Buffalo: The land of chicken wings, snowstorms — and grid computing?

BUFFALO, N.Y. — The 100-acre medical campus in downtown Buffalo is considered by many here to be the rose amid the rubble of this rusty industrial city still recovering from an economic collapse that took place 30 years ago. The Buffalo Niagara Medical Center, called the corridor, employs 8,000 people among four main healthcare and research institutions and has a supercomputing center that could be the envy of the Northeast.

The Center for Computational Research (CCR) at the State University of New York’s University at Buffalo operates a 1,200-server system that supports about 100 research groups spanning nearly 40 departments at the university, as well as more than 20 companies and institutions in the Buffalo-Niagara region. Among them are the world-renowned Roswell Park Cancer Institute, the Hauptman-Woodward Research Institute (HWI) and the new New York State Center for Excellence in Bioinformatics & Life Sciences, where the system is housed.

The CCR system also serves as the hub of a statewide grid connecting 18 educational and research institutions. But in its primary role as the computational heart of the medical campus, CCR’s system can produce the complex structure of cells and proteins in days vs. months or even a year using a series of workstations, says Director Thomas Furlani.

Click to see: The University at Buffalo's "U2" cluster of 1,056 Dell servers is the computational heart of the city's medical campus and could play a key role in Buffalo's revitalization.

In addition to bioinformatics, which includes DNA and protein sequence, gene expression and biological pathway analysis, CCR’s system supports computational chemistry, data mining and database development, earthquake engineering, environmental modeling and simulation, grid computing, homeland security, visualization and urban planning, and virtual reality and animation.

On the homeland security front, the Jacksonville, Fla., city school district is having CCR construct a prototype visualization of its schools so if there’s a shooting, for example, law enforcement and school officials can virtually look in every nook and cranny for the assailants or available exits.

“You never know where this is going to lead," Furlani says.

Grid close-up

CCR’s system consists of parallel processing servers connected by 2Gbps bidirectional links, with a 100BaseT connection for maintenance and administration. It also includes sequential processing servers linked via 1Gbps Ethernet.

The largest cluster in the group includes 1,056 Dell PowerEdge SC1425 servers, each of which has two 3.0GHz or 3.2GHz Xeon processors, and varying amounts of main memory: 964 nodes configured with 2GB; 64 nodes configured with 4GB; and 32 nodes configured with 8GB. The servers are interconnected with a pair of Force10 Terascale E1200 Gigabit Ethernet switches and run the Red Hat Linux operating system.

The peak performance of this cluster is just over 13 teraflops per second — or 13 trillion operations every second — and all machines run at 85% to 90% of capacity, Furlani says. The University at Buffalo acquired the bulk of these servers in 2005, and the remainder in 2006.

CCR also employs a 35TB EMC storage-area network with I/O performance of 3G bytes/sec. In all, CCR has more than 300TB of storage, and combining this with the 13 teraflops of compute power makes it No. 87 on the list of the top 100 supercomputing centers in the world, according to supercomputing site tracker Top500.org.