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					 Computing for Research:
simulation and visualisation

     Bernard Pailthorpe
       (and Nicole Bordes)
   Research Computing Centre, UQ

                bap@uq.edu.au


                                   www.rcc.uq.edu.au
                                   vislab.uq.edu.au
                                   qcif.edu.au
Outlin
e• Computer Simulation & Visualisation
      - medical imaging; history; Data & Sim in science & engineering
      - eg. projects: research, industry, community impact

 • Computational Science:              3rd route to scientific discovery
   Computational Engineering: design new products, services
rcc.uqedu.au
  web site
  - Research Gallery
  - Education
   -- (student projects)
Types of Visualization
          • Image Processing – medical, satellite, etc;
          • Data Visualisation
              • Rendering: surface, volume;
          • Molecular Modelling
          • Info Vis
          • GIS.
          • Note also:
              o Animation;
             o Virtual Environments - Cave; Stereo
             o PowerWalls, OptIPortal display, Access Grid.
Visualisation in Medicine    (1992)




Ultrasonic imaging,
 inside human artery
  - plaque deposits
 - Sci Vis for
  surgical planning


                       Dr. Richmond Jeremy, Dept Medicine (Cardiology),
                         U. Sydney & RPAH (1992).




                         was www.vislab.usyd.edu.au; now rcc.uq.edu.au/
Medical Imaging: Cancer Cells                              (at UCSD)

1. Confocal microscopy
Optical (Nomarski interference)
  512 x 512 pixels (0.09um);
   25 layers (0.125 um slices)

2. Fluorescence microscopy
   3D, time lapse imaging;


> function localized
     in 3D structure

 NPACI Volume Vis toolkit:
   composite
   & reconstruct image stacks           Jim Feramisco et al, UCSD Cancer Center
           50 frames (320x234 pixels)   - data by Jag Shah; Cleveland Lab, LCIR (2000)

                                        J V Shah & D W Cleveland, Cell, 103, 997 (22 Dec 2000)
Filtered image of CT scan slice: Liver

                                                            Cancer of the Liver
                                                            CAT scan
                                                            Liver surgery




   7
       R. Martin, N. Bordes, B. Pailthorpe (USyd & UQ), Dr. T. Hugh (RNSH)
Image processing – done by astronomy student;
Semi-automatic image segmentation




                                                                  All done in Matlab


   R. Martin, N. Bordes, B. Pailthorpe (UQ), Dr. T. Hugh (RNSH)

                                          Published: Australian Computer Society (2004)
Liver surgery planning: 3D image (matlab)




     9
  R. Martin, N. Bordes, B. Pailthorpe (UQ), T. Hugh (RNSH)
  Fluid flow in complex biological systems
      Simulating the beating heart                              (Charles Peskin & David McQueen, Courant Institute,
      NY; NPACI support team;                                     Computer Graphics 34, p56, (2000)




                                                                         Mitral Valve Flow: heart section showing flow patterns during
Ventricular Vortices: patterns during early diastole                     early diastole (ventricular filling): vortices behind the leaflets of the
(ventricular filling) - vortex motion in the right ventricle.            mitral valve in the left ventricle
                                                                          …. improving design of artificial mechanical heart valves.
Improving health care                     3D MRI imaging:
                                             breast cancer
 Public health benefits
       (11,000 new cases pa)
   vs. Proj. cost




      2D slice visualisation
                                             EMI, School of ITEE, UQ Prof. Stuart Crozier &
Resolve 15 pixel suspicious ROI (~ 2mm)                              Dr. Andrew Maenart &, ITEE, UQ
                                                                      + Dr Kerry McMahon, Qld. X-Ray
Scientific Visualisation




     Imagination or visualisation, and in particular
    the use of diagrams, has a crucial part to play
    in scientific investigation.

                               Rene Descartes, 1637
                                            Lascaux (12,000 BC)




www.culture.fr/culture/arcnat/lascaux/en/
   Thanks to N Bordes
Visualisation and health sciences




Right shoulder anatomy
(c.1510-11)
                         Heart and lungs of an Ox
                                                       Vessels of the liver
                         (c.1512-13)
                                                       (1507-08)


                                                    Courtesy of Leonardo da Vinci
 Thanks to N Bordes
  Human Suffering: Napoleon’s Russia Campaign
                                (19th century)




         15
Thanks to N Bordes   C Minard, 1869. Ref. Eg.   www.edwardtufte.com/tufte/minard
Improving
Health
Care:




            Source: D Spiegelhalter, Science 333, 1391 (9 Sept 2011)
Discovery of x-rays




   Radiograph of the hand of anatomist Albert von Kolliker
   taken by Wilhelm Conrad Röntgen on January 23, 1896.
   Image courtesy of American College of Radiology
   Archives




                              1st Nobel prize in physics, 1901
 Thanks to N Bordes
     London Underground

               Harry Beck,
               1931




                Refs – eg.
                London
18              Transport
                Museum
Visualising natural phenomena                    …long history

    Michael Faraday in his lab
    at the Royal Institution,
    London, 1870.




                                 “ ..magnetic field lines
                                     can be visualised
                                     by use of iron filings…”
Visualisation         - users interacting with data & computers




                                                       ARC + USyd
                                                        & partners:
                                                       1992-2002




         was www.vislab.usyd.edu.au/
Desktop software
Tera-scale Vis software                    OSS Toolkits

 • SciRUN
  Utah: Chris Johnson, et al    http://www.sci.utah.edu/
   eg.. BioTensor, BioFEM

 • VisTools
  NPACI (UCSD): B Pailthorpe, A. Olson, S. Cutchin, et al

 • vtk
  mcs@anl.gov: + Kitware Inc.
 • Shastra
  C. Bajaj, UT, Austin +

 • DoE ASCI Tri-Lab VIEWS program: VisIT
    Volume Rendering        R. Frank, et al; LLNL, LANL

                                                            + Paraview
Bioinformatics:                        Rob Beiko & Mark Ragan (IMB, ARC Centre Bioinformatics, UQ)

 Lateral Gene Transfers in Prokaryotes
- organisms transmits DNA to non offspring
    common in bacteria
   develop resistance to antibiotics

• BLAST alignment:
  track 423,000 predicted proteins
  from 144 organisms;
- 22k evolutionarily related
- build phylogenetic trees for each Protein

• Bayesian sampling: search the trees
  - probable pathways of gene sharing

   “.. thousand-dollar genome and
   million-dollar interpretation…”                                    'Highways of gene sharing in prokaryotes',
     Nature, 483, 21 (1 March 2012).                               Proc Natl Acad Sci USA 102, 14332-7 (2005).
Chem Eng:            Suresh Batia (UQ)
Transport and Adsorption in Nanomaterials

Pores diam ~ 5 - 50 ångström, molec ~3-5 Å
Monte Carlo & molecular
dynamics (MD) simulations

Molecular sieving in
microporous materials
- method of separation
  many industrial applications:
  separations, catalytic processing.
                                                   Zeolite rho structure

                                            Phys. Rev. Lett., 91, 0126102 (2003);
                                            95, 245901 (2005).
Astronomy: Telescope mirror + mounts:
                                                       Design
                                                       - for manufacture




           Numerical modelling + visualisation:   Anna Moore, N. Bordes, USyd
Physics - BEC:                Chao Feng & Mike Malone    ... working at the Optiportal display Wall




Simulation of a Bose Einstein
Condensate (BEC), showing
- density of a cylindrically
  symmetric BEC after a laser
  beam excited the condensate.

Visualised in vtk, Paraview




                                                Movie at: www.rcc.uq.edu.au/gallery/bec/ - pto:
Physics: Chao Feng & Mike Malone   (Centre for Quantum-Atom Optics & RCC, UQ, 2012)




                                                    Movie at: www.rcc.uq.edu.au/gallery/bec/
                     Fluid Turbulence
                           Fundamental physics
                           problems




                         DNS - solve
                         Navier Stokes eqn.

                         Vorticity field
                          on 2563 - 10243 mesh

                         Perspective-view
                         Volume rendering



Numerical modelling: K. Nomura, P. Diamessis, UCSD
Visualisation: N. Bordes, UCSD (1999).
Numerical weather prediction

                                                         CFD: hi res grid
                                                         - resolve phenomena

                                                         SciVis:
                                                         - more info: arrows
                                                         - weightless “particles”
                                                           follow tradjectories




               Perth, WA: Hazard reduction burn, 14-15 Nov. 1995
               (Lance Leslie: UNSW & BoM)               > movie: later slide
Granular flows in hoppers:                                                industry competitiveness

Dalrymple Bay Coal Loader- coal jams in chute (~10m)
  6000 tonne/hr throughput; ~ US$50/t;                                4-5 tonne dump from rail wagon
  Payback time ~ 69 sec. of operations




                                                                  Prof. Jeff Logheran, JCU (2005)
B. Pailthorpe & N Bordes, UQ at Info Emergency Response July’11                                     www.qcif.edu.au/Coal_flow_modelling
                                                                   Peter Wotherspoon, BBI DBCT
Hypersonic flight:
Multi-Disciplinary Design Optimization




                                          CFD pressure contours in the inlet and combustion chamber




                                                                        Russel Boyce
                                                                        & team (Mech Eng, UQ)

                            Ogawa, H. and Boyce, Russell R. Proc.. ICFD2010, Sendai, Japan,. Nov. 2010.
New companies in town: Aerospace
     GKN AES                                                                               composite materials


                                                                                                               3D reconstruction showing the
                                                                                                               outer surface of the cylinder




Joint Strike Fighter F-35, Lightning II (Image courtesy of
the Joint Strike Fighter Program Office, United States Government/Department of Defence)




                                                       Manufactured parts require 100% inspection
                                                        … in real time
                                                       Ultrasound scan of inner surface of a tubular
                                                        part, showing impact damage
                                                         - Matlab Image Processing toolbox
              Raw C-scan of a damaged                                                      Brett Petersen (UQ & GKN), Adrian Smith (GKN), BP, NB.
              half-cylinder(CCI Pope)
                                                                 B. Pailthorpe, QciF, Aug24, 06
New industries:                                Medical Imaging                          MRI scanners
superconducting magnets




 Dr. Riyu Wei (UQ & Magnetica),                                                                          3D magnetic fields
 Nicky Milson (Magnetica Pty. Ltd.).
                                       B. Pailthorpe & N Bordes, UQ at Info Emergency Response July’11
                                                                  Olympic sculptures,
                                                                       Sydney 2000.
                                                                              Artworks
                                                                         & Public safety




 Mechanical design
 for public safety:
  - 15m, 4.5t, on AMP Tower
   - wind loading (1/ 50 yr)
 Source: Strand7

 Sculptor: Dominique Sutton
 Engineers: Hyder Consulting


B. Pailthorpe & N Bordes, UQ at Info Emergency Response July’11
Human society: Mill Point Archaeological Project




                                                      Photos
                     B. Pailthorpe, QciF, Aug24, 06   Nicole Bordes & Sean Ulm
3D interactive       • digital collections: dissemination and
model of the           interchange of archaeological data
archaeological dig
                        (maps, GIS, satellite images, photos, audio,
                         artefacts):
                          – across disciplines & institutions,
                          – across public & private sectors;
                     • enable archaeological research to reach its
                       full potential;
                     • contributes to discourses about Australian
                       history, cultural heritage & identity.

                     Bordes, N., S. Ulm, O. Pettersen, K. Murphy, D.
                     Gwynne, W. Pagnon, S. Hungerford, P. Hiscock, J. Hall
                     and B. Pailthorpe. “Data grid for the management,
                     reconstruction, analysis and visualisation of
                     archaeological data”.
                      in S. Ulm and I. Lilley (eds), An Archaeological Life:
                     Papers in Honour of Jay Hall, pp.251-264 (UQ, 2006).
                     An ARC e-Research project (2005).

                                     www.rcc.uq.edu.au/vislab/archaeology/
Floodwise project – urban storms, floods
                                                               Integrate BCC water level gauges
                                                                at bridges, etc
                                                                to BoM weather radar
                                                               - anticipate flooding patterns (1-2 hr),
                                                                 for civil emergency response
                                                                  .. Call centre staff
                                                                  .. Maintenance staff




Joshua Soderholm, Nick Beaton; UQ, QCIF (2008)
Ken Morris; BCC
BOM’s Thunderstorm Identification Tracking
Analysing and Nowcasting (TITAN)
- analyse & track storm cells
- one hour rainfall predictions along path
                                                   WebSite GUI

                                             GIS      www.qcif.edu.au/Thunderstorm_identification_and_tracking
                                                      Computational Linguistics:
                                                              digital scholarship
                                                                  Analysis of 5.2M books: a “cultural genome”;
                                                                   4% of books published (1500’s –now)
                                                                    x1000 longer than human genome




                                                                                                            Extinction ->
                                                    + TED talk
“Tens of thousands of books appear in this photograph of
the interior of the sculpture Idiom, by Matej Krén; ..
in the Municipal Library of Prague.” …

                                                                  E Lieberman et al “Quantifying the evolutionary
                                                                  dynamics of language”
                                                                  Nature, 449, 713 (11 Oct 2007).
J-B Michel, et al. “Quantitative Analysis of Culture         M Pagel et al “Frequency of word-use predicts rates of
 Using Millions of Digitized Books”,                         lexical evolution throughout Indo-European history”
Science, 331, 176 (14 Jan 2011).                              Nature, 449, 717 (2007).
www.ted.com/speakers/jean_baptiste_michel.html (June 2011)
Why animation in vis?                                           Mathematics example:
                                                                    … as they do it




           R. Bartnik, Aust. Mathematical Society Gazette, 31(3), 161 (2004)
Mathematics: concept illustration


 Diffeomorphism of space
    ~ mobius strip

        720o rotation
A well known party trick, which has on
occasions been used to motivate the use of
spinors in physics, is shown to have a
counterpart in certain one-parameter families
of diffeomorphisms of R3. One such family is
constructed and then visualized as an animated
sequence of deformations applied to
                                                                  Andrew Norton & Gavin Brown
parametric surfaces in R3.
                                                                  Mathematics, UNSW (later USyd)
A. Norton, “Spinors and Entanglement”,
     Mathematica J. 5(2) (Spring 1995).




                                             was www.vislab.usyd.edu.au/   - now: www.rcc.uq.edu.au/gallery/diffeo/
Planetary Scale Oceanographic Simulations
Goal: to understand the ocean’s role in climate variability
      CFD simulations, bc: satellite altimetry, observational data (buoys, etc)




    1997 El Nino event: relative sea surface temperature (color) and height (x 10 8 in relief)
    (C Wunsch, MIT; D Stammer, SIO; N Bordes, SDSC)
                         In 1999 (Cray T90):                 … with Tera-flops (IBM 1200 Proc):
                         2o Lat, Long. -> 2 GB files         0.25o lat, long grid -> 200 GB files 64-bit
                High resolution oceanographic
                         simulations
   Full Planet @ (1/6)o lat, long   - sea surface temperature & height




turbulent features:                 (D Stammer & Arne Biastoch, SIO; R. Charles & N Bordes, SDSC)
southern ocean ~ energy transfer
                                                                    OpenDX, 1GB files
Collaboration: Access Grid - Aust. Tech. Park, Sydney
the 1st in Austr.        .. participating in SC-Global confr. (Nov 2001) : Beijing – Syd – US - UK




    B Pailthorpe, QCIF
                                                                                   ARC funding, 2001
 Collaborative working:                                         An ARC e-Research project

 B Pailthorpe, Chris Willing, N Bordes (UQ),          I   Atkinson (JCU)
Beyond sharing ppt for meetings …
- molecular viewers (chem, bio)
- Geographic Information Systems
 (GIS) for urban planning, logistics,
 mapping, resources, response, ….



             Currently > 30 AG nodes in Australia,
                    10 in Qld, and > 200 worldwide




                                                     Shared Grass     (GIS software app), within AG environment
      shared workrooms                               Stéphane Bidet, VisLab UQ + Downloads at:
                                                           http://www.vislab.uq.edu.au/research/accessgrid/software/

     B. Pailthorpe, QciF, AHM, Aug’06
OptIPortal displays: CalIT2 (UCSD & UCI) & EVL (UCI)
                                OptiPuter project: NSF, 2003-08
                                T A Defanti et al, Future Gen Comp Sys
                                                    25, 114-1123 (2009)




              UCI HIPerWall
 Porting scientific apps to the OptIPortal – demo at QuestNet-09
                                                                                                   iCluster
                                                                                                    - IMB, UQ
                                                                                                   Classify 100s-1000s
                                                                                                   of cell images on the fly,
                                                                                                   with humans in the loop

                                                                                                   Also
                                                                                                    Paraview / vtk
                                                                                                    Mayavi/ vtk
                                                                                                    .. for general purpose
                                                                                                       Sci Vis


                                                                                                     Run “natively”
                                                                                                     in OptIPortal
                                       i -Cluster: Nick Hamilton (IMB), R Hammond, Chris Willing
                                       & B Pailthorpe (UQ Vislab)
                                                                                                     … breaking out of
                                                                                                     desktop limitations




B. Pailthorpe, UQ at SAGE BoF, SC-11
iCluster workflow
– high throughput classification
of EM images




Figure 2: Nick Hamilton et al,
BMC Bioinformatics, 10, 94 (‘09).
iCluster workflow
 - image classification.
(1) Treated/untreated images
(2) Images stored
(3) And loaded into iCluster, TAS
stats generated automatically.
Initially images are randomly
placed in 3D.
(4) “Adjacency mapping” 3D
spatial layout - by statistical
                                                                               In OptIPortal:
similarity using 'Sammon Map'.
                                                                               moving up from
…..                                           http://icluster.imb.uq.edu.au/   thumbnail images…
                                                                               + humans in the loop
B. Pailthorpe, UQ at IEEE e-Science, Dec’10
 Genome Browser (UCSC) in the OptIPortal              (Mike Pheasant, Chris Willing)
                                            Run “natively”
                                            in OptIPortal

                                            … breaking out of
                                            desktop limitations




    a very “long” image
      & GUI, with clickable links




B. Pailthorpe, UQ   at SAGE BoF, SC-11   www.rcc.uq.edu.au/vislab/genome-browser/
   END
& extra slides
Computational Science
Numerical solution to the equations of
 maths, physics, chemistry, biology, engineering.. eg.

 • Newton’s eqns: F = ma
      - FEA: engineering structures
      - CFD: fluid dynamics ~ Navier Stokes eqns
      - turbulence
• Maxwell’s equations: Electromagnetism
     - wireless networks, photonics
• Schroedinger eqn.: Quantum mechanics
      - electronic structure
* Challenges: Non-linear, interacting;
        multi-component; multi-resolution; multi-domain
                … ie. they are complex systems
Computational Engineering



   • Numerical solution of those equations
     .. for industrial design
         -> new products, better processes

    • optimised design
        faster and
        lower cost to market
UQ HPC infrastructure                         (with QCIF funding):

Supercomputers (Rackable/ sgi), Data


                                                                     25 kW
                                                        Sun/Oracle StorageTek SL8500 (2009)


                         30 kW
                         x many                                          @UQ:
             (2007-10)
                                                                         3,400 TB
            2010: 3,000 cores, 25 TeraFlops
                                                                             400 TB discs
Data archives: StorageTek tape robots                                     I/O (32) servers



                                                                          + new 500 TB disc

                                                                          Power: upgrade ?
(2000-08)                                                                    3-yr ops cost
                                                                               = equip cost
IMPACT:
• $65m of ARC + NH&MRC grants to UQ in past 2 years
     by Top20 RCC Users    (Groups), at Apr 2012.

                          • Qld. Govt. $16m investment (2000-06)
                                -> GSP + $12.7m pa x 10 yrs

                          Employment:
                          Researchers:
                          PhD students:
                          Productivity:
                          Cost savings (avoided costs):
                           – travel:      $2m pa (2006)
                            - health care: $8m pa



                           Report (2006) available at:   www.rcc.uq.edu.au/about-rcc
 Geometry: Surface model example

         3D primitives can be joined together using various
         techniques to produce more complex surfaces.


                                           rotated copies

                   original curve       skinning generates
                                        surface




Thanks to N Bordes (Cosc3000 class)
Geometric Modelling: Crystal palace, London
                         Crystal palace




                            Courtesy C. Jesse and W. Rourk, U of Virginia
Radiosity calculations
Numerical weather prediction
                                    CFD: hi res grid
                                    - resolve phenomena

                                    SciVis:
                                    - more info
                                    - weightless “particles”
                                      follow tradjectories




                    Perth, WA: Hazard reduction burn
                    Feb’96 (Lance Leslie: UNSW & BoM)

				
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