B. Pailthorpe, UQ at IEEE e-Science, QUT Dec’10

OptIPortals: visualisation for

Scientific applications

vislab.uq.edu.auqcif.edu.au

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Prof. Bernard Pailthorpe, U Qld.with Richard Hammond, Nick Hamilton, Chris Willing

bap@uq.edu.au

Outline• OptIPortals: ultra-scale tiled displays

… wall-sized desktops; collaboration spaces

- SAGE: visualcasting: demo events - driving network performance: tuning for real-time collaboration

• Scientific applications:

- porting to Optiportal / SAGE environment

- general: Matlab, Paraview

& bio-imaging: iCluster

• Scalable I/O - GUIs, parallel rendering (CW)

B. Pailthorpe, UQ at IEEE e-Science, Dec’10

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)

OptIPuter: creating a Planetary Scale CyberInfrastructure: … enabling Collaborative, Data-Intensive e-Research

www.evl.uic.edu/cavern/sage

“OptIPlanet: The OptIPuter Global Collaboratory” –

Special Section of Future Generations Computer

Systems, 25 (2), February 2009

Calit2 (UCSD, UCI), SDSC, and UIC Leads—Larry Smarr PIUniv. Partners: NCSA, USC, SDSU, NW, TA&M, UvA, SARA, KISTI, AIST

Industry: IBM, Sun, Telcordia, Chiaro, Calient, Glimmerglass, Lucent Source: Larry Smarr

OptiPortal Display at UQ VisLab (50 MegaPixel)

Constructed by Chris Willing, Jonathon White, Imran Syed(Dec 2007)

+ OptiPortable

- joint with AARNet

- demos at QuestNet …

www.vislab.uq.edu.au/research/optiputer/

Tiled 4 x 5 24'' LCD display7680 x 6000 pixels Cluster, Cent-OS ROCKS SAGE, CGLX

~ A$50k for 50 Mpx

B. Pailthorpe, UQ at IEEE e-Science, Dec’10

OptIPortable: UQ, QCIF &AARNet - at QuestNet-08

Tom DefantiCalIT2 / UCSD2008 Keynote

National Exposure:Touring conferences& events (AALD, Educause..)

B. Pailthorpe, UQ at IEEE e-Science, Dec’10

Network performance (1. SC-08 Bandwidth Challenge):

Austr “speed record” (21 Nov, 2008) 3 Gbps sustained UQ – Austin – EVL (Chicago)

S. Korea

EU

USA

Austr.

Global collaboration via 10 Gig networks:

UQ/ QCIF, AARNet - PacWave, Cenic, StarLight - Austin, Tx.

1st direct 10 G bps to an

Austr lab - UQ (15 Nov, 2008)

B. Pailthorpe, UQ at IEEE e-Science, Dec’10

2. SC-09 TACC, UQ and SARA Demo led by Byungil Jeong, TACC, UT Austin (17-19 Nov’09)

U Qld

SC

TACC

SARA

Real-time scientific visualizations on Longhorn

ParaView + SAGE

8K scientific animation

DXT-compressed and uncompressed live HD

video streams

Bitplayer, Mplayer + SAGE

HDS + SAGE

TACC booth#1545

SARA booth#2154

Tue : 2:00 ~ 4:00pmWed : 2:00 ~ 4:00pmThu : 1:00 ~ 2:30pm

B. Pailthorpe, UQ at IEEE e-Science, Dec’10

UQ user tests (19-20 Nov, 2009) ~ 3 Gbps sustained UQ – AARNet-Portland

Network performance (SC-09 Portand, Or):

UQ – USA 2.79 Gbps (19 Nov’09 2.98 Gbps (20 Nov)

Austr. network performance (previous): 900 Mbps AAO –Swinburne (Oct’08) 3 Gbps QCIF/UQ – USA (Nov’08) 3.4 Gbps Curtin- CSIRO ATNF, (Aug’09)

B. Pailthorpe, UQ at IEEE e-Science, Dec’10

3. APAN-29 (Sydney, Feb’10, Intercontinental hotel):

Links:

Brisb – Syd – Melb - Austin – Seoul;

+ Saudi Arabia: KAUST

Chris Willing: setting up

Greg Wyckham .. at Kaust Saudia Arabia

APAN-29 (Sydney, Feb’10, Intercontinental hotel):

UQ – AARNet-TACC-GIST (9-10 Feb, 2010) ~ 5.5 Gbps sustained, 12 hrs & 6 G peak ex Brisb

UQ – AARNet/UTS tests (2-3 Feb, 2010) ~ 4.1 Gbps sustained for 8 hrs, Brisb - Syd

Brisb– Syd - Austin - Seoul

t (sec)/ /

www.aarnet.edu.au

t (UTC)

B. Pailthorpe, UQ at IEEE e-Science, Dec’10

4. Osaka Event (June 10 -11, 2010 Shinji Shimozo: NICT, Tokyo & Cybermedia Lab, Osaka)

Knowledge Capital – launch events

Setting up on site

B. Pailthorpe, UQ at IEEE e-Science, Dec’10

OptIPortal & SAGE Bridge joint demo in Osaka (June 10 -11, 2010 Shinji Shimozo)

Goal is showing the interactivity of SAGE Content flows via Sage bridges - from UQVislab, NCHC, Calit2: to Osaka

UQVislabBrisbane, Austr.

NCHCHsinchu, Tw

OsakaKnoweldge Precinct

SAGE Machine

SAGE BridgeIn NICT (Tokyo)

SAGE BridgeAARNet (Sydney)

Large images and HD movies(ImageViewer & VLC < 1 Gbps )

Live Video & Mayavi2(Decklinkcapture:200-250 Mbps x2)

EVLUCI, Chicago, USA

Calit2San Diego, USA

B. Pailthorpe, UQ at IEEE e-Science, Dec’10

Osaka event: on the showroom floor (10 June ’10)

Shinji Shimozo

iCluster software - from Brisb. Austr.

Traditional culture - from Hsinchu, Taiwan

Osaka event: on the showroom floor (10 June ’10)

Satellite imaging - N Qld. Austr.

Network traffic monitoring - from Internet2, USA

Shinji Shimozo

B. Pailthorpe, UQ at IEEE e-Science, Dec’10

xx

Osaka event: from CalIT2 (UCSD) to Showroom floor (11 June ’10)

Osaka

BrisbBP presenting from CalIT2, San Diego

B. Pailthorpe, UQ at IEEE e-Science, Dec’10

B. Pailthorpe, UQ at IEEE e-Science, Dec’10

B Jeong et al, IEEE Comp Graphics 30, 71-83 (2010)

SAGE Architecture

evl.uic.edu/cavern/sage

code.google.com/p/sage-graphics

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 IEEE e-Science, Dec’10

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

Rendering pipelines in SAGE

evl.uic.edu/cavern/sagecode.google.com/p/sage-graphics

Source: SAGE Documentation, EVL (2005)

RemoteDisplay

The Challenge: scalable I/O ?

B. Pailthorpe, UQ at IEEE e-Science, Dec’10

Scalable I/O for software apps in SAGE

Head Node {a0}

{Cluster mpi slaves }

Tiled D

isplay: Ou

tpu

t (50-100 Mpx)

Mouse, keyboard

Inputs (WIMP model)

(2-4 Mpx)

3D navigation

Inputs (“wall” model)

- rotate 3D object

- zoom, pan

- resize windows

(50-100 Mpx)

{a1}

{a2}

{a3}

{Master}

ContentNode

B. Pailthorpe, UQ at IEEE e-Science, Dec’10

Scalable I/O – the challenge?

HeadNode {a0}

{Cluster mpi slaves }

Tiled D

isplay: Ou

tpu

t (50-100 Mpx)

Mouse, keyboard

Inputs (WIMP model)

(2-4 Mpx)

3D navigation

Inputs (“wall” model)

- rotate 3D object

- zoom

- resize windows

(50-100 Mpx)

{a1}

{a2}

{a3}

{Master}

How to map 3D pointer back to control window?

Work in progress – User apps

Paraview/ vtk & Mayavi/ vtk iCluster Matlab

B. Pailthorpe, UQ at IEEE e-Science, Dec’10

3D Interactions with scalable display walls

breaking out from desktop limitations

Nintendo WiiMote; Tutorial: C A Wingrave et al, IEEE Comp Graphics & Apps, 30, 71-85 (2010)See www.wiimotelab.org

3D gyro mousewww.gyration.com

Pointing: natural; long history - long understood by us primates

chriscollison.wordpress.com

chimp using stick as tool

Also VR devices:Magnetic head trackers,Wands, …

maybe an iPhone app ?

B. Pailthorpe, UQ at IEEE e-Science, Dec’10

3D Interaction with the OptIPortal, SAGE & apps: Input

3D gyro mousewww.gyration.com

Richard Hammond UQ Vislab

Pointing &Navigating at large scale

Input. Activating menu control buttons in app’s window (copied from head Node) – separate from 3D navigation.

Output. Atlantis, Paraview - mpi distributed across cluster (Chris Willing: talk + demos)

B. Pailthorpe, UQ at IEEE e-Science, Dec’10

Content Node{2 x a0}

{Display Nodes Cluster}

(2-4 Mpx)

{a1}

{a2}

{a3}

Interacting with the OptIPortal, SAGE & apps: OutputWrite/ Draw simultaneously to 2 Output “windows”

1. Draw to local screen buffer, with Window Manager - to Content Node Display Tiled Display (Local, or Remote)

2. Draw to Xvfb: virtual frame buffer (can be very large) - thence to Tiled Display; but no Window Manager?

+ Needs to be scalable:

migrate rendering from Content (“Head”) node to the cluster nodes; & draw to tiled display

+ needs to couple to3D navigation devices

Mouse, keyboard Inputs

Progress: Atlantis, Paraview mpi distributed (Chris Willing: talk + demo)

… underway ….

2a. Draw to XDMX - Distributed MultiHead X - proxy X server - not a Window Manager - 16 tile limit

B. Pailthorpe, UQ at IEEE e-Science, Dec’10

Acknowledgements• Work

– Chris Willing, Richard Hammond, Doug Kosovic, Nicole Bordes, Mathieu Klug (VisLab, UQ), Nick Hamilton (IMB, UQ);

– Larry Smarr, Tom Defanti (CalIT2, UCSD), Luc Renambot (EVL,

UIC), Byongill Jeong (TACC, UT Austin);

– Brett Rosolen (AARNet).And formerly: Jonathon White, Imran Syed, Jean Francillard (UQ); Greg Wickham

• Support

– Australian Research Council

– UQ

– QCIF

– AARNet; UQ ITS network team;

B. Pailthorpe, UQ at IEEE e-Science, Dec’10