The Pacific Research Platform Two Years In
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This document provides an overview of the Pacific Research Platform (PRP) after two years of operation. It describes several science drivers that are using the PRP, including biomedical research on cancer genomics and microbiomes, earth sciences like earthquake modeling, and astronomy. It highlights how the PRP is connecting sites like UC San Diego, UC Santa Cruz, UC Berkeley to share and analyze large datasets using high-speed networks. The PRP is expanding to support new areas like deep learning, cultural heritage projects, and connecting additional UC campuses through network upgrades.
The Pacific Research Platform Two Years In
- 1. “The Pacific Research Platform Two Years In” Welcome and Overview Talk to the Pacific Research Platform “PRPv2” Workshop 2017 University of California, San Diego February 21, 2017 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 http://lsmarr.calit2.net
- 2. Initially Proposed PRP Multi-Campus Science Driver Teams • Biomedical – Cancer Genomics Hub/Browser( UCSC/SDSC project over, connecting PRP to U. Chicago) – Microbiome and Integrative ‘Omics (UCSD, Caltech, UCSF, UCD) – Integrative Structural Biology (UCSF, NERSC, SDSC) • Earth Sciences – Data Analysis and Simulation for Earthquakes and Natural Disasters (Phase II) – Climate Modeling: NCAR/UCAR (UCSD, NCAR) – California/Nevada Regional Climate Data Analysis (UCI, UCSD, NCAR) – CO2 Subsurface Modeling (SDSC) • Particle Physics (UCD, UCI, UCSC, UCSD, others soon) • Astronomy and Astrophysics – Telescope Surveys (NERSC connected to PRP) (Phase II) – Galaxy Evolution (UCI, UCSC) (Phase II) – Gravitational Wave Astronomy (Caltech, UCSD) • Scalable Visualization, Virtual Reality, and Ultra-Res Video (UCB, UCLA, UCM, UCSD)
- 3. 100 Gbps FIONA at UCSC Connects the UCSC Hyades Cluster to the NERSC Supercomputer at LBNL Supporting UCSC Remote Access to Large Data Subsets of the Dark Energy Spectroscopic Instrument (DESI) and AGORA Galaxy Simulation Data Produced at NERSC. 250 images per night 800GB per night Shawfeng Dong, UCSC Cyberengineer UCSC Feb 7, 2017
- 4. Global Scientific Instruments Will Produce Ultralarge Datasets Continuously Requiring Dedicated Optic Fiber and Supercomputers Square Kilometer Array Large Synoptic Survey Telescope https://tnc15.terena.org/getfile/1939 www.lsst.org/sites/default/files/documents/DM%20Introduction%20-%20Kantor.pdf Tracks ~40B Objects, Creates 10M Alerts/Night Within 1 Minute of Observing 2x40Gb/s
- 5. 40G FIONAs 20x40G PRP-connected WAVE@UC San Diego PRP Will Enable Distributed Virtual Reality PRP MerWAVE @UC Merced
- 6. UC Merced’s VR CAVE: Merced WAVE • Transferring 5 CAVECam Images Over 10 Gbit/sec Fiber Path From UCSD to UC Merced: – Total Data Size: 1.96 GBytes – Transfer Took 2.17 seconds – Transfer Rate: 924.49 MBytes/sec (~8Gbit/sec) • This Transfer Would Have Taken: – 21 Seconds Over 1Gbit/sec Connection (Regular Ethernet) – 5.35 Minutes Over 50Mbit/sec Connection (Residential Internet)
- 7. PRP Will Link the Laboratories of the Pacific Earthquake Engineering Research Center http://peer.berkeley.edu/
- 8. The Second FIONette was Deployed at the PEER Facility at UC Berkeley, and its Performance is Being Monitored John Graham Installing FIONette at PEER Feb 10, 2017
- 9. Cancer Genomics Hub (UCSC) is Housed in SDSC: Large Data Flows to End Users at UCSC, UCB, UCSF, … 1G 8G Data Source: David Haussler, Brad Smith, UCSC 15G Jan 2016 30,000 TB Per Year
- 10. Slide on Cancer Genomics
- 11. Newly Added PRP Multi-Campus Science Driver Teams • Biomedical – Cryo Electronic Microscopy (UCB/LLNL, UCD,UCLA, UCSD, UCSF) – Bioinformatics (UCD) – High-Resolution Microscopy (UCR, UCSD, NSCC) • Computer Science and Engineering /Electrical and Computer Engineering, etc. – JupyterHub (UCB, UCSD) – Deep Learning (UCB, UCSD, UIC) – Drones, Terrestrial Modeling/GIS (UCSD, UCM) – Contextual Robotics (new) • High Performance Wireless Research and Education Networks – UCSD/SIO, UCI, UCR, UCM, CENIC, others tbd. • Humanities and Social Sciences – Preserving Cultural Heritage
- 12. PRP First Application: Distributed IPython/Jupyter Notebooks: Cross-Platform, Browser-Based Application Interleaves Code, Text, & Images IJulia IHaskell IFSharp IRuby IGo IScala IMathics Ialdor LuaJIT/Torch Lua Kernel IRKernel (for the R language) IErlang IOCaml IForth IPerl IPerl6 Ioctave Calico Project • kernels implemented in Mono, including Java, IronPython, Boo, Logo, BASIC, and many others IScilab IMatlab ICSharp Bash Clojure Kernel Hy Kernel Redis Kernel jove, a kernel for io.js IJavascript Calysto Scheme Calysto Processing idl_kernel Mochi Kernel Lua (used in Splash) Spark Kernel Skulpt Python Kernel MetaKernel Bash MetaKernel Python Brython Kernel IVisual VPython Kernel Source: John Graham, QI
- 13. GPU JupyterHub: 2 x 14-core CPUs 256GB RAM 1.2TB FLASH 3.8TB SSD Nvidia K80 GPU Dual 40GbE NICs And a Trusted Platform Module GPU JupyterHub: 1 x 18-core CPUs 128GB RAM 3.8TB SSD Nvidia K80 GPU Dual 40GbE NICs And a Trusted Platform Module PRP UC-JupyterHub Backbone UCB Next Step: Deploy Across PRP UCSD Source: John Graham, Calit2
- 14. Cryo-electron Microscopy (cryo-EM) Has Driven a “Resolution Revolution” in the Last Five Years Exposure (every 60 seconds): X & Y dimensions: 7420 x 7676 pixels Frames per movie: 10 - 50 Size: 3 - 10 GB per movie Every 24 hours: Number of movies: ~1400 Data size: ~5 TB Typical datasets: Length of time: 2 - 6 days Total size: 10 - 30 TB Each Cryo-EM ‘Image’ is Actually a Movie Source: Michael A. Cianfrocco, Elizabeth Villa, & Andres Leschziner, UCSD
- 15. ~20 microscopes in CA UCLA UC Davis UC Santa Cruz SF Bay UC Berkeley, LBNL, UCSF, Stanford San Diego UCSD, TSRI, Salk * * SDSC NERSC *Xstream Using PRP to Connect Cryo-EM across California With End Users and Computational Facilities Long term: ‣ Partner with cryo-EM facilities to stream data straight from microscopes (over PRP) to SDSC ‣ Perform all cryo-EM analysis (from micrographs to 3D models) via web browser on SDSC ‣ Expand computing to other XSEDE resources (e.g. Xstream) Short term: ‣ Provide 2D and 3D analysis on particle stacks on Comet at SDSC Source: Michael A. Cianfrocco, UCSD3 supercomputer centers cosmic-cryoem.org
- 16. UCD UCSF Stanford NASA AMES/ NREN UCSC UCSB Caltech USC UCLA UCI UCSD SDSU UCR Esnet DoE Labs UW/ PNWGP Seattle Berkeley UCM Los Nettos Internet2 Internet2 Seattle Note: This diagram represents a subset of sites and connections. * Institutions with Active Archaeology Programs “In an ideal world – Extremely high bandwidth to move large cultural heritage datasets around the PRP cloud for processing & viewing in CAVEs around PRP with Unlimited Storage for permanent archiving.” -Tom Levy, UCSD PRP is NOT Just for Big Data Science and Engineering: Linking Cultural Heritage and Archaeology Datasets Building on CENIC’s Expansion To Libraries, Museums, and Cultural Sites
- 17. Linking Libraries at UCB, UCLA, UCM and UCSD with CAVE Kiosks 48 Megapixel CAVE Kiosk for UCSD Library UCSD Library Review, June 24 Megapixel UCM Library Installation, July
- 18. PRP Backbone Sets Stage for 2017 Expansion of HPWREN, Connected to CENIC, into Orange and Riverside Counties • PRP CENIC 100G Link UCSD to SDSU – DTN FIONAs Endpoints – Data Redundancy – Disaster Recovery – High Availability – Network Redundancy • Anchor to CENIC at UCI – PRP FIONA Connects to CalREN-HPR Network – Data Replication Site • Potential Future UCR CENIC Anchor UCR UCI UCSD SDSU Source: Frank Vernon, Greg Hidley, UCSD
Editor's Notes
- #3: Campus Cyberinfrastructure – Network Infrastructure and Engineering (CC-NIE) Campus Cyberinfrastructure – Infrastructure, Innovation, and Engineering (CC-IIE) Campus Cyberinfrastructure – Data, Networking, and Innovation (CC-DNI) NSF 15-534 incorporates Data Infrastructure Building Blocks (CC-DNI-DIBBs) – Multi-Campus / Multi-Institution Model Implementation from Program Solicitation NSF 14-530
- #12: Campus Cyberinfrastructure – Network Infrastructure and Engineering (CC-NIE) Campus Cyberinfrastructure – Infrastructure, Innovation, and Engineering (CC-IIE) Campus Cyberinfrastructure – Data, Networking, and Innovation (CC-DNI) NSF 15-534 incorporates Data Infrastructure Building Blocks (CC-DNI-DIBBs) – Multi-Campus / Multi-Institution Model Implementation from Program Solicitation NSF 14-530
- #17: We already have 11 major research universities in California poised to partner.