Environmental research performed since the Deepwater Horizon oil spill in the Gulf of Mexico has uncovered fundamental changes to the microbes in the Louisiana marshes. Supercomputing is advancing DNA analyses involved in the work.

This podcast features interview comments from Annette Engel, associate professor of earth and planetary sciences at the University of Tennessee, Knoxville.

Link to feature story: https://www.nics.tennessee.edu/gulf-coast-research

Link to publication: http://dl.acm.org/citation.cfm?id=2616505

Image courtesy of Annette Engel

Oil Spill Research Gets a Boost from Supercomputing

Computer scientist Doug Jennewein's working environment is, in more ways than one, a great frontier. Situated at the University of South Dakota (USD) on America's wind-swept plain, he is in a job that is allowing him to pursue his passion for science and technology, and be a pioneer in growing the use of computationally assisted research.

In this podcast, he discusses how the Extreme Science and Engineering Discovery Environment (XSEDE) has enhanced his work as USD's research computing manager.

Link to XSEDE website: https://www.xsede.org
Link to the University of South Dakota website: http://www.usd.edu

Spurring Scientific Exploration on the Great Plains with XSEDE and HPC

Unanticipated firestorms can take lives and destroy property, equipment, and other resources. With help from the eXtreme Science and Engineering Discovery Environment (XSEDE), researchers are working to improve wildfire forecasts and give firefighting professionals a more powerful tool.

XSEDE is a single, virtual system funded by NSF for scientists to interactively share resources, data, and expertise. People around the world use XSEDE’s resources and services—things like supercomputers, collections of data, and new tools—to improve our planet.

The Joint Institute for Computational Sciences (JICS) was established by the University of Tennessee and Oak Ridge National Laboratory (ORNL) to advance scientific discovery and leading-edge engineering, and to further knowledge of computational modeling and simulation. JICS realizes its vision by taking full advantage of petascale-and-beyond computers housed at ORNL and by educating a new generation of scientists and engineers well-versed in the application of computational modeling and simulation for solving the most challenging scientific and engineering problems. JICS operates the National Institute for Computational Sciences (NICS), which had the distinction of deploying and managing the Kraken supercomputer. NICS is a leading academic supercomputing center and a major partner in XSEDE. In November 2012, JICS sited the Beacon system, which set a record for power efficiency and captured the number one position on the Green500 list of the most energy-efficient computers.

Founded in 1985, the San Diego Supercomputer Center (SDSC) enables international science and engineering discoveries through advances in computational science and data-intensive, high-performance computing.

Article link: 
Earth, Wind, & Fire: A Computer Model Combination Could Unravel the Mysteries of Sudden Firestorms
By Scott Gibson
https://www.nics.tennessee.edu/wildfire-modeling

Research journal article citation: 
"Coupled fire–atmosphere modeling of wildland fire spread using DEVS-FIRE and ARPS"
Nathan Dahl • Haidong Xue • Xiaolin Hu • Ming Xue
http://link.springer.com/article/10.1007/s11069-015-1640-y

Earth, Wind, & Fire: A Computer Model Combination Could Unravel the Mysteries of Sudden Firestorms

This podcast episode focuses on a recent XSEDE Campus Bridging Success involving a site visit.

The National Science Foundation-funded eXtreme Science and Engineering Discovery Environment (XSEDE) is a single virtual system that scientists can use to interactively share computing resources, data and expertise. People around the world use these resources and services—things like supercomputers, collections of data and new tools—to improve our planet.

XSEDE’s Campus Bridging aims to make cyberinfrastructure—whether local, regional, national, or international—feel close at hand to students, researchers, and staff. Computational systems, data and information management, advanced instruments, visualization environments, and people are all linked together by software for a sense of virtual proximity akin to accessing a peripheral device plugged into the back of a laptop.

Campus Bridging helps institutions with their computer clusters, or sets of computers that work together, by providing an open-source toolkit called Rocks for deploying, managing, upgrading, and scaling applications in parallel across the cluster. Each release of Rocks has core and optional “Rolls” that provide the operating system and other applications integral to cluster computing. So, Rocks Rolls helps institutions build an XSEDE-compatible basic cluster, or XCBC. 

Campus Bridging also offers on-site visits for software installations.  

The first of such visits took place in April at Marshall University in Huntington, West Virginia. The project involved increasing the cluster’s capabilities and enhancing system management. 


An XSEDE Campus Bridging Success Story: Installation at Marshall University

The research interests of Wladimir Lyra revolve around the theory of planet formation and a very ancient question: How was planet Earth formed?

Lyra is an assistant professor at California State University at Northridge, Department of Physics and Astronomy. He is also a research associate at NASA’s Jet Propulsion Laboratory and a visitor at Caltech’s Division of Geological and Planetary Sciences. A native of Rio de Janeiro, Brazil, he received his Ph.D. in February 2009 from Uppsala University, Sweden. Lyra is a recipient of the Sagan Fellowship, the prestigious postdoctoral research grant named after the famous astronomer and science communicator Carl Sagan.

As Lyra says via telephone in this podcast, virtually every society in recorded history, every culture known to anthropology, has attempted at some point to find the answer. In modern times, the quest has been stirred by the discovery of the roughly 2,000 planets around other stars known as extrasolar planets or exoplanets.

The vast majority of these exoplanets lie in planetary systems remarkably different from our own. But despite those dissimilarities, the same approach to research and the results it yields also apply to the origin of our planet. Thus, a major goal of Lyra’s research is to understand the diversity of the planetary systems while simultaneously tracing the origins of Earth.

The National Science Foundation’s eXtreme Science and Engineering Discovery Environment (XSEDE) is instrumental in Lyra’s research. XSEDE is a single virtual system that scientists can use to interactively share computing resources, data, and expertise. People around the world use these resources and services—things like supercomputers, collections of data and new tools—to improve our planet.

Podcast host: Scott Gibson, Science Writer, National Institute for Computational Sciences (NICS) at the University of Tennessee

The Origins of Home (Planet Earth) with Astronomer Wladimir Lyra

The “small talk” of researchers in nanotechnology is extremely small. Their interest is in the physical phenomena occurring with things one-billionth of a meter in size, a million times shorter than the length of an ant, and up to 100,000 times thinner than a human hair. But the benefits to society of the science, engineering, and technology they’re doing at such tiny scales are huge.

In fact, more than 800 everyday commercial products rely on nanoscale materials and processes, according to the National Nanotechnology Initiative (nano.gov).

A central aspect of nanotechnology is that it allows essential structures of materials to be tailored to achieve specific properties that improve a variety of applications in medicine, energy, information technology, and many other areas.

One method of nanotechnology research involves the use of short laser pulses at minuscule fractions of a second to produce structural changes in thin, localized surface regions of various materials, such as gold, silver, or silicon.

Leonid Zhigilei, who heads the Computational Materials Research Group at the University of Virginia, says via telephone in this podcast that what attracted him to this type of research is the ability of lasers to excite and change materials in ways not possible with any other technique.

Dr. Zhigilei discusses the practical applications of zapping surfaces with short laser pulses. Laser ablation, which refers to the ejection of materials from the irradiated target, generates chemical-free nanoparticles that can be used in medical applications, for example.

Zhigilei says that because laser-induced processes are complex and happen so fast, experimentation cannot provide a detailed understanding of the structural transformations triggered by the rapid laser energy deposition.

Supercomputers provide the needed perspective.

The supercomputing resources of the National Science Foundation's eXtreme Science and Engineering Discovery Environment (XSEDE) have played a critical role in many of the projects of Zhigilei's group.

Podcast host: Scott Gibson, Science Writer, National Institute for Computational Sciences (NICS) at the University of Tennessee

Written story: https://www.nics.tennessee.edu/zhigilei-laser-nanotechnology


Tiny Zaps, Big Results: Laser–Materials Research with Guest Leonid Zhigilei

The story in this podcast revolves around a collaboration of social scientists, humanities scholars, and digital researchers directed at using advanced computing to find and understand the historical experiences of Black women by searching two massive databases (HathiTrust and JSTOR) for written works from the 18th through the 20th centuries. The team also is developing a common toolbox that can help other digital humanities projects.

The research is supported by the National Science Foundation's eXtreme Science and Engineering Discovery Environment (XSEDE), the preeminent collection of integrated digital resources and services in the world. (xsede.org)

Participating in the podcast's discussion are the following: Ruby Mendenhall, an associate professor at the University of Illinois, Urbana-Champaign, and the project's principal investigator; Nicole M. Brown, a postdoctoral researcher at the National Center for Supercomputing Applications (NCSA); Michael Black, an assistant professor of English at the University of Massachusetts, Lowell; and Mark Vanmoer, a senior visualization programmer at NCSA.

Links to stories that have been written about this project:

http://www.nsf.gov/discoveries/disc_summ.jsp?cntn_id=137797&org=NSF

http://www.ncsa.illinois.edu/news/story/word_search

Recovering Lost History

Most of the podcasts presented here convey activities of the National Institute for Computational Sciences (NICS), a project of the Joint Institute for Computational Sciences (JICS). JICS was established by the University of Tennessee and Oak Ridge National Laboratory (ORNL) to advance scientific discovery and leading-edge engineering, and to further knowledge of computational modeling and simulation. JICS realizes its vision by taking full advantage of petascale-and-beyond computers housed at ORNL and by educating a new generation of scientists and engineers well versed in the application of computational modeling and simulation for solving the most challenging scientific and engineering problems. JICS runs NICS, which had the distinction of deploying and managing the Kraken supercomputer. NICS is a leading academic supercomputing center and a major partner in the National Science Foundation's eXtreme Science and Engineering Discovery Environment (XSEDE). In November 2012, JICS sited the Beacon system, which set a record for power efficiency and captured the number one position on the Green500 list of the most energy-efficient computers.

Spurring Scientific Exploration on the Great Plains with XSEDE and HPC

Tennessee Supercomputing