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Networked Data Storage and Analysis for the Wisconsin Regional Materials Network

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NDA presentation given by Dr. Jon McCarthy, Senior Scientist at Wisconsin Materials Institute

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Networked Data Storage and Analysis for the Wisconsin Regional Materials Network

  1. 1. Networked Data Storage and Analysis for the Wisconsin Regional Materials Network 6/3/2015 M&M 2015 Portland 1 Jon J. McCarthy, Paul M. Voyles, Julie A. Last, Davis R. Bittner, Ian W. Sadkovich Wisconsin Materials Institute, University of Wisconsin, Madison WI, USA Materials Science and Engineering Department, University of Wisconsin, Madison WI, USA Materials Science Center, University of Wisconsin, Madison WI, USA Computer-Aided Engineering Department, University of Wisconsin, Madison WI, USA
  2. 2. Our “big” data issues at UW Madison Instrument data output is growing…. FAST! Issues with continuing to transfer data the “Same Old Way” The importance of including “off the local computer “Analysis Capability A couple examples Things we have learned so far… M&M 2015 Portland 26/3/2015
  3. 3. Problem Statement: Large Images/multispectral data sets • Need to be stored…OFF the Instrument COMPUTER • Virus avoidance is critical • Dedicated sub networks • How Large is large? EM Tomography data • Now 0.5 Gb per 100 slice stack, soon to be 2 to 16+ GB per stack • But also Processed …. • Which leads to even more images…and more storage space • Often Proprietary commercial software required…. • How many licenses can you afford? Can your collaborators access data and analysis it output easily? • Without access to rest of your computer networks and restricted software? M&M 2015 Portland 36/3/2015 Wi Regional Materials Network
  4. 4. EM Tomography Data Storage Requirements: • Electron Tomography of Cryo Sections : What is Next? Happening now in fact! 6/3/2015 M&M 2015 Portland 4 The Output is 0.5 GB of raw Image data in a single tilt series. With no binning its 2 GB of data. K2 16 Megapixel Direct Electron Detector The Output is potential for 4 to 32 GB for a single tilt series! GIF: binned 2X2
  5. 5. AP Tomography Data Storage Requirements: 6/3/2015 M&M 2015 Portland 5 The Output is 2.8 GB of raw Image “hit” data file that is processed to generate this image.
  6. 6. Getting data off the instrument: No Portable Drives! The trouble with Thumb and Portable Drives: Viruses and Limited Capacity M&M 2015 Portland 66/3/2015 NOT Acceptable, but all to common!
  7. 7. Getting data off the instrument: Limited LAN Internal sub-net to another Lab PC for Storage; Lock rack door to the both Instrument PC’s! M&M 2015 Portland 76/3/2015 Instrument Control PC Support PC (crossover Cable) This was a satisfactory solution for several years BUT…issues are: • LAN running out of disk Storage • 20 users, output is 4 TB per year. Limited LAN host is maxed out below that level! • Duplicating hosts and more storage and Licensed processing software quickly becomes cost prohibited ! • SO users bring out the portable drives AGAIN …. OR • Users must come to the host to process data. • One user at a time can process data (its not a server, just a host) • Access for outside UW Collaborators very difficult! We needed a scalable Solution!
  8. 8. Networked Data and Analysis Solution A data storage and processing on a secure, networked platform: We chose the Citrix XenAPP Platform M&M 2015 Portland 86/3/2015 Citrix XenAPP provides delivery over the Internet of data analysis applications with access to a central data repository. • Users acquire their data on the instrument. • Data is copied off the instrument computers to a centralized data store. • The data store is connected to an analysis software server. • Users can connect to the analysis software server from any Windows or Mac computer with Internet connection faster than 1 Mbit/sec. • Raw data and analysis Output are stored on the server, or copied back to the client computer.
  9. 9. NDA Advantages • The Instrument control computers do not see Thumb Drives, USB Storage, or even the UW Network! • Secure Login, accesses only client machine and the XenAPP server. • Hardware easy to expand as storage needs grow; Currently, 24 cores on two processors and 256 MB of RAM, 4 TB of storage. EASY to SCALE! • Data can be sent to server directly from instrument Support Computer and downloaded to client computer as needed. • The XenApp client runs on the user’s computer, but the application runs on a University (CAE) managed Windows server. • XenApp delivery is legal for most end user license agreements (EULAs) for data analysis applications. • Outside users cannot access other UW resources or other computers on the CoE network. 6/3/2015 M&M 2015 Portland 9
  10. 10. Example: Launching XenAPP 6/3/2015 M&M 2015 Portland 10 Secure Login Access to only these applications
  11. 11. Client and Server Drives auto-mapped 6/3/2015 M&M 2015 Portland 11 Client drives XenAPP Server Drives NO Access to UW computers
  12. 12. Example: EM Tomography 6/3/2015 M&M 2015 Portland 12 On my desktop but running on XenAPP Server Tomogram created with IMOD/etomo on XenAPP! Made into an AVI with Fiji
  13. 13. Frame from a FIJI movie of a rendered Tomogram 6/3/2015 M&M 2015 Portland 13 Movie of FHV rendered stack running in XenAPP • On my laptop (i7, 8GB Dell) • At home, 11 Mbps download speed!
  14. 14. Collaborator Access Example 6/3/2015 M&M 2015 Portland 14 UW Milwaukee/UW Madison/Thermo Scientific Collaborators Li Cells, Built, Charged In Milwaukee. Anodes extracted in Glove Box, Loaded into Thermo Vacuum Transfer Vessel in Madison XPS Spectral Imaging Data Data on Instrument Computer transferred to NDA Server
  15. 15. Collaborator Access Example 6/3/2015 M&M 2015 Portland 15 Spectral Images Processed, Quantified entirely on Thermo Avantage on XenAPP Server Atomic % for all elements from three anodes determined, and plotted in Excel, by collaborators in MKE and Madison!
  16. 16. TIPS: What we have Learned so far  Unless you can manage the Server yourself, get a key contact in your IT group to be the “owner” of XenAPP administration.  Admin and negotiation of License and EULA  How do you load and configure plug’s or upgrades?  Commercial Software seems to be more likely to be easy to configure on a LAN and XenAPP o Many packages (with a LAN License) work “out of the box” o Shareware is often configured for a single user and a desktop/laptop  Often use code or scripts that select specific files or path names that may be blocked on the Server!  It took three rounds to get 3DMOD to work, then 3 more to get etomo to work  Have a Skilled User do testing of any new XenAPP application!  IT folks are computer savvy, but not experts on your application!  You don’t want to learn the software and debug XenAPP install issues at the same time!  Have the tester user write up “how to use IMOD on XenAPP” tutorial document. 6/3/2015 M&M 2015 Portland 16
  17. 17. Acknowledgements 6/3/2015 M&M 2015 Portland 17 Co-Authors Paul M. Voyles Materials Science and Engineering Department Julie Last, Alex Kvit and John Jacobs Materials Science Center Davis R. Bittner and Ian W. Sadkovich Computer-Aided Engineering Department Special Thanks (for tomography work) to: Ken J. Ertel Fellow, Institute For Molecular Virology UW Madison Desiree Benefield Post Doc Research Associate Morgridge Institute for Research Weixin Chen, Research Associate Materials Science and Engineering Department UW Madison External Collaborators: Xingkang Huang Mechanical Engineering Department University of Wisconsin-Milwaukee Bill Sgammato Thermo Fisher Scientific
  18. 18. 6/3/2015 M&M 2015 Portland 18 QUESTIONS?
  19. 19. Movie is so Cool I have to show you! 6/3/2015 M&M 2015 Portland 19
  20. 20. 6/3/2015 M&M 2015 Portland 20
  21. 21. Motivation for moving from Limited LAN to NDA System 6/3/2015 M&M 2015 Portland 21 Data Output and Processing bottlenecks: • Quickly running out of disk space—if one user produces 16.5 GB in a week, and you have 20 user-> 4 TB per year. Limited LAN host is maxed out below that level. The data output will quadruple with the direct electron detector! • Duplicating hosts and more storage and Licensed processing software quickly becomes cost prohibited ! • Users must come to the host to process data. Only one user at a time can process data (its not a server, just a host) • It often takes as long (or longer!) to process tomograms as to collect the data! • If Host is in the lab (Atom Probe) , it is cold and noisy and crowded. The next user is collecting their data, space is crowded! SO what Happens? • Users get a license for their PC and use the Portable Drives again to move data to their own machine. • Multiple licenses for software raise cost for each user group, so still have the one person in the lab processing at a time!
  22. 22. 22 Materials Science Center (MSC) • Three FESEMs and AURIGA FIB, PHI Auger, 4 XRDs, including Bruker Discover D8 (microfocus source, automated stage, WAXs detector) JY Horiba Micro-imaging Raman and Micro FT-IR, UV/VIS/NIR spectroscopy, DI Multimode AFM, Bruker Catalyst Bio AFM, Zeiss META CLSM, Thermo Imaging XPS, FEI 200KV Titan, FEI TF-30 CryoTEM for electron tomography, Cameca LEAP 3000si Atom Probe. Soft Materials Laboratory (SML) • Rheometer, Dynamic Mechanical Analysis, 2 HPLC, TGA, DSC, contact angle, Ellipsometry, Zeiss 1550 VPSEM, Thermo Scientific Micro-Imaging Raman Wisconsin Center for Advanced Microelectronics (WCAM) • Seven Bay, 10,000 Square foot clean room Facility, over 60 fab tools • CMOS devices, MEMS, soft lithography, DC/RF sputter deposition tool. UW College Of Engineering Shared Facilities Instruments in Blue (most recent!) create Analytical Spectral Images and Image stacks -which brought us to a tipping point, but Electron Tomography pushed us over the edge!
  23. 23. Loading an IMOD stack from client HD 6/3/2015 M&M 2015 Portland 23
  24. 24. Getting data off the instrument: Solution #2 Local 1 to 2 TB portable hard disk • It stays in the instrument room - always! • But does It really?? M&M 2015 Portland 246/3/2015 ISSUES: • Researchers must come here to Process • It often takes as long (or longer!) to process tomograms as to collect the data! • Only one user at a time! • For the Atom Probe; • Its cold and noisy in the lab • The next user is collecting their data, space is crowded!  NEED to Process the data somewhere ELSE!
  25. 25. Getting data off the instrument: Limited LAN A support computer, with crossover Ethernet cable to instrument control computer! M&M 2015 Portland 256/3/2015 Instrument Control PC Support PC (crossover Cable) ISSUES: • Better than solution 2, but one thumb drive inserted in the wrong computer brought down our Titan! Led to a Disk Rebuild! • It often takes as long (or longer!) to process tomograms as to collect the data! • Only one user at a time • Run out of disk space on the support Computer—if one user generates 16.5 GB, and you have 20 users…  NEED to process Data somewhere ELSE Support computer monitor

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