Researching the structure and behavior of human proteins presents super problems that require a supercomputer and...
a monumental amount of storage capacity to solve. So when the University at Buffalo's (UB) main technology partner, Dell, "lost interest" in it, UB turned instead to IBM for a computing cluster and SAN storage to beef up its infrastructure.
Dr. Jeffrey Skolnick, director of the Center of Excellence in Bioinformatics at UB, spends his days trying to unlock the secrets of life. His ultimate goal is to aid in the development of more targeted drugs to treat diseases such as cancer, Alzheimer's, AIDS and multiple sclerosis. But analyzing protein structures and mapping molecules was monopolizing the Center's 4652 processors and 15 TB of EMC SAN storage 24 hours a day.
"Our systems are completely full 100% of the time," he said. At the time of our interview, Skolnick had 5400 jobs in the queue and 3944 of his 4000 active processors were running jobs (the IBM systems are still being tested). "This thing is pegged twenty-four-seven. That's why we needed the additional 542 processors from IBM."
Interoperability was a major concern because the majority of the Center's legacy systems are Dell servers backed by storage arrays from EMC Corp. Adding the new IBM gear was a necessary "expansion" of the Center's IT resources.
Skolnick signed a deal with IBM instead of buying more Dell and EMC systems because Dell "lost interest in the installation. Unfortunately, the level of customer service and technical support that Dell provided was not what I had hoped for," said Skolnick. However, he stressed that while his EMC arrays were purchased through Dell, he has never had a problem with EMC's customer service. "Our interactions with EMC were extremely positive. This is by no means a reflection on EMC."
The new IBM systems will enhance and not replace the existing Dell and EMC hardware. "Our Dell and EMC systems have another year of good life," said Skolnick.
Before the Center signed on with IBM, Skolnick's team established a tough product screening process. "We obviously looked at the standard cast of characters. The vendors had to provide us a working architecture to test and if they didn't they were immediately disqualified. IBM passed muster.
The new supercomputer, capable of a peak performance of more than 1.32 TeraFlops, will consist of a cluster of 266 IBM eServer BladeCenter HS20 systems running Red Hat Advance Server 2.1 Linux, each with two 2.8 GHz Intel Xeon processors and 1 GB of memory. Seven IBM xSeries 345 Intel processor-based servers connect to 5 TB of IBM TotalStorage FAStT700 storage servers to house the Center's large volumes of biological and research data. The supercomputer forms the basis of the IBM eServer Cluster 1350, a pre-packaged and tested supercluster.
Skolnick has two people maintaining his massive IT infrastructure and no one person dedicated to storage management. Though Skolnick did not disclose how much the IBM hardware cost, he said "the system had to be as automated and easy to manage as possible and it had to [fit] into my budget."
Although the Center's IT budget is "on the order of millions of dollars," Skolnick said cost was not the overriding factor in his buying decision. He said IBM's involvement in Life Sciences was compelling. Subsequently, IBM has entered into a research partnership with Skolnick's group. IBM will share computing algorithms for discovering patterns and correlations among protein data in exchange for Skolnick's input on future IBM technologies. He said "they have no commitment to actually listen to what I have to say, but it's an opportunity to offer an end user opinion [on where IBM is going with its architecture]."