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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
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