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OptIPortals: visualisation for Scientific applications

This article discusses the use of OptIPortals, ultra-scale tiled displays, for scientific applications. It covers topics such as collaboration spaces, driving network performance, and porting scientific applications to the OptIPortal/SAGE environment. The article also explores scalable I/O and parallel rendering techniques.

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OptIPortals: visualisation for Scientific applications

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  1. Prof. Bernard Pailthorpe, U Qld. with Richard Hammond, Nick Hamilton, Chris Willing bap@uq.edu.au OptIPortals: visualisation for Scientific applications Queensland Cyber-infrastructure vislab.uq.edu.au qcif.edu.au B. Pailthorpe, UQ at IEEE e-Science, QUT Dec’10

  2. 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

  3. 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

  4. 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 PI Univ. Partners: NCSA, USC, SDSU, NW, TA&M, UvA, SARA, KISTI, AIST Industry: IBM, Sun, Telcordia, Chiaro, Calient, Glimmerglass, Lucent Source: Larry Smarr

  5. OptiPortal Display at UQ VisLab (50 MegaPixel) Tiled 4 x 5 24'' LCD display 7680 x 6000 pixels Cluster, Cent-OS ROCKS SAGE, CGLX ~ A$50k for 50 Mpx Constructed by Chris Willing, Jonathon White, Imran Syed (Dec 2007) + OptiPortable - joint with AARNet - demos at QuestNet … www.vislab.uq.edu.au/research/optiputer/ B. Pailthorpe, UQ at IEEE e-Science, Dec’10

  6. OptIPortable: UQ,QCIF &AARNet - at QuestNet-08 National Exposure: Touring conferences & events (AALD, Educause..) Tom Defanti CalIT2 / UCSD 2008 Keynote B. Pailthorpe, UQ at IEEE e-Science, Dec’10

  7. Network performance (1. SC-08 Bandwidth Challenge): Austr “speed record” (21 Nov, 2008) 3 Gbps sustained UQ – Austin – EVL (Chicago) 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) Austr. USA S. Korea EU B. Pailthorpe, UQ at IEEE e-Science, Dec’10

  8. 2. SC-09 TACC, UQ and SARA Demoled by Byungil Jeong, TACC, UT Austin (17-19 Nov’09) Bitplayer, Mplayer + SAGE SARA booth #2154 TACC booth #1545 SARA SC 8K scientific animation TACC DXT-compressed and uncompressed live HD video streams ParaView + SAGE Real-time scientific visualizations on Longhorn HDS + SAGE U Qld Tue : 2:00 ~ 4:00pm Wed : 2:00 ~ 4:00pm Thu : 1:00 ~ 2:30pm B. Pailthorpe, UQ at IEEE e-Science, Dec’10

  9. Network performance (SC-09 Portand, Or): UQ user tests (19-20 Nov, 2009) ~ 3 Gbps sustained UQ – AARNet-Portland 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) UQ – USA 2.79 Gbps (19 Nov’09 2.98 Gbps (20 Nov) B. Pailthorpe, UQ at IEEE e-Science, Dec’10

  10. 3. APAN-29 (Sydney, Feb’10, Intercontinental hotel): Links: Brisb – Syd – Melb - Austin – Seoul; + Saudi Arabia: KAUST Greg Wyckham .. at Kaust Saudia Arabia Chris Willing: setting up

  11. APAN-29 (Sydney, Feb’10, Intercontinental hotel): UQ – AARNet/UTS tests (2-3 Feb, 2010) ~ 4.1 Gbps sustained for 8 hrs, Brisb - Syd Brisb– Syd - Austin - Seoul UQ – AARNet-TACC-GIST (9-10 Feb, 2010) ~ 5.5 Gbps sustained, 12 hrs & 6 G peak ex Brisb t (UTC) www.aarnet.edu.au / / t (sec) B. Pailthorpe, UQ at IEEE e-Science, Dec’10

  12. 4. Osaka Event (June 10 -11, 2010 Shinji Shimozo: NICT, Tokyo & Cybermedia Lab, Osaka) Knowledge Capital – launch events Setting up on site www.kita-yard.com/kc B. Pailthorpe, UQ at IEEE e-Science, Dec’10

  13. 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 EVL UCI, Chicago, USA UQVislab Brisbane, Austr. NCHC Hsinchu, Tw Calit2 San Diego, USA Large images and HD movies (ImageViewer & VLC < 1 Gbps ) Live Video & Mayavi2 (Decklinkcapture: 200-250 Mbps x2) SAGE Bridge AARNet (Sydney) HD stream (1Gbps) (< 10 Gbps) (10 Gbps) Osaka Knoweldge Precinct SAGE Machine SAGE Bridge In NICT (Tokyo) Skype: audio B. Pailthorpe, UQ at IEEE e-Science, Dec’10

  14. Osaka event: on the showroom floor (10 June ’10) iCluster software - from Brisb. Austr. Traditional culture - from Hsinchu, Taiwan Shinji Shimozo

  15. Osaka event: on the showroom floor (10 June ’10) Shinji Shimozo Network traffic monitoring - from Internet2, USA Satellite imaging - N Qld. Austr. B. Pailthorpe, UQ at IEEE e-Science, Dec’10

  16. Osaka event: from CalIT2 (UCSD) to Showroom floor (11 June ’10) Osaka Brisb BP presenting from CalIT2, San Diego xx B. Pailthorpe, UQ at IEEE e-Science, Dec’10

  17. SAGE Architecture B Jeong et al, IEEE Comp Graphics 30, 71-83 (2010) • evl.uic.edu/cavern/sage • code.google.com/p/sage-graphics B. Pailthorpe, UQ at IEEE e-Science, Dec’10

  18. 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 IEEE e-Science, Dec’10

  19. 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

  20. Rendering pipelines in SAGE The Challenge: scalable I/O ? Source: SAGE Documentation, EVL (2005) Remote Display • evl.uic.edu/cavern/sage • code.google.com/p/sage-graphics B. Pailthorpe, UQ at IEEE e-Science, Dec’10

  21. Scalable I/O for software apps in SAGE (50-100 Mpx) (2-4 Mpx) Head Node {a0} Content Node {Master} {a1} Mouse, keyboard Inputs (WIMP model) 3D navigation Inputs (“wall” model) - rotate 3D object - zoom, pan - resize windows Tiled Display: Output (50-100 Mpx) {a2} {a3} {Cluster mpi slaves } B. Pailthorpe, UQ at IEEE e-Science, Dec’10

  22. Scalable I/O – the challenge? (50-100 Mpx) (2-4 Mpx) How to map 3D pointer back to control window? Head Node {a0} {Master} {a1} Mouse, keyboard Inputs (WIMP model) 3D navigation Inputs (“wall” model) - rotate 3D object - zoom - resize windows Tiled Display: Output (50-100 Mpx) {a2} {a3} {Cluster mpi slaves } Work in progress – User apps Paraview/ vtk & Mayavi/ vtk iCluster Matlab B. Pailthorpe, UQ at IEEE e-Science, Dec’10

  23. Pointing: natural; long history - long understood by us primates 3D Interactions with scalable display walls chriscollison.wordpress.com chimp using stick as tool 3D gyro mouse www.gyration.com Also VR devices: Magnetic head trackers, Wands, … Nintendo WiiMote; Tutorial: C A Wingrave et al, IEEE Comp Graphics & Apps, 30, 71-85 (2010) See www.wiimotelab.org maybe an iPhone app ? breaking out from desktop limitations B. Pailthorpe, UQ at IEEE e-Science, Dec’10

  24. 3D Interaction with the OptIPortal, SAGE & apps: Input Pointing & Navigating at large scale Richard Hammond UQ Vislab 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) 3D gyro mouse www.gyration.com B. Pailthorpe, UQ at IEEE e-Science, Dec’10

  25. Interacting with the OptIPortal, SAGE & apps: Output Write/ Draw simultaneously to 2 Output “windows” • Draw to local screen buffer, • with Window Manager • - to Content Node • Display 2. Draw to Xvfb: virtual frame buffer (can be very large) - thence to Tiled Display; but no Window Manager? (2-4 Mpx) Tiled Display (Local, or Remote) 2a. Draw to XDMX - Distributed MultiHead X - proxy X server - not a Window Manager - 16 tile limit Content Node {2 x a0} + needs to couple to 3D navigation devices {a1} Mouse, keyboard Inputs + Needs to be scalable: migrate rendering from Content (“Head”) node to the cluster nodes; & draw to tiled display {a2} Progress: Atlantis, Paraview mpi distributed (Chris Willing: talk + demo) … underway …. {a3} {Display Nodes Cluster} B. Pailthorpe, UQ at IEEE e-Science, Dec’10

  26. 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

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