Supercomputer provides massive computational boost to biomedical research at TGen

October 29, 2008

In less time than the blink of an eye, the Translational Genomics Research Institute's new supercomputer at Arizona State University can do operations equal to every dollar in the recent Wall Street bailout.

That would be 700 billion computations in less than 1/60th of a second, says Dan Stanzione, director of the High Performance Computing Initiative at ASU's Ira A. Fulton School of Engineering.

The "Saguaro 2" supercomputer, housed on the first floor of ASU's Barry M. Goldwater Center for Science and Engineering, is capable of 50 trillion mathematical operations per second.

"That's the equivalent of taking a calculator and doing one operation per second, by hand, continuously for the next one and a half million years," Stanzione said.

Although the computing world changes daily, and measurements depend on numerous factors, Stanzione said, for some functions, ASU's new computer may be among the top five in the world.

TGen will need that speed as it continues its research into a variety of human diseases through the use of data-rich DNA sequencing, genotyping, microarrays and bioinformatics.

"This is really a remarkable testament," to the cooperative efforts of ASU and TGen, said Dr. Jeffrey Trent, President and Scientific Director of TGen, especially in a tight funding environment.

The new supercomputer will help TGen's efforts in translational biomedicine, developing new therapies targeted for individual patients suffering from Alzheimer's, autism, diabetes, coronary heart disease, melanoma, pancreatic cancer, prostate cancer, colon cancer, multiple myeloma, and breast cancer.

Dr. Edward Suh, TGen's Chief Information Officer, said a joint TGen-ASU computer support team is being assembled, and he urged the creation of more partnerships between TGen and ASU.

"I am confident this new supercomputer system will help the ASU and TGen scientists expedite their research, and accelerate innovation in biomedical and engineering research," Suh said. "It is my hope to see this supercomputer system, and a supporting informatics program which Dan and I are putting together, bring the ASU and TGen scientists closer than before for even greater success."

Saguaro 2 - a partially water-cooled set of 7-foot-tall black monolith computer racks, each with as many as 512 processor cores, and linked by ultra-high-speed Infiniband cables - was funded in part by a nearly $2 million grant in July by the National Institutes of Health. The grant was in response to a wide range of scientific activities proposed by TGen, the Ira A. Fulton School of Engineering, and ASU's BioDesign Institute.

The new system doubles the capabilities of ASU's High Performance Computing Initiative (HPCI). The system consists of Intel microprocessors, servers from Dell, storage from Data Direct Networks, and components from a number of other partners, including fiber optic cables from Phoenix-based Zarlink.

More importantly for TGen, the new system has 20 times the previous computational power available to TGen researchers, said James Lowey, director of TGen's High Performance Biocomputing Center.

The new supercomputer also adds to the storage capacity of the HPCI, bringing the total storage to 1.5 quadrillion bytes, or 1.5 petabytes -- or 15 followed by 14 zeroes (1,500,000,000,000,000). That's enough storage space to record nearly a quarter million DVD discs.

The HPCI storage will be used to store a vast array of data from TGen's sequencers and simulations, as well as other large datasets from ASU researchers, including a high resolution mapping of the moon to be performed in 2009 by NASA's Lunar Reconnaissance Orbiter.

Stanzione said the dedication marked the start of "our next era in supercomputing," and of three ASU milestones:

* The start of production operations of Saguaro 2.

* The beginning of a new and stronger partnership with TGen.

* The nearly three years since the start of ASU's High Performance Computing Initiative.

"I firmly believe that computation is crucial to the competitiveness of our research at TGen and at ASU, and is increasingly crucial to our economic competitiveness as a state, and nation, as well," Stanzione said.

High performance computing addresses the needs of science beyond theory and experimentation to "the ever more important role of simulation," which he called the "Third Mode" of scientific progress.

"As we move in science into the nano scale of materials and molecular design and diagnostics, or into the macro scale of global climate or the motion of the galaxies, experimentation becomes more expensive and difficult, and simulation becomes invaluable," Stanzione said. "The speed of those simulations determine the speed of progress."

The computational speed of Saguaro 2 is especially critical to the work of TGen.

"In 2009, more genome sequence data will be generated than all the words spoken by humans in all of history. Teasing meaningful understanding from this avalanche of data is also the role of HPC (high performance computing)," Stanzione said.

The Translational Genomics Research Institute

---

---

	Computer Architecture: From Microprocessors to Supercomputers (Oxford Series in Electrical and Computer Engineering) by Behrooz Parhami (Author) Computer Architecture: From Microprocessors to Supercomputers provides a comprehensive introduction to this thriving and exciting field. Emphasizing both underlying theory and actual designs, the book covers a wide array of topics and links computer architecture to other subfields of computing. The material is presented in lecture-sized chapters that make it easy for students to understand the relationships between various topics and to see the "big picture." The short chapters also allow instructors to order topics in the course as they like. The text is divided into seven parts, each containing four chapters. Part I provides context and reviews prerequisite topics including digital computer technology and computer system performance. Part II discusses instruction-set...
	The Supermen: The Story of Seymour Cray and the Technical Wizards Behind the Supercomputer by Charles J. Murray (Author) The SUPERMEN "After a rare speech at the National Center for Atmospheric Research in Boulder, Colorado, in 1976, programmers in the audience had suddenly fallen silent when Cray offered to answer questions. He stood there for several minutes, waiting for their queries, but none came. When he left, the head of NCAR's computing division chided the programmers. 'Why didn't someone raise a hand?' After a tense moment, one programmer replied, 'How do you talk to God?'" -from The SUPERMEN The Story of Seymour Cray and the Technical Wizards behind the Supercomputer "They were building revolutionary, not evolutionary, machines. . . . They were blazing a trail-molding science into a product. . . . The freedom to create was extraordinary." -from The Supermen In 1951, a...
	Understanding Supercomputing by Scientific American (Author), editors at Scientific American (Author) In this book you'll discover what constitutes a 'supercomputer', how the supercomputers of today function, how you can make your own computer into a super machine - through networking - and what tomorrow holds in store for computer usage in terms of hardware, software and everyday applications.
	The Whale and the Supercomputer: On the Northern Front of Climate Change by Charles Wohlforth (Author) Scientists and natives wrestle with our changing climate in the land where it has hit first --and hardest A traditional Eskimo whale-hunting party races to shore near Barrow, Alaska-their comrades trapped on a floe drifting out to sea-as ice that should be solid this time of year gives way. Elsewhere, a team of scientists transverses the tundra, sleeping in tents, surviving on frozen chocolate, and measuring the snow every ten kilometers in a quest to understand the effects of albedo, the snow's reflective ability to cool the earth beneath it. Climate change isn't an abstraction in the far North. It is a reality that has already dramatically altered daily life, especially that of the native peoples who still live largely off the land and sea. Because nature shows her...
	SUPERCOMPUTER #39 (Choose Your Own Adventure) by Edward Packard (Author)
	A Scientist's and Engineer's Guide to Workstations and Supercomputers: Coping with Unix, RISC, Vectors, and Programming by Rubin H. Landau (Author), Paul J. Fink (Author), Paul J. Landau (Author), Rubin H. Fink (Author) A scientist’s and engineer’s guide to Workstations and Supercomputers Crack the Unix code and put its power to work for you. If you’re seeking such clear-cut guidance, your search will end with the first Unix survival manual designed specifically for practicing scientists and engineers like you. Avoiding the narrower concerns and complicated jargon of computer science, this guide shows you how to master the complexities of accomplishing computer projects—from start to finish—predominantly under a Unix operating system. With the help of clarifying examples and tutorials, you’ll learn how to write and organize files and programs as well as run, debug, and visualize the results of scientific programs on workstations and supercomputers. At the same time, you’ll discover how to...
	Peer-to-Peer Computing: Building Supercomputers with Web Technologies (Computer Communications and Networks) by Alfred Wai-Sing Loo (Author) Communications of ACM Internet Research IEEE Transactions on Parallel and Distributed Systems Parallel Computing IEEE Transactions on Computers ACM Transactions on Computer Systems
	Optimizing Supercompilers for Supercomputers (Research Monographs in Parallel and Distributed Computing) by Michael Wolfe (Author) Effective use of a supercomputer requires users to have a good algorithm and to express this algorithm in an appropriate language, and requires compilers to generate efficient code. This book investigates several problems facing compiler design for supercomputers, including building efficient and comprehensive data dependence graphs, recurrence relations, the management of compiler temporary variables, and WHILE loops. The book first proposes an efficient means of representing the flow of data in a program by labeling the arcs in a data dependence graph with "direction vectors" to show how the flow of data corresponds to the loop structure of the program. These data dependence direction vectors are then used in several high level compiler loop optimizations:...
	Parallel Processing for Supercomputers and Artificial Intelligence (Mcgraw-Hill Series in Supercomputing and Parallel Processing) by Kai Hwang (Author), Doug Degroot (Editor)
	The Supercomputer Era by Sidney Karin (Author), Norris Parker Smith (Author)