Koniak
• Collaborators
• Charles Weeks
• Dave Pape
• Bill Furey
• Steve Potter
• NSF, NIH, NYS, DOE