Cyberinfrastructure News

To see past content, see the blog archive.

PolarGrid Equipment Heads to Greenland

Indiana University-led PolarGrid cyberinfrastructure project will reach a major milestone this month, as researchers take the new PolarGrid computing equipment to the ice sheets of northern Greenland.

Expedition scientists from PolarGrid partner organizations, the Center for the Remote Sensing of Ice Sheets and Elizabeth City State University, will collect data from Greenland's shrinking ice sheets in an effort to better understand the effects and implications of rising global temperatures.

The new PolarGrid equipment will allow scientists to process data in the field during the course of the expedition and use the results to direct their data collection strategies. The ability to analyze data while still in the field will also help the research team assess the quality of the data and adjust sensors as needed. This is a significant improvement over past methods, in which data was taken back to the U.S. for later analysis.

Technologists from Indiana University have been working throughout the spring to prepare the field equipment, which includes IBM servers and storage arrays, as well as Dell and Panasonic laptops, designed to withstand hard use in extremely harsh conditions. The equipment recently left Indiana University, and is expected to arrive in Greenland later this month. PolarGrid is funded by a grant from the National Science Foundation under award number CNS-0723054.

Watch a new video about the PolarGrid project at www.polargrid.org .

Posted on: 07/01/2008 | 0 comments

National Biorepository for Gene Therapy

Indiana University's School of Medicine will be home to the National Gene Vector Biorepository and Coordinating Center (NGVB) for gene therapy research. Researchers use gene vectors, such as disabled viruses, to carry genetic materials in the body in hopes of treating or preventing disease. For example, genes important for fighting infections may be inserted into immune system cells that have been rendered inactive by genetic mutations.

The NGVB at Indiana University will help university scientists share research information and substances to promote discoveries, patient safety and compliance with regulations of the Food and Drug Administration. The NGVB's services will include maintaining a warehouse of important reagents, disseminating the results of safety studies, and the storage of biological materials and patient specimens in accordance with FDA regulations.

Scientists are using gene transfer techniques in studies involving a broad range of diseases including cancer, heart disease, cystic fibrosis, immune disorders including arthritis, and infectious diseases. An NIH database lists more than 500 such trials currently under way.

Research Technologies staff, in collaboration with the IU School of Medicine's Bioinformatics Core, are building the web-based systems that will be used to manage and share this information.

For more information, see http://medicine.indiana.edu/news_releases/viewRelease.php4?art=887.

Posted on: 07/01/2008 | 0 comments

I-Light backbone completed

The backbone of a high-speed, fiber-optic network has been completed that will provide every public and private college campus in Indiana with digital communications at least 20 times faster than a typical home Internet connection. Known as I-Light, the network involves more than 1,000 miles of fiber-optic cable reaching every corner of the state. It is larger, per capita, than similar networks in neighboring states. More than 40 higher education institutions will use the system for educational and research purposes.

In addition to providing more bandwidth than most Indiana colleges and universities could otherwise afford, the system offers a variety of other capabilities, including:

Connecting classrooms at distant locations with high-quality video-streaming,
Allowing researchers at any location to exchange large digital data files and access supercomputers and scientific data storage facilities at IU and Purdue,
Making possible multi-campus collaborative research projects,
Enabling the use of high-definition learning tools, such as telepresence, a new way of videoconferencing that gives the users the appearance of being at the same location.

I-Light web page More information

Posted on: 07/01/2008 | 0 comments

Calendar - July 2008

Research Technologies Round Table

Thursday, July 31, 12:30-1:30pm
IUB: Radio-TV Building Room 180
IUPUI: ICTC Room 497
Live URL: mms://wms.indiana.edu/rt_round_table

The Indiana Spatial Data Portal

The Indiana Spatial Data Portal provides students, staff, researchers, and the general public access to terabytes of Indiana geospatial imagery. Geographic Information Systems staff will describe the current database and online services and their plans.

Staff from the Indiana Geological Survey and The Polis Center will also be on hand to discuss their projects which rely on these services.

IEEE 2008 eScience Conference Call for Participation

Organizing committees for the 2008 IEEE eScience Conference are now accepting papers and proposals for tutorials; posters, exhibits, and demos; workshops and special sessions on topics related to eScience, grid, and cloud computing. The conference is being hosted by Indiana University in partnership with Microsoft Research and will take place on December 7-12, 2008 at the University Place Conference Center in Indianapolis, Indiana.

Submission Deadlines:

Workshops and Special Sessions: June 20, 2008
Papers and Tutorials: July 20, 2008
Exhibits, Demos, and Posters: September 14, 2008

For more information please visit the Conference Web site.

Posted on: 07/01/2008 | 0 comments

TeraGrid Allocation Proposal Deadline

TeraGrid proposals for the allocation period from Oct. 1, 2008 thru Sept. 30, 2009, are now being accepted. The proposal deadline is July 15th, midnight local time.

You should submit your proposals at the URL:

https://pops-submit.teragrid.org/.

Please note the availability of these new resources:

Purdue's Dell 1950 Cluster, Steele,
for Gateways, IU's IBM HS21 Bladeservers, Quarry.

This is for medium and large allocations [MRACs and LRACs]; development allocations [DACs] are accepted and approved at any time.

Posted on: 07/01/2008 | 0 comments

Source code repository service introduced

The Core Services group in Research Technologies is now offering source code repository services for Indiana University researchers' software projects. If you write your own code for research projects that you run on IU systems, and would like to manage source code revisions under subversion, you can request a project by sending email to rtadmin at rtinfo.indiana.edu.

Subversion is already installed on Big Red and Quarry. If you want to use subversion on your personal computer you will need to install subversion on your system. Documentation for subversion is available at http://svnbook.red-bean.com/.

Posted on: 07/01/2008 | 0 comments

IU's Advanced Cyberinfrastructure Systems back in service

Big Red and Quarry were placed in service last night, June 18. The Data Capacitor Lustre-WAN system is curently being used as parallel I/O filesystem while we complete recovery of the GPFS system. The Data Capacitor Lustre-WAN system has been online since Tuesday June 16th.

The Data Capacitor Project space and GPFS are currently undergoing system recovery and we expect those systems to be online in the near future. Users are now fully able to run jobs and do their work on IU's advanced cyberinfrastructure with the exception of the Data Capacitor Project space.

If you encounter any problems or need help, please send email to: researchtechnologies@iu.edu

Posted on: 06/19/2008 | 0 comments

Weather disaster impacts IU, Big Red, Quarry, and Data Capacitor

IU Bloomington has faced a series of severe weather events that started June 4, and extended to the 15th. The repeated severe weather events have resulted in a series of failures in the electrical power infrastructure supporting Bloomington generally, including IU's advanced computing systems. The events were so severe that Bloomington and surrounding counties have been declared a federal disaster area.

IU's major research computing systems -- Big Red, Quarry, and the Data Capacitor -- were out of service after the initial power outages on June 4. The time from the 4th to the 15th was a repeated cycle of putting systems back in production, facing additional weather-related power events, and starting over again. The power event on the 14th of June was the most damaging since the severe weather started.

IU is renting emergency generators in order to assure reliable power to restart these systems. These arrived on site Monday (6/16), and we will have systems up and running as quickly as possible. Our best current estimate is that we will be in operation again as of the end of the week (6/21).

We recognize the impact that this downtime is having on researchers within IU and nationally. Our teams are working as hard as we can with all the resources we can bring to bear to get IU research systems running again as quickly as possible.

If you face deadlines in the next few days, please contact us at researchtechnologies@iu.edu and we will work with you to find alternate solutions for your immediate computing needs.

We will update the status of IU's advanced cyberinfrastructure systems each day at 9 am and 4 pm EDT, on this web site.

IU's new Data Center, currently under construction, will be a hardened facility. It is designed in such a way that it will not be subject to even the extraordinary series of weather events that brought about the current situation.

Posted on: 06/19/2008 | 0 comments

Calendar - June 2008

Research Technologies Round Table

Thursday, June 26th, 12:30-1:30pm
IUB: Radio-TV Building Room 180
IUPUI: ICTC Room 497
Live URL: mms://wms.indiana.edu/rt_round_table

Howto: Manage thousands of job submissions on Big Red

Dick Repasky, Matt Allen and Yu Ma

Some researchers need to run thousands of jobs on Big Red. For example, a recent project to annotate the Maize genome required that 25,000 jobs be run. That many jobs is difficult to manage.

The Research Technologies division is designing a facility that will allow users to manage thousands of jobs, and we want your input. RT staff will present the design goals of the project, outline how users would specify a pool of thousands of jobs, and describe plans for how users would process a pool of jobs and monitor progress.

Please note the new Radio-TV Building location for IUB. Videoconferencing equipment will broadcast to the IUPUI location.

Posted on: 06/02/2008 | 0 comments

HPC bootcamp at IU Northwest

Attend the SC08 Summer Workshop: Introduction to Modeling, Simulation, and Computational Methods, being held July 28-30, 2008 at Indiana University Northwest, in Gary, IN. The three-day workshop is designed for faculty from a broad range of disciplines: science, technology, engineering, mathematics, and also humanities, arts, and social sciences.

The material covers a broad range of modeling and simulation techniques, including cellular automota, dynamic systems, agents, and Monte Carlo methods. An introduction to using large-scale computational resources will be provided along with credentials and support for continued use of the computational resources after the workshop.

Participants are asked to pay a $75 registration fee which will be refunded upon completion of the workshop. Room, board, most meals and other costs are covered by the SC Education Program. Participants must cover their own travel expenses.

To register please visit

http:// sc08.sc-education.org/workshops/schedule.php

and choose the workshop held at IU Northwest in Gary, IN.

Posted on: 06/01/2008 | 0 comments

New resources to support Lustre over wide area networks

University Information Technology Services (UITS) has dedicated over 350 terabytes of new storage platforms to support collaborative research projects mounting Lustre file systems across the TeraGrid network and other national high speed networks. The ability to use Lustre over a wide area network (WAN) is a significant advancement in the ongoing struggle to meet user demand for easier and faster access to stored research data.

Indiana University has made several notable achievements related to the use of Lustre over a WAN in the past year. In November, a team led by Indiana University was awarded first place in the annual Bandwidth Challenge at the SC07 Conference in Reno, Nevada; using the Data Capacitor, the IU team achieved a peak transfer rate of 18.21 Gigabits/second (Gb/s) out of a theoretically possible 20 Gbs, nearly twice the peak rate of the nearest competitor.

More information is available.

Posted on: 06/01/2008 | 0 comments

IU named National Center of Academic Excellence in Information Assurance Research

The National Security Agency and Department of Homeland Security announced that Indiana University is among the first universities to be designated National Centers of Academic Excellence in Information Assurance Research.

The designation complements IU's selection in August 2007 as a National Center of Academic Excellence for Information Assurance Education. Fred H. Cate, director of the Center for Applied Cybersecurity Research and distinguished professor of law at the IU School of Law, Bloomington, said the designation for both research and education "reflects our twin goals of developing new knowledge and translating that knowledge into practical benefits for the public by educating students, professionals, policymakers, the press and the public."

More information is available.

Posted on: 06/01/2008 | 0 comments

Places & Spaces in Beijing

In collaboration with Chinese researchers at the Research Center for Grid and Service Computing at the Institute of Computing Technology of the Chinese Academy of Sciences in Beijing, and with support from a grant by the National Science Foundation, the "Places & Spaces: Mapping Science" exhibit opened on May 17, 2008 at The National Science Library of the Chinese Academy of Sciences in Beijing. This will be the debut for the 4th iteration of this 10-year project, "Science Maps for Economic Decision Makers".

Weixia (Bonnie) Huang, from the Cyberinfrastructure for Network Science Center at the Indiana University School of Library and Information Science, travelled with the exhibit and will work with colleagues to introduce the maps. This is the first major showing of the exhibit outside of the U.S., and the maps have been translated into Chinese to aid in the sharing of information.

For more information, see http:// scimaps.org/nslc.

Posted on: 06/01/2008 | 0 comments

IEEE 2008 eScience Conference CFP

For more information on topics of interest, submission guidelines and deadlines please visit the conference Web site at http://escience2008.iu.edu.

Posted on: 06/01/2008 | 0 comments

Calendar - May 2008

Learn about IU's supercomputers from the experts!

Monday, May 12, 11:00am-1:00pm - ICTC Main Lobby, IUPUI

You're invited to stop by and visit with the system administrators who run IU's supercomputers, Big Red and Quarry -- two of the most powerful supercomputers in the world.

You're welcome to ask questions, share ideas, or just chat in aninformal setting. This is an opportunity for you to learn how these centralized research computing resources can help support your work.

Research Technologies Round Table

Thursday, May 29, 12:30-1:30pm
IUB: Radio-TV Building Room 180
IUPUI: ICTC Room 497
Live URL: mms://wms.indiana.edu/rt_round_table

Science Gateways

Marlon Pierce

After more than a decade of development, tools for Web-based access to computing resources and data archives are now very mature. This month's Roundtable will include discussion of these Science Gateways and the Grid middleware that they access, architecture and standards used by the science portal community, component-based Web portals, Web Services, and workflow (or service orchestration) tools. Also discussed will be Web 2.0 and Cloud Computing approaches to resource and data access, and these tools' eventual merger into Science Gateways and portals.

Please note the new Radio-TV Building location for IUB. Videoconferencing equipment will broadcast to the IUPUI location.

Posted on: 05/01/2008 | 0 comments

Don't forget to optimize!

When you submit a job to one of IU's supercomputers, there will be hundreds of jobs in front of yours and more lining up behind. Optimization ensures all these jobs will run as quickly as possible.

How can you simply and quickly optimize your program? Let the compiler help. By using three types of compiler switches - machine, usage, and optimizing - you can make your program fast and sleek without a lot of work. In this article, we'll look at optimizing switches only, with a C program compiled using Big Red's IBM compilers as an example.

Not all switches improve a program's performance. Some are neutral, some will help or hurt based on combinations, and some will slow a code down dramatically on their own. Safe bets include -Q to replace function calls with the function's source code, and -qunroll to unroll loops as if they were sequentially written source code. Those that should be used with care include -qhot for combining loops.

The -O switch is a set of macros for these types of smaller optimizations. This switch optionally includes a digit (e.g., -O3) which increases optimization risks as it increases. To offset this, IBM offers the -qstrict switch, which tells the compiler not to take risks if there is some doubt. A good first test of our sample C program might be:

xlc -q64 -O3 -Q -qunroll -qstrict -qarch=ppc970 -qtune=ppc970 -qenablevmx -qaltivec -o my_project my_project.c -lm

Every program is unique, but a good compiler can typically improve the performance of even a well-written program by 1/3. Reading your compiler's man page and experimenting with a few simple optimization switches may even cut your job's run time in half.

IU's High Performance Applications group may be able to help with compiling and optimizing your programs.

Posted on: 05/01/2008 | 0 comments

Old GPFS scratch files to be deleted

Beginning June 1, 2008, files that haven't been accessed in more than 180 days will be automatically removed from IU's General Parallel File System (GPFS) scratch file system.

The GPFS scratch file system is accessible from Big Red, Quarry, and Libra.

Please be sure to back up important data stored on GPFS since it is a temporary scratch file system and is not intended for long-term storage.

For information on backing up data to the Massive Data Storage Service (MDSS), see the KB article "At IU, how do I use SFTP or SCP to access my MDSS account?."

Posted on: 05/01/2008 | 0 comments

New job type on Big Red

A recent update to Big Red's LoadLeveler resource manager includes a new job type: MPICH. LoadLeveler jobs of type MPICH, as opposed to "parallel", automatically generate host files for use with mpirun's "-machinefile" switch.

A job's host file can be referred to via the new $LOADL_HOSTFILE variable; use of the llmachinelist command and subsequent cleanup are no longer necessary!

In addition, the variable $LOADL_TOTAL_TASKS may be used with mpirun's "-np" switch. $LOADL_TOTAL_TASKS is calculated from the LoadLeveler job script keywords "node" and "tasks_per_node". As a result, changes to job geometry only need to be made with these keywords; the mpirun command's arguments will be modified automatically.

Finally, the MPICH job type provides support for some additional MPI application enhancements which we intend to implement in the coming weeks. We encourage all of our MPICH users to modify their job scripts accordingly.

Posted on: 05/01/2008 | 0 comments

IEEE 2008 eScience Conference Call for Participation

For more information on topics of interest, submission guidelines and deadlines please visit the conference Web site.

Posted on: 05/01/2008 | 0 comments

Drug Discovery on Big Red

The continued rise in computational power is significantly enhancing medical research and promises to expedite the process of translating research in basic science to the clinic. High throughput computational screening as well as highly intensive biomolecular simulations are accelerating the process of drug discovery to a new level. Blessed with the nation's second largest School of Medicine, as well as a rich high performance computing cyberinfrastructure, such activity is a natural fit for IU.

Showcasing this is work by Dr. Samy Meroueh and his group in the IU School of Medicine's Department of Biochemistry and Molecular Biology, along with the Center for Computational Biology and Bioinformatics. He is using IU's Big Red supercomputer in research aimed at the discovery and design of small molecules that can be used for the treatment of various diseases.

Big Red allows Dr. Meroueh to multiply many times the rate at which he can identify potentially useful molecules, a process that involves screening millions of candidate compounds and computing how well the candidate molecule shuts down the disease causing agent. His work has led to the discovery of highly potent agents that block processes that tumors must undergo to metastasize. Dr. Meroueh is now working in collaboration with various faculty at the world- renowned Simon Cancer Center at the Indiana University School of Medicine to assess the effectiveness of these molecules in animal models.

For more information, please visit the Meroueh web page.

Posted on: 05/01/2008 | 0 comments

Bulk email from Big Red

If you run a large number of jobs through Big Red (or any other supercomputer), you should include the line

# @notification = never

in your job scripts, unless you're absolutely positive your email server will accept a large number of emails. Read on to learn why.

Recently, a prominent research group stepped up testing of their system, running close to 9,000 jobs on Big Red each day. Each job sent a notification of the result to the group's Gmail account. Thousands of emails in a short time, forwarded to an external mail server, led to Big Red being classified as a spammer by SpamHaus. This meant that anyone at any organization using SpamHaus to create its blacklists couldn't receive email from Big Red - including Big Red users at IU!

IU sysadmins can't make sure every server out there will accept large numbers of emails. And since "Big Red" is not a real email server - it's an alias that aggregates the notification email from1024 nodes - we cannot use a standard bulk emailer setup to become a "legitimate" bulk emailer. If you run a lot of jobs, please help us to help you - turn off job notifications so you can still get the mail that you need.

Posted on: 04/04/2008 | 0 comments

Student in Open Systems Lab wins Microsoft Award

Congratulations to Joseph Cottam, of the Pervasive Technology Labs at Indiana University, on receiving the first ever Microsoft Award,from the International Network of Social Network Analysis (INSNA) for his paper "Extended Assortivity and the Structure in the Open Source Development Community." The award, given to authors of outstanding papers that address social relations aspects of softwaredevelopment, includes a $1,000 cash prize.

Cottam wrote the winning paper with Professor Andrew Lumsdaine, Director of the Open Systems Lab where Cottam works as a Graduate Research Assistant. The Cottam and Lumsdaine paper introduces a set of tools they call "Developmetrics" to investigate community formation and product development in the open source software community. Read the paper at http:// cs.indiana.edu/~jcottam/pubs/sunbelt2008.pdf

Posted on: 04/01/2008 | 0 comments

Big Red & Quarry queue changes

Big Red has a new SERIAL queue that includes all the nodes from theNORMAL and LONG queues. This will allow users to submit to the SERIAL queue single node jobs that are ideal for backfilling withouthaving to choose which queue will start a batch job sooner. An IEDC queue has also been added that will allow access to Big Red through the Indiana Economic Development Corporation in partnership with Purdue University.

Quarry also has a serial queue to serve the same purpose that includes all the nodes from the normal and long queues in addition to 5 dedicated nodes. A normal queue has also been added for jobs less than 7 days and includes 33 dedicated nodes in addition to the nodes from the long queue. In order to make these changes possible the long queue has been reduced to 42 nodes.

Please see the following Knowledge Base documents for more details:

Posted on: 04/01/2008 | 0 comments

The least you need to know updated!

The general introduction to Indiana University's Advanced Cyberinfrastructure is frequently updated, and has been recast in audio and audio/video format, for those who want to learn about computing, data storage, visualization and consulting while working on their aerobics (or who prefer a non-visual modality, for whatever reason).

These items are available from http:// rtinfo.uits.indiana.edu/documentation/.

Posted on: 04/01/2008 | 0 comments

Calendar - April 2008

Digital Library Brown Bag

Wednesday, April 2, 2008, 12:00-1:15pm
Wells Library E174

The Digital Library Program's Project Proposal Process
Stacy Kowalczyk and Michelle Dalmau

Learn about IU's supercomputers from the experts!

Thursday, April 10, 11:00am-1:00pm
Jordan Hall Atrium, IUB

You're invited to stop by and visit with the system administrators who run IU's supercomputers, Big Red and Quarry -- two of the most powerful supercomputers in the world.

Digital Library Brown Bag

Wednesday, April 16,, 2008, 12:00-1:15pm
Wells Library E174

Sakaibrary Update: Integrating Library Resources with Sakai
Jon Dunn

Research Technologies Round Table

Thursday, April 24, 12:30-1:30pm
IMU Persimmon Room & ICTC 497

Why optimize my code? It works already!

John Samuel, Director of the Center for Statistical and Mathematical Computing, will discuss Star-P, a software package designed to extend and parallelize high-level languages, including

a discussion of Star-P and how it extends Matlab,
optimizing Matlab code by incorporating Star-P data types, and
a review of Star-P availability on the IU campuses.

Posted on: 04/01/2008 | 0 comments

UITS provides support for award-winning IU musicologist

Congratulations to IU Jacobs School of Music musicologist Thomas Mathiesen, who in December 2007 took home his third Deems Taylor award from the American Society of Composers, Authors and Publishers for his work as an editor of the book Music and Ideas in the Sixteenth and Seventeenth Centuries.

Mathiesen serves as director for the IU Center for the History of Music Theory and Literature (CHMTL), a joint venture of the Jacobs School of Music and the Office of Research and the University Graduate School. With support from UITS Core Services, which provides hardware and server administration, Mathiesen and associate director Peter Slemon maintain the CHMTL Web site. The CHMTL site provides scholars from around the world with electronic access to doctoral dissertations in musicology and texts on music theory, aesthetics, history and literature, as well as historical music texts.

Posted on: 03/03/2008 | 0 comments

Fetal alcohol spectrum disorder data repository

For the past four years Indiana University researchers from the departments of Computer Science, Psychology, Anthropology, Anatomy and Cell Biology, and Medical and Molecular Genetics have been part of the Collaborative Initiative on Fetal Alcohol Spectrum Disorders (CIFASD), funded by the National Institute on Alcohol Abuse and Alcoholism. CIFASD, which includes researchers from 21 institutions in eight countries, was recently renewed for five years.

According to CIFASD Administrative Core Director Ed Riley of San Diego State University, "Fetal alcohol spectrum disorder is a major, worldwide public health issue and fetal alcohol syndrome is among the most common known causes of mental retardation in the western world. The work being done by the CIFASD is an international collaboration to study this problem using a multidisciplinary approach and should help define the spectrum of effects resulting from prenatal alcohol exposure. This includes providing better diagnostic protocols and an enhanced understanding of the changes in brain and behavior that occur following prenatal alcohol exposure, with the hopes of translating these findings into enhanced interventions."

CIFASD researchers are collecting a wide variety of data, including results from questionnaires, physical examinations, neuropsycho- logical test batteries, three dimensional facial images, brain images, and ultrasound movies. Data are collected at sites around the world using a variety of methods and then uploaded to the CIFASD Central Repository at Indiana University. CIFASD researchers can then use the Central Repository to join data from different locations and of different modalities. Members of the Research Technologies' Biomedical Applications group created the Central Repository and a variety of related software. A member of the Research Technologies' Advanced Visualization Laboratory developed the procedure used to capture three dimensional facial images.

The Central Repository for the CIFASD is hosted by the Indiana University Research Database Cluster, and makes use of the Indiana University Massive Data Storage System. The IU Research Database Cluster provides both an Oracle relational database management system and a Web application hosting environment used by the Central Repository. The Massive Data Storage System holds backups of the data in the Central Repository, providing highly resilient disaster recovery due to its geographically distributed nature.

More information is available on the Biomedical Applications group.

Posted on: 03/01/2008 | 0 comments

Indiana Academy students step into their virtual worlds at IU

Students from the Indiana Academy for Science, Mathematics, and Humanities may be a few years away from owning their own homes, but six juniors and seniors, with support from Indiana University's Advanced Visualization Lab (AVL), are able to step into a virtual kitchen of their own design.

The experience is part of an ongoing AVL project with an advanced computer class offered at the Muncie residential high school for gifted and talented students. Students from the program receive instruction from their computer science teacher, Susie Sechrest, and expert advice from IU's AVL staff, in creating a virtual environment of their own imagination.

Using programming knowledge in languages such as Java and C++, the students work in teams to create a variety of virtual environments, such as a mad scientist lab, an apartment, and a village. The students develop their projects in Virtual Reality Modeling Language (VRML) on a standard personal computer, and then interact with their creations in immersive 3D in the AVL=92s state-of the-art virtual reality theater.

Sechrest said her students have greatly benefited from their experience. "I could never relay the amount of information that can be absorbed through the use of the 3D glasses, the theater, and the big computer screen," she said. "This experience will stay with the students for a lifetime."

For more information on the Indiana Academy for Science, Mathematics, and Humanities or IU's Advanced Visualization Lab.

Posted on: 03/01/2008 | 0 comments

IU SPEA class invites you to take a survey

Staff from the UITS Research Technologies division have been working with a graduate level SPEA class this semester. The students are doing research on "green computing" and are studying efficiency and energy use in the IU data center. In an effort to learn more about high performance computing at IU and the people that use those resources, the students have put together a short survey which takes less than 5 minutes to complete. To request a copy please send email to hps-admin.

Posted on: 03/01/2008 | 0 comments

Calendar - March 2008

Digital Library Brown Bag

Wednesday, March 5, 2008, 12:00-1:15pm
Wells Library E174

The NEW IUScholarWorks: Repositories, Journals, and Scholarly Publishing
Julie Bobay and Randall Floyd

This talk is co-sponsored by the Continuing Education Committee of the Bloomington Library Faculty Council.

CGB Roundtable: Marlon Pierce

Tuesday, March 18, 12:00-1:00pm
MY 209

Tools for Web-based access to computing resources and data archives have been developed for over a decade and are now very mature. This talk will briefly review examples of these "gateways" and the associated grid middleware, and then delve into the architecture and standards used by the science portal community to develop reusable software components. Topics to be discussed include component-based Web portals, Web Services, and workflow (or service orchestration) tools.

Systems based on heavy-weight "enterprise" standards are being challenged by lighter-weight "Web 2.0" approaches that incorporate social networks, gadgets, content syndication, rich client interfaces (based on the resurgence of JavaScript), and REST-based services. The talk will review these and discuss the eventual merger of these technologies into science portals and gateways.

Digital Library Brown Bag

Wednesday, March 19, 2008, 12:00-1:15pm
Wells Library E174

The Evolution of Library Descriptive Practices
Jenn Riley

Research Technologies Round Table

Thursday, March 27, 12:30-1:30pm
IMU Persimmon Room & ICTC 497

Why optimize my code? It works already!

Ray Sheppard, Acting Manager of the High Performance Applications group, will discuss compilers and optimization. This talk will center on when it would be beneficial to spend time optimizing source code (and when it would not). Discussion of the time spent vs. gain realized will include case examples from users of Big Red. Simple tricks which may be used and some of the possible pitfalls to watch out for will be discussed as well.

Posted on: 03/01/2008 | 0 comments

TeraGrid '08 - Call extended

June 9-13, 2008 - Las Vegas, NV, USA

The Call for Participation for TeraGrid '08 has been extended, and all interested individuals and organizations are invited to participate. New deadlines are:

Proposals for papers on original, innovative work will be received and reviewed in three tracks: Science, Technology, and Education. All papers will be peer-reviewed. The Call for Participation is available at: http://www.tacc.utexas.edu/tg08/

Posted on: 03/01/2008 | 0 comments

TeraGrid workshop at AAAS meeting

Technologists from Indiana University Information Technology Services will inform some of the nation's top research scientists about advanced cyberinfrastructure at the annual meeting of the American Association for the Advancement of Science (AAAS) being held next month in Boston. IU is sponsoring a tutorial and workshop titled "The TeraGrid: An essential tool for 21st century science," on Sunday, February 17, from 10:30-noon.

"The AAAS meeting is among the largest gatherings of the best scientific minds in the world," said Craig Stewart, Associate Dean for Research Technologies and chief operating officer for Pervasive Technology Labs at Indiana Unversity. "This workshop provides a tremendous opportunity to inform scientific researchers across a wide spectrum of disciplines about the TeraGrid, and to show how it can help accelerate innovation and enable new discoveries."

Workshop attendees will learn how the TeraGrid can support virtual organizations - distributed teams and communities of scientists that share common interests or needs for data and computing resources. Noted Stewart, "The NSF is promoting the concept of virtual organizations as a way of responding rapidly to today's scientific, medical, and security challenges. The TeraGrid's combination of computing power, storage capability, and science gateways offers an unparalleled mechanism for enabling virtual organizations to solve some of the most challenging problems facing scientists today.

This workshop will also show how the TeraGrid is becoming more accessible to all scientists - even those without computer science expertise - through Science Gateways, tools that make it easier to access and use supercomputers. Any scientist whose research is slowed or inhibited by limitations on computer power or storage capabilities will find this workshop and tutorial valuable.

For more information, visit the Research Technologies home page.

Posted on: 02/01/2008 | 0 comments

Calendar - February 2008

Lunch with a system administrator

Come and have lunch with an IU cluster admin. Mid-February, details in the Message of the Day.

Cell/Broadband Engine programming workshop

On February 4 and 5, the IBM Future Technology Solutions Center team will be conducting a workshop on Cell/Broadband Engine programming at IUPUI. Another workshop will be scheduled later this spring.

Digital Library Brown Bag

Wednesday, February 27, 2008, 12:00-1:15pm
Wells Library E174

The Digital Library Federation Aquifer Initiative
Jon Dunn and Jenn Riley

This talk is co-sponsored by the Continuing Education Committee of the Bloomington Library Faculty Council.

Research Technologies Round Table

Thursday, February 28, 12:30-1:30pm
IMU Walnut Room & ICTC 497

Grid Tools
George Turner

The power of today's computing technology is in its diverse and distributed nature. Tying together this vast cyberinfrastructure are tools such as Globus, GridFTP, and GSI-SSH. Research Technologies will offer a brief introduction into these grid tools, with a goal of stimulating discussion on how they can be used to increase research productivity.

Posted on: 02/01/2008 | 0 comments

Institute for Digital Arts and Humanities created

A newly established Indiana University institute is set to digitally redefine scholarship and creative activity in literature, music, dance, and many other arts and humanities fields.

The Institute for Digital Arts and Humanities (IDAH) will enable and expand digitally-based arts and humanities projects by bringing together scholars, artists, librarians and IT experts. The Institute draws on established strengths at the IU Bloomington campus in combining arts and humanities disciplines and information technology such as the Variations digital music library, the EVIA digital video archive of ethnographic music and dance, 3-D virtual reality work by IU artists and the IU Digital Library Program.

For more information, see the the press release or visit the IDAH home page.

Posted on: 02/01/2008 | 0 comments

TeraGrid Knowledge Base taking off

There were more than 19,000 accesses to the TeraGrid Knowledge Base during the month of December, which now has 291 entries. Here's one of the newest: "On Big Red or Quarry, why is my job sitting in the queue, and when will it run?" The answer involves the commands showq, checkjob, and showstart; it can be found at


      http://www.teragrid.org/cgi-bin/kb.cgi?docid=awgw

or by searching the Knowledge Base for 'job queue' (for example).

Posted on: 02/01/2008 | 0 comments

Star-P available on Quarry

Star-P, from Interactive Supercomputing, Inc., is now available for user access on the Quarry cluster. Star-P is a client-server parallel computing platform that=92s been designed to work with Very High Level Language client applications such as Matlab or Python. Star-P makes parallel application development much more accessible than traditional programming models.

Vectorized Matlab code adapts well to Star-P's structures. Star-P supports parallelism by overloading core Matlab functions, so Matlab users should have little trouble incorporating Star-P. While not every Matlab Toolbox has explicit support for parallelism, seventeen commonly-used toolboxes do, including the neural network and signal processing toolboxes. A web-based tutorial on =20 using Star-P with Matlab is available.

Star-P's support for Python is also stable. We are interested in contacting active Python users for testing purposes. At present R support is in the development stage.

If you are interested in trying Star-P, the SoftEnv keyword for is +Starp. Once this key is added to your .soft file, you can start Star-P using =20= a command such as


      starp -j'-l nodes=3D1:ppn=3D2' -p 2

If you need additional information on Star-P, please don't hesitate to contact the Stat/Math Center (statmath @ indiana.edu).

Posted on: 02/01/2008 | 0 comments

System Administration

The maintenance window for all systems is the first Tuesday of each month, 7am - 7pm EDT.
This includes the Massive Data Storage System!

Outage reports are available online for Big Red, Libra, and Quarry.

How To Contact Us And Get Help

If you have questions pertaining to IU's cyberinfrastructure, or you are encountering some difficulty, there are several ways to obtain help.

An introduction and overview titled "Indiana University's CyberInfrastructure: The least you need to know" has been updated and is available along with other introductory resources.

The IU Knowledge Base is an excellent source of help on how to do things.

If you have problems which the KB does not enable you to solve, questions about system outages, or if you just have a problem and you don't know who to contact, send email with the RT contact form.

This is an official publication of Indiana University produced by the Research Technologies division, University Information Technology Services, Indiana University.

Subscription is automatic when you receive an account on IU's advanced cyberinfrastructure. Please email comments, questions, and subscribe/unsubscribe requests, using the RT contact form.

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