UB bolsters its supercomputer
Increases its power, relocates it to medical corridor
By Fred O. Williams, BUFFALO NEWS BUSINESS REPORTER
Updated: 03/04/07 4:47 PM
Walk with Thomas Furlani between racks and racks of computers and you feel a blast of scorching heat.
Furlani, director of the supercomputer center, seems used to it. "You know they're working," he says - meaning either the machines or the far-flung research scientists who use them.
The energy thrown off by more than 2,000 processor chips is a measure of the computational work being done on the University at Buffalo's supercomputer - now in a new location near downtown Buffalo.
UB has finished moving its big Dell number-cruncher to its bioinformatics center in the city's medical corridor. The move - from the university's Amherst campus to a developing commercial district - gives a push to life science research and marks another step in the bio center's development, officials said.
Connected to the main campus by fiber-optic cable, the supercomputer was moved without depriving scientists in other fields of the resource, according to university officials. Highend computation is a critical tool for engineering, physics and other fields besides life science.
"There was never an issue in terms of access - the machines could be pretty much anywhere," Furlani said. The center's staff of 14 has opened a satellite office on campus, where they help scientists get their projects to run on the supercomputer.
While it may not matter to researchers where the equipment is, having it physically in the medical corridor adds to the city's commercial drawing power, development experts said.
"It really is a great showcase to have, to show we're really on the cutting edge," said Matthew Enstice, director of the Buffalo Niagara Medical Campus, a non-profit group that is coordinating the district's development.
Part of the supercomputer center's mission is to work with local companies, making it a resource for business as well as academia.
With the computer center's move came an upgrade giving its main "cluster," called U2, a capacity of 13 trillion calculations per second. The upgrade came after the computer was already ranked at number 87 on the widely watched Top500.org list of the world's fastest machines. Even so, the ranking puts U2 among an exclusive group of government research labs and a few top universities in terms of computing power.
During a tour one day last week, U2 was 96 percent busy working on 176 projects, with hundreds more in line. That marked a sharp contrast from 2005, when more than a third of the machine sat idle for months because it lacked sufficient electricity at the Amherst campus.
The newly built home has onethird more electric capacity than the present machine needs, "so we have some room to grow," Furlani said.
Last month, the machine missed another mishap when a cold snap caused a water pipe to burst. The breach sent water cascading into the center's ground floor, but the 4,000- square-foot machine room wasn't affected.
The supercomputer center - formally known as the Center of Computational Research - also houses supplemental highend computers, a high-capacity data storage system, and a visualization center for displaying graphical representations and computer simulations. Running one project, for example, its big screens give an animated view of what Buffalo's Main Street pedestrian zone would look like if it were opened to rush-hour traffic.
Hosting the supercomputer marks another milestone in the development of the 150,000- square-foot bioinformatics center, officials said. Announced with fanfare by former Gov. George Pataki in 2001, the fourstory center is the middle of a $200 million trio of research buildings at Virginia and Ellicott streets, bracketed by the Hauptman Woodward Medical Research Institute and Roswell Park Cancer Institute's gene research center.
"The center of excellence has become actually much more key than was originally envisioned as the facilitator of that industry, government and university partnership," center director Bruce Holm said.
With its combination of labs, offices and now computing power, the bioinformatics center is a place where scientific research can meet the business culture necessary to get discoveries from the lab to the bedside, he said. Next door to Holm's office on the center's top floor is space for biotech management consultants from Buffalo Biosciences LLC, a commercialization consultant.
The new Spitzer administration in Albany is following a national trend among universities to pull back from aggressive university involvement in commercialization efforts, Holm said. As a result, the bioinformatics center has received a commitment for $1.4 million a year in state development funds to support commercialization work apart from the university.
"You get a natural tension that's going to occur between the core mission of a university and the next step [after scientific discovery]," he said.
The scientific goal behind the research complex - to unlock the genetic secrets behind human health and disease with the aid of powerful computers - is starting to play out, researchers said.
Geneticist Norma Nowak explained how her project looks at human tissue samples, but needs silicon computing power to yield results.
She examines cells from thousands of cancer patients, each one with some 38,000 genetic variables that need to be examined and matched to their medical history. Connecting genetic abnormalities to disease should uncover important patterns that point to better treatments, she said. Finding disease- linked genes can also lead to new, more targeted drugs than current chemotherapy, whose battle with tumors wreaks collateral damage on the rest of the body.
"We have all these tumor types in a database," she said. "We're trying to look at what is in common across all these tumor types, and what discriminates between tumor types." The complex job would be impossible without high-end computing resources, she said.
Another project at the center looks at fruit flies - that staple of college biology labs - to study genetic regulators. Understanding the chemical mechanisms that turn genes on and off is seen as a key to understanding birth defects and evolutionary processes as well as disease.
UB switched on its supercomputer center in 1999 to support the rapidly growing field of computational modeling. When launched, its two main computers had a combined capacity of 60 billion calculations per second; upgrades have boosted the center's current speed to about 200 times that.