A New Era for Computational Science

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A New Era for Computational Science

• NPACI Parallel Computing Institute
• August 28, 2000
• Sid Karin
• Director, NPACI/SDSC skarin_at_sdsc.edu

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SDSC
A National Laboratory for Computational Science
and Engineering
Leading-Edge Site for NPACI
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Continuing Evolution
NPACI
NPACI
SDSC
Resources
Resources
Education Outreach Training
Technology applications thrusts
Enabling technologies
Applications
Individuals
Partners
1985
2000
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A Distributed National Laboratory for
Computational Science and Engineering
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NPACI is a Highly Leveraged National Partnership
of Partnerships
46 institutions 20 states 4 countries 5 national
labs Many projects Vendors and industry Government
agencies
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Accelerate Scientific Discovery
Mission

• Through the development and implementationof
  computationaland computerscience techniques

By creating a ubiquitous, continuous, and
pervasive national infrastructure the grid
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Changing How Science is Done
Vision

• Collect data from digital libraries,
  laboratories, and observation
• Analyze the data with models run on the grid
• Visualize and share data over the Web
• Publish results in a digital library

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Embracing the Scientific Community
Goals Fulfilling the Mission

• Capability Computing
• Provide compute and information resources of
  exceptional capability
• Discovery Environments
• Develop and deploy novel, integrated, easy-to-use
  computational environments
• Computational Literacy
• Extend the excitement, benefits, and
  opportunities of computational science

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Partnership Organizing Principle Thrusts
Computational Literacy EOT
Discovery Environments APPLICATIONS
Discovery Environments TECHNOLOGIES
Molecular Science Neuroscience Earth Systems
Science Engineering
Metasystems Programming Tools
Environments Data-intensive Computing Interaction
Environments
Capability Computing RESOURCES
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Projects Meld Applications and Technology
Brain databases
Data-IntensiveComputingNeuroscience
Metasystems andParallel Tools Engineering
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Leadership Team

• Susan Graham, UC Berkeley Chief Computer
  Scientistgraham_at_cs.berkeley.edu
• Peter Taylor, SDSCChief Applications
  Scientisttaylor_at_sdsc.edu
• Wayne Pfeiffer, SDSCDeputy Directorpfeiffer_at_sdsc
  .edu
• Greg Moses, U WisconsinEducation, Outreach, and
  Training Leadermoses_at_engr.wisc.edu

Sid Karin, SDSCDirectorskarin_at_sdsc.edu Peter
Arzberger, SDSC Executive Directorparzberg_at_sdsc.e
du Paul Messina, CaltechChief Architect(on
leave)
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NPACI Executive Committee

• Leadership Team plus

Andrew Grimshaw, U VirginiaMetasystems Joel
Saltz, U MarylandProgramming Tools and
Environments Reagan Moore, SDSCData-Intensive
Computing Arthur Olson, TSRIInteraction
Environments William Martin, U MichiganResource
Representative
Russ Altman, Stanford UMolecular Science Mark
Ellisman, UCSDNeuroscience Bernard Minster,
UCSD (SIO)Earth Systems Science Tinsley Oden, U
Texas (TICAM)Engineering James Pool,
CaltechResource Representative
Aron Kuppermann, Caltech User Representative
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NPACI Oversight
Institutional Oversight Board External Visiting
Committee
Directors Advisory Committee Users Advisory
Committee
UAC
EVC
IOB
DAC
Executive Committee
Leadership Team
Resource Partner Representatives
Applications Thrust Leaders
Technologies Thrust Leaders
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Budget Balance
SDSC
Partners
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Complementary rolesof five compute resource sites

• Leading-edge site (SDSC)
• Very high-performance resources
• IBM SP teraflops system
• Mid-range sites (U Texas U Michigan)
• Smaller systems compatible with LES
• Support for applications with limited
  scalability, large-memory jobs, application
  development, OS testing, and education
• Alternate architecture research systems
• Caltech, UC Berkeley, SDSC
• Support for leading-edge applications, thrusts,
  and evaluation

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Leading-Edge Site Supercomputer Roadmap
1 TFLOPSIBM SP1999
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NPACIs balanced complement ofhigh-end resources
for 2000

• Compute resources (SDSC 4 partners)
• IBM SP Teraflops system at SDSC
• Complementary systems at partner sites
• Data resources (SDSC 10 partners)
• gt180 TB mass store at SDSC
• gt100 GB data sets at partner sites
• Network resources (SDSC all partners)
• gt100 Mbps access to compute data resources
• Communications backbone for metacomputing

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IBM Selected as First NPACI Teraflops Vendor

• Strong commitment to high end by IBM
• Technology being developed through ASCI
• SDSC has largest system in US academia
• Growing partnership with IBM

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1st Teraflops System for US Academia
Nov 1999

• 1 TFLOPs IBM SP
• 144 8-processor compute nodes
• 12 2-processor service nodes
• 1,176 Power3 processors at 222 MHz
• gt 640 GB memory (4 GB/node), upgrade to gt 1 TB
  later
• 6.8 TB switch-attached disk storage
• Largest SP with 8-way nodes
• High-performance access to HPSS
• Trailblazer switch interconnect with subsequent
  upgrade

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Current Large SP Allocations

• Fundamental Physics
• T. Kinoshita, Cornell University
• R. Sugar, UC Santa Barbara
• Ab initio Biochemistry
• H. Scheraga, Cornell University
• A. McCammon, UC San Diego
• M. Klein, Univ. of Pennsylvania
• M. Gordon, Iowa State University
• Biomedicine
• A. Garfinkel, UCLA
• B. Pettitt, University of Houston

• Materials Science
• F. Abraham, IBM Almaden
• J. Kim, Ohio State University
• Fluid Dynamics
• K. Gubbins, Cornell University
• J. Kim, UCLA
• G. Karniadakis, Brown University
• Astrophysics
• P. Hauschildt, Univ. of Georgia
• J. Raeder, UCLA
• M. Ashour-Abdalla, UCLA

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NPACI alpha projects

• Bioinformatics Infrastructure for Large-Scale
  Analyses
• Protein Folding in a Distributed Computing
  Environment
• Telescience for Advanced Tomography Applications
• Multi-Component Models for Energy and the
  Environment
• Scalable Visualization Toolkits for Bays to Brains

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Bioinformatics Infrastructure for Large-Scale
Analyses

• Next-generation tools for accessing,
  manipulating, and analyzing biological data
• Russ Altman, Stanford University
• Reagan Moore, SDSC
• Analysis of Protein Data Bank, GenBank and other
  databases
• Accelerate key discoveries for health and medicine

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Protein Folding in a Distributed Computing
Environment

• Simulating protein movement governing reactions
  within cells
• Andrew Grimshaw, U Virginia
• Charles Brooks, The Scripps Research Institute
• Bernard Pailthorpe, UCSD/SDSC
• Computationally intensive
• Distributed computing power from Legion

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Telescience for Advanced Tomography Applications

• Integrates remote instrumentation, distributed
  computing, federated databases, image archives,
  and visualization tools.
• Mark Ellisman, UCSD
• Fran Berman, UCSD
• Carl Kesselman, USC
• 3-D tomographic reconstruction of biological
  specimens

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Multi-Component Modeling for Energy and the
Environment

• Simulating contaminant movement through
  ecosystems
• Leaders Joel Saltz, U Maryland and Johns Hopkins
  U Mary Wheeler, U Texas
• Will assist environmental cleanup efforts and
  strategies
• Engineering and environmental models linked
  through metasystems and data manipulation tools

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Scalable Visualization Toolkits

• Vast data collections and large-scale simulations
  require scalable visualization tools
• Art Olson, The Scripps Research Institute
• Bernard Pailthorpe, SDSC/UCSD
• Art Toga, UCLA
• Carl Wunsch, MIT
• 3-D reconstruction, time-dependent modeling

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Examples of Additional Projects

• NPACI and SDSC activities

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MICE Transparent Supercomputing

• Molecular Interactive Collaborative Environment
• Gallery allows researchers, students to search
  for, visualize, and manipulate molecular
  structures
• Integrates key SDSC technological strengths
• Biological databases
• Transparent supercomputing
• Web-based Virtual Reality Modeling Language

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The Protein Data Bank

• Worlds single scientific resource for depositing
  and searching protein structures
• Protein structure data growing exponentially
• 10,500 structures in PDB today
• 20,000 by the year 2001
• Vital to the advancement of biological sciences
• Working towards a digital continuum from primary
  data to final scientific publication
• Capture of primary data from high-energy
  synchrotrons (e.g. Stanford Linear Accelerator
  Center) requires 50Mbps network bandwidth

1CD3 The PDBs 10,000th structure.
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New Mode of Visualization

• Network-accessible TeleManufacturing
• 3-D hardcopy for visualization
• Used by many disciplines
• Molecules to Hurricanes
• Death Valley to Venus
• Reimann Zeta Function to Ozone Hole

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Digital Galaxy

• Collaboration with Hayden Planetarium
• American Museum of Natural History
• Support from NASA
• Linking SDSCs mass storage to Hayden Planetarium
  requires 155 Mbps
• MPIRE Galaxy Renderer
• Scalable volume visualization
• Linked to database of astronomical objects
• Produces translucent, filament-like objects

• An artificial nebula, modeled after a planetary
  nebula

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The Digital Sky

• Billions of objects can be detected with optical,
  infrared, and radio telescopes
• Tens of terabytes of image and catalog data
• Digital Sky federating four sky surveys to allow
  multi-wavelength studies across the data sets
• DPOSS, 2MASS, NVSS, FIRST
• Tom Prince, Caltech, leading federation effort
• Uses MIX, SDSC SRB, and NPACI mass storage systems

A globular cluster from the DPOSS archive. Such
clusters provide a minimum age for the universe.
Image by Thomas Handley, Caltech.
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Looking out for San Diegos Regional Ecology

• Unique partnership
• 31 federal, state, regional,and local agencies
• John Helly, et al., SDSC
• Combines technologies and multi-agency data
• Sensing, analysis, VRML
• Physical, chemical, and biological data
• Web-based tool for science and public policy

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AMICO The Art of Managing Art

• Art Museum Image Consortium (AMICO)
• 28 art museums working toward educational use of
  digital multimedia
• Launch of the AMICO Library includes more than
  50,000 works of art
• AMICO, CDL, SDSC
• XML information mediation
• SDSC SRB data management
• Links between images, scholarly research,
  educational material

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Mapping the Nets Terra Incognita

Nature Web Matters, 1/7/99. Science 10/16/98
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This is Only the Beginning...
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