Entries filed under “Computing Research”

While the Tree of Life film bares the rare distinction of being the only movie to put me to sleep three times in one sitting, the study of evolution through Phylogenetics is a very lively topic these days thanks to the power of HPC.

Researchers are using now TACC supercomputers to develop and test smarter, faster, and more accurate genetic alignment and tree-building algorithms and apply them to some of the largest biological datasets ever created.

The most accurate trees are estimated using methods that try to solve hard optimization problems,” said Tandy Warnow, professor of computer science at The University of Texas at Austin and a Guggenheim Fellow. “While those solutions can be done on small datasets or moderate sized data sets, on large datasets, they can take a very long time — weeks to months to years of computational time. The Texas Advanced Computing Center ends up being essential for those problems.”

Collaborating with evolutionary biologists, the software they developed is leading to new insights into the Tree of Life and the relationships among species.

Read the Full Story.

A Texas Tech researcher is using TACC supercomputers to explore chemical reactions at the atomic level. Empowered with the computation might of Lonestar, Ranger, and Kracken, Dr. William Hase is now able to examine the dynamics of individual molecules when they collide.

For molecules to react, they need specific types of geometries, specific types of energies, and certain types of motion,” Hase explained. “Reactions are often not random. They’re very specific in terms of what’s going to react.”

Hase’s work spawned recent articles in Nature Chemistry, the Journal of Physical Chemistry, the Journal of Chemical Physics, and the Journal of the American Chemical Society (JACS). Read the Full Story.

Gregory Scott Jones from NICS writes that researchers are using the Kraken supercomputer to model hazardous material explosions with an eye on greater safety for the nation’s highways.

Thanks to the University of Tennessee’s Cray XT5 Kraken supercomputer and the hard work of a research team from the University of Utah, accidents such as the one in Spanish Fork Canyon may soon become better understood, and hopefully, one day, a near impossibility. The team, led by Martin Berzins and Charles Wight, is using the processing power of Kraken to simulate burning and detonation processes in transportable explosives in hopes of one day making catastrophes like the one in Spanish Fork Canyon a thing of the past. Recent simulations have led the team to believe that the key to preventing these types of detonations is to pack the trucks transporting the explosives in such a way that temperatures and pressures are vented so as to avoid a chain-reaction explosion-to-detonation scenario.

The University of Utah team used 3.5 million hours on Kraken in 2010 alone, and the simulations have given the group the computational knowledge to expand its algorithms to ensure that its codes continue to scale to tomorrow’s even larger computing architectures. Read the Full Story.