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A New Era for Computational Science. NPACI Parallel Computing Institute August 28, 2000 Sid Karin Director, NPACI/SDSC skarin@sdsc.edu. SDSC. A National Laboratory for Computational Science and Engineering. Leading-Edge Site for NPACI. NPACI. Continuing Evolution. NPACI. SDSC.

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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@sdsc.edu


SDSC

A National Laboratory for Computational Science and Engineering

Leading-Edge Site for NPACI


NPACI

Continuing Evolution

NPACI

SDSC

Resources

Resources

Education

Outreach & Training

Enabling technologies

Technology & applications thrusts

Applications

Individuals

Partners

1985

2000


A Distributed National Laboratory for Computational Science and Engineering


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


Mission

Accelerate Scientific Discovery

Through the development and implementationof computationaland computerscience techniques

By creating a ubiquitous, continuous, and pervasive national infrastructure: the grid


Vision

Changing How Science is Done

  • 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


Goals: Fulfilling the Mission

Embracing the Scientific Community

  • 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


Partnership Organizing Principle: “Thrusts”

Computational Literacy

EOT

Discovery Environments

TECHNOLOGIES

Discovery Environments

APPLICATIONS

Metasystems

Programming Tools & Environments

Data-intensive Computing

Interaction Environments

Molecular Science

Neuroscience

Earth Systems Science

Engineering

Capability Computing

RESOURCES


Projects Meld Applications and Technology

Brain databases

Data-IntensiveComputing+Neuroscience

Metasystems andParallel Tools

+

Engineering


Leadership Team

Sid Karin, SDSCDirectorskarin@sdsc.edu

Peter Arzberger, SDSC Executive Directorparzberg@sdsc.edu

Paul Messina, CaltechChief Architect(on leave)

Susan Graham, UC Berkeley Chief Computer Scientistgraham@cs.berkeley.edu

Peter Taylor, SDSCChief Applications Scientisttaylor@sdsc.edu

Wayne Pfeiffer, SDSCDeputy Directorpfeiffer@sdsc.edu

Greg Moses, U WisconsinEducation, Outreach, and Training Leadermoses@engr.wisc.edu


NPACI Executive Committee

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

Leadership Team plus:

Aron Kuppermann, Caltech

User Representative


NPACI Oversight

Institutional Oversight Board

External Visiting Committee

Director’s Advisory Committee

Users’ Advisory Committee

EVC

UAC

IOB

DAC

ExecutiveCommittee

Leadership Team

Resource Partner Representatives

Technologies

Thrust Leaders

Applications

Thrust Leaders


EOT

Applications

Technologies

Resources

Budget Balance

SDSC

Partners


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


14

10

13

10

World's fastest

12

10

supers

Peak speed (flops)

11

10

SDSC's

vector

supers

10

10

9

10

8

10

1980

1985

1990

1995

2000

2005

Year installed

Leading-Edge Site Supercomputer Roadmap

1 TFLOPSIBM SP1999


NPACI’s 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)

    • >180 TB mass store at SDSC

    • >100 GB data sets at partner sites

  • Network resources (SDSC & all partners)

    • >100 Mbps access to compute & data resources

    • Communications backbone for metacomputing


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


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

    • > 640 GB memory (4 GB/node), upgrade to > 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


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

Current Large SP Allocations


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


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


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


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


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


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


Examples of Additional Projects

  • NPACI and SDSC activities


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


The Protein Data Bank

  • World’s 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 PDB’s 10,000th structure.


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


Collaboration with Hayden Planetarium

American Museum of Natural History

Support from NASA

Linking SDSC’s 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

Digital Galaxy


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.


Looking out for San Diego’s 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


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


Mapping the Net’s Terra Incognita

Nature: Web Matters, 1/7/99. Science 10/16/98


This is Only the Beginning...

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