Transcript A Vision for a New Era in Computational Science
Cyberinfrastructure and California
Dr. Francine Berman
Director, San Diego Supercomputer Center Professor and High Performance Computing Endowed Chair, UC San Diego
SAN DIEGO SUPERCOMPUTER CENTER
Fran Berman
UCSD UNIVERSITY OF CALIFORNIA
The Digital World
Science Commerce Information
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Fran Berman
UCSD UNIVERSITY OF CALIFORNIA
Entertainment
Today’s Technology is a Team Sport
•
Today’s “computer” is a coordinated set of hardware, software, data, and services providing an “end-to end” resource.
•
Cyberinfrastructure
captures the integrated character of today’s IT environment
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Fran Berman wireless DATA Field instrument computer computer network computer DATA storage sensors network DATA viz computer network field instrument The “computer” as an integrated set of resources
UCSD UNIVERSITY OF CALIFORNIA
Cyberinfrastructure -- An Integrating Concept
Cyberinfrastructure = Resources
(computers, data storage, networks, scientific instruments, experts, etc.)
+ “Glue”
(integrating software, systems, and organizations)
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Fran Berman
UCSD UNIVERSITY OF CALIFORNIA
How does Cyberinfrastructure Work?
Cyberinfrastructure-enabled Neurosurgery
Radiologists and neurosurgeons at Brigham and Women’s Hospital, Harvard Medical School exploring
transmission of 30/40 MB brain images
(generated during surgery) to SDSC for analysis and alignment
• • •
PROBLEM:
Neuro-surgeons seek to remove as much tumor tissue as possible while minimizing removal of healthy brain tissue
Brain deforms during surgery
Surgeons must align preoperative brain image with intra-operative images to provide surgeons the best opportunity for intra-surgical navigation
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Fran Berman
Transmission repeated
every hour
during 6-8 hour surgery.
Transmission and output must take on
the order of
minutes
Finite element simulation
biomechanical model for volumetric deformation surgeons on performed at SDSC; output results are sent to BWH where updated images are shown to
UCSD UNIVERSITY OF CALIFORNIA
SDSC is a National Cyberinfrastructure Center
• • • •
SDSC
National facility funded by NSF, NIH, DOE, Library of Congress, NARA, etc.
Employs nearly 400 researchers, staff and students National Facility and UCSD Organized Research Unit Home to many associated activities including
• • Protein Data Bank Biomedical Informatics Research Network (BIRN) Coordinating Center • • Geosciences Network (GEON) NEES IT Center, etc.
Data and Knowledge Systems Grid and Cluster Computing SW tools, workbenches, toolkits Community Databases and Data Collections
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High Performance computing
UCSD
Data oriented Science and Engineering Networking Computational Science and Engineering
UNIVERSITY OF CALIFORNIA
Fran Berman
SDSC Resources Are Available to the Community
• • •
COMPUTE SYSTEMS DataStar
• • • • 2,528 Power4+ processors IBM p655 8-way and p690 32-way nodes 7 TB total memory Up to 3 GBps I/O to disk
TeraGrid Cluster
• 512 Itanium2 IA-64 processors • • 1 TB total memory Also 128 2-way data nodes
Blue Gene Data
• • • First academic IBM Blue Gene system 2,048 PowerPC processors 128 I/O nodes
http://www.sdsc.edu/ user_services/
• • • • • • • •
DATA ENVIRONMENT
1.4 PB Storage-area Network (SAN) 6 PB StorageTek tape library HPSS and SAM-QFS archival systems DB2, Oracle, MySQL Storage Resource Broker 72-CPU Sun Fire 15K IBM p690s – HPSS, DB2, etc
http://datacentral.sdsc.edu/ SAN DIEGO SUPERCOMPUTER CENTER UCSD
Support for community data collections and databases Data management, mining, analysis, and preservation
• • • • • •
SCIENCE and TECHNOLOGY STAFF, SOFTWARE, SERVICES
User Services Application/Community Collaborations Education and Training SDSC Synthesis Center Community SW, toolkits, portals, codes
http://www.sdsc.edu/
Fran Berman
UNIVERSITY OF CALIFORNIA
• • •
Cyberinfrastructure Can Help Harness Today’s Deluge of Data
Over the next decade, data will
• • • •
come from everywhere Scientific instruments Experiments Sensors and sensornets New devices (personal digital devices, computer enabled clothing, cars, …)
• • • •
And be used by everyone Scientists Consumers Educators General public Data from simulations Cyberinfrastructure must support unprecedented diversity, globalization, integration, scale, and use Volunteer Data Data from sensors Data from instruments Data from analysis SAN DIEGO SUPERCOMPUTER CENTER
Fran Berman
UCSD UNIVERSITY OF CALIFORNIA
How much Data is there?*
iPod Shuffle (up to 120 songs) = 512 MegaBytes Printed materials in the Library of Congress = 10 TeraBytes 1 human brain at the micron level = 1 PetaByte
Kilo
10 3
Mega
10 6
Giga
10 9 1 novel = 1 MegaByte
Tera
10 12 1 Low Resolution Photo = 100 KiloBytes
Peta Exa
10 10 15 18
* Rough/average estimates
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Fran Berman
SDSC HPSS tape archive = 6 PetaBytes
UCSD UNIVERSITY OF CALIFORNIA
All worldwide information in one year = 2 ExaBytes
Cybeirnfrastructure and Data: Using Data for Analysis and Simulation
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Fran Berman
UCSD UNIVERSITY OF CALIFORNIA
Cyberinfrastructure – enabled Disaster Preparedness
• • •
The SCEC TeraShake simulation is a result of immense effort from the Geoscience community for over 10 years
Focus is on understanding big earthquakes and how they will impact sediment-filled basins.
Simulation combines massive amounts of data, high-resolution models, large-scale supercomputer runs
1906 M 7.8
Major Earthquakes on the San Andreas Fault, 1680-present
1857 M 7.8
How dangerous is the southern San Andreas Fault?
1680 M 7.7
?
• •
TeraShake results provide new information enabling better
• Estimation of seismic risk • Emergency preparation, response and planning • Design of next generation of earthquake-resistant structures
Such simulations provide potentially immense benefits in saving both many lives and billions in economic losses SAN DIEGO SUPERCOMPUTER CENTER
Fran Berman
UCSD UNIVERSITY OF CALIFORNIA
Domain: 600Km x 300km x 80km Mesh Dimension: 3000x1500x400 Spatial resolution = 200m Simulated time = 200s Number of time steps = 20,000
•
What you’re looking at:
•
L.A. experiences strong ground motion from the S->N scenario
•
The N->S rupture generates strong reverberations in the Imperial Valley, ultimately hitting Mexicalli and other northern Mexico cities.
•
Large local peaks in ground motion near Palm Springs, resulting in immense damage.
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Fran Berman
UCSD UNIVERSITY OF CALIFORNIA
Making Terashake Resources Work --
• •
Computers and Systems
• 80,000 hours on 240 processors of DataStar • 256 GB memory p690 used for testing, p655s used for production run, TG used for porting • • 30 TB Global Parallel file GPFS Run-time 100 MB/s data transfer from GPFS to SAM-QFS • 27,000 hours post-processing for high resolution rendering
People
• 20+ people involved in information technology support • 20+ people involved in geoscience modeling and simulation
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Fran Berman
• •
Data Storage
• 47 TB archival tape storage on Sun StorEdge SAM-QFS • 47 TB backup on High Performance Storage system HPSS • SRB Collection with 1,000,000 files
Funding
• SDSC Cyberinfrastructure resources for TeraShake funded by NSF • Southern California Earthquake Center is an NSF-funded geoscience research and development center
UCSD UNIVERSITY OF CALIFORNIA
Cyberinfrastructure and Data: Preserving our Scientific and Cultural Heritage
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Fran Berman
UCSD UNIVERSITY OF CALIFORNIA
Data Preservation
• • • Many Science, Cultural, and Official Collections must be sustained for the foreseeable future
Critical collections must be preserved:
•
community reference data collections
(e.g. Protein Data Bank) •
irreplaceable collections
(e.g. Shoah collection) •
longitudinal data
(e.g. PSID – Panel Study of Income Dynamics)
No plan for preservation often means that data is lost or damaged
“….
the progress of science and useful arts … depends on the reliable preservation of knowledge and information for generations to come.”
“Preserving Our Digital Heritage”, Library of Congress SAN DIEGO SUPERCOMPUTER CENTER
Fran Berman
UCSD UNIVERSITY OF CALIFORNIA
Key Challenges for Digital Preservation
•
What should we preserve?
• What materials must be “rescued”?
• How to plan for preservation of materials by design?
•
How should we preserve it?
• Formats • Storage media • Stewardship – who is responsible?
•
Who should pay for preservation?
• The content generators?
• The government?
• The users?
•
Who should have access?
Print media provides easy access for long periods of time but is hard to data-mine Digital media is easier to data-mine but requires management of evolution of media and resource planning over time
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Fran Berman
UCSD UNIVERSITY OF CALIFORNIA
Planning Ahead for Preservation
• • • •
Comprehensive approach to infrastructure for long-term preservation requires the integration of Collection ingestion Access and Services Research and development
for new functionality and adaptation to evolving technologies •
Business model, data policies, and management
issues critical to success of the infrastructure
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Fran Berman
Services Policy
UCSD UNIVERSITY OF CALIFORNIA
Ingestion R&D
Consortium
Cyberinfrastructure Resources at SDSC
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Fran Berman
UCSD UNIVERSITY OF CALIFORNIA
• •
SDSC Data Central
First program of its kind to support research and community data collections and databases
•
Comprehensive resources
•
Disk:
400 TB accessible via HPC systems, Web, SRB, GridFTP • • •
Databases:
DB2, Oracle, MySQL
SRB:
Collection management
Tape:
6 PB, accessible via file system, HPSS, Web, SRB, GridFTP
Data collection and database hosting
• • • Batch oriented access Collection management services
Collaboration opportunities:
• Long-term preservation • Data technologies and tools
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Fran Berman
• • • • • • • • • • •
New Allocated Data Collections include
Bee Behavior (Behavioral Science) C5 Landscape DB (Art) Molecular Recognition Database (Pharmaceutical Sciences) LIDAR (Geoscience) LUSciD (Astronomy) NEXRAD-IOWA (Earth Science) AMANDA (Physics) SIO_Explorer (Oceanography) Tsunami and Landsat Data (Earthquake Engineering) UC Merced Library Japanese Art Collection (Art) Terabridge (Structural Engineering)
UCSD UNIVERSITY OF CALIFORNIA
SDSC Academic Associates Program Targets Enabling Cyberinfrastructure Collaborations
• • • • • • •
SDSC/UC Academic Associates Program Cyberinfrastructure and “Seeding” Activities
Targeted workshops Priority SW installation
and
support Priority participation
Summer Institute for Cyberinfrastructure
Focused assistance
with developing successful proposals for national allocation programs
Targeted user services
Special
UC compute
and
data allocations Priority for “early usage”
resources of new national • • •
SDSC Cyberinfrastructure Resources Heavily Used by UC faculty and students
UC PIs account for
329+ trillion bytes of data
stored at SDSC In FY05, over
5 million CPU hours
on HPC machines at SDSC were used by UC faculty and students at all campuses UCSD faculty make up
40% of among top users
of SDSC compute resources
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Fran Berman
UCSD UNIVERSITY OF CALIFORNIA
Cyberinfrastructure is Fundamental for California
• • •
Cyberinfrastructure captures the practice and potential of modern science and engineering Cyberinfrastructure is the focus of increasing number of federal programs
• NSF (all directorates), NIH (BISTI, Bioinformatics, Computational Biology, etc.), DOE (Science Grid), etc.
Cyberinfrastructure is critical for success in modern research and education initiatives
• Stem cell research • Grid computing • Multi-disciplinary science and engineering
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Fran Berman
Leadership in Cyberinfrastructure provides a competitive edge to California researchers, educators, practitioners, and business leaders
UCSD UNIVERSITY OF CALIFORNIA
Thank You
www.sdsc.edu
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Fran Berman
UCSD UNIVERSITY OF CALIFORNIA