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IMPACTS Annual Report FY2018


Number of IU departments supported by RT in 2017


From students using virtual reality goggles for the first time to IU medical researchers trying to solve some of humankind’s most pressing problems, Research Technologies at Indiana University is there to support the basic and the most complex scientific and educational challenges with sophisticated tools, powerful high performance computing (HPC) resources, and talented, supportive people. This is their story.

Overall increase in RT users from 2008–17


University Information Technology Services’ (UITS) arm of Research Technologies (RT) develops, delivers, and supports advanced technology solutions that enable new possibilities in research, scholarly endeavors, and creative activity at Indiana University and beyond.

FY18 grant dollars: Total IU grants


RT provides services that benefit fields ranging from astronomy to zoology and has developed a new suite of systems and services to address the needs of disciplines like the arts, cinema, humanities, and recreation. Services range from software consulting and workshops to computing and creating new software tools that meet researchers’ needs wherever they are, and at whatever technical grasp they may have. RT complements these efforts with education and technology translation activities to improve the quality of life for people in the community, state, the nation, and the world.

RT supported



User Status



Number of Users




Faculty Affiliate


Staff 600

Group Account TeraGrid/XSEDE



200 0












This diagram indicates both the increase in individuals using RT services from 2008–17 and a breakdown of those user groups. 2

Jetstream Research Experience for Undergraduates (REU) 2018 interns gain cloud computing experience

Research Technologies support We provide A to Z services in


Connecting you with software, computing, tools, and other resources to advance your work


Enabling fast calculations, advanced simulations, and massive secure storage


Delivering tools for analytics and big data research; distributing stat/numerical and open-source software


Promoting interactive models, virtual and augmented reality, advanced digital arts and media, as well as secure data analysis


Connecting you with the research services you need to reach discovery through targeted training, seminars, workshops, and tours

five major categories. No matter the tool, service, or support application, our goal is to benefit the entire IU community.


Data transferred from DC2 to HPC

124PB Time it would take to play 124PB of music

250,000 years ...the first Homo Sapiens would just be finishing up their jams

Number of years it would take you to send 124PB of email if you sent 50 emails a day

100 million Years it would take to tweet 124PB if every person in the world tweeted once a day

17 years DC2 is 5PB, that’s filling and emptying the entire filesystem

24 times or 2x a month

High performance computing (HPC) machines at the IU Data Center

Example of Tableau visualizations using data from Big Red II. Available online to users, these provide both a broad overview and detailed usage statistics for every RT system.

Research at scale Indiana University is one of the few institutions where any student or faculty member can access high performance computing resources without grant funding, project proposals, or review and approval. Research Technologies takes this unique standing to heart, supporting not only large-scale projects but also an ever-increasing scope of users. Reaching out to new potential users—especially those in fields not typically associated with high performance computing like the humanities and arts—involves consulting, support, and education, as well as creating tools for these powerful systems that are user-friendly. By providing a diversity of research tools, innovative software approaches, and levels of support, Research Technologies strives to ensure that IU’s high performance computing bursts beyond the data center walls.

Franco Pestilli, assistant professor of psychological and brain sciences, uses Jetstream for precision brain mapping



Supporting research at IU






Real-time world seismic monitor available on the IRIS website 6

IRIS-EARTHSCOPE USARRAY SHORT COURSE This workshop on seismology and supercomputing at IU Bloomington was assisted by Karst Desktop. It focused on the Oklahoma Wavefields experiment, targeting data from an active seismic area in north central Oklahoma in 2016.

Number of elite seismologists from around the US

29 1TB of USArray data from 400 seismographs studying over

2,000 locations

“It was perfect. A terabyte of data is not easy to stage, so the Data Capacitor II was an essential tool to stage and work with it.” Gary Pavlis, IU professor of Geological Sciences

Background image: Detail of Data


Capacitor II at the IU Data Center

DC2 Data Capacitor II (DC2) is a large-capacity, high-throughput, high-bandwidth Lustre-based file system serving all IU campuses.


Karst A high-throughput computing cluster designed to deliver large amounts of processing capacity over long periods of time, Karst provides batch processing and node-level co-location services, making it especially suited for high-throughput, data intensive parallel computing jobs. • • • •

Remote access from Karst Desktop 228 general-access compute nodes 28 condominium nodes 16 dedicated data nodes: each with 64GB RAM and 24TB local storage Each node: IBM NeXtScale nx360 M4 server with two Intel Xeon E5-2650 v2 8-core processors, 32GB RAM, 250GB local disc storage

“Karst Desktop provides an ease of collaboration across scholars and also unrestricted access to a computational capability.” Nikolaos Zirogiannis, IU researcher

UNDERSTANDING EXCESS EMISSIONS IU researcher Nikolaos Zirogiannis studied “excess emissions”—an EPA category of pollutants that are beyond Clean Air Act standards that occur during startups, shutdowns, or malfunctions, Zirogiannis expected to find spikes during emergencies like hurricane Harvey in 2017, analyzing data from the Texas Commission of Environmental Quality using Karst Desktop. His research instead found these types of emissions are far more routine than expected, and cost around $150 million in health damages annually.



Carbonate A large memory computer cluster configured to support high performance, data-intensive computing, Carbonate handles tasks for researchers using genome assembly software, large-scale phylogenetic software, and other genome analysis applications that require large amounts of computer memory. • • •

72 general-purpose nodes, each with 256GB RAM 8 large-memory compute nodes, 512GB RAM each Each node: Lenovo NeXtScale nx360 M5 server with two 12-core Intel Xeon E5-2680 v3 CPUs and four 480GB SSDs


Karst Desktop A remote desktop service for users with accounts on the Karst research supercomputer, Karst Desktop lets you open and control a remote session from a graphical desktop window running on your personal computer.


COMPUTATIONAL ANALYSES OF DNA IU Biology graduate Jeffery Adrion developed TEFLoN—a software package that allows researchers to see where the transposable elements of DNA (a.k.a. “junk DNA”) have cut themselves, and where they have migrated to, on the scale of population genetic data. Overall, the goal is to learn how so-called junk DNA might influence evolution. Adrion used Karst to run and debug his program and Carbonate for memory-intensive simulations to test its accuracy and sensitivity.

“It’s nice that I can have access to everything from home, office, everywhere [with Karst Desktop].” Jeffery Adrion, IU Biology graduate



Supporting research at IU

IU Bioinformatics Ph.D. student Gregg Thomas analyzed large files of encoded genomic data to identify differences and similarities between genomes, to map out and explore the history of life through genomics. Genomes at a time =

30 1 genome =

Detail of Thomas’ work—


a phylogeny of 76 insects inferred using Carbonate



“The large memory capacity of Carbonate means I’m able to analyze large chunks of the genome at once without worrying about running out of RAM, and the many processors available mean I can analyze several genomic chunks at once,




which vastly cuts down on run times.” Gregg Thomas, IU Bioinformatics Ph.D. student Background image: Detail of Carbonate at the IU Data Center 9


Tools for teachers and students in focus IQ -WALLS At Indiana University, IQ-Walls help you visualize data, display images, documents, and web pages in large format and with tons of detail. With side-by-side viewing, you can compare content and collaborate with others. An image can be displayed on one monitor, a combination of monitors, or on all of the monitors for one gigantic image.


The IQ-Wall at IU’s Wells Library in Bloomington makes use of 3D tracking and stereoscopic 3D technologies, providing a large-format interactive virtual reality experience. The user’s perspective changes depending on which direction they’re looking and where they are standing within the tracked space.






The IQ-Wall at the Advanced Visualization Lab (AVL) facility in Indianapolis is multi-touch enabled. The touch interface allows for natural gestures that zoom and manipulate data on the displays. IU’s AVL developed and supports Indiana University’s IQ-Walls. Any IU student, faculty, or staff can investigate data and collaborate in new and exciting ways—and on any campus, in the near future. IQ-Walls will soon be constructed at each regional IU campus, beginning with IU East.

REALITY LABS Research Technologies created Reality Labs from existing classroom or lab spaces. Each one contains an instructor station, plus up to a dozen student stations. Each of these stations includes an Acer G1 Predator or MSI Aegis gaming computer and an HTC Vive or Oculus Rift head-mounted VR display. A shared, room-wide VR tracking space facilitates immersion in virtual simulations. Any IU-affiliated student, faculty, or staff member with an IU network ID can access the systems. They simply find an available Reality Station and log in. They can engage the VR capabilities as part of a class curriculum or on their own—for testing or development or for a class project or capstone.

Ultra-resolution imagery on the 66 million pixel ConCAVE IQ-Wall at IUPUI

At the same time, many labs offer a large-format display, such as a projector or tiled video wall, which allows non-VR-fitted users to share in the virtual experience and also supports collaborative critiques and reviews. Reality Labs can also provide complete educational functionality for classes that do not require VR.

“I’ve been using VR in my classroom and I’ve seen students demonstrate a richer understanding of their designs through the use of VR.” Jon Racek, senior lecturer, IU School of Art, Architecture + Design

Students demonstrate their final projects in AVL staff member Bill Sherman’s “Introduction to Virtual Reality” IU School of Informatics, Computing, and Engineering course 11


Connecting IU and the community UITS Campus Networks staffer Tony Brazzell helping Mitchell Junior High students with LEGO Mindstorms® robots

“These robots are very cool, definitely! There are endless possibilities of what you can do with this technology: you can program them to go through the maze here or grab your water bottle. Robots are our future.” Cody Cox, 7th grader



Training & outreach Research Technologies strives to serve both IU and our local community by providing training and outreach programs. Programs that teach, inform, and convey the role that technology can play in research and discovery continue to evolve. In the coming year, we plan to extend our outreach to local educators by providing more hands-on technology experiences for young students. We will also engage more directly with the IU community to expand our reach, building partnerships with faculty and researchers to support them in their quest for new knowledge.

LEGO MINDSTORMS This spring in partnership with Lawrence County STEAM and Naval Surface Warfare Center Crane Division, Research Technologies loaned eight LEGO Mindstorms® programmable robots (normally used for Ready, Set, Robots! camp) to a local junior high school in Mitchell and helped science teacher Amy Glassco teach the kids about programming.


MAKEVENTION Sponsored by Research Technologies, Makevention is an annual event where local maker groups come together to celebrate their DIY spirit. The 1,200 participants range from artists to educators to tech enthusiasts and tinkerers of all ages. RT’s Jenett Tillotson and Nathen Heald are lead supporters of Bloominglabs, a local makerspace for sharing tools and knowledge, and organized the event this year.





READY, SET, ROBOTS! Now in its 12th consecutive year, this two-day summer camp requires no prerequisites, just a curious mind and an interest in technology. Kids grades 7–12 learn basic computer programming skills as they work in teams alongside RT staff to command LEGO Mindstorms® robots, simulating a Mars rover mission. The camps end with a Robot Grand Challenge, where parents and friends gather to see the kids’ newly acquired skills. They also get a tour of the IU Data Center, RT high performance computers, and the Big Red II supercomputer.

“We’re thrilled that students are able to learn so much in a really short period of time. From computer programming terminology to public speaking and respect for equipment and the facilities, there is something for everyone, even if they don’t decide to pursue a career in science or technology.” Robert Ping, education and outreach manager for UITS Research Technologies



OPTIMISTIC For nursing home residents, being transferred to a hospital is disruptive and expensive. And in some cases, it’s potentially avoidable—but only with a better understanding of circumstances. OPTIMISTIC, a project led by Dr. Kathleen Unroe and Dr. Greg Sachs of IU Centers for Medicare & Medicaid Services, seeks to improve nursing facility care by untangling the complicated conditions behind hospital transfers—exploring the relationship between symptoms and diagnoses of avoidable conditions, and identifying associations between risk factors and diagnoses using REDCap.

When it comes to infant mortality, Hoosier babies are faring worse than the national U.S. average. In an effort to combat this, researchers created WeCare, a program that provides evidence-based health education and connects women with community organizations and health coaches. To help coaches understand their clients’ situations and provide the appropriate resources, WeCare Indiana turned to REDCap. Now WeCare researchers can get real-time data from coaches, organizations, and the over 1,300 enrolled women, and keep it securely, using the data to identify areas of greatest need, and greatest potential impact.


REDCap Research Electronic Data Capture (REDCap) is a self-managed, secure, web-based platform designed to support data collection and data management for research, operations support, and quality improvement projects. REDCap’s easy-to-use, intuitive features allow users to rapidly build and manage secure online surveys and databases. REDCap’s streamlined, intuitive functionality and features enable you to rapidly develop surveys and databases for collecting and managing research data. No programming experience is needed to start creating data entry forms and surveys. 14

“REDCap has been a life saver for this project.” Rachel Gruber, WeCare data manager


Surveying a healthier Indiana


INFANT SLEEP STUDY Sleep-deprived parents of infants have new hope through the research of Dr. Sarah Honaker, who used devices to track infants’ movements at night and REDCap to log parents’ sleep diaries in real time. Science has long shown that behavioral sleep interventions can help babies and parents sleep better and reduces parents’ stress. Using REDCap allows researchers to acquire up-to-date sleep data. Dr. Honaker’s team can then respond right away to parents’ questions or concerns—even the very next morning.





Dr. Sarah Honaker and her team of dedicated infant sleep researchers 15


Addressing Indiana’s toughest challenges Flooding along the Ohio River in Utica, Indiana. The Ohio River reached its highest crest in 21 years during February 2018

PREPARED FOR ENVIRONMENTAL CHANGE As the Earth undergoes a changing climate, devastating hurricanes appear to be getting more frequent and deadlier, leading scientists to wonder about their relationship to future climates. IU researcher Chanh Kieu aims to understand if and how hurricanes will change as a result of future rising temperatures. Kieu and his team run atmospheric simulations of hurricanes under different hypothetical future climate states to see how it affects the strength, structures, movement, and frequency of hurricanes. His group is also working on climate modeling under the IU Grand Challenge Project “Prepared for Environmental Change” to similarly study future climate scenarios in Indiana. Kieu’s high-resolution simulations require high-performance storage at large capacities to handle the high volume of data and—using Big Red II and Big Red II+—thousands of computer cores to run their modeling systems for several months.

“The computing infrastructure we have here at IU is among the best ones because of the consistency, the maintenance, and the upgrades that we have. You cannot find it anywhere else that is all free for the faculty members and students like here.” Chanh Kieu, Ph.D., IU Department of Earth and Atmospheric Sciences



IU GRAND CHALLENGES PROGRAM Grand Challenges are defined as major, focused, and large-scale problems facing humanity that can only be solved by the application of dedicated research findings in collaboration with community partners. IU is pioneering the approach of pairing faculty and students from all disciplines in partnership with cross-sector teams of community and business leaders. The Grand Challenges Program is a bold commitment to address these issues that impact Indiana—and the world. The challenges are split into three main categories: the Precision Health Initiative, Prepared for Environmental Change, and Responding to the Addictions Crisis. Many projects within these programs are planned and spinning up, but some are already underway. For example, Research Technologies is supporting a project analyzing genes associated with addiction under the Precision Health Initiative, while also helping Chanh Kieu’s work simulating hypothetical future climates for the environmental challenge. As these large-scale programs and projects ramp up in size and scope, Research Technologies at UITS is committed to providing support to the IU Grand Challenges and stands ready to assist with the high performance computing needs that may arise.





FINDING THE ADDICTION GENE Substance abuse causes millions of illnesses and injuries for Americans and results in thousands of deaths every year. As part of the Precision Health Initiative, medical genomics researchers at IU from Dr. Tatiana Foroud’s laboratory are making great strides in helping medical researchers and clinicians to better understand the genetic underpinnings of drug addiction and alcohol dependence. Leah Wetherill, a researcher working with Dr. Foroud at IU School of Medicine, is utilizing Research Technologies high performance computing and storage systems to identify genes associated with alcohol, drug, and behavioral disorders. Using IU’s newest supercomputer Big Red II+, genomic data of more than 12,000 individuals—with more than 12 million total genetic markers—need to be cleaned, processed, and analyzed. The data volumes are huge and the computational resources needed even more immense, but increasing the size and complexity of analyses yield more reliable results, and Big Red II+ is up to the task.



High Performance Computing (HPC) in focus

“What do I like about the Jetstream REU experience? Everything! I love being able to just be in an environment where I’m surrounded by a bunch of people interested in different types of computing—it’s beautiful to see everyone working together.” Steven O’Riley, Jetstream REU student






Background image: Jetstream at the IU Data Center 18

REU PROGRAM Six college students from across the country got the chance of a lifetime—getting embedded with Research Technologies staff in active research projects and learning how to use HPC systems in the inaugural National Science Foundation (NSF)-funded Jetstream Research Experience for Undergraduates (REU) program.

UNIVERSITY OF ARKANSAS HPC WORKSHOP The workshop, led by IU staff from NCGAS and Jetstream, was held at the Engineering Research Center and was attended by 30 faculty, staff, and graduate students. The primary focus was to apply bioinformatic tools in the analysis of genomic data within the Jetstream environment.

NCGAS National Center for Genome Analysis Support (NCGAS) is a collaboration between the lead institution, Indiana University (IU), and the Pittsburgh Supercomputing Center (PSC) at Carnegie Mellon University and is affiliated with the IU Pervasive Technology Institute and Research Technologies. NCGAS has continued to use NSF funding—with additional funding and facilities from IU and PSC—to aid discovery and innovation in biological sciences that use genomic methods. Through collaborative efforts with PSC, NCGAS has aided works ranging from ecology, to physiology, to economically important animals and plants. NCGAS’ most significant accomplishments continue to be those of the researchers, assisting discoveries from RNA and DNA transcriptome, and metagenome and metatranscriptome assemblies.



Jetstream is a user-friendly cloud environment created to give researchers and students access to computing and data analysis resources on demand—from their tablets, laptops, or desktop computers. Research Technologies, an IU Pervasive Technology Institute center, is the lead institution on the $11 million NSF grant to create, implement, and operate Jetstream. The service is colocated at IU and the University of Texas at Austin’s Texas Advanced Computing Center (TACC). Jetstream extends the reach of the NSF’s eXtreme Science and Engineering Discovery Environment (XSEDE) project, which supports most of the largest NSF-funded computing systems serving the national research community. More than 2,400 researchers and educators use Jetstream, with nearly 900 student users. The Jetstream cloud system won a 2018 Campus Technology Impact Award. The award honors the work of those who have made Jetstream a success in reaching underserved colleges and universities.

Jetstream was developed with support from NSF grants ACI1445604 and OCI-1053575. Access to Jetstream is available to XSEDE researchers with Startup allocations. Visit jetstream-cloud. org. NCGAS was developed with support from NSF grants DBI1062432 2011, ABI-1458641 2015, ABI-1759906 2018. NCGAS resources are available to researchers with current NSF funding (or working in areas that qualify for NSF funding) typically at no cost. Visit



OPERATION ICE BRIDGE For nine years, Research Technologies has provided IT support for the Center for Remote Sensing of Ice Sheets (CReSIS) at the University of Kansas and NASA’s effort to collect polar ice cap data. Known as Operation IceBridge, a fleet of research aircraft flies out of Antarctica, Chile, Argentina, and Greenland to gather data to help improve scientific models of physical interactions between glaciers, sea ice, and ice sheets. It’s the largest airborne survey of Earth’s polar ice ever flown, offering unprecedented threedimensional detail and critical data used to predict polar response to climate change and resulting sea-level rise. Onboard are three radar systems that can produce up to 5 terabytes of data per flight, and a supercomputer called Forward Observer— specially designed by Research Technologies’ Matt Standish, Rich Knepper, and Matt Link to capture the data streams and create multiple copies, eliminating the risk of losing valuable data to unexpected, harsh elements in the arctic and Antarctic fields. It also gives scientists nearly instant access to preliminary images while they’re still in the air, allowing for the possibility of in-flight adjustments of a planned route if problems or opportunities arise. The data is later transferred to DC-WAN2 for researchers to access. Once the data is processed, images showing slices of snow, ice, and bedrock are used by scientists to study the year-to-year changes in this vital part of the planetary ecosystems.

Forward Observer A cluster-based highperformance data duplication, storage, and processing system that fits into an aircraft-rated machine rack, routinely performs in polar turbulence well in excess of what is allowed in commercial flights, and runs on limited aircraft-generated power. Receiving data streams from three advanced sensor systems, the Forward Observer creates checksums for assurance, multiple copies for redundancy, and processes the data into visuals so researchers can monitor results in real time.


DC-WAN2 The Data Capacitor Wide Area Network 2 is a large, high-speed data storage facility serving all IU campuses and several research centers throughout the nation. It allows researchers to access remote data as if it were stored locally and share large amounts of data with researchers at multiple remote sites. 20


Partnership on a global scale

MAPPING WORKSHOP Research Technologies’ Tassie Gniady quickly organized and led an emergency humanitarian mapping workshop at the Scholar’s Commons IQ-Wall in the Herman B Wells Library in response to a deadly earthquake near the Iraq/Iran border the previous weekend. The goal was to use satellite imagery to tag areas of visible destruction or flooding, and to improve maps of remote areas so that first responders can get to those in need more effectively.







Thinking forward: anticipate and delegate As high performance computing continues to grow in capability and research needs become more diverse and complex, Research Technologies is determined to anticipate and respond to new challenges and demands. For example, with research projects expanding in data volume, the demand on the horizon for higher capacity and more agile high-performance storage is presently being addressed by the upcoming storage systems, Slate and Geode.

Background image: Geode at the IU Data Center 22

SLATE A follow-on to the Data Capacitor II—the high-performance, high-throughput parallel file systems used by IU’s HPC resources—Slate’s forward-thinking persistent storage technology brings extreme scalability and faster speeds. It will enable: •

Measured speeds up to two times faster than the Data Capacitor II

New individual storage allocations up to 1.6TB at no cost

15TB Project Space allocation—50% more shared storage for IU research projects at no cost

Additional shared storage for $0.07 per GB per year above the 15TB allocation

RESEARCH DESKTOP (RED) Research Desktop (RED) is a graphical desktop service for users with accounts on the Carbonate research supercomputer at Indiana University. UITS developed RED, which is replacing Karst Desktop, to reduce the learning curve for users who are unaccustomed to working in Unix-like command line environments. Most research supercomputers, including those at IU, run Unixlike operating systems that, by default, require you to type commands into a command processor, or shell. However, RED lets you use a graphical user interface (similar to Windows and macOS) and run it on your personal device to launch and control a remote session on one of more than a dozen dedicated compute nodes. You can also run graphical applications remotely without noticeable latency and without needing to submit an interactive compute job. RED helps users with little or no command line experience and, as a result, promotes broader use of IU’s research cyberinfrastructure.

GEODE Known as Home Directories in its current incarnation, Geode allows you to access your home directory and/or project directory from any of IU’s research supercomputers. It’s in the process of getting a hardware refresh, which will enable: •

Replicated persistent storage for user home directories

Desktop mounted access

Individual allocations up to 200GB—two times the current quota

Speeds up to 4 times faster than Home Directories

Data encrypted at rest

Snapshots with self-restore capability

Geode Project Space available for $0.20 per GB per year

ADS management of Geode Project Space


Research Technologies is a division of Research Technologies is a division of University University Information Technology Servicesof the Information Technology Services and an affiliate Pervasive TechnologyInstitute Institutecenter and a IU Pervasive Technology

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IU Research Technologies Impacts Annual Report FY2018  

IU Research Technologies Impacts Annual Report FY2018  

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