Foreword from the Directors
Michael Levine and Ralph
PSC co-scientific directors.
Twenty-five years ago, with a grant from the National Science Foundation, the Pittsburgh Supercomputing Center (PSC) was born. Since then we’ve participated in breathtaking technological change, and it’s still happening. This year, with partner sites around the country, we embark on the adventure of XSEDE, the Extreme Science and Discovery Environment, the most powerful collection of integrated computational resources in the world.
Two supercomputing systems that we host and make available to the national research community this year came into productive maturity. With Anton, the world’s most effective system for simulation of proteins and nucleic acids, computational biologists have opened a new view into protein dynamics. We briefly describe in this booklet the unique story of Anton and findings from four of these projects.
Blacklight, the world’s largest shared-memory system, has rapidly become a force across a wide and interesting spectrum of fields — including genomics, machine learning, natural language processing, geophysics and astrophysics.
As a tool for assembly of sequence data from next-generation sequencing tools, Blacklight enabled remarkably fast results in two projects. One, led by James Vincent, is the sequencing of an NIH model organism, a fish called the little skate. Similarly, Blacklight accelerated sequence assembly in the work of Cecilia Lo at the University of Pittsburgh Medical School on congenital heart defects.
With limitless quantities of text available on World Wide Web, Blacklight’s shared memory is a powerful tool for sifting words as data — as Noah Smith showed in four papers in diverse fields of “natural language processing” within six months of access to Blacklight.
For astrophysicists Tiziana Di Matteo and Rupert Croft, Blacklight has revolutionized discovery from large-scale simulations of how the cosmos evolves. The ability to hold an entire snapshot of MassiveBlack, their huge simulation, in memory at one time was instrumental in their ability to reveal “cold gas flows” as a phenomenon that accounts for supermassive black holes in the early universe.
With help from PSC scientist Marcela Madrid, Catalina Achim solved the structure of a fascinating molecule called peptide nucleic acid, a close cousin structurally to DNA, but with important advantages for research in electron transport.
In a major accomplishment, Art Wetzel and Greg Hood, scientists in PSC’s National Resource for Biomedical Supercomputing, co-authored a paper that appeared as a cover story in Nature, the prestigious international journal of science. Their collaboration with Clay Reid and colleagues at Harvard is a milestone in brain research.
Along with these scientific advances, PSC continues to be a resource for research and education in Pennsylvania. Through the Three Rivers Optical Exchange, PSC’s networking group serves the Pennsylvania-West Virginia region and carries out nationally recognized research in next-generation, high-bandwidth Internet resources. This booklet also highlights our important work to help educate the upcoming generation of scientists and science-literate citizens.
Much more than technology per se, it’s PSC’s staff who make all of this possible. It’s our privilege to work with a collection of people second-to-none in world-class talent and experience in high-performance computing. We’re grateful also for support from the National Science Foundation, the U.S. Department of Energy, the National Institutes of Health, the Commonwealth of Pennsylvania and many others.