Cyberinfrastructure and California Dr. Francine Berman Director, San Diego Supercomputer Center Professor and High Performance Computing Endowed Chair, UC San Diego
The Digital World Science Entertainment Commerce Information
wireless sensors computer Field instrument network computer network DATA computer DATA DATA storage computer viz network fieldinstrument 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 The “computer” as an integrated set of resources
Cyberinfrastructure -- An Integrating Concept Cyberinfrastructure = Resources (computers, data storage, networks, scientific instruments, experts, etc.) + “Glue”(integrating software, systems, and organizations)
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 Transmission repeated every hour during 6-8 hour surgery. Transmission and output must take on the order of minutes Finite element simulation on biomechanical model for volumetric deformation performed at SDSC; output results are sent to BWH where updated images are shown to surgeons How does Cyberinfrastructure Work?Cyberinfrastructure-enabled Neurosurgery • 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
Data andKnowledge Systems High Performance computing Data-orientedScience and Engineering Grid andClusterComputing SW tools,workbenches,toolkits Networking Community Databasesand Data Collections Computational Science and Engineering 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.
SDSC Resources Are Available to the Community 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/ Support for community data collections and databases Data management, mining, analysis, and preservation 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/ 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/
Data from sensors 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 • Cyberinfrastructure must support unprecedented diversity, globalization, integration, scale, and use Data from simulations Data from instruments Volunteer Data Data from analysis
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 SDSC HPSS tape archive = 6 PetaBytes 1 novel = 1 MegaByte All worldwide information in one year = 2 ExaBytes 1 Low Resolution Photo = 100 KiloBytes * Rough/average estimates
Cyberinfrastructure – enabled Disaster Preparedness Major Earthquakes on the San Andreas Fault, 1680-present • 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 • 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 1906 M 7.8 1857 M 7.8 ? 1680 M 7.7 How dangerous is the southern San Andreas Fault?
Domain: 600Km x 300km x 80kmMesh Dimension: 3000x1500x400Spatial resolution = 200mSimulated time = 200sNumber 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.
Making Terashake Work -- Resources • 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 • 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
Cyberinfrastructure and Data: Preserving our Scientific and Cultural Heritage
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
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
Consortium Planning Ahead for Preservation • Comprehensive approach to infrastructure for long-term preservation requires the integration of • Collection ingestion • Access and Services • Research and developmentfor new functionality and adaptation to evolving technologies • Business model, data policies, and managementissues critical to success of the infrastructure Services Ingestion Policy R&D
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 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) email@example.com
SDSC Academic Associates Program Targets Enabling Cyberinfrastructure Collaborations SDSC/UC Academic Associates Program Cyberinfrastructure and “Seeding” Activities • Targeted workshops • Priority SW installationand support • Priority participation for Cyberinfrastructure Summer Institute • Focused assistance with developing successful proposals for national allocation programs • Targeted user services • Special UC computeanddata allocations • Priority for “early usage” of new national resources 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
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 Leadership in Cyberinfrastructure provides a competitive edge to California researchers, educators, practitioners, and business leaders
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