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High Performance Cyberinfrastructure Enables Data-Driven Science in the Globally Networked World

High Performance Cyberinfrastructure Enables Data-Driven Science in the Globally Networked World. Keynote Presentation Sequencing Data Storage and Management Meeting at The X-GEN Congress and Expo San Diego, CA March 14, 2011. Dr. Larry Smarr

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High Performance Cyberinfrastructure Enables Data-Driven Science in the Globally Networked World

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  1. High Performance Cyberinfrastructure Enables Data-Driven Science in the Globally Networked World Keynote Presentation Sequencing Data Storage and Management Meeting at The X-GEN Congress and Expo San Diego, CA March 14, 2011 Dr. Larry Smarr Director, California Institute for Telecommunications and Information Technology Harry E. Gruber Professor, Dept. of Computer Science and Engineering Jacobs School of Engineering, UCSD Follow me on Twitter: lsmarr

  2. Abstract High performance cyberinfrastructure (10Gbps dedicated optical channels end-to-end) enables new levels of discovery for data-intensive research projects—such as next generation sequencing. In addition to international and national optical fiber infrastructure, we need local campus high performance research cyberinfrastructure (HPCI) to provide “on-ramps,” as well as scalable visualization walls and compute and storage clouds, to augment the emerging remote commercial clouds. I will review how UCSD has built out just such a HPCI and is in the process of connecting it to a variety of high throughput biomedical devices. I will show how high performance collaboration technologies allow for distributed interdisciplinary teams to analyze these large data sets in real-time.

  3. Two Calit2 Buildings Provide Laboratories for “Living in the Future” “Convergence” Laboratory Facilities Nanotech, BioMEMS, Chips, Radio, Photonics Virtual Reality, Digital Cinema, HDTV, Gaming Over 1000 Researchers in Two Buildings Linked via Dedicated Optical Networks UC San Diego UC Irvine www.calit2.net Over 400 Federal Grants, 200 Companies

  4. The Required Components ofHigh Performance Cyberinfrastructure High Performance Optical Networks Scalable Visualization and Analysis Multi-Site Collaborative Systems End-to-End Wide Area CI Data-Intensive Campus Research CI

  5. The OptIPuter Project: Creating High Resolution Portals Over Dedicated Optical Channels to Global Science Data Scalable Adaptive Graphics Environment (SAGE) OptIPortal Picture Source: Mark Ellisman, David Lee, Jason Leigh Calit2 (UCSD, UCI), SDSC, and UIC Leads—Larry Smarr PI Univ. Partners: NCSA, USC, SDSU, NW, TA&M, UvA, SARA, KISTI, AIST Industry: IBM, Sun, Telcordia, Chiaro, Calient, Glimmerglass, Lucent

  6. Visual Analytics--Use of Tiled Display Wall OptIPortal to Interactively View Microbial Genome (5 Million Bases) Acidobacteria bacterium Ellin345 Soil Bacterium 5.6 Mb; ~5000 Genes Source: Raj Singh, UCSD

  7. Use of Tiled Display Wall OptIPortal to Interactively View Microbial Genome Source: Raj Singh, UCSD

  8. Use of Tiled Display Wall OptIPortal to Interactively View Microbial Genome Source: Raj Singh, UCSD

  9. Large Data Challenge: Average Throughput to End User on Shared Internet is 10-100 Mbps Tested January 2011 Transferring 1 TB: --50 Mbps = 2 Days --10 Gbps = 15 Minutes http://ensight.eos.nasa.gov/Missions/terra/index.shtml

  10. Solution: Give Dedicated Optical Channels to Data-Intensive Users (WDM) Source: Steve Wallach, Chiaro Networks “Lambdas” 10 Gbps per User ~ 100-1000x Shared Internet Throughput Parallel Lambdas are Driving Optical Networking The Way Parallel Processors Drove 1990s Computing

  11. Dedicated 10Gbps Lightpaths Tie Together State and Regional Fiber Infrastructure Interconnects Two Dozen State and Regional Optical Networks Internet2 Dynamic Circuit Network Is Now Available NLR 40 x 10Gb Wavelengths

  12. The Global Lambda Integrated Facility--Creating a Planetary-Scale High Bandwidth Collaboratory Research Innovation Labs Linked by 10G Dedicated Lambdas www.glif.is Created in Reykjavik, Iceland 2003 Visualization courtesy of Bob Patterson, NCSA.

  13. Launch of the 100 Megapixel OzIPortal Kicked Off a Rapid Build Out of Australian OptIPortals January 15, 2008 January 15, 2008 No Calit2 Person Physically Flew to Australia to Bring This Up! Covise, Phil Weber, Jurgen Schulze, Calit2 CGLX, Kai-Uwe Doerr , Calit2 http://www.calit2.net/newsroom/release.php?id=1421

  14. “Blueprint for the Digital University”--Report of the UCSD Research Cyberinfrastructure Design Team April 2009 No Data Bottlenecks--Design for Gigabit/s Data Flows Focus on Data-Intensive Cyberinfrastructure research.ucsd.edu/documents/rcidt/RCIDTReportFinal2009.pdf

  15. Campus Preparations Needed to Accept CENIC CalREN Handoff to Campus Source: Jim Dolgonas, CENIC

  16. Current UCSD Prototype Optical Core:Bridging End-Users to CENIC L1, L2, L3 Services Enpoints: >= 60 endpoints at 10 GigE >= 32 Packet switched >= 32 Switched wavelengths >= 300 Connected endpoints Approximately 0.5 TBit/s Arrive at the “Optical” Center of Campus. Switching is a Hybrid of: Packet, Lambda, Circuit -- OOO and Packet Switches Lucent Glimmerglass Force10 Source: Phil Papadopoulos, SDSC/Calit2 (Quartzite PI, OptIPuter co-PI) Quartzite Network MRI #CNS-0421555; OptIPuter #ANI-0225642

  17. Calit2 SunlightOptical Exchange Contains Quartzite Maxine Brown, EVL, UIC OptIPuter Project Manager

  18. UCSD Planned Optical NetworkedBiomedical Researchers and Instruments CryoElectron Microscopy Facility San Diego Supercomputer Center Cellular & Molecular Medicine East Calit2@UCSD Bioengineering Radiology Imaging Lab National Center for Microscopy & Imaging Center for Molecular Genetics Pharmaceutical Sciences Building Cellular & Molecular Medicine West Biomedical Research • Connects at 10 Gbps : • Microarrays • Genome Sequencers • Mass Spectrometry • Light and Electron Microscopes • Whole Body Imagers • Computing • Storage

  19. UCSD Campus Investment in Fiber Enables Consolidation of Energy Efficient Computing & Storage WAN 10Gb: CENIC, NLR, I2 N x 10Gb/s DataOasis(Central) Storage Gordon – HPD System Cluster Condo Triton – PetascaleData Analysis Scientific Instruments Digital Data Collections Campus Lab Cluster OptIPortal Tiled Display Wall GreenLight Data Center Source: Philip Papadopoulos, SDSC, UCSD

  20. Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis http://camera.calit2.net/

  21. Calit2 Microbial Metagenomics Cluster-Next Generation Optically Linked Science Data Server Source: Phil Papadopoulos, SDSC, Calit2 ~200TB Sun X4500 Storage 10GbE 512 Processors ~5 Teraflops ~ 200 Terabytes Storage 1GbE and 10GbE Switched/ Routed Core 4000 Users From 90 Countries

  22. OptIPuter Persistent Infrastructure EnablesCalit2 and U Washington CAMERA Collaboratory Photo Credit: Alan Decker Feb. 29, 2008 Ginger Armbrust’s Diatoms: Micrographs, Chromosomes, Genetic Assembly iHDTV: 1500 Mbits/sec Calit2 to UW Research Channel Over NLR

  23. Creating CAMERA 2.0 -Advanced Cyberinfrastructure Service Oriented Architecture Source: CAMERA CTO Mark Ellisman

  24. The GreenLight Project: Instrumenting the Energy Cost of Computational Science • Focus on 5 Communities with At-Scale Computing Needs: • Metagenomics • Ocean Observing • Microscopy • Bioinformatics • Digital Media • Measure, Monitor, & Web Publish Real-Time Sensor Outputs • Via Service-oriented Architectures • Allow Researchers Anywhere To Study Computing Energy Cost • Enable Scientists To Explore Tactics For Maximizing Work/Watt • Develop Middleware that Automates Optimal Choice of Compute/RAM Power Strategies for Desired Greenness • Data Center for School of Medicine Illumina Next Gen Sequencer Storage and Processing Source: Tom DeFanti, Calit2; GreenLight PI

  25. Moving to Shared Enterprise Data Storage & Analysis Resources: SDSC Triton Resource & Calit2 GreenLight Source: Philip Papadopoulos, SDSC, UCSD http://tritonresource.sdsc.edu • SDSC • Large Memory Nodes • 256/512 GB/sys • 8TB Total • 128 GB/sec • ~ 9 TF • SDSC Shared Resource • Cluster • 24 GB/Node • 6TB Total • 256 GB/sec • ~ 20 TF x256 x28 UCSD Research Labs • SDSC Data OasisLarge Scale Storage • 2 PB • 50 GB/sec • 3000 – 6000 disks • Phase 0: 1/3 TB, 8GB/s Campus Research Network N x 10Gb/s Calit2 GreenLight

  26. NSF Funds a Data-Intensive Track 2 Supercomputer:SDSC’s Gordon-Coming Summer 2011 • Data-Intensive Supercomputer Based on SSD Flash Memory and Virtual Shared Memory SW • Emphasizes MEM and IOPS over FLOPS • Supernode has Virtual Shared Memory: • 2 TB RAM Aggregate • 8 TB SSD Aggregate • Total Machine = 32 Supernodes • 4 PB Disk Parallel File System >100 GB/s I/O • System Designed to Accelerate Access to Massive Data Bases being Generated in Many Fields of Science, Engineering, Medicine, and Social Science Source: Mike Norman, Allan Snavely SDSC

  27. Data Mining Applicationswill Benefit from Gordon • De Novo Genome Assembly from Sequencer Reads & Analysis of Galaxies from Cosmological Simulations & Observations • Will Benefit from Large Shared Memory • Federations of Databases & Interaction Network Analysis for Drug Discovery, Social Science, Biology, Epidemiology, Etc. • Will Benefit from Low Latency I/O from Flash Source: Mike Norman, SDSC

  28. Rapid Evolution of 10GbE Port PricesMakes Campus-Scale 10Gbps CI Affordable • Port Pricing is Falling • Density is Rising – Dramatically • Cost of 10GbE Approaching Cluster HPC Interconnects $80K/port Chiaro (60 Max) $ 5K Force 10 (40 max) ~$1000 (300+ Max) $ 500 Arista 48 ports $ 400 Arista 48 ports 2005 2007 2009 2010 Source: Philip Papadopoulos, SDSC/Calit2

  29. 10G Switched Data Analysis Resource:SDSC’s Data Oasis 10Gbps UCSD RCI OptIPuter Radical Change Enabled by Arista 7508 10G Switch 384 10G Capable Co-Lo 5 CENIC/NLR Triton 8 2 32 4 Existing Commodity Storage 1/3 PB Trestles 100 TF 8 32 2 12 Dash 40128 8 2000 TB > 50 GB/s Oasis Procurement (RFP) Gordon • Phase0: > 8GB/s Sustained Today • Phase I: > 50 GB/sec for Lustre (May 2011) • :Phase II: >100 GB/s (Feb 2012) 128 Source: Philip Papadopoulos, SDSC/Calit2

  30. Calit2 CAMERA Automatic Overflows into SDSC Triton @ SDSC Triton Resource @ CALIT2 CAMERA -Managed Job Submit Portal (VM) Transparently Sends Jobs to Submit Portal on Triton 10Gbps Direct Mount == No Data Staging CAMERA DATA

  31. California and Washington Universities Are Testing a 10Gbps Connected Commercial Data Cloud • Amazon Experiment for Big Data • Only Available Through CENIC & Pacific NW GigaPOP • Private 10Gbps Peering Paths • Includes Amazon EC2 Computing & S3 Storage Services • Early Experiments Underway • Robert Grossman, Open Cloud Consortium • Phil Papadopoulos, Calit2/SDSC Rocks

  32. Academic Research OptIPlanet Collaboratory:A 10Gbps “End-to-End” Lightpath Cloud HD/4k Live Video HPC Local or Remote Instruments End User OptIPortal National LambdaRail 10G Lightpaths Campus Optical Switch Data Repositories & Clusters HD/4k Video Repositories

  33. You Can Download This Presentation at lsmarr.calit2.net

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