In conducting research on how global warming and toxic waste affect the world's microorganisms, the University...
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of Houston chose to use a cluster of Intel Itanium servers rather than x86 commodity hardware, largely because of memory considerations.
The university uses five Itanium-based systems running Red Hat Enterprise Linux to conduct its research. The hardware includes a four-way HP rx5670, a 16-way HP rx8620, and a 64-way SGI Altix 3700. Lennart Johnsson, a computer science professor at the university and the project's director, said that the University of Houston has worked with three generations of Itanium machines, and the newest ones are the reigning kings, no doubt.
But why not go with an x86 Linux cluster based on commodity hardware? Johnsson said the memory performance isn't quite there yet on x86, and the memory caches on Itanium are even better than its EPIC/RISC competitors: IBM's Power and Sun Microsystems' Sparc.
The applications that the university runs are memory hogs. The average microbial genome has 5 million base pairs, which researchers manipulate from within data structures that can require more than 200 GB of RAM. The Itanium systems – and in particular the SGI server – can handle that kind of load.
"One of the weak points with computing resources are memory systems," Johnsson said. "Some are quite good, but even when they are good, memory access is not so good. If you have a large cache, you have a much faster cache and faster performance."
The university has run on Itanium for three generations of the chip, dating back to the initial processor that came out in 2001. Before that, it ran Linux on PA-RISC and 32-bit x86 Intel processors.
Johnsson acknowledged that Itanium systems cost more up front than x86-based systems, but said that lifetime cost "considering price performance, availability and support for applications requiring 64-bit precision made the convincing argument."Kudos from Itanium Alliance
The University of Houston was one of three recipients of the Itanium Solutions Alliance Innovation Awards.
The alliance began giving out awards to Intel Itanium users last year and followed that up this year with another group of three award-winners. The University of Houston won for humanitarian impact, while Protégésoft won for enterprise business application achievement, and S7 Software Solutions won the entrepreneurial innovation award.
"We started a year ago to recognize work being done on Itanium systems, said Joan Jacobs, executive director of the alliance. "We thought it would be interesting to see how Itanium systems are being used."
The University of Houston is trying to figure out how big microbial communities are and how the diversity of the communities is affected by external factors, such as human activities and global warming.
"All these ways to measure things becomes possible because we could do heavy analysis of the genome characteristics to figure out how many are distributed in random fashion," said Yuriy Fofanov, director of Bioinformatics Laboratory, University of Houston.
The award comes with a $50,000 prize. The university hasn't decided what it will do with the money, but suggested that it could go toward attending industry conferences and buying more Itanium systems.