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Matthew Dublin is a senior writer at Genome Technology. |
Galaxy Gets an HPC Injection
June 06, 2012
Researchers can thank the Pittsburgh Supercomputing Center, or PSC, for seriously ramping up the Galaxy platform. The folks at PSC have just completed a new super high-speed link from Galaxy to the National Science Foundation's Extreme Science and Engineering Discovery Environment, or XSEDE using their Three Rivers Optical Exchange, a 10-gigabit per second fiber-optic high-performance Internet networking hub.
There are currently over 10,000 Galaxy users running 4,000 to 5,000 analyses per day, and that number is growing, so the need for a HPC resource on steroids is clear.
"The network connection to XSEDE through PSC is a huge breakthrough," says Anton Nekrutenko, Galaxy co-developer and associate professor at Penn State. "It provides us with the ability to run up to 150,000 jobs per month, and we expect to quadruple that as this link gets fully up and running. It allows biologists to take advantage of HPC resources in ways they otherwise could not, not only the computing, but the storage resources at XSEDE sites. It democratizes research by making XSEDE useful for a scientific community that traditionally has not been a heavy user of high-performance computing."
The new bandwidth hookup is made possible with a four-year $1.5-million NSF's Academic Research Infrastructure program grant.
What parts of the pipeline
What parts of the pipeline are the bottleneck with Galaxy?