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Supercomputer Dedicated To Bioengineering, Computational Biology Installed

available to computational biologists and bioengineers across the country as part of a new paradigm often referred to as grid computing.

The new cluster, which was purchased from Dell for less than $180,000 per Teraflops (trillion floating point operations per second), is a distributed-memory parallel computer. It is valued not only for its speed, but also because its 428 gigabytes of memory capacity and 20 terabytes of storage will enable researchers to solve ever larger and more sophisticated problems. "It's not always just a matter of computational speed with some of our models -- some are memory limited," said McCulloch. "For example, our models of the propogation of an electrical impulse thorough the heart wall require us to generate matricies with millions of individual cells, and our ability to solve such problems is limited by the memory available. This new cluster will enable completely new simulations of the heart and other biological systems."

Traditional supercomputer centers have historically been the workhorses of computational biology, but McCulloch said the drive to build ever faster and more specialized supercomputers has required computational biologists to continually reinvent their modeling software. "It's not new that science has been developing large computational challenges, but what is new is the commoditization of supercomputing," said McCulloch. "These commodity clusters running with an open source operating system and management software can provide a stunning degree of performance that a few years ago simply couldn't be found in a small room in the basement of a bioengineering building."

The cluster's management tool is called Rocks, an award winning toolkit developed at UCSD by a team led by Philip Papadopoulos, director of the Advanced CyberInfrastructure Lab at the San Diego Supercomputer Center and associate research scientist in the Department of Computer Science and Engineering. The open-source Rocks toolkit
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Source:UC San Diego


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