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Eight-Way Intel-Based Servers Offer New Choices for Bioinformatics Departments


SANTA CLARA, Calif.--More options are available for bioinformatics departments now that Intel and its partners have launched machines that use eight microprocessors working together in a server to equal the power of more expensive high-end computers. The much lower cost of these 8-way Intel-based servers is expected to put a considerable amount of price pressure on vendors of the most powerful systems such as Sun Microsystems, Silicon Graphics, IBM, Hewlett-Packard, and the Digital Equipment division of Compaq Computer.

Intel released its Profusion chipset and architecture last month, enabling up to eight Pentium III Xeon processors running at 550 MHz to support demanding enterprise-level applications, such as web server functions. According to Pat Buddenbaum, Intel's marketing manager, server components division, the new systems are a continued evolution of the standard high-volume server, going from 4-way to 8-way. He claimed the equipment is "on par" with performance but, on average, 3-4 times less costly than other comparable high-performance servers.

With about 20-25 system vendors slated to be selling these servers by year-end, they are available now from Compaq, NEC, Fujitsu, Hitachi, and Siemens, while Hewlett-Packard, IBM, Dell Computer and others are expected to begin shipping them later this month. As for operating systems, the servers can run a variety of operating environments including Microsoft's Windows NT, Novell's Netware, Linux, Sun's Solaris, and Santa Cruz Operation's Unixware, Buddenbaum added.

"It's going to have a big impact," said Nat Goodman, director of Compaq's bioinformatics solutions center, commenting on the news from a cost and performance standpoint. "The issue for bioinformatics is going to be the operating system issue," he added. Because most software developers in this field prefer to use one of the variants of the Unix operating system, Goodman sees a big opportunity for Linux to expand its presence in bioinformatics, given its low cost. Linux is an open-source system that is given away for free and developed by volunteer programmers in the computing community, which gives it a "whole different ethic" than that of the commercial Unix systems, remarked Goodman. Even though it is available for free, there are a number of companies selling the software at low prices along with support and other add-on features.

Linux is already popular and becoming more so in bioinformatics, said Goodman. Compaq is seeing some of its customers using Linux in Beowulf clusters--a loosely coupled cluster of Linux machines running on Pentium-based hardware--for tasks that can be separated into many small pieces. Incyte is the "premier example" of a Beowulf cluster site where the cluster is used to run software that generates Incyte's databases and analyzes data for them. Pentium machines running Linux do the number crunching, while Digital Alpha chip-based computers act as master and intermediate-level controllers, said Goodman.

David McAllister, director of strategic technologies at SGI, echoed many of Goodman's comments about the Intel servers being an inexpensive way to get a lot of power and a "distributed share model" for solving a problem. The servers may have limitations but they appear to be well-suited for certain chores, he remarked, adding that that goes for Linux as well. In his view, Linux has about a 20 percent market share of the entire scientific computing space, what he calls a "reasonably large impact." He noted that 8-way Linux servers are available today.

While it remains to be seen how the Intel-based machines affect Sun's hardware business, the company said it doesn't see the 8-way servers as a threat from the software side, because Solaris runs on the Sun Sparc chips as well as on those from Intel. "We actually see Intel 8-way machines as an opportunity because we scale so well on 64-way machines today. The software's had years of tuning for scaling across large numbers of processors," said Paul Steeves, Sun's group marketing manager for Solaris. He explained that all the work that's been done to get Solaris to run properly on multiple processors is inherited by the Intel 8-way box when Solaris is installed on it.

Sun also has an unexpected approach towards Linux, viewing it as a "Unix brother," stated Steeves. "We're currently looking at opportunities where we can actually take source code from Linux and contribute source code to Linux," he revealed. Because Linux is an open-source system, Sun can use any gains made by Linux and also make "donations" to it, he explained.

--Matthew Dougherty

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