Biomedical Computing and Visualization

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Problem Solving Environments for Scientific
Computing
Chris Johnson
Scientific Computing and Imaging Institute School
of Computing University of Utah
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Computational Cardiology
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Computational Neuroscience
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Biomedical Visualization
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DOE ASCI Center CSAFE
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Time Dependent Combustion
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Fracture Close-Up
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DOE SciDAC Center Nuclear Fusion
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Seismic Simulation and Visualization
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Elastohydrodynamic Lubrication (EHL)
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CFD Time Dependent Visualization
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Genetics
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Surgical Planning
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Computational Science
Computational X - Chemistry - Physics -
Biology - Medicine - Fluid Dynamics -
Geoscience -

• Common Tools
• Image Processing
• - Mesh Generation
• - Approximation
• - Linear Algebra
• - Visualization

Infrastructure - Memory Mgmt - Process Mgmt -
Framework
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Problem Solving Environments (PSEs)
Chemistry
Physics
Core Memory Mgmt Process Mgmt Framework Libraries
Biology
Geoscience
Medicine
Fluid Dynamics
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Problem Solving Environments

• Computational Workbench
• Modeling, Simulation,
• Visualization Tools
• Dataflow Programming
• Modules
• Spatial/Temporal Coherence
• Computational Steering
• What if..? Problem Exploration
• Flexible, Extensible Environment
• Module Development Tool

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Problem Solving Environments
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SCIRun

• Modules - functional elements
• Computation
• Visualization
• Modeling
• Imaging
• Data flows through ports
• Fields - the main data model
• Nets - are the application

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Packages

• Encapsulated project
• Hierarchical organization of modules
• Packages enabled via configure options
• configure --enable-packageBioPSE mypackage

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Dataflow Datatypes
Matrix
Field
ColorMap
Geometry
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Matrices Class Hierarchy

• Matrix base class
• get, put, , nrows, ncols, get_row, get_col,
  get_val, zero, mult, mult_transpose, print,
  is_,as_,sparse,dense,column, cg_solve,
  bicg_solve, scalar_multiply
• SparseRowMatrix
• int rows, int cols, double a, int nnz
• ColumnMatrix
• double data
• DenseMatrix
• double data

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Matrices External Libraries

• PETSc
• Preconditioners jacobi, bijacobi, sor,
  eisenstat, icc, ilu, asm, sles, lu, mg, spai,
  milu, nn, cholesky, ramg
• Solvers KSRICHARDSON, PSPCHEBYCHEV, KSPGG,
  KSPGMRES, KSPTCQMR, KSPBCGS, KSPBGS, KSPTFQMR,
  KSPCR, KSPLSQR, KSPBICG, KSPPREONLY
• BLAS and Atlas
• Faster linear-algebra via loop unrolling

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Fields Mesh Data
Data int, float, double, Vector, Tensor,
Geometry Regular Irregular
Properties Data_at (center)
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Example Datasets - On Line
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Algorithm Structure

• Templated Algorithm
• Composed with Field classes to provide optimized
  implementation
• Uses dynamic compilation to create required
  combinations
• Potentially specialized for specific field type

templateltclass Fieldgt RenderField public
RenderFieldBase
virtual void render(FieldBase)0
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Visualization at All Levels

• Application level
• Streamlines, cutting planes, isosurfaces, volume
  rendering, etc.
• System level
• Module profiling
• Memory allocator visualization
• Links to TAU

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Error Messages

• Run-time messages are sent to the modules log

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Interactive Large-Scale Visualization
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SCIRun/BioPSE Extensibility

• Leverage existing utilities/programs
• Extensibility through bridges

GENESIS
Matlab
NetSolve
SQL
lib
socket
BioPSE
PETSc
lib
ITK
lib
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Adding a Module to SCIRun/BioPSE

• Rapid development/protyping tool
• ModuleMaker ComponentWizard
• Start with a generic template
• Design ports, interface, callback
• Compile on-the-fly
• Dynamically reload

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Component Wizard

• Creating a new module

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Adaptive Finite Elements
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Inverse EEG Simulation
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Source Localization Algorithm
Data
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Forward/Inverse EEG Simulation

• Apply source location
• 3D adaptive mesh generation
• Finite element simulation (forward and inverse
  solution)
• Linear system solve
• Visualization

400,000 Tetrahedral Elements, SGI and Linux PC
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Cardiac Defibrillation Device Design
300,000 Tetrahedral Elements, SGI and Linux PC
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Software Engineering
Software Engineering is Often Overlooked! Software
Engineering is Hard! Software Engineering is
Important!
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Internal Software Management

• Shared Software System
• CVS
• Log, Track, and Manage Bugs
• Bugzilla
• Automated Documentation
• doxygen
• Automated System Testing
• Custom scripts
• Tinderbox
• Development Management
• SCIRun Exec / NCRR Exec
• Master task list
• Weekly meetings
• MS Project

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Current SCIRun/BioPSE Research

• Bridging to other Applications and Components
• Detachable interface
• Reproducibility
• CCA compatibility
• Remote vis
• Custom UI
• Scripting
• Focused applications!

BioPSE
GUI
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DOE Common Component Architecture Project

• A CA for large-scale Scientific Computation
• Component Characteristics
• May be SPMD or multi-threaded parallel objects
• Heterogeneity
• Parallel platforms to desktops and any language
• Local and Remote
• Parallel communication for remote parallel
  interfaces and 0-copy in-process connection
• Dynamic Composition and Integration
• Hot-swapable components, shared instances
• www.cca-forum.org

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Building Applications by Composition

• Components can be linked along share
  interfaces (Ports) where one component invokes
  the services of another

Remote component
Direct connect
setImage()
Image Database Component
getImage()
doFFT()
ACME FFT Component
adjustColor()
Single address space
Image tool graphical interface component
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Abstraction - Picasso
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SCIRun2 Overview

• Design Goals
• Distributed memory parallel components
• Grid computing
• Meta components to combine
• CCA
• SCIRun
• VTK
• Other component systems

SCIRun2
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Component Bridges
Bridges adapt component interactions Automatically
or semi-automatically generated
Maps semantics between multiple software domains
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Managing Complexity Subnets
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Managing Complexity Subnets
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Managing Complexity Subnets
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Managing Complexity Annotations
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All Modules are Generic
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Power Apps
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PowerApps User-Friendly, Domain-Specific
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BioPSE
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BioFEM - PowerApp
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BioTensor - PowerApp
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ITK Insight Toolkit
www.itk.org
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SCIRun and ITK Integration
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More Apps, More Bridges
NCMIR
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Documentation
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Acknowledgements

• NIH NCRR, NLM and BISTI
• DOE ASCI and SciDAC
• DARPA
• NSF
• Utah Centers of Excellence
• Visual Influence

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More Information
www.sci.utah.edu