1. Advanced Computing Resources for IU Researchers
Anurag Shankar
University Information Technology Services
Indiana University
March 2, 2012

2. Outline IU’s Research Cyberinfrastructure Research LifeCycle Support
University Information Technology Services
September 16, 2018
Outline
IU’s Research Cyberinfrastructure
- People, hardware, software, services, training & support
Research LifeCycle Support
- Solutions for your research workflows
Scope & Scale
- Boundaries & growth
Costs
- Who pays what
Benefits
- The difference it makes

3. What is Cyberinfrastructure (CI)?
University Information Technology Services
9/16/2018
What is Cyberinfrastructure (CI)?
Federal funding agencies define “Cyberinfrastructure” as a technological and sociological solution to the problem of efficiently connecting laboratories, data, computers, and people with the goal of enabling derivation of novel scientific theories and knowledge

4. Cyberinfrastructure …
University Information Technology Services
9/16/2018
Cyberinfrastructure …
Consists of research environments that support advanced data acquisition, storage, management, integration, mining, visualization and other computing and information processing services distributed over the network within (local CI) or beyond a single institution (global CI)

5. IU’s Research Cyberinfrastructure
University Information Technology Services
9/16/2018
IU’s Research Cyberinfrastructure
Provided by the Research Technologies (RT) division of UITS
Dedicated to supporting research, no matter the area
Strives to help you get recognition & funding (“make you shine”)

6. People RT consists of around 90 staff
University Information Technology Services
9/16/2018
People
RT consists of around 90 staff
Staff are both base and grant funded
RT is divided into thirteen logical units
Units cover generic to very specific areas
Staff are distributed across IUB and IUPUI
We are available at a moment’s notice

7. Research Technologies Units
University Information Technology Services
9/16/2018
Research Technologies Units
Advanced IT Core
Advanced Visualization Lab
Biomedical Applications
Computational Biology
Core Services
Digital Library Program
High Performance Applications
High Performance File Systems
High Performance Systems
Open Science Grid
Research Storage
Science Gateways Group
Statistical & Mathematical Computing

8. University Information Technology Services
9/16/2018
RT Units …
Advanced IT Core – An IU School of Medicine service core to assist researchers in using RT resources
Advanced Visualization Laboratory - Consulting and support for scientific visualization, virtual reality, high-end computer graphics, and visual tele-collaboration
Biomedical Applications - Consultation on access and management of biomedical data
Computational Biology – Application/technical support and software development for biological computing (particularly in genomics, cell biology, and molecular biology)
Core Services – Applications/hosting for researchers & RT
Digital Library Program - Services for digital library development

9. University Information Technology Services
9/16/2018
RT Units …
High Performance Applications – Programming support for IU’s parallel supercomputers Big Red and Quarry
High Performance File Systems – High-speed, parallel file systems (Data Capacitor)
High Performance Systems – Administration of central research computing systems
Open Science Grid – Large-scale, high-throughput grid computing for science
Research Storage – Data storage resources for research
Science Gateways Group – Software development & consulting for grid and cloud applications
Statistical and Mathematical Computing – Support and licenses for statistical, mathematical, and GIS software

10. University Information Technology Services
9/16/2018
RT Hardware
Data Analysis, Simulation & Storage - supercomputers, disk & tape-based storage systems, database servers
Data Publishing – web and application servers
Data Visualization – virtual reality theater, high-resolution display wall, stereo wall, 3D scanner, 3D printer, haptics, stereo video rigs

11. University Information Technology Services
9/16/2018
RT Software
Statistics – Amos, Eviews, GAUSS, HLM, LISREL, Minitab, Mplus, R, RATS, SAS, SPSS, Stata, S-PLUS
Mathematics – Maple, MATLAB, Mathematica, Geometer’s Sketchpad, LINDO, LINGO
GIS – Alta4, ESRI, ERDAS, Pictometry
Other – AutoCAD, Nvivo, SigmaPlot, Scientific WorkPlace, Stat/Transfer

12. University Information Technology Services
9/16/2018
Software
Databases – Oracle, MySQL, Oracle Application Express, phpMyAdmin
High Performance Computing – ATLAS, BLAS, Cern Program Library, Chaco, Charm, Cmake, FFT, FDPR, Global Arrays, GNU c compiler collection, Hadoop, IMSL/C, MPA library, Science library, HDF5, LAPACK, NAG Fortran library, NetCDF, Octave, PyACTS, R, SCALAPACK, SPRNG, SVDPACK, SWIG
Debuggers – TotalView, Valgrind, Vampir Trace

13. University Information Technology Services
9/16/2018
Software
Graphing/Visualization – BoxShade, Grace, Graphviz, Mesa 3D, Qt, Raster3D, Visualization Toolkit
Chemistry - Amber, AutoDock, AutoDock-Vina,CPMD, Gamess, MolPro, MolScipt, NAMD, Procheck, Quantum ESPRESSO, Siesta, STRIDE, VMD
Physics/Engineering - ANSYS, FLUENT, GAMBIT, LS-DYNA, Trillinos

14. University Information Technology Services
9/16/2018
Software
Biology – BioPerl, BLASTZ, CAP3, ClustalW, EMBOSS/wEMBOSS, FASTA, fastDNAml, GARLI, IMPUTE, MACH, McMCcoal, MEME, MIGRATE, MPI-HUMMER, MrBayes, MULTICLUSTAL, MUMMER, NCBI, PAML, PAUP, PHYLIP, Phrap, PLINK, RepeatMaster, structure, TREE-PUZZLE
Users can also request software installation on IU supercomputers
See

15. University Information Technology Services
9/16/2018
Services
Data Storage – Research File System (RFS), Scientific Data Archive (SDA), Research Database Complex (RDC)
Data Sharing & Management – Alfresco Share, Research Electronic Data Capture (REDCap)
Data Publishing – Discern Application Server, RDCWeb, Virtual Servers
Data Visualization – Advanced Visualization Lab (AVL), GIS

16. University Information Technology Services
9/16/2018
Services …
Simulation & Data Analysis – Big Red, Quarry supercomputers, high-performance I/O, xSEDE & OSG national computational grids, Stat/Math Center
Software Development – Custom software development
Consulting – Requirements gathering, database administration, data management, data visualization, parallel programming, computational biology, grid computing, & more

17. RT Services (more info at http://kb.iu.edu)
University Information Technology Services
9/16/2018
RT Services (more info at
Service Type
Service
Details
Data Storage
RFS
Ubiquitous, disk based storage for in-work files
SDA
Cached, tape-based, large-scale archival storage
Database Storage
RDC
Oracle & MySQL databases, remote access from applications, Unix command line, ODBC, SQL*Plus/Aqua Data Studio/Oracle client (Oracle), phpMyAdmin (MySQL)
Data Sharing
Alfresco Share
Document sharing with IU and non-IU collaborators
Data Management
REDCap
Creation and management of online surveys and databases; DBs from spreadsheets, exports to Excel, SAS, R, etc., data sharing with IU and non-IU users
Data Publishing
Discern
PHP/Java applications serving viaApache/Tomcat
RDCWeb
Serving PHP/Java applications accessing databases on RDC via Apache/Tomcat
Visualization
AVL
Provides AVL hardware for visualizing data

18. RT Services (more info at http://kb.iu.edu)
University Information Technology Services
9/16/2018
RT Services (more info at
Service Type
Service
Details
Data Analysis & Simulation
Big Red (IBM)
1025 nodes (2048 PowerPC 970 CPUs), 8GB RAM/node, 73GB disk, high speed Myricom interconnect
Quarry (IBM)
140 nodes (560 Intel Xeon 5410 CPUs), 8/16GB RAM/node, 73GB disk, 340TB scratch, GB ethernet interconnect
230 nodes (460 Intel Xeon 5410 CPUs), 16GB RAM/node, 160GB disk, 360TB scratch, GB ethernet interconnect
Extreme Science and Engineering Discovery Environment (xSEDE)
A national grid of 16 supercomputers, data storage & visualization resources (time allocation through formal proposal submission, but startup allocations are easy to get)
Open Science Grid (OSG)
An international grid of a large number of compute resources for large scale grid computing

19. University Information Technology Services
9/16/2018
Training & Support
Customized training (virtually, at IUB/IUPUI, or on campus)
General support for all research IT issues
Software support for RT installed/developed software
Database (DBA) support
System administration support for virtual servers
Grant support

20. Research LifeCycle Support
University Information Technology Services
9/16/2018
Research LifeCycle Support
RT can support you comprehensively, at every step of your research workflow, by leveraging its own and/or national resources to provide or build solutions ranging from simple to complex, from modest to immense, and from local to national to international

21. University Information Technology Services
9/16/2018
Data LifeCycle
The research lifecycle from RT’s perspective consists of a data lifecycle, representing the sequence from data creation to archival/disposal

22. The Research/Data LifeCycle
University Information Technology Services
9/16/2018
The Research/Data LifeCycle
Pre-Grant
Preliminary Investigation
Cyberinfrastructure Design
Proposal
Proposal Prep
Budget
Funding
Execution
Data Acquisition
Data Analysis
Data Management
Data Sharing
Data Visualization
Post-Grant
Data Publishing
Data Archival
Data Disposal

23. Research LifeCycle Support – Pre-Grant
University Information Technology Services
9/16/2018
Research LifeCycle Support – Pre-Grant
Preliminary Investigation:
Support your preliminary investigation (for little or no cost)
Make you aware of how RT can help the project
Help you explore technology options

24. Research LifeCycle Support – Grant Proposal
University Information Technology Services
9/16/2018
Research LifeCycle Support – Grant Proposal
Proposal Preparation:
Actively partner as co-investigators
Provide support letters
Provide text on how IU’s massive cyberinfrastructure will support your specific project or a standard RT template
Develop a budget
Cyberinfrastructure Design:
Initial consulting
Gather requirements
Research options
Design solutions

25. Research LifeCycle Support – Grant Execution
University Information Technology Services
9/16/2018
Research LifeCycle Support – Grant Execution
Data Acquisition
Provide data capture application (REDCap)
Optimize data flows
Data Analysis
Migrate your analysis or other compute-intensive application to IU supercomputers, with potentially significant (say 10X) speedups to result
Accelerate your application further by parallelizing it
Supply optimized (parallel) versions (if available) of commonly used libraries & tools

26. Grant Execution … Data Storage: Data Management:
University Information Technology Services
9/16/2018
Grant Execution …
Data Storage:
Provide secure, regularly backed up disk storage of and ubiquitous access to data in work (RFS)
Provide massive amounts of disaster-proof (IUB & IUPUI mirrored), secondary, archival storage (SDA)
Provide large spaces and support for Oracle and MySQL databases (RDC)
Data Management:
Help you manage your data using professional data management paradigms such as metadata and tags, data provenance, data dictionaries (REDCap)
Design data management systems/applications

27. Grant Execution … Data Sharing: Data Visualization:
University Information Technology Services
9/16/2018
Grant Execution …
Data Sharing:
Provide collaborative spaces you can create instantly to invite others at IU or outside IU to share work documents or structured data over the web (Alfresco Share)
Data Visualization:
Help you explore and use visualization to assist your analysis and/or decision making
Provide a place to expose yourself and students to the latest, high-end visualization technologies
Present you visualization at conferences

28. Research LifeCycle Support – Post-Grant
University Information Technology Services
9/16/2018
Research LifeCycle Support – Post-Grant
Data Publishing:
Design of data dissemination environments – web application design, development, hosting, web publishing of data in Oracle/MySQL databases, web portals
Hassle-free virtual servers for you to run your own applications, system administration for these servers
Data Archival:
Long-term (decades), massive storage (TBs) of web-accessible secondary storage
Help you consolidate ALL your data in a SINGLE location.
Data Disposal:
Dispose off your data securely and professionally

29. University Information Technology Services
9/16/2018
Scope & Scale
Project scope is bounded only by funding & resource limits, but both can be raised
IU’s massive cyberinfrastructure allows us to help you plan for future growth, be it data storage, analysis, or dissemination
Supported projects currently scale up to petabytes (a million GB) of storage, months of running analysis applications on supercomputers, etc.
Geographically, we have built and run highly distributed cyberinfrastructure for national and international collaborations

30. University Information Technology Services
9/16/2018
Costs
Nearly all of the RT services described here (supercomputers, storage, visualization resources) are provided free of charge to any IU researcher
Projects that require significant RT commitment, for instance software development, system administration, etc., are provided at cost, but usually have RT written into grants to cover costs
Consulting up to a reasonable limit, especially in preliminary phases to help you attract funding, is free

31. University Information Technology Services
9/16/2018
Benefits
There is evidence that including RT in grant proposals has enhanced funding prospects
Speedups in the research workflow allows you to accomplish more and to think bigger
You don’t need local hardware or system administration resources
RT solutions are built professionally and for production use
RT provides high security for your data – it has done the hard work to align itself with HIPAA

32. University Information Technology Services
9/16/2018
Contact
Your single point of contact for all things RT: Anurag Shankar Local Contact: Carol Wood