• ARSC Installs Two New Systems
• From the Director
• Horner-Miller Named SC2006 Chairperson
• ARSC Holds Third Annual Faculty Camp
• ARSC at SC2003
• ARSC Adds Resources to UAF Mac Lab
• Portable Cray Bioinformatics Library Released

ARSC Installs Two New Systems

ARSC staff were hard at work during the summer of 2003 installing two major new systems that will soon increase the center’s computational power tenfold. A Cray X1 was installed and has become generally available, while an IBM p655+/p690 is currently undergoing effectiveness level testing.

ARSC staff spent much of the summer working with Cray engineers, researchers and specialists to configure the X1 to run in the ARSC computing environment. The system underwent significant testing to ensure that it would be stable and efficient for users.

“This was a challenging project because the X1 is probably one of the most leading-edge technologies ARSC has been involved in,” said ARSC systems analyst Liam Forbes. “We were able to participate in the development cycle and work with Cray, and other centers, to create a better product. It was a growing opportunity for ARSC, and for me as an HPC system administrator. It was kind of fun to have the fastest performing Cray in the world, even if it was only for a day or two.”

The ARSC Cray X1, called Klondike, is equipped with 128 multi-streaming processors and has a theoretical peak performance of 1.6 teraflops. Pioneer users were allowed onto the system in early October, and it will be opened to all users in early November. Already, ARSC oceanographer Kate Hedstrom’s Regional Ocean Modeling System (ROMS) is running six times faster than her earlier runs on the IBM SP.

ARSC’s newest IBM, called Iceberg, arrived at the center in the early fall 2003. The IBM is being configured in the former ARSC visualization laboratory, which is located in the Butrovich building next to the existing machine room. Each p655+ weighs in at 3,000 pounds, for a total of just over 15 tons for the eleven frames that make up the entire system. Iceberg requires about 18 kilowatts of power to operate, and produces 825,000 BTUs of heat.

The p655+/p690+ system is currently running using an interim switch. In late November, a Federation Switch will be installed. Following this upgrade, the system will begin undergoing testing and acceptance. ARSC hopes to allow pioneer users on the IBM in early 2004. [Back to Top]

From the Director

As we carry out the daily activities of keeping our growing supercomputing center running and moving forward, it is always rewarding to stand back and look at the big picture. The reason we work so hard to help users get their codes running, to keep our machines functioning at their highest levels, or even to keep our accounts up to date, is that each of these actions is contributing to a larger whole—the science that our users are able to accomplish with ARSC resources. It is this science, and its contribution to discovery, that really defines supercomputing.

ARSC has been involved in increasing the center’s direct contributions to scientific discovery significantly over the last year. Specialists and research faculty are joining the center to complement and work with the center’s users and joint faculty. And, we are currently undergoing a national search for a chief scientist who will lead our computational science team.

Next semester, ARSC will be expanding to new office space in the nearly-finished West Ridge Research Building on the University of Alaska Fairbanks campus. Already, we have renovated a portion of our current home, the Butrovich building, to accommodate our growing staff. We have moved our visualization and teaching lab out of that same building to make room for an 800-processor IBM system, which is currently undergoing installation. Over the last year, and especially the last few months, ARSC staff have worked hard to bring three major new systems and the Discovery Lab online, and to ensure that those systems meet or exceed the rigorous standards we uphold for our users’ benefit.

While we go about accomplishing the tasks to make these projects happen, our users are soaring forward with our machines, studying intricacies of biological molecules in hopes of achieving new understanding of hibernation, modeling the workings of the physical environment and making predictions about how tsunamis inundate coastal communities, or exploring virtual environments and designing innovative ways to interact in these new spaces. But it is these moments when researchers are able to see their data in a way that they had previously only imagined that we are reminded of the reason we are here carrying out our everyday tasks.

Looking back on ARSC’s tenth year, and looking forward to the possibilities of the next ten, I’m excited about the ways our center has developed opportunity and facilitated discovery, and how we will continue to contribute to the future. [Back to Top]

Horner-Miller Named SC2006 Chairperson

Arctic Region Supercomputing Center associate director, Barbara Horner-Miller, has been elected chair of the international high performance supercomputing and networking conference, SC2006.

“This is an exciting opportunity,” said Horner-Miller. “SC is an incredible volunteer-driven organization that significantly contributes to the fields of high performance computing and networking.”

The SC conference, originally called The Supercomputing Conference at its inception in 1988, was re-named in 1997 to reflect the growth of the high performance computing industry. The international conference now annually brings together thousands of experts from high performance computing and networking industries to learn about new scientific applications and listen to other experts present their most recent research. The conference’s showroom floor boasts exhibits from organizations such as NASA, IBM and Cray, Inc. Each year, conference organizers temporarily construct the fastest network in the world for the week of the conference.

Horner-Miller has served in various committee roles including Research Exhibits Chair, Masterworks Chair, Panels Chair and currently Technical Program Co-Chair. She is also on the SCXY steering committee.

“We’re excited to see Barbara share her talent with such a first rate organization,” said ARSC Director Frank Williams.
The SC conference is sponsored by the Institute of Electrical and Electronics Engineers (IEEE) Computer Society and the Association for Computing Machinery’s Special Interest Group on Computer Architecture (ACM SIGARCH). [Back to Top]

ARSC Holds Third Annual Faculty Camp

The summer of 2003 marked the third year of ARSC’s Faculty Camp, an event that draws researchers and faculty from the University of Alaska Fairbanks (UAF) campus and other affiliated federal and academic research organizations to the center to learn about the resources available at ARSC. The annual Faculty Camp was initiated to familiarize UAF faculty with the computing resources available at the center, and give those users whose projects might benefit the training to begin using those resources. Participants attend classes in vector programming, code optimization, visualization, animation, code debugging, and more. In addition, each participant works one-on-one with ARSC staff members, who can help the user troubleshoot particular questions or ideas.

During the three-week event, attendees work in a hands-on lab setting and attend classes on various topics pertaining to high performance computing, taught by ARSC staff. Between classes, attendees have a chance to work on their own projects, allowing them to apply new skills and come back to labs with questions.

“I’m now going to go off and do something that I have all the tools I need to accomplish,” said Eric Anderson of the U.S. Army Cold Regions Test Center after completing this year’s camp.

Faculty Camp is an important activity that allows ARSC to strengthen its user-base and ties with particular users and their projects. The center plans to continue the camp in the coming years. Check the ARSC website this spring for announcements and applications for Faculty Camp 2004. [Back to Top]

ARSC at SC2003

ARSC vector specialist Ed Kornkven and Andrew Johnson of the Army High Performance Computing Research Center (AHPCRC) will present a tutorial at the SC2003 conference. SC2003 is the premier annual conference in high performance computing and networking. Tutorial acceptance at the conference is highly competitive, with approximately 25% of the applicants being accepted.

The tutorial, titled “Vector Performance Programming,” will provide an overview of vector computing with an emphasis on programming for high performance on today’s vector platforms. Included in the tutorial will be a history of vector hardware, architectural features, and how speedup is achieved on a vector machine. An in-depth discussion of the capabilities and limitations of modern vectorizing compilers will include techniques for restructuring code to enable vectorization. The tutorial will end with a pair of application case studies and a discussion of how vector computing is being combined with parallel and multi-streaming methods on the new Cray X1.

Ed Kornkven began working with supercomputers at the National Center for Supercomputing Applications while doing programming of insect pest models at the Illinois Natural History Survey. His teaching experience includes courses in compilers, programming languages and parallel and vector computing. Since 2002 he has been a vector specialist at ARSC. [Back to Top]

ARSC Adds Resources to UAF Mac Lab

In late fall 2003, ARSC and the University of Alaska Fairbanks (UAF) made available new Macintosh computer resources to support classes and training sponsored by the center and UAF. The lab is equipped with ten student and one instructor Macintosh G5 2GHz dual processor systems. Currently, ARSC/art department joint appointee Miho Aoki is using the lab to teach a computer animation, 3D design class.

ARSC staff began working with Robert Hale of UAF’s Department of Computing and Communications this summer when it became necessary to relocate the training lab. The existing SGI systems in the Butrovich building needed to be moved to make room for the center’s new IBM system (see page 1). It soon became apparent that there was a need on campus and in ARSC classes for more powerful computers. The G5s were purchased to meet this requirement.

“The location of the new lab in the main part of campus will make it more accessible to students,” said Aoki. “It is also within walking distance of the Discovery Lab, where they will be working during the last part of the semester.”

The lab, located in the Gruening building on the UAF campus, also houses UAF Macintosh and Windows-based PCs. The lab is open to classes and training activities, and will be staffed by ARSC students at scheduled times throughout the semester. For more information, call 907-474-5102. [Back to Top]

Portable Cray Bioinformatics Library Released

ARSC announced in August the release of a new portable version of the Cray Bioinformatics Library (CBL). The library, which was developed in cooperation with Cray Inc. by ARSC MPP Specialist James Long, contains the same functions as the CBL, and is compatible with hardware systems other than Cray.

The original CBL is a set of fundamental library routines that take advantage of proprietary Cray hardware to implement some common nucleotide/protein sequence manipulations typically used in a bioinformatics context. This library was optimized for the Cray SV1 and Cray X1 platforms and is available from Cray. The Portable CBL is written in C and implements the computational primitives of the original library in a generic fashion with little regard to specific hardware. The Portable CBL routines facilitate performance by operating on compressed data whenever possible.

“It has been a wonderful opportunity for ARSC to work together with Cray Inc. to contribute to the field of bioinformatics,” said ARSC director Frank Williams. “We hope to see this library continue to grow as additional biological computational primitives are identified and implemented.”

The Portable Cray Bioinformatics Library was made available on SourceForge.net and can be downloaded for use by researchers at cbl.sourceforge.net. [Back to Top]