Clusters at IGPP

1
(No Transcript)
2

• Biomedical Imaging Data -
• Distributed Instrumentation
• Seismic Data Analysis

• Mark Ellisman, Ph.D.
• Debi Kilb, Ph.D.
• David Lee and Atul Nayak
• (who did the work)

http//www.nbirn.net
3
GOALS Overarching Aim is to bring the
challenges of Biomedical and Earth sciences to
help shape the development of the OptIPuter.
Will here summarize the accomplishments and plans
of the applications teams -- including the
linkages to education and outreach.
4
Year 3 2004 Accomplishment Highlights

• Continue testing and usability studies of the
  simultaneous use of DMX and EVL visualization
  software with the same tiled display supporting
  EVL OptIPuter applications in addition to
  standard Linux compatible software. (done)
• Channel bonding of front-end node using multiple
  port GigE cards for use in applications such as
  DMX where many nodes are requesting information
  from the front end simultaneously. (Done on
  Brainywall/IBM T221 cluster) (done)
• Build and deploy a 20-tile BioWall based on
  GeoWall2 technology. (done)
• Build and deploy a 21-computer Opteron cluster
  with QuadroFX 3000G graphics cards to power the
  BioWall display. (done)
• Install EVLs JuxtaView and Vol-a-Tile
  applications on the BioWall cluster. (done)
• Install and test other tiled display software
  such as DMX and Chromium. (done)
• Develop a point-and-click web interface allowing
  users to launch JuxtaView from the Telescience
  web portal. (done)
• Develop a point-and-click web interface allowing
  users to launch SAGE from the Telescience web
  portal, allowing users to click and choose
  rendering resources as well as what visualization
  endpoint to display to. (Sept)
• Upgrade of the IBM T221 OptIPuter visualization
  node to the latest version of the Rocks software
  with the viz roll. (Sept)
• Include EVL and SIO computational and
  visualization resources into the Telescience
  portal. (Sept)
• Allow the Rocks group to use the Raster cluster
  to develop a 64-bit version of the Viz Roll for
  Rocks, allowing for rapid deployment of
  visualization clusters on 64-bit platforms.
  (Sept)
• Develop the Interactorium room for simultaneous
  2D and 3D data exploration using OptIPuter
  technologies (Sept)
• Installed and tested TeraVision server for
  transport of microscope video to remote
  collaborators. (done)

5
High Data Rate Instruments are driving the
Requirements for Optical Networks

• Three Dimensional Imaging with High Energy
  Electron Microscopes
• High speed camera
• 1K x 1K, 12bit, 12frame/sec 24MByte/sec
• High resolution camera
• 4K x 4K, 16bit 32MByte
• Remote control capability
• New camera coming online within the next 18
  months
• 8K x 8k, 16bit 122MByte
• High Throughput Laser Scanning Light Microscope
• Useful for live 4D cell imaging
• Require high computation process
• Remote control capability

6
Synchrotrons, Microscopes and MRIs Tools for
the Nano, Meso and Macro Scales of Biological
Systems
Molecules
Synchrotrons
Macromolecular Complexes, Organelles, Cells
Microscopes
Organs, Organ Systems, Organisms
Magnetic Resonance Imagers
7
2-photon montage of mouse cerebellum using
quantum dots Anti-IP3 receptor QD 565, anti-GFAP
QD 655 and Hoechst 44432
Extremely Large Brain Image Data Sets are Driving
the Requirements for Optical Networks
512 x 512 x100,000

.
5um
8
NCMIR Biowall

• In production use by NCMIR staff on a regular
  basis
• Widely adopted by staff within its first week of
  operation
• Uses the OptIPuter Storage Cluster
• Enables high resolutions views and perspectives
  otherwise not possible

21 node Opteron Rocks cluster powering 40
million pixels on 20 UXGA displays
Sun Screen spf40
9
(No Transcript)
10
OptIPuter Visualization Environments at NCMIR
11
Single click interface to the OptIPuter
Clicking on a thumbnail transparently launches
JuxtaView utilizing the following OptIPuter
components
Browser Page

• Optical networks
• UCSD Extreme 10GigE chain
• Tiled displays
• NCMIRs Biowall
• OptIPuter Storage cluster
• EVL Visualization Applications
• JuxtaView
• Distributed Virtual Computer (being integrated
  now)
• Providing services for JuxtaView

Clicking on a thumbnail in the Telescience Portal
launches JuxtaView, displaying the image on the
tiled display.
12
Prime Program Education and Outreach
Undergraduate students were sent to the Pragma
member Cybermedia Center at Osaka, Japan where
they developed IPv6 technologies with SRB and
Globus to be integrated into remote work with the
microscopes at NCMIR and a part of OptIPuter
Ramsin Khoshabeh Stephen Geist
13
iGrid 2005
Plans
We will demonstrate a five layer demonstration
spanning the entire stack of OptIPuter
technologies, performing a real scientific
experiment

• Scientific Applications
• 2. Photonic layer
• 3. Protocols
• 4. Dist. Virtual Computer
• 5. Visualization - Lambda-powered Interactoriums

Technology collaboration between EVL, UCSD-CSE,
and NCMIR Collaboration between Amsterdam, Korea,
Taiwan, Chicago, San Diego
14
The BIRN is Expanding with NIH ProgramsOptIPuter-
based Infrastructure will Link Key Sites
Will Connect New NIH Program for National
Centers for Biomedical Computation
www.nbirn.net
15
OptIPuter Clusters at IGPP

• SIO OptIPuter Visualization Cluster
• 10 node Linux cluster 2 IBM displays setup is
  being upgraded to Rocks 3.3 and viz roll
• G5 Cluster for USArray
• 2 x 2 tiled display of 30 Apple monitors driven
  by 3 node G5 cluster being set up for Earthscope
  project.

16
Applications on Clusters

• High resolution imagery Juxtaview (EVL, UIC)
• eg., 36 Gb San Diego Aerial Photos
• Volume visualization of seismic cubes Vol-a-Tile
  (EVL, UIC) GVU (ISI, USC)
• eg., 2Gb seismic cube
• Graduate student projects
• Imaging detailed structure within large scale
  fault zones

17
What a Dip!
Fault Orientations Visualizing Large and Small
Scale Structure Within Fault SystemsDebi Kilb
(SIO) Charles Zhang (EVL)
But what we are after are the small scale 3D
details not the over all trend.
The average fault dip is 69.67 and the standard
deviation is 35.70. Got it?
optIPuter
Earths Surface
Earthquake hypocenter Fault orientation Inferred
orientation based on hypocenters
18
Fault Tour ..
19
The orientations of some faults can be estimated
from the earthquake hypocenters, but this is
relatively rare (and can be wrong!)
San Andreas Fault Simple fault orientation
San Jacinto Fault Complex fault orientation
San Andreas Fault
20
(No Transcript)
21
Work in Progress
Generation of movies from real time images (
ROADnet).
Volumetric visualization of conductivity models
22
Education Outreach
Lincoln Elementary School
23
Project Plan
Giving students access to phenomena through
networking visualization technologies.
24
EVL Focus FromEmbedded PhenomenatoPhenomenon
Servers
Development work HelioRoom (Solar system),
RoomTraces (migratory patterns), RoomQuake 2.0
(seismology) Research in students learning
Content knowledge (e.g. distribution of
earthquake amplitudes), Process knowledge (e.g.
determination of epicenter), Attitudes toward
science (TOSRA) Expanding partnerships Galileo,
National Teachers Academy
25
NCMIR Development of tools (hardware/software)
for outreach/education in the San Diego Community

26
Preuss Year 3 FocusLong-Distance
Collaborations/Learning

• Ship-2-Shore Real-time conversations between
  students at Preuss and teacher at sea Debra
  Brice.

27
Preuss (students/teachers) SIO (researchers)
Real-time 3D data exploration and data
manipulation.
28
Scripps Institution of Oceanography Visualization
Center
29
GEOWALL at the Birch Aquarium at Scripps
30
The Magic Planet at the Birch Aquarium at
Scripps
31
SIO Focus Linking Projects Together

• Annual Earthquake Education Workshop
• Annual Graduate Student Visualization Competition
• Museum Exhibits
• Earthquake! Life on a restless planet (BAS)
• IMAX opening (Reuben H. Fleet Science Museum)

32
(No Transcript)