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Research Technologies

Systems and Services Overview. Research Technologies. Kristy Kallback-Rose, Marlon Pierce, George Turner. Divisions within UITS. Learning Technologies Technology in teaching and learning

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Research Technologies

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  1. Systems and Services Overview Research Technologies Kristy Kallback-Rose, Marlon Pierce, George Turner

  2. Divisions within UITS • Learning Technologies Technology in teaching and learning • Communication and Support Communication and support services for students, faculty, and staff; licensing agreements • Enterprise Software Vendor products, proprietary systems, community source projects • Networks Advanced networking engineering services, international initiatives • Enterprise Infrastructure Management of infrastructure for university services and software applications • Research Technologies Systems and services in support of leading edge research

  3. Units within Research Technologies (RT) • Advanced Visualization Laboratory - Consulting and support for scientific visualization, virtual reality, high-end computer graphics, and visual telecollaboration • Biomedical Applications - Consultation on access and management of biomedical data • Computational Biology - Application support, technical support, and software development for biological computing, particularly in the areas of genomics, cell biology, and molecular biology • Core Services - provides services to Researchers at IU, Faculty, Staff, and Students, and Research Technologies Units • Digital Library Program - Services for digital library development • ScienceGateway - consulting and software for scientific communities who want to develop Web-based mechanisms for accessing and managing scientific applications • High Performance Applications - Programming support for IU's parallel supercomputers, Big Red and Quarry • High Performance Systems - Central research computational & database resources • Open Science Grid - Enables large-scale high-throughput computing for science • Research Storage - Provides storage infrastructure to support teaching, research, and administrative computing • Stat/Math - Support for statistical and mathematical software

  4. Working with Research Technologies • We are here to support research computing • Staff at IUPUI and IUB, but support for all 8 campuses • Opportunities to Interact in person http://pti.iu.edu/calendar • RT Fair • Visiting departments and labs by request • Workshops • Electronically • Email (listed at end of presentation)

  5. Today’s focus… • High Performance Systems • High Performance Applications • Research Storage • Data Capacitor • Core Services • Science Gateway • Visualization

  6. High Performance Systems - Big Red • Main compute resource for large compute tasks (parallel & serial) • 1024 JS21 Blades • Dual PowerPC 970 MP dual-core CPU (4 cores / server) • 8GB RAM • GigE ethernet • PCI-X Myrinet 2000 switch fabric (high-bandwidth, low-latency MPI) • 70 GB local scratch • SUSE Linux Enterprise Server 9 • NFS home directory (10GB quota) /N/u/$USER/BigRed • GPFS volume (346TB) /N/gpfs/$USER • Data Capacitor (339TB) /N/dc/scratch/$USER, /N/dc/project/$PROJECT • Data Capacitor WAN (339TB) /N/dcwan/scratch/$USER, /N/dcwan/project/$PROJECT

  7. High Performance Systems - Quarry • General access computing • 140 IBM HS21 Blade servers (b/q nodes) • Dual 2.0GHz Intel Xeon 5335 (Clovertown) quad-core processors • 8GB (default) or 16GB (himem) RAM • Gigabit Ethernet • RHEL 4 • 36 or 73GB local scratch • 230 IBM dx340 servers (p/pg nodes) • Dual 2.3GHz Intel Xeon E5410 (Harpertown) quad-core processors • 16GB RAM • Gigabit Ethernet • RHEL 5 • 94GB local scratch • NFS home directory (10GB quota) /N/u/$USER/Quarry • GPFS volume (346TB) /N/gpfs/$USER • Data Capacitor (339TB) /N/dc/scratch/$USER, /N/dc/project/$PROJECT • Data Capacitor WAN (339TB) /N/dcwan/scratch/$USER, /N/dcwan/project/$PROJECT • Research File System /afs/iu.edu/….

  8. Using Big Red and Quarry • Available to faculty, staff and graduate students • BigRed : undergraduates can be sponsored by faculty or staff • Queueing and Resource Management • Big Red = LoadLeveler, Moab • Quarry = TORQUE/PBS, Moab • Scheduling strategies • Fairshare • Backfill • Interactive processes on Head node • 20 minute limit • WildWest nodes; ssh from head nodes, see MOTD • Reservations and Priority increases are available for time-critical  projects • “Condo” computing possibilities

  9. High Performance Systems - Mason • Large Memory Jobs Only • 18 HP DL580 G7 servers • 2 head nodes, 16 compute nodes • Quad 1.87GHz Intel Xeon L7555 (Beckton/Nehalem-EX) oct-core CPU (32/server) • 512GB RAM • 10 Gigabit Ethernet • ½ to 1TB local scratch (TBD) • RHEL 6 • TORQUE + Moab • NFS home directory (10GB quota) /N/u/$USER/Mason • Data Capacitor (339TB) /N/dc/scratch/$USER, /N/dc/project/$PROJECT • Data Capacitor WAN (339TB) /N/dcwan/scratch/$USER, /N/dcwan/project/$PROJECT • Account request mechanism TBD • Available spring 2011

  10. High Performance Systems – Research Database Complex (old) • Dedicated to : • research-related databases • data-intensive applications using database. • Two IBM p575 servers • Eight 1.9 GHz Power5 CPU per server • 64 GB RAM per server • Two 146 GB local disks • AIX 5.3 • Oracle • MySQL • NFS home directory (10GB quota) /N/u/$USER/BigRed • GPFS volume (~300 TB) /N/gpfs/$USER • Retire Spring 2011

  11. High Performance Systems – Research Database Complex (new) • Dedicated to : • research-related databases • data-intensive applications using database. • Four (4) HP DL180 G6 • Dual 2.4GHz Intel Xeon E5620 (Gulftown/Westmere-EP) Oct-core • 64 GB RAM • 218 GB local disk • GigE networking • 48 TB SAN attached • RHEL 5 Linux • NFS home directory (10GB quota) /N/u/$USER/RDC • Oracle • MySQL • Web Applications front end • Available Spring 2011

  12. High Performance Systems – Research Database Complex (Web) • Apache & TomCat servers • Single Dell 2950 server • 1.6 GHz Intel Xeon CPU • 8 GB RAM • Two 146 GB local disks • RHEL 5 • NFS home directory (10GB quota) /N/u/$USER/RDC • Web frontend requested when RDC account is requested

  13. High Performance Systems – TeraGrid • NSF funded HPC systems and support infrastructure • 11 resource providers • Compute, Visualization, Data • http://www.teragrid.org/ • See HPA (hpahelp@iu.edu) for assistance

  14. High Performance Systems - TeraGrid • IU AMD (Quarry – Gateways Only) • IU e1350 (Big Red) • LONI Intel 64 Linux Cluster (Queen Bee) • NCAR Blue Gene/L (Frost) • NCSA Altix UV (Ember) • NCSA Intel 64 Linux Cluster (Abe) • NCSA PowerEdge 1950 with NVIDIA Tesla S1070 (Lincoln) • NICS SGI/NVIDIA, Visualization and Data Analysis System (Nautilus) • NICS XT4 (Athena) • NICS XT5 (Kraken) • ORNL IA-32 Cluster (NSTG Cluster) • PSC Altix 4700 (Pople) • PSC Altix UV (Blacklight) • Purdue 1950 Cluster (Steele) • Purdue Cloud (Wispy) • Purdue Condor Pool (Condor Pool) • Purdue TeraDRE (TeraDRE) • SDSC (Trestles) • SDSC (Dash) • TACC DELL/NVIDIA Visualization & Data Analysis Cluster (Longhorn) • TACC PowerEdge Westmere Linux Cluster (Lonestar) • TACC Sun Constellation Linux Cluster (Ranger) • TACC Visualization Cluster (Spur) • TeraGrid Clusters (AQS)

  15. Getting Started Getting Started on BigRed http://kb.iu.edu/data/avjx.html At IU, what is BigRed http://kb.iu.edu/data/aueo.html Getting Started on Quarry http://kb.iu.edu/data/avkx.html At IU, what is Quarry http://kb.iu.edu/data/avju.html Getting Started on IU’s Research Database Complex http://www.kb.iu.edu/data/awmv.html E-mail hps-admin@iu.edu for any problems or concerns regarding Big Red, Quarry or the RDC.

  16. High Performance Applications Support users of IU's HPC and TeraGrid systems help IU researchers make efficient use of IU and TeraGrid compute resources Migrate applications to HPC systems Installation and configuration Optimization for the target architecture Performance analysis Profiling and tracing of serial and parallel codes Extended Consulting Support national community through TeraGrid In depth collaborations with scientists at IU Consulting for grant proposals

  17. Research Storage • Scholarly Data Archive (aka Massive Data Storage System) • Research File System

  18. Scholarly Data Archive (SDA) • Massive data archive for Indiana University • Currently can hold over 5,700 Terabytes (TB) • Operating since 1999 • Primarily tape storage • Fronted by over 220TB of disk cache • HIPAA aligned

  19. SDA Details • Data is safe • By default two copies of data • IUB and IUPUI each get a copy • checksum storing and server-side validation available • SDA: Best Uses • Files of at least 1MB • Single file can be up to 10TB • Archive files • Files rarely updated • Files need to be kept long time • Files are read often • frequently accessed files tend to stay on disk cache • SDA: Poor Uses • Small files • small files should be aggregated with a tool like WinZip or tar • Files that will frequently change • do not edit files in place

  20. SDA Access Methods & Quotas • Fast access: 100‘s MB/sec • hsi and htar command line tools • GridFTP clients • Kerborized FTP • Convenience protocols: 10 - 20 MB/sec • Web access via browser • requires authentication - no public access • upload and download • Sftp • mount to desktop via CIFS (mapped drive) • files and directories can be shared between SDA users with ACL’s • default quota 5TB • 2nd copy of data is not counted • additional storage is readily available

  21. RFS Details • disk based system - 60TB total • available to faculty, staff and graduate students • undergraduates can be sponsored by faculty or staff • data is backed up nightly • backups are kept for 2 months • changes from the previous day kept in 1day-backup directory • HIPAA aligned

  22. Using RFS RFS: Best Uses • relatively small files • should stay under a few hundred MB in size • files that are updated frequently • files can be edited in place on RFS • frequently accessed files • files that need to be shared, especially group project work RFS: Poor Uses • Backups • RFS is intended as working space • SDA works better for backups • concurrently updated files • multiple people updating same file at once, i.e. Access databases • relational database, i.e. mysql or postgres

  23. RFS Access Methods & Quotas • mount on the desktop (map a drive) • OpenAFS client • Available for Windows, Macs, Linux • Requires getting kerberos tickets which is automatic with Windows authentication to ADS • Available on Quarry • Web access from browser • sftp access • Can request project space • default project quota is 50GB • can define own groups of RFS users • no shared accounts required • users can be revoked access • Default personal quotas are 10GB • Additional space is generally available upon request

  24. Data Capacitor (DC) • Short term storage (~700 TB) • DC-WAN added in Spring of 2008 • Increased usable capacity by 360TB • Mountable across long distances, facilitates workflows that require unique, geographically distributed resources • Allows users to obtain high read/write speeds for their data as well as support for very large files. • DC Project and Scratch • Available on Big Red and Quarry • Projects with storage requirements that cannot be met with other existing systems • default size 10 TB • default time limit 30 days • Other arrangements can usually be made

  25. Data Capacitor WAN (DC-WAN) • Short term storage (~340TB) • Mountable across long distances, facilitates workflows that require unique, geographically distributed resources • Allows users to obtain high read/write speeds for their data as well as support for very large files. • DC-WAN Project and Scratch • Available on Big Red, Quarry, and various TeraGrid sites • Scratch space is available now to all Big Red and Quarry users • Available at /N/dcwan/scratch/<username> • Files in scratch space may be purged after 14 days. • Project space is available upon request • Available at /N/dcwan/projects/<projectname> • Default size 10 TB • Files in project space with access times greater than 30 days may be purged. • Arrangements for more space can usually be made • Application available at http://pti.iu.edu/dc/allocrequest

  26. Core Services • Provides services to Researchers at IU, Faculty, Staff, and Students, and Research Technologies Units • Some examples: • Web application hosting on the Research Database Complex • Wiki hosting • Subversion source code repository, GitHub software project service • Open Source Mirror (OpenOffice, GNU, etc.) • Red hat Enterprise Linux license and management

  27. Science Gateway Group • We assist groups who want to provide Web-based access to IU and TeraGridcomputing resources for scientific communities. • We lead the Open Gateway Computing Environments project. • Open source software for science gateways • Partners include Purdue, NCSA, UIUC, UTHSCSA • Apache incubators in preparation • Software Resources • Google/OpenSocial gadgets • Scientific workflows and application management on clusters, supercomputers • Hardware Resources • Gateway Hosting Environment • VMs for both development and production web server hosting

  28. Visualization • Areas of Expertise • Visualization – both scientific and information • Virtual reality – projection-based displays, head-mounted displays, navigation and interaction methodologies • Advanced displays – stereoscopic, ultra resolution, haptic (force feedback) • Spatial input/output technologies – 3D scanners, 3D printers, motion tracking systems • Advanced graphics – modeling, animation, rendering • Stereoscopic video and animation • Visual telecollaboration • Available Equipment and Facilities • Multi-screen stereoscopic displays • Ultra-resolution displays • Portable single-screen stereoscopic displays • Acquisition devices: 3D scanners, stereo cameras, motion tracking systems • Output devices: 3D printer, haptic (force feedback) devices

  29. Help & Additional Information IU KB - http://kb.iu.edu/ “Indiana University’s Advanced CyberInfrastructure: The Least You Need To Know.” document • http://pti.iu.edu/cyberinfrastructure.pdf Advanced IT Core (w/IU School of Medicine) – http://uits.iu.edu/page/avoh barnettw@indiana.edu ashankar@indiana.edu Advanced Visualization Lab (AVL) – https://pti.iu.edu/rtv vishelp@indiana.edu Core Services - https://pti.iu.edu/cs • rtadmin@rtinfo.indiana.edu Data Capacitor - http://pti.iu.edu/dc dc-team-l@indiana.edu High Performance - Applications (HPA)- https://pti.iu.edu/hpa • hpahelp@iu.edu High Performance - Systems (HPS) – https://pti.iu.edu/hps • hps-admin@iu.edu Research Storage - https:/pti.iu.edu/storage • store-admin@iu.edu Research Technologies Division - http://pti.iu.edu/rt • researchtechnologies@iu.edu Science Gateways - https://pti.iu.edu/sgg ogce-discuss@googlegroups.com StatMath Center - http://www.indiana.edu/~statmath/ • statmath@iu.edu • IUB phone 812-855-4724, IUPUI phone 317-278-4740 Google

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