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JGI Consolidates High-Performance Computing Operations into NERCS

By Alex Philippidis

NEW YORK (GenomeWeb News) – The Joint Genome Institute says the torrent of sequencing data it has generated, and plans to generate this year, explains its decision to consolidate its high-performance scientific computing operations into the US Department of Energy's National Energy Research Scientific Computer Center (NERSC).

JGI has agreed to transfer to NERSC six Lawrence Berkeley National Laboratory employees specializing in scientific computing, including computer and network security and instrumentation computer systems. JGI's desktop support services will remain under the control of the institute, which is located in Walnut Creek, Calif.

The consolidation, announced April 12, follows JGI's expectation this year that it will multiply the quantity of data it expects to generate through its sequencing of plant, microbe, fungal, and metagenomes. That quantity surpassed 1 terabase, or 1 trillion bases, in 2009, an eight-fold increase over 2008 — with "maybe 4 to 5 trillion [bases] this year" expected to be sequenced, JGI spokesman David Gilbert told GenomeWeb Daily News.

"In that alone, you can tell why we need that computational horsepower that we could handle on our own, but now it's getting to the point where it's just crazy. Why build something in house when we've got a partnership where all the folks who are, in effect, being transferred over to NERSC? They've been Lawrence Berkeley people anyhow, so it's not a major change from their perspective," Gilbert said.

The institute's current data center lacks the capacity to store the exponentially higher amount of data projected, and JGI staff did not have the same breadth of experience with running very large-scale systems that staffers at the computer center have, Jeff Broughton, systems department head at NERSC, told GWDN.

Under the consolidation, NERSC will be responsible for existing JGI scientific computing equipment and new equipment to be procured, which will be housed about 16 miles southwest of Walnut Creek, at the computer center's Oakland facility.

Broughton said the new equipment will include 500 dual-socket, quad-core Nehalem processor nodes from SGI — of which 160 nodes are in place, with the remaining 340 nodes "expected to arrive within the next six weeks, by the end of May" — as well as a 120 nodes from the IBM iDataPlex system already in use at NERSC's "Magellan" cloud computing cluster, part of a joint research effort between NERSC and the Argonne Leadership Computing Facility, funded with $32 million from the $862 billion American Recovery and Reinvestment Act.

"In general, genomics is a pretty good fit for cloud computing, and they were able to take advantage of that," Broughton said.

"The new sequencers are producing ever-increasing flows of data, and it's important to make sure that the computational infrastructure scales appropriately to match it," he added.

He said NERSC runs "in excess of" 50,000 cores for high-performance computing now, a figure expected to quadruple by the end of the year. JGI would account for about 10 percent of NERSC's total computing power, based on core count.

By teaming with NERSC, JGI can enjoy access to a dedicated 10 Gbps-per-second link between both institutions on the Science Data Network of the Energy Sciences Network, as well as other benefits, such as redundant cooling systems, an uninterruptible source of power, environmental and energy-use monitoring, and a central help desk.