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August 4, 2010
Feature - The sun never sets on the GreenStar Network

Feature - The sun never sets on the GreenStar Network The GSN project is lead by Quebec Ecole de technologie superieure in Montreal. In this picture, the team behind the GreenStar Network pose next to the Communications Research Centre Canada's GSN node. From left to right: Martin Brooks, Mathieu Lemay, Michel Savoie, John Spence, Bobby Ho. Image courtesy of John Spence. When the sun sets on the Communications Research Centre in Ottawa, Canada, the solar-powered computational jobs might be sent across the high-speed connection to the Cybera data center in Calgary, where it’s still bright and sunny. And when the sun stops shining in Calgary, if the wind is blowing at the wind-powered BastionHost facility in Truro, Nova Scotia, then the jobs could be sent back east. Most forms of renewable energy are not reliable – at any given location. But Canada’s Green Star Network aims to demonstrate that by allowing the computations to follow the renewable energy across a lar

August 4, 2010
Opinion - A round-up of the grid in Chile

Opinion - A round-up of the grid in Chile

Palacio de la Moneda, the seat of government in Chile. Image courtesy Max Cossio, stock.xchng.

I was lucky enough to be a guest of REUNA in Chile, and make a presentation at their eScience Workshop in Santiago.
REUNA is a not-for-profit organization connecting 16 universities in Chile, working to promote and advance grid computing in the region and bring together science and business to exchange ideas. REUNA is the original NREN in Chile, connecting the country to the 20,000 gridified institutions around the world via RedCLARA and the ALICE2 project.
The organization has been investigating the state of the art in the region, setting up grid pilot projects in areas such as climate change, bioscience and grid technology, in which they transfer expertise through training and setting up an action plan for the future.
Many other areas of research are ripe for grid computing, including astronomy, engineering, education and physics. REUNA

July 28, 2010
Back to Basics - How hardware virtualization works: Part 2

Back to Basics - How hardware virtualization works: Part 2

BY GREG PFISTER Since retiring from his position as an IBM Distinguished Engineer, Greg Pfister has worked as an independent consultant as well as serving as research faculty at Colorado State University. Pfister is the author of “In Search of Clusters,” and over his 30-year career, he has accrued over 30 patents in parallel computing and computer communications.

It is possible to find many explanations of hardware virtualization on the Internet and, of course, in computer science courses. Nonetheless, there remains a great deal of confusion regarding this increasingly popular technology.
This multi-part series attempts to provide an approachable explanation of hardware virtualization. You can see Part 1 here.
The Goal
The goal of hardware virtualization is to maintain, for all the code running in a virtual machine, the illusion that it is running on its own, private, stand-alone piece of hardware. What a pr

July 28, 2010
Feature - Fighting pesticide resistance

 

Feature - Fighting pesticide resistance

The tobacco hornworm is a large caterpillar, that can swiftly defoliate other plants as well, such as tomato plants. Image courtesy Jan Stipala, University of Exeter

Pesticide resistance is becoming more of a problem throughout the world as the use of pesticides continues, and insects evolve to accommodate them.
Consequently, pesticides that were once effective at killing crop pests are now no longer effective, leading to an increase in damaged or destroyed crops.
To try to understand the mechanics of how this resistance develops, a group of researchers led by Richard ffrench-Constant at the University of Exeter in the UK are using the country’s National Grid Service. Wilkinson and his research group are analyzing the transcriptomes of insects that are major crop pests, such as Manduca sexta — the tobacco hornworm moth — as seen in the picture at right. (A transcriptome is the set of all messenger RNA molecules, or

July 28, 2010
Feature - Predicting the almost un-predictable

Feature - Predicting the almost unpredictable

Tornado observed on the slopes of Pambak mountain, Armenia, June 6, 2005. All images courtesy Zaruhi Petrosyan, Operational Hydrometeorological Center, Armenian Hydrometeorological and Monitoring Service.

Weather forecasters do not always get their predictions right, especially when it comes to “severe weather events” that pose a hazard to life and property.Western Europe is no stranger to such very rare but extremely dangerous weather, as demonstrated by the ‘deep freeze’ that the UK experienced in January earlier this year. With temperatures dropping to -21C (-6 degrees F), the UK encountered its coldest weather front in 30 years. The country’s  Federation of Small Businesses said that by the time all the economic costs of the three-week cold spell were added up, they topped 1.2 billion pounds — the equivalent of 1.4 billion euros, or $1.8 billion dollars (US), as of the exchange rates at pr

July 21, 2010
Back to Basics - How hardware virtualization works, Part 1: Virtualization and cloud computing

Back to Basics - How hardware virtualization works
Part 1: Virtualization and cloud computing

BY GREG PFISTER Since retiring from his position as an IBM Distinguished Engineer, Greg Pfister has worked as an independent consultant as well as serving as research faculty at Colorado State University. Pfister is the author of “In Search of Clusters,” and over his 30-year career, he has accrued over 30 patents in parallel computing and computer communications.

It is possible to find many explanations of hardware virtualization on the Internet and, of course, in computer science courses. Nonetheless, there remains a great deal of confusion regarding this increasingly popular technology.
This multi-part series attempts to provide an approachable explanation of hardware virtualization. But before explaining hardware virtualization, we will have to put it in the context of cloud computing and other forms of virtualization.

Virtualization is not a mathematical prerequisite for c

July 21, 2010
Feature - On a grid and a prayer

Feature - On a grid and a prayer

Predictect rainfall in cm (color scale) over the Indonesian island of Java and part of Sumatra. Magnitude and strength of the wind at ten meters about the ground is also shown.

In Indonesia, weather forecasts powered by grid computing are being distributed twice a day using Google Maps, along with Imsakiyah, the calendar of Muslim prayer times as well as an earthquake update.
Because Indonesia straddles the equator, the temperature is roughly constant all year round — typically a balmy 28°C in coastal regions. So, the most interesting part of a weather forecast is usually how much rain it predicts.
There are often torrential rains between December and March, when the monsoon winds blow from the north and west, while some parts of the country suffer drought when dry air blows north from the Australian continent, between June and September.
Predicting local rainfall is, however, a tricky business, as sudden tropical storms are a typic

July 21, 2010
Feature - The reports of grid's death are greatly exaggerated

Opinion – Reports of grid’s death are greatly exaggerated

BY CRAIG LEE
Craig Lee was named President/CEO of the Open Grid Forum in October 2007. He is a Senior Scientist in the Computer Systems Research Department of The Aerospace Corporation, a non-profit research and development center funded by the US government. At the Aerospace Corporation, Lee advises civil, commercial and governmental agencies on all issues relating to high-performance parallel and distributed computing and is responsible for the transfer of maturing technologies into new application domains. This work has led naturally to Lee’s involvement in the Open Grid Forum where he was a working group chair and an area director prior to becoming president.

Last week, Amazon Web Services announced the launch of Cluster Compute Instances for Amazon EC2, which aims to provide high-bandwidth, low-latency instances for high performance computing.
The announcement was met with a variety of responses from the

July 14, 2010
Feature - Fruitfly plus flight studies plus grid equals flying robots?

Feature: Fruitfly + flight studies + grid = flying robots?

The GUI pre-processor used to generate the geometry of the fly wings. (Click on image to enlarge.) All images courtesy Diego Scardaci, INFN

The study of the flight of a fruit fly may one day lead to the development of autonomous ‘Micro-air vehicles’ (MAVs), or independent ‘flying robots,’  if scientists in Argentina have their way.
Working in conjunction with the Italian Institute of Nuclear Physics (INFN) under the EELA-2 initiative, they are conducting the study to understand the flight mechanisms of insects and small birds. Their hope is that someday, 'flying robots' could be developed with maneuvering capabilities similar to insects — the most agile flying creatures on Earth.
MAVs could be used to study and explore places that are too dangerous or inhospitable for humans to tread; examples include search-and-rescue teams exploring buildings to detect fires, or scientists investiga

July 14, 2010
Feature - RadiotherapyGrid

Feature - RadiotherapyGrid Gamma-ray map for treatment. Image courtesy BEinGRID Cancer is Europe’s second largest cause of death. One of the most common and effective treatments is external radiotherapy, where a Linear Accelerator (Linac) attacks the cancerous tissue with radiation delivered from several different directions. The treatment plan — the direction, size and length of dosages — has to be carefully calculated to avoid damaging healthy tissue. These calculations can take a long time — speeding up this process would allow earlier treatment and more patients to be treated.RadiotherapyGrid is a solution based on grid technology that helps hospitals plan the best possible treatment for each patient. It has two core functions: verification of plans using accurate — but computationally expensive — techniques; and searching for the optimal treatments. These tools improve the efficiency and effectiveness of planned treatm

July 7, 2010
Feature - Australians launch new Compute Cloud

Feature - Australians launch new Compute Cloud

Image courtesy of ilco.

With the launch of their new Compute Cloud last month, the Australian Research Collaboration Service aims to bring user friendly grid and cloud computing to a whole new level.
“For the high-power HPC users, people who want to use all the features, GRISU provides a graphical user interface,” said Jim McGovern, a systems services manager at ARCS.
ARCS’ grid service GRISU, which sits atop Globus, provides Australian researchers and their colleagues with access to over 18,000 cores distributed across the nation. The Compute Cloud provides another layer, ultimately connecting researchers to the same resources GRISU accesses.
The Compute Cloud, McGovern explained, is ideally suited for less advanced users using standard packages.
As computational power has increased, computational methods have likewise become increasingly feasible for scientific disciplines not traditionally connected with grids,

July 7, 2010
Feature - Next week: Chat live with experts about computational resources

Next week: Chat live with experts about computational resources

Image courtesy brainloc.

What makes a grid perfect for one project, but a cloud better for another? When is a high-performance computer wasteful overkill, or a small cluster underpowered?
To answer these questions, iSGTW has invited experts from around the world to join us on Wednesday, 14 July 2010 at 10:30 a.m. CDT/4:30 p.m. CEST for a one-hour live chat - and you’re invited.
Can’t make it to the chat? No problem. For a week following the chat, an even larger host of experts will join us in our online forums to answer questions. To volunteer to serve as an expert, please email us at [email protected].
We’ll be announcing the identity of our experts throughout the week by adding them to this page. But in the meantime, we’d like to offer you a preview of some of the experts you can expect to hear from next week.

Steven Newhouse
Director, European Grid Initiative
I

July 7, 2010
Feature - Volunteer computing helps rescue oiled Gulf Coast wildlife

Feature - Volunteer computing helps rescue oiled Gulf Coast wildlife

Map indicating position fo Deepwater Horizon oil spill as of June 8, and globally important bird areas considered most at risk. Image courtesy American Bird Conservancy. Click on image to enlarge.

iPhone users who come upon oiled birds and other wildlife in the Gulf Coast region can immediately transmit the location and a photo to animal rescue networks using a free new iPhone application called MoGO (Mobile Gulf Observatory). It was developed by four University of Massachusetts-Amherst researchers to make it easier for the public to help save wildlife exposed to the oil spill in the Gulf of Mexico. With support from the National Fish and Wildlife Foundation, the UMass-Amherst researchers hope the MoGO app will draw on the large network of “citizen scientists” who are as heartbroken as they are to witness the disaster for marine life, and who are actively looking for ways to help save wildlife along

June 30, 2010
Feature - Computing a way out of poverty

Feature - Computing a way out of poverty

In northwest Bangladesh, 72% of the population live below the poverty line, according to the Asian Development Bank. Photo here and on front page courtesy of ADB and Eric Sales, from an ADB Photo Essay entitled New Hope for Bangladesh’s Extreme Poor. 

In the Philippines, the Asian Development Bank and grid specialists are getting together to figure out best investment strategies for Asia’s poorest regions.
One of the outcomes of the EUAsiaGrid Project, funded by the European Commission under Framework Program 7, has been to spark new grid-based collaborations in Southeast Asia.
One example is the result of a meeting that occurred last October, when representatives from EUAsiaGrid partners went to the Asian Development Bank (ADB) Headquarters in Manila, The Phillipines, to explore ways to model the impact of poverty alleviation investments that ADB makes.
In the past, investments by development banks such as the ADB and the

June 30, 2010
Feature - Distributed computing experts gather in Chicago

Feature - Distributed computing experts gather in Chicago

At OGF29, Mark Morgan demonstrates XCG, a production grid maintained by the Genesis II team at the University of Virginia.
Image courtesy Miriam Boon, iSGTW.

Last week, distributed computing experts from around the world converged on Chicago to attend OGF29 and the ACM International Symposium on High Performance Distributed Computing 2010 (HPDC).
“It’s been a quite successful HPDC,” said Peter Dinda, the event’s program chair. “In terms of the grid context, it’s good to have it co-located with Open Grid Forum.”
Both events benefited from the co-location, reporting increases in attendance.
Although the conference chairs did not actively seek out programming on the topic of clouds, this emerging technology became a major theme throughout both conferences.
OGF29’s second day featured a status update on the Open Cloud Computing Interface, and cloud technology demonstrations by t

June 30, 2010
Feature - Project profile: ESFRI

Feature - Project profile: ESFRI

Image courtesy GridTalk

So, just what is ESFRI?The European Strategy Forum on Research Infrastructures (ESFRI) is a European Commission initiative whose role is to guide policymaking on Research Infrastructures (RIs) in Europe. ESFRI projects span social and biomedical sciences, earth and physical sciences, energy, infrastructures and analytical facilities.
The ESFRI projects are detailed in the ESFRI Roadmap, which was last updated in 2008. A new version of this document is due to be released in 2010 and will include also input from the e-Infrastructure Reflection Group (e-IRG), a body which defines and recommends best practices for pan-European e-Infrastructure efforts.
But with such wide scope and vision, the ESFRI projects will place large demands on the storage, processing and networking services of Europe’s e-Infrastructures. To address this, the European e-Infrastructure Forum (EEF) has released a report addressing the future requiremen

June 23, 2010
Feature - Cancer researchers speed crystallography using grid

Feature - Cancer researchers speed crystallography

Scientists have trained a system to recognize the formation of 3-D protein crystals, automating a time-intensive, manual process necessary for scrutinizing the structure of cancer-related proteins.
Image courtesy of IBM and the World Community Grid.

Using the World Community Grid, scientists at the Help Conquer Cancer Project have found a way to automate and speed up protein crystallography, according to a recent paper in the Journal of Structural and Functional Genomics.
X-ray crystallography is the process of using x-rays to map the structure of crystals. Although biological molecules such as proteins and DNA are not normally crystalline in form, they can be prompted to form crystals through exposure to the right chemical compounds. Once crystallized, the scientists can use x-rays to map the protein; knowing the structure of a protein is invaluable to scientists who are trying to understand how a protein interacts with the human

June 23, 2010
Feature - John Shalf talks parallel programming languages

Q & A - John Shalf talks parallel programming languages

As with parallel programming languages, a lexicon of moves designed for jugging in pairs would help these jugglers plan their performances. Image courtesy Dave Herholz, CC 2.0

Whether on a grid, cloud, or cluster, today’s science software runs in parallel, executing many calculations simultaneously. Programmers have found many ways to create parallel programs in traditional programming languages. Nevertheless, today there are a number of emerging languages that are designed specifically for programming in parallel. To learn more about these unusual programming languages, iSGTW caught up with John Shalf, the team lead of the Advanced Technologies Group at the National Energy Research Scientific Computing Center.
iSGTW: Thanks for joining us today, John.
Shalf: It’s my pleasure to talk to you.
iSGTW: We’ve heard about parallel programming languages. Could you explain to us what that is?
Shalf: A sequentia

June 23, 2010
Feature - Just what do you think you're doing, Dave?

Just what do you think you’re doing, Dave?

Anyone who has seen the movie 2001: A Space Odyssey remembers the phrase “Just what do you think you’re doing, Dave?” While it looks similarly futuristic, ATLAS (above) is the setting for something completely different — the ‘Dave’ dataset. Photo courtesy CERN

What is 45 days old, has visited 22 countries and already has close to 500 children but will outlive them all?
Dave the ATLAS dataset.
Born on the 30th of March, 2010 to his proud parents, the ATLAS detector and the LHC, Dave weighed in at just over 3 Terabytes. Very soon after that, he was sent to the Rutherford Appleton Laboratory (RAL) grid operations center,  and the team there have been tracking his progress through the grid world ever since.Dave is the result of accelerating two beams of protons in the Large Hadron Collider (LHC) and colliding them in the center of the ATLAS detector.
He is a selection of the collisions chosen by

June 16, 2010
Back to Basics - Q&A on meshes

Back to Basics – Q&A on meshes

The geometry and adapted mesh for a patient-specific abdominal aorta aneurysm. Image courtesy of Min Zhou, Onkar Sahni, H. Jin Kim, C. Alberto Figueroa, Charles A. Taylor, Mark S. Shephard and Kenneth E. Jansen.

The word “mesh” seems to pop up all over the place. What exactly is a mesh? How about an adaptive mesh? Who uses them, and for what? This week, iSGTW interviewed Mark Shephard to learn more about meshes. Mark Shephard is the director of the Scientific Computation Research Center (SCOREC) at Rensselaer Polytechnic Institute. His primary area of interest is the development of techniques to reliably automate multiscale simulations..
iSGTW: So, what is a mesh? When do you use these?
Shephard: In the context of modeling physical behavior over complex geometric domains that can be modeled by partial differential equations (PDEs), meshes are used to support the application of methods that can provide approximate but accurate sol

June 16, 2010
Feature - Open Nebula becomes what you want

Open Nebula becomes what you want

An intricate sand castle sculpture, about 10 feet (over 3 meters) high, in Victoria, Australia. Photo courtesy Wikipedia, under Creative Commons license.

As children, our sand castles were limited only by our imaginations. Sand is a great building material, making it possible to do almost whatever you wanted. It is abundant, easy to shape and, if the tower, outer wall or turret didn’t turn out as you hoped, easy to re-shape. It might not be very permanent, but for the job at hand — it worked great. The stuff of computing should be a bit more durable, but similarly flexible. The demands of today will not be the same as those of tomorrow, and the computing underpinnings should adapt as needed. Companies who manage a lot of data can now hire the support of a start-up business, C12G Labs, to help them design and construct a custom-fit cloud infrastructure. The people behind OpenNebula — an open-source toolkit to build cloud computi

June 16, 2010
Grid makes drug discovery "crystal clear"

Feature - Grid makes drug discovery “crystal clear” Real crystals grown in the lab overlaid with a computer-generated crystal structure. Image courtesy OMII-UK From aspirin to the most sophisticated and specialized drugs, it is difficult to overstate the impact that pharmaceutical chemistry has made on modern medicine. Less widely known is that a drug’s operation is dictated by a host of properties that depend on the drug’s crystal structure. A new drug might be the silver bullet for a killer virus, but if it dissolves at the wrong rate in the human bloodstream, it may be useless - or dangerous. In legal matters, patents apply only to a single crystalline form. It’s therefore no surprise that big pharmaceutical companies and other researchers are eager for a computational technique that can predict the possible crystal structures of amolecule. Crystal-structure prediction aims to provide that technique.The hitch has been harnessing the computing resour

June 9, 2010
Feature - BP oil spill: Scientists mobilize to create new disaster response science

BP oil spill: Scientists mobilize to create new disaster response science

The Gulf's wildlife is increasingly being affected by the spill. Image courtesy of NOAA.

Less than two weeks after the BP Deepwater Horizon oil rig explosion killed 11 and began leaking between two and four million liters of oil per day, the calls started coming in. The oil would soon reach the Louisiana coast, where it would do untold amounts of damage to the local marshes, wetlands, and channels. Could the team that successfully modeled hurricane storm surges along the Louisiana, Mississippi, and Texas coastlines help?
“We started working on the project fairly quickly, probably around the 10th of May,” said Clint Dawson, head of the Computational Hydraulics Group at the Institute for Computational Engineering and Sciences at The University of Texas at Austin.
With the highly accurate descriptions of the Gulf of Mexico’s coastline Dawson and his colleagues previously used for hurricane si

June 9, 2010
Feature - Seeing particles with VPM

Feature - Seeing particles with VPM

VPM Interview from Renaissance Computing Institute on Vimeo.

Before we can make use of data, we need to make sense of it. But with complex concepts such as particulate air pollution, you could just as easily drown in the data.
And that’s exactly what was happening when NASA first approached Uma Shankar, an atmospheric scientist at the Institute for the Environment at UNC Chapel Hill, to ask what sort of advanced visualizations the particulate matter research community needed.
After some thought, Shankar suggested an application to visualize particulate matter across the range of sizes in which it occurs.
“Particulate matter has such important impacts on a variety of air quality issues, especially human health” Shankar explained. “Now we better understand the connection between particulate matter and climate, so its importance is even greater than we originally understood.”
Despite this better understanding, the existing visu

June 9, 2010
News Round-Up - ISC10 in the news

News Round-Up - International Supercomputing Conference 2010 in the news

Computing researchers and video co-hosts John Shalf and Heike Jagode discuss the day's activities at ISC'10.
Screenshot of video captured on 4 June 2010. To see these videos, visit the YouTube video channel.

Last week, nearly 1800 researchers descended upon Hamburg, Germany, to attend the annual International Supercomputing Conference.
Naturally, there has been a great deal of information coming out of the conference in the form of videos of sessions, blogs, Twitters, videos, press releases, and news stories.
Here are some of our favorite sources of information about ISC'10.

Keynote videos - Visit this page for three keynotes, plus a video showing the highlights of the 35th TOP500 List. The videos are long, but worth the time! Note that the first video starts play automatically.
ISC10 Twitter search - For bite-sized information on anything and everything related to ISC'10, search Twitter for ISC10, or si