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Computing for Research: simulation and visualisation

Computing for Research: simulation and visualisation. Bernard Pailthorpe (and Nicole Bordes) Research Computing Centre, UQ bap@uq.ed u.au . www.rcc.uq.edu.au vislab.uq.edu.au qcif.edu.au. Outline. • Computer Simulation & Visualisation

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Computing for Research: simulation and visualisation

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  1. 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

  2. Outline • 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

  3. rcc.uqedu.au web site - Research Gallery - Education -- (student projects)

  4. Types of Visualization • Image Processing – medical, satellite, etc; • Data Visualisation • Rendering: surface, volume; • Molecular Modelling • Info Vis • GIS. • Note also: • Animation; • Virtual Environments - Cave; Stereo • PowerWalls, OptIPortal display, Access Grid.

  5. Visualisation in Medicine (1992) Ultrasonic imaging, inside human artery - plaque deposits - Sci Vis forsurgical planning Dr. Richmond Jeremy, Dept Medicine (Cardiology), U. Sydney & RPAH (1992). was www.vislab.usyd.edu.au; now rcc.uq.edu.au/

  6. 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; > functionlocalized in 3D structure NPACI Volume Vis toolkit: composite & reconstruct image stacks 50 frames (320x234 pixels) Jim Feramisco et al, UCSD Cancer Center - data by Jag Shah; Cleveland Lab, LCIR (2000) J V Shah & D W Cleveland, Cell, 103, 997 (22 Dec 2000)

  7. Filtered image of CT scan slice: Liver Cancer of the Liver CAT scan Liver surgery R. Martin, N. Bordes, B. Pailthorpe (USyd & UQ), Dr. T. Hugh (RNSH)

  8. 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)

  9. Liver surgery planning: 3D image (matlab) R. Martin, N. Bordes, B. Pailthorpe (UQ), T. Hugh (RNSH)

  10. 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 early diastole (ventricular filling): vortices behind the leaflets of the mitral valve in the left ventricle …. improving design of artificial mechanical heart valves. Ventricular Vortices: patterns during early diastole (ventricular filling) - vortex motion in the right ventricle.

  11. Improving health care3D MRI imaging: breast cancer Public health benefits (11,000 new cases pa) vs. Proj. cost 2D slice visualisation Prof. Stuart Crozier & Dr. Andrew Maenart &, ITEE, UQ + Dr Kerry McMahon, Qld. X-Ray EMI, School of ITEE, UQ Resolve 15 pixel suspicious ROI (~ 2mm)

  12. Scientific Visualisation Imagination or visualisation, and in particular the use of diagrams, has a crucial part to play in scientific investigation. Rene Descartes, 1637

  13. Lascaux (12,000 BC) www.culture.fr/culture/arcnat/lascaux/en/

  14. Visualisation and health sciences Right shoulder anatomy (c.1510-11) Heart and lungs of an Ox (c.1512-13) Vessels of the liver (1507-08) Courtesy of Leonardo da Vinci

  15. Human Suffering: Napoleon’s Russia Campaign (19th century) C Minard, 1869. Ref. Eg. www.edwardtufte.com/tufte/minard Thanks to N Bordes

  16. ImprovingHealthCare: Source: D Spiegelhalter, Science 333, 1391 (9 Sept 2011)

  17. 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

  18. London Underground Harry Beck, 1931 Refs – eg. London Transport Museum

  19. 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…”

  20. Visualisation - users interacting with data & computers ARC + USyd & partners: 1992-2002 RCC Website - examples was www.vislab.usyd.edu.au/

  21. Desktop software

  22. 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

  23. 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…” Nature, 483, 21 (1 March 2012). 'Highways of gene sharing in prokaryotes', Proc Natl Acad Sci USA102, 14332-7 (2005).

  24. 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).

  25. Astronomy: Telescope mirror + mounts: Design - for manufacture Numerical modelling + visualisation: Anna Moore, N. Bordes, USyd

  26. 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 Physics - BEC:Chao Feng & Mike Malone... working at the Optiportal display Wall Movie at: www.rcc.uq.edu.au/gallery/bec/ - pto:

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

  28. 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).

  29. 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

  30. 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) Peter Wotherspoon, BBI DBCT www.qcif.edu.au/Coal_flow_modelling B. Pailthorpe & N Bordes, UQ at Info Emergency Response July’11

  31. 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.

  32. 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 Brett Petersen (UQ & GKN), Adrian Smith (GKN), BP, NB. Raw C-scan of a damaged half-cylinder(CCI Pope) B. Pailthorpe, QciF, Aug24, 06

  33. New industries:Medical ImagingMRI scanners superconducting magnets Dr. Riyu Wei (UQ & Magnetica), Nicky Milson (Magnetica Pty. Ltd.). 3D magnetic fields B. Pailthorpe & N Bordes, UQ at Info Emergency Response July’11

  34. 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

  35. Human society: Mill Point Archaeological Project Photos Nicole Bordes & Sean Ulm B. Pailthorpe, QciF, Aug24, 06

  36. 3D interactive model of the archaeological dig • • digital collections: dissemination and • interchange of archaeological data • (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/

  37. 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

  38. Computational Linguistics: digital scholarship Analysis of 5.2M books: a “cultural genome”; 4% of books published (1500’s –now) x1000 longer than human genome + TED talk Extinction -> “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 Using Millions of Digitized Books”, Science, 331, 176 (14 Jan 2011). www.ted.com/speakers/jean_baptiste_michel.html(June 2011) M Pagel et al “Frequency of word-use predicts rates of lexical evolution throughout Indo-European history” Nature, 449, 717 (2007). “culturomics”

  39. Why animation in vis? Mathematics example: … as they do it R. Bartnik, Aust. Mathematical Society Gazette, 31(3), 161 (2004)

  40. 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 parametric surfaces in R3. A. Norton, “Spinors and Entanglement”, Mathematica J.5(2) (Spring 1995).
 Andrew Norton & Gavin Brown Mathematics, UNSW (later USyd) was www.vislab.usyd.edu.au/ - now: www.rcc.uq.edu.au/gallery/diffeo/

  41. Planetary Scale Oceanographic Simulations Goal: to understand the ocean’s role in climate variability CFDsimulations, 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) … with Tera-flops (IBM 1200 Proc): 0.25o lat, long grid -> 200 GB files 64-bit In 1999 (Cray T90): 2o Lat, Long. -> 2 GB files

  42. High resolution oceanographic simulations Full Planet@(1/6)o lat, long - sea surface temperature & height turbulent features: southern ocean ~ energy transfer (D Stammer & Arne Biastoch, SIO; R. Charles & N Bordes, SDSC) OpenDX, 1GB files

  43. Collaboration: Access Grid - Aust. Tech. Park, Sydney the1st in Austr... participating in SC-Global confr. (Nov 2001): Beijing – Syd – US - UK ARC funding, 2001

  44. Collaborative working:An ARC e-Research projectB Pailthorpe, Chris Willing, N Bordes(UQ), I Atkinson(JCU) Currently > 30 AG nodes in Australia, 10 in Qld, and > 200 worldwide Beyond sharing ppt for meetings … molecular viewers (chem, bio) Geographic Information Systems (GIS) for urban planning, logistics, mapping, resources, response, …. Shared Grass (GIS software app), within AG environment Stéphane Bidet, VisLab UQ + Downloads at: http://www.vislab.uq.edu.au/research/accessgrid/software/ shared workrooms B. Pailthorpe, QciF, AHM, Aug’06

  45. 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

  46. 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 … breaking out of desktop limitations i -Cluster: Nick Hamilton (IMB), R Hammond, Chris Willing & B Pailthorpe (UQ Vislab) B. Pailthorpe, UQ at SAGE BoF, SC-11

  47. 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 similarity using 'Sammon Map'. ….. In OptIPortal: moving up from thumbnail images… + humans in the loop http://icluster.imb.uq.edu.au/ B. Pailthorpe, UQ at IEEE e-Science, Dec’10

  48. 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 www.rcc.uq.edu.au/vislab/genome-browser/ B. Pailthorpe, UQ at SAGE BoF, SC-11

  49. END & extra slides

  50. 3rd route to Discovery 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

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