Content about Project Profile

  Opinion - The role of open source in grid computing: past, present and future Open source software allows individual users to work with an initial shared material, adapt and tailor it to suit their own specific needs, and pass on their improvements to the rest of the community for continued improvement.Image courtesy of Eric Gjerde It is not long now until the first Open Source Grid and Cluster Conference, to be held in Oakland, California from 13-15 May 2008. This upcoming event got me thinking about the role of open source in grid and cluster computing, in the past, present, and future.    My involvement with open source dates to the early days of Globus, in the late 1990s. At that time, I (and my colleagues Carl Kesselman and Steve Tuecke) resolved that, in order to reduce barriers to grid technology adoption, Globus software should be freely available to anyone. To this end, we chose to release Globus software under a variant of the BSD Unix license. (Later we moved to the more modern

  Opinion - International Summer School on Grid Computing: looking back, one year on Thanks to his ISSGC’07 experience, Andrew Jamieson and his colleagues are actively pursuing the possibility of gridifying aspects of their medical research work.Image courtesy of Andrew Jamieson Deadlines for the 2008 International Summer School on Grid Computing close on 5 May. Here, former student Andrew Jamieson reflects on his experiences at the 2007 summer school, held in Sweden. In 2007, with the aid of the Open Science Grid, I attended the International Summer School on Grid Computing in Sweden. Today, just over a year later, I am still involved in grid computing.My scientific background as a medical physicist researcher involves developing accurate computer-aided diagnosis (CAD) algorithms for breast mass lesions in X-ray mammography, ultra sound and MRI images. My colleagues and I are interested in using grid computing to push CAD and image analysis to a new level of exploratory power and scientific evalua

  Feature - The dynamics of dark energy: ZEN probes the limits Data from the Wilkinson Microwave Anisotropy Probe spacecraft, illustrated here leaving the Earth/Moon orbit, will be used to fine-tune our understanding of the Universe in the hunt for dark matter.Images courtesy of NASA/WMAP Science Team The answers are out there somewhere, and researchers with the ZEN project are keen to find them.  ZEN—standing for Zoom sur l’Energie Noire or “zoom on dark energy”—is a computer model designed to enable new estimates about the nature of dark energy.Mysterious, not dark “Dark energy has a very surprising property: it acts like negative pressure,” says ZEN project leader Andre Tilquin of the Marseilles Centre for Particle Physics in France. “This means the expansion of our universe is accelerating; before we thought the expansion of the universe was decelerating due to its own mass.” Tilquin’s goal is to calculate the dynamics of this force with new accuracy, usi

Link of the week - Salute to SALUTE

The Bulgarian team in charge of the SALUTE project is developing algorithms for studying quantum effects in semiconductor structures. These effects influence the design of nano-devices with improved performance.Images courtesy of SALUTE and Obscura

SALUTE—or Stochastic ALgorithms for Ultra-fast Transport in sEmiconductors—is a pilot grid application developed to solve computationally intensive problems in semiconductor physics.
Semiconductors—materials that can both conduct and insulate electricity—are invaluable to modern electronics. Their ability to conduct depends on the ability of “carriers”—electrons or phonons—to transport electrical charge.This carrier transport occurs on a quantum level: the temporal scale is so short it is measured in femtoseconds, where one femtosecond is 10-15 seconds, or one millionth of a nanosecond.
Simulations on this sort of scale rely on complicated integral eq

Feature - Introducing Condor at RIT

The Condor team at RIT: from left, Bill Hoagland, Paul Mezzanini and Brent Strong.Image courtesy of RIT

Grid computing at the Rochester Institute of Technology, New York, is not a new initiative, but with the advancement of technology and recent additions to the resource pool, RIT is setting its sights on further expanding its grid presence and contributions.
The Condor computing infrastructure harnesses the power of idle computers across the RIT campus, and has been in use sporadically since 1999. It has recently gained a campus-wide foothold thanks to a pushstart from Research Computing at RIT.
The Condor network has expanded to over 1000 processors among three flocks, with a goal of reaching 2000 processors in the near future.
This computing network spans a multitude of operating systems and machine architectures, with installations on dedicated clusters, personal workstations and in a large number of computer labs on campus.
New horiz

Feature - Never-born proteins: predicting protein structures from your web browser By predicting the structure and functional properties of “never born proteins” scientists can learn more about the structure and function of actual existing proteins.Image courtesy of INFN While the number of known natural protein sequences is quite large, it is infinitely small compared to the number of proteins theoretically possible using the 20 natural amino acids. Thus, there exist a huge number of protein sequences that have never been observed in nature, the so-called “never born proteins.” If we can study the structural and functional properties of these “never born proteins,” we can improve our knowledge of the fundamental properties that make existing protein sequences so unique. Where these studies would take years on a single CPU, grid infrastructures make it feasible to approach this problem in an acceptable time frame. The Rosetta softwareThe Rosetta ab initio module is a software application developed by David Baker at the Univers

Image of the week - FOCUS on fire This image shows a flame held by a flameholder. The FOCUS project simulations have demonstrated that taking radiation into consideration when making calculations modifies the dynamics of the flame. Image courtesy of FOCUS Combustion is hot stuff, playing a part in more than 80 percent of primary energy conversion processes worldwide; however, the way things burn remains a complex phenomenon, characterized by instabilities and side effects, such as pollutant formation and radiative heat transfer.Hot computingComplex numerical simulations are used to aid the design of industrial combustors, and now a team of researchers is using Europe’s DEISA e-infrastructure to make these simulations even more accurate.The team, a collaboration between Olivier Gicquel’s team at the EM2C laboratory of the Ecole Centrale Paris and the IDRIS team at CNRS in France, say CPU-power fueled their results. “The DEISA project gave us access to the coupling technology that we required,” says Gicquel. “It also provided u

Feature - Cutting edge computing helps discover the origin of life A snapshot from a large-scale molecular dynamics simulation of a 480 base pair DNA plasmid sandwiched between two sheets of a clay mineral. The plasmid structure remains essentially stable and intact at the elevated temperatures and pressures of deep ocean hydrothermal vents, where life on Earth may have originated. Image courtesy of P V Coveney. The National Grid Service in the UK and the TeraGrid in the U.S. have joined forces to help University College London scientists shed light on how life on earth may have originated.  Deep undersea secretsDeep ocean hydrothermal vents have long been suggested as possible sources of biological molecules, such as RNA and DNA, but it was unclear how they could survive the high temperatures and pressures that occur round these vents.Peter Coveney and colleagues at the UCL Centre for Computational Science have used computer simulation to provide insight into the structure and stability of DNA while inserted into layered

  Feature - Powerful pollution model moves to the grid High ozone levels threaten Bulgaria’s most important agricultural crop, wheat, with yields down by ten to twenty percent.Image courtesy Tzvetan Ostromsky In January 2008, Bulgarian authorities installed a public air pollution monitoring system in Sofia, the country’s capital. The system allows passing citizens to check air quality and keeps authorities informed of current pollution levels.  Computer scientist Tzvetan Ostromsky is also keeping an eye on pollution levels. Ostromsky is working at the Bulgarian Academy of Sciences to gridify a large-scale air pollution model. Called the Danish Eulerian model, it combines data on convection, diffusion, precipitation, emissions and more to predict future air pollution trends.“For a small country like Bulgaria it’s especially important to know what pollutants we’ll receive and from where,” says Ostromsky. “Emissions can travel thousands of kilometers—most of what Bulgaria get

  Feature - An orange in the emergency room: grids join the race against viral epidemics The race to stay one step ahead of evolving plant viruses is one that requires new and innovative methodologies.Images courtesy of Alessandro Lombardo Have you ever seen an orange in the emergency room? Have you ever diagnosed a tomato on a computer?            These things have been reality in Sicily for a long time. Biologists at the University of Catania, Italy, are involved in the PI2S2 project, studying the virulence and spread of plant viruses using bioinformatics applications created for grid computing. The testbed viruses—cucumber mosaic virus, tomato yellow leaf curl virus,  tomato yellow leaf curl sardinia virus, tomato spotted wild virus and citrus tristeza virus—are, at least from an economic point of view, the causal agents of  some of the most important plant pathologies in the Mediterranean region. Forewarned is forearmed To help farmers withstand possi

  Opinion - New developments in teaching grid computing across North Carolina A slide from a presentation by Ian Foster given as part of the 2005 grid computing course,  Image courtesy of Ian Foster Grid computing is now part of the curriculum, thanks to a distributed grid computing course run by the University of North Carolina at Charlotte. The course was first taught in 2004, then again in 2005 and 2007, involving the creation of a virtual organization and the broadcast of lectures across the state using the North Carolina Research and Education Network. A total of 90 students distributed across 14 institutions have so far been involved. In with the newIn 2007, we taught the course for a third time, adopting a new approach. Previous courses had employed a bottom-up perspective, where students began with low-level details before moving to higher-level tools. Our revised course reversed this, beginning with more complex interfaces, such as the Gridsphere-based portal to access grid resources and the PURSe-based registra

Feature - EnVision: from data to discoveries EnVision makes it easier than ever before for scientists to visualize their data. This dynamic webpage shows a catalogue of visualization snapshots.Images courtesy of TACC Visualization allows scientists to transform massive amounts of raw data into a visual format, helping researchers to explore data and fuel discoveries. And now, thanks to EnVision, a grid-enabled visualization tool released late in 2007, creating interactive visualizations has never been easier. Developed by the team at the Texas Advanced Computing Center, EnVision is a web-based software tool that simplifies the tasks of data management, analysis and interpretation involved in visualization.Visualize this  EnVision dramatically simplifies the visualization process by semi-automating data importation and providing powerful, easy-to-use tools. “The goal of EnVision is to make the scientific visualization process so easy that a researcher can pick up the tool without ever having done visualizat