Computing for Research:

rangebeaverMécanique

22 févr. 2014 (il y a 3 années et 7 mois)

92 vue(s)

Computing for Research:


simulation and visualisation


www.rcc.uq.edu.au

vislab.uq.edu.au

qcif.edu.au

Bernard Pailthorpe

(and Nicole Bordes)

Research Computing Centre, UQ












bap@uq.ed
u.au



Outlin
e

• Computer Simulation & Visualisation


-

medical imaging; history; Data & Sim in science & engineering


-

eg. projects: research, industry, community impact

• Computational Science
: 3
rd

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
.

Ultrasonic imaging,


inside human artery


-

plaque deposits


-

Sci Vis for


surgical planning

Dr. Richmond Jeremy, Dept Medicine (Cardiology),


U. Sydney & RPAH (1992).

Visualisation in Medicine
(1992)

w
as
www.vislab.usyd.edu.au
; now rcc.uq.edu.au/



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


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)

Medical Imaging: Cancer Cells
(at UCSD)

NPACI Volume Vis toolkit:


composite


& reconstruct image stacks



50 frames (320x234 pixels)

7

Filtered image of CT scan slice: Liver

R. Martin, N. Bordes, B. Pailthorpe (U
S
yd & UQ), Dr. T. Hugh (RNSH)

Cancer of the Liver

CAT scan

Liver surgery

Image processing


done by astronomy student;

Semi
-
automatic image segmentation

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

Published: Australian Computer Society (2004)

All done in Matlab

9

Liver surgery planning: 3D image
(matlab)

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)

Ventricular Vortices:
patterns during early diastole

(ventricular filling)
-

vortex motion in the right ventricle.

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.



Public health benefits



(11,000 new cases pa)

vs. Proj. cost


Improving health care



3D MRI imaging:







breast cancer

Prof. Stuart Crozier &

Dr. Andrew Maenart &, ITEE, UQ


+
Dr Kerry McMahon,
Qld. X
-
Ray

2D slice visualisation

EMI, School of ITEE, UQ

Resolve 15 pixel suspicious ROI (~ 2mm)

Scientific Visualisation




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


Rene Descartes, 1637

Thanks to N Bordes

Lascaux (12,000 BC)

www.culture.fr/culture/arcnat/lascaux/en/

Visualisation and health sciences

Vessels of the liver
(1507
-
08)

Heart and lungs of an Ox
(c.1512
-
13)

Right shoulder anatomy
(c.1510
-
11)

Courtesy of Leonardo da Vinci

Thanks to N Bordes

15

Human Suffering: Napoleon’s Russia Campaign

(19th century)

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

18

London Underground

Harry Beck,

1931

Refs


eg.

London

Transport
Museum


…long history


Visualising natural phenomena

“ ..magnetic field lines


can be visualised


by use of iron filings…”

Michael Faraday
in his lab

at the Royal Institution,

London, 1870.

Visualisation
-

users interacting with data & computers

was www.vislab.usyd.edu.au/

ARC + USyd


& partners:

1992
-
2002

Desktop software


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

OSS Toolkits

Tera
-
scale Vis software

+ Paraview


'Highways of gene sharing in prokaryotes',

P
roc Natl Acad Sci

USA

102
, 14332
-
7 (2005).

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



“..
t
housand
-
dollar genome and

million
-
dollar interpretation
…”


Nature
,
483
,
21 (1 March 2012).

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.


Phys. Rev. Lett
.
,
91
, 0126102 (2003);

95
, 245901 (2005).

Zeolite rho structure

Astronomy: Telescope mirror + mounts:

Numerical modelling + visualisation:
Anna Moore, N. Bordes, USyd

Design


-

for manufacture

Physics
-

BEC:

Chao Feng & Mike Malone

... working at the Optiportal display Wall

Movie at:
www.rcc.uq.edu.au/gallery/bec/

-

pto:

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:

Chao Feng & Mike Malone

(Centre for Quantum
-
Atom Optics & RCC, UQ, 2012)

Movie at: www.rcc.uq.edu.au/gallery/bec/

Fluid Turbulence

Numerical modelling: K. Nomura, P. Diamessis, UCSD

Visualisation: N. Bordes, UCSD (1999).

DNS
-

solve

Navier Stokes eqn.


Vorticity field


on 256
3

-

1024
3

mesh


Perspective
-
view

Volume rendering

Fundamental physics

problems

Numerical weather prediction

Perth, WA: Hazard reduction burn, 14
-
15 Nov. 1995

(
Lance Leslie: UNSW & BoM)

> m
ovie: later slide

CFD: hi res grid


-

resolve phenomena


SciVis:


-

more info: arrows


-

weightless “particles”


follow tradjectories

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

Ogawa, H. and Boyce, Russell R.

Proc.
.
ICFD2010
,

Sendai, Japan,. Nov. 2010
.

CFD pressure contours in the inlet and combustion chamber

Hypersonic flight:

Multi
-
Disciplinary Design Optimization

Russel Boyce


& team
(Mech Eng, UQ)


B. Pailthorpe, QciF, Aug24, 06

New companies in town:

Aerospace



GKN AES




composite materials

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)

3D reconstruction showing the

outer surface of the cylinder

Dr. Riyu Wei (UQ & Magnetica),

Nicky Milson (
Magnetica Pty. Ltd.
).

New industries:

Medical Imaging

MRI scanners
superconducting magnets

3D magnetic fields

B. Pailthorpe & N Bordes, UQ at Info Emergency Response July’11

Mechanical design

f
or 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

Olympic sculptures,

Sydney 2000.


Artworks

& Public safety


B. Pailthorpe, QciF, Aug24, 06

Human society:
Mill Point Archaeological Project


Photos

Nicole Bordes & Sean Ulm

3D interactive


model of the

archaeological dig

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/

• 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.

Floodwise
project


urban storms, floods

Joshua Soderholm, Nick Beaton; UQ, QCIF (2008)

Ken Morris; BCC

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

www.qcif.edu.au/Thunderstorm_identification_and_tracking

BOM’s Thunderstorm Identification Tracking

Analysing and Nowcasting (TITAN)


-

analyse & track storm cells


-

one hour rainfall predictions along path

WebSite GUI

GIS

Computational Linguistics
:

digital scholarship

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).

Analysis of 5.2M books: a “cultural genome”;


4% of books published (1500’s

now)


x1000 longer than human genome

+ TED talk

E Lieberman
et al “Quantifying the evolutionary
dynamics of language”


Nature
,
449
, 713 (11 Oct 2007).

“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.” …

Extinction
-
>

Why animation in vis?

R. Bartnik,
Aust. Mathematical Society Gazette
,
31
(3), 161 (2004)

Mathematics example:


… as they do it


Diffeomorphism of space


~ mobius strip




720
o

rotation

Andrew Norton & Gavin Brown

Mathematics, UNSW (later U
S
yd)

Mathematics:

concept illustration

w
as
www.vislab.usyd.edu.au/

-

now:
www.rcc.uq.edu.au/gallery/diffeo
/



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 R
3
. One such family is
constructed and then visualized as an animated
sequence of deformations applied to
parametric surfaces in R
3
.


A. Norton, “
Spinors and Entanglement
”,


Mathematica J.

5
(2) (Spring 1995).


In 1999 (Cray T90):

2
o

Lat, Long.
-
> 2 GB files

… with Tera
-
flops (IBM 1200 Proc):

0.25
o

lat, long grid
-
> 200 GB files
64
-
bit

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)


Goal
: to understand the ocean’s role in climate variability

CFD

simulations,

bc:
satellite altimetry, observational data

(buoys, etc)

Planetary Scale Oceanographic Simulations

High resolution oceanographic
simulations



turbulent features:


southern ocean
~ energy transfer

Full Planet

@

(1/6)
o

lat, long
-

sea surface temperature & height

(D Stammer & Arne Biastoch, SIO; R. Charles & N Bordes, SDSC)


OpenDX, 1GB files

B Pailthorpe, QCIF

Collaboration: Access Grid
-

Aust. Tech. Park, Sydney


the

1st in Austr.

.. participating in
SC
-
Global
confr. (Nov 2001)

: Beijing


Syd


US
-

UK

ARC

funding, 2001


B. Pailthorpe, QciF, AHM, Aug’06

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, ….


Shared Grass

(GIS software app), within AG environment


Stéphane Bidet
, VisLab UQ +
Downloads

at:


http://www.vislab.uq.edu.au/research/accessgrid/software/

Currently > 30 AG nodes in Australia,


10 in Qld, and > 200 worldwide

shared workrooms

OptIPortal displays:
CalIT2 (UCSD
&
UCI) & EVL (UCI)

OptiPuter project: NSF, 2003
-
08

UCI HIPerWall

T A Defanti et al,
Future Gen Comp Sys

25
, 114
-
1123 (2009)

Porting scientific apps to the OptIPortal


demo at QuestNet
-
09


i
-
Cluster
: Nick Hamilton (IMB), R Hammond, Chris Willing


& B Pailthorpe (UQ Vislab)

Run “natively”


in OptIPortal



… breaking out of
desktop limitations

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

B. Pailthorpe, UQ at SAGE BoF, SC
-
11


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

iCluster
workflow



high throughput classification
of EM images


http://icluster.imb.uq.edu.au/


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

B. Pailthorpe, UQ at SAGE BoF, SC
-
11


www.rcc.uq.edu.au/vislab/genome
-
browser/

a very “long” image


& GUI, with clickable links

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


Data archives:
StorageTek tape robots

Sun/Oracle StorageTek SL8500 (2009)

(2000
-
08)


@UQ:


3,400 TB

400 TB
discs


I/O (32)
servers


(2007
-
10)

25 kW

2010
: 3,000 cores, 25 TeraFlops

30 kW


x many

Power: upgrade ?


3
-
yr ops cost


= equip cost


+ new 500 TB disc

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.



original curve

rotated copies

skinning generates
surface

Thanks to N Bordes (Cosc3000 class)

Crystal palace

Courtesy C. Jesse and W. Rourk, U of Virginia

Radiosity calculations

Geometric Modelling:

Crystal palace, London

Numerical weather prediction

Perth, WA: Hazard reduction burn

Feb’96

(
Lance Leslie: UNSW & BoM)

CFD: hi res grid


-

resolve phenomena


SciVis:


-

more info


-

weightless “particles”


follow tradjectories