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August 8, 2012
Building a new bridge between XSEDE and PRACE

At the XSEDE’12 conference in mid-July, John Towns, principal investigator for XSEDE discussed the challenges and successes of the US high-performance computing network's first year. XSEDE is building bridges between universities, users, and other cyber-infrastructures including the Open Science Grid for high throughput computing. Towns also mentioned the collaboration between XSEDE and the European computing infrastructure called PRACE and unveiled a new joint call to enable users to use both sets of resources.

October 12, 2011
Don’t stop the beat

40% of rejected drugs developed by the pharmaceutical industry fail due to their adverse affects on the heart. Now, researchers from the preDiCT project have built the most accurate computer models ever to help the pharmaceutical industry know which drugs are more likely to disrupt electrical activity in the heart. 

PreDiCT is just one of 26 projects that are part of the Virtual Physiological Human Initiative - it's goal is the creation of a 'virtual you', down to your face, skin, muscle, bones and DNA. These simulations will greatly improve disease, drug and health treatments for the public.

March 2, 2011
Opinion: A Rich Port for Puerto Rican Science

The name “Puerto Rico” means “Rich Port.” Recently, the island was rich in computing education.

February 16, 2011
Back to Basics: Supercomputing

Just what is supercomputing, or “big iron?” E-ScienceTalk’s Manisha Lalloo explains.

December 8, 2010
Finding a leader in a crowd

Commentators suggest that Wikipedia and other collaborative network-driven projects, such as the Linux computer operating system, could be an emerging socioeconomic paradigm no less radical and disruptive than the Industrial Revolution.

Wikipedia is meant to be a new way of doing things in a world of ubiquitous electronic information and social networks, one that may be changing the conduct of everything from scientific research to political campaigns.

Sociological commentary and predictions aside, however, do Wikipedia and other “crowd-sourced” efforts really function so differently? Purdue communications researcher Sorin Adam Matei and his team are testing the concept by analyzing Wikipedia articles and revisions produced between 2001 and 2008 – a computationally demanding task. They’re finding that Wikipedia may have more in common with an old-fashioned factory floor than we think.

In theory, the collaborative online encyclopedia’s entries are created, edited and maintained with little in the way of traditional, hierarchical organizational and leadership structures. The production of Wikipedia has been characterized as an emergent system, like an ant colony, resulting from collective actions of individual participants with the “wisdom of the crowd” yielding a viable outcome.

October 27, 2010
Feature - DEISA and TeraGrid host joint EU/US Summer School in Italy

DEISA and TeraGrid host joint EU/US Summer School in Italy

Attendees outside the  Santa Tecla Palace on Sicily’s southeastern shore. Image courtesy Summer School

The Santa Tecla Palace on Sicily’s southeastern shore was recently a classroom for a summer school dedicated to fostering collaboration and innovation in computational science among graduate and postdoctoral scholars from Europe and the United States.
A joint effort of the EU’s DEISA and America’s TeraGrid, it provided a multicultural student community the opportunity to learn about high performance computing (HPC) resources, tools and methods.
“We hope to continue with such events every year — alternating between EU and US destinations,” said Hermann Lederer, who presented a DEISA infrastructure and service overview.
Sixty graduate and postdoctoral scholars from 20 nations were selected from more than 100 applications. Participant expenses were paid by DEISA and TeraGrid. &

September 15, 2010
Feature - Neighborly efficiency: Scaling kNN problems using GPUs

Feature - Neighborly efficiency: Scaling kNN problems  (nearly) linearly using GPUs

This image depicts an example of a two-dimensional feature space. In this case, the unknown dot would be classified as “green,” because three of the five nearest neighbors are green.
Image courtesy of Cyrus Stoller and Libin Sun.

What is k-Nearest Neighbor?
The class of machine learning algorithms known as kNN classifies objects based on the closest training examples in the feature space. What does that mean? Let us illustrate that with an example.
Imagine you have a large set of digital images of friends and family. Many of them have already been tagged according to the person in the image. You would like a way to automate the tagging of the remaining photographs.
First, you would need a program that can analyze images of faces, quantifying features such as eye color, the distance between the eyes, and so on. The program would take in each image – say, 1000 – and re

September 1, 2010
Announcement - Gordon Conference 2010 abstracts due 16 September

Announcement - Gordon Conference 2010 abstracts due 16 September

The Grand Challenges in Data-Intensive Discovery conference (or Gordon Conference for short) will be held 26-28 October 2010 at the San Diego Supercomputer Center on the campus of UC San Diego.
Science has entered a data-intensive era, driven by a deluge of data being generated by digitally based instruments, sensor networks, and simulation devices. Hence, a growing part of the scientific enterprise is associated with analyzing such data, and such analysis places special demands on computer architectures because the associated calculations have frequent I/O accesses, large memory requirements, and often limited parallelism.
In mid 2011, SDSC will deploy a unique data-intensive high performance computing system called Gordon. Gordon will be a peer-reviewed allocated resource on the National Science Foundation's TeraGrid available to any US researcher. It will have a peak speed of 245 Teraflops and feature very large shared memo

August 25, 2010
Feature - OSG and TeraGrid join forces for ExTENCI

Feature - OSG and TeraGrid join forces for ExTENCI

Image courtesy of Jayanta Behera.

Last week marked the kick-off for ExTENCI, the first major technical collaboration between TeraGrid and Open Science Grid.
“The idea is to have Open Science Grid and TeraGrid work together on a joint project as an experiment,” explained Paul Avery, the principle investigator for ExTENCI (which stands for Extending Science Through Enhanced National CyberInfrastructure). Although the two infrastructures have worked together to agree on principles and attend each others’ meetings, ExTENCI marks the first time that they will work together, sharing milestones and goals.
In order to make the partnership possible, the National Science Foundation’s Office of Cyberinfrastructure and Math and Physics Directorate each awarded ExTENCI approximately one million U.S. dollars over two years, for a grand total of just over two million U.S. dollars.
The limitations imposed by a small budget

August 18, 2010
Announcement - DEISA-TeraGrid HPC school applications due

Announcement - DEISA-TeraGrid HPC school applications due

The Hotel Santa Tecla Palace, where the event will take place. Image courtesy of the Hotel Santa Tecla Palace.

Applications for the joint EU-US school on High Performance Computing Challenges in Computational Sciences are due 29 August.
The school, which is sponsored by the Distributed European Infrastructure for Supercomputing Applications (DEISA) and TeraGrid, will take place 4-7 October 2010 in Acireale, Catania, Italy.
High-level speakers from the US and Europe will address the following areas in computational science with high relevance for HPC simulations:

HPC Challenges and Technology
Challenges by Scientific Disciplines
Programming
Performance Analysis & Profiling
Algorithmic Approaches & Libraries
Data Intensive Computing and Visualization

Leading scientists in the fields of astrophysics, materials science, nanotechnology, quantum chromodynamics, and plasma physics will present discipl

August 18, 2010
Feature - First OSG Summer School a success

Feature - OSG Summer School a success

The summer school in progress. Image courtesy of OSG.

Last month, Open Science Grid hosted its first summer school, and by all reports, it was a hit with both teachers and students.
“The OSG Summer School was a great experience,” said Vishagan Ratnaswamy, who will begin work on his doctorate in aeronautics this fall at Caltech. “I was able to learn more about the script files I was using as well as the systems I was running my simulations on.”
Before attending the summer school at the University of Wisconsin-Madison, Ratnaswamy was already an OSG user. But by attending, he said, he learned more about the available computational resources and the many ways in which grid computing can be applied to various types of research.
Ratnaswamy was one of 17 students chosen from a pool of 45 applicants to receive funding to attend the summer school, the TeraGrid ’10 conference, and next year’s OSG All-Hands Meeting. At

August 18, 2010
Link of the week - TeraGrid 10 proceedings

 

Link of the Week - TeraGrid ’10 Proceedings

People mingle as they browse the research projects on display at the TeraGrid ’10 poster session. Image courtesy of Miriam Boon, iSGTW.

Earlier this month, researchers and computer experts gathered in Pittsburgh for TeraGrid ’10, the annual conference organized and sponsored by TeraGrid.
Not everyone could attend, of course, so it’s a good thing that the proceedings are now available online at this week’s link of the week.
The conference included a wide variety of programming, including tracks dedicated to science, technology, science gateways, and EOT (education, outreach and training). A poster session and visualization showcase featured posters and visualizations related to computational biology, molecular dynamics, computational chemistry, signal processing, computer science, computational fluid dynamics, computational multi-body dynamics, computational materials (nano-composites), grid computing

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

May 26, 2010
Announcement - TeraGrid '10 contest for high school, undergraduate, and graduate students

Announcement - TeraGrid '10 contest for high school, undergraduate, and graduate students

TeraGrid ’10 is seeking students to participate in this year’s 5th Annual TeraGrid Conference. As a student, you can participate in several ways:
Poster Contest How do you use computational science to solve science, engineering or mathematics problems? Let us know by submitting a poster that demonstrates your models, simulations, or visualizations. Awards will recognize the best poster in each of three categories: high school, undergraduate, and graduate.
Programming Contest Showcase your team’s programming skills by participating in this exciting, fast-paced on-site contest. With access to computing resources, teams (of up to five members, plus one coach) will receive a variety of interesting science and parallel computation problems to address at the conference. Awards will recognize creativity, quality of the solutions and innovative excellence of the teams who solve the most problems during

May 19, 2010
Technology roundup: Science gateways and portals may level the playing field

Feature - Technology roundup: Science gateways and portals may level the playing field

Baseball diamond in a small town at night. Image courtesy Joe Y Jiang, Creative Commons

Our guest writer is Elizabeth Leake of TeraGrid — the high-performance, distributed computing network in the US. At the recent EGEE User Forum in Sweden, attendees had a chance to learn about two general-purpose portal engines and two domain-oriented portals. What these technologies have in common is the ability to act as “science gateways,” ultimately allowing new communities of researchers better access to advanced computing, thus leveling the playing field — a key part of “eScience.” Here is a round-up of some of the features pf these gateways, and who is developing them:VCR
Milan Prica from Sincrotrone Trieste, an independent laboratory in Italy, presented an advanced web portal with virtual collaboration features. The latest version of Virtual Control Room (VCR) inc

April 28, 2010
Opinion - What would Linnaeus do?

Opinion: What would Linnaeus do?

Carl Linnaeus on his wedding day, holding in his right hand a specimen of Linnear borealis — his favorite plant, said Magnus Lidén, curator of the Uppsala University Botanic Garden. Image courtesy Uppsala University Art Collection

Elizabeth Leake of TeraGrid — the high-performance, distributed computing network in the USA — was a guest at the EGEE User Forum, the recent conference in Europe on high-throughput computing. Here, she gives her impressions about a technology challenge faced by both types of computing: Long-term, persistent storage.
 
One of the highlights of visiting the conference venue in Uppsala, Sweden, was learning about Carl Linnaeus.
Born in nearby Råshult in 1707, Linnaeus  moved to the college town of Uppsala to study, and quickly became a cornerstone of the university. He died in 1778 and was laid to rest in Uppsala Cathedral — largest in all of Scandinavia.
Linnaeus was fam

March 3, 2010
Feature - Black holes and their jets

Feature - Black holes and their jets

This simulation depicts a black hole with a dipole as a magnetic field. This system is sufficiently orderly to generate gamma ray bursts that travel at relativistic speeds of over 99.9% the speed of light. (To see what happens with a more complex magnetic field, see the next video below!)
The black hole pulls in nearby matter (yellow) and sprays energy back out into the universe in a jet (blue and red) that is held together by the magnetic field (green lines).
The simulation was performed on the Texas Advanced Computing Center resources via TeraGrid, consuming approximately 400 000 service units.
Video courtesy of Jonathan McKinney and Roger Blandford.

Jets of particles streaming from black holes in far-away galaxies operate differently than previously thought, according to a study published recently in Nature.
High above the flat Milky Way galaxy, bright galaxies called blazars dominate the gamma-ray sky, discrete spots on the da

February 3, 2010
Announcement - Call for submissions: TeraGrid 2010

Announcement - Call for submissions: TeraGrid ’10

Participants can now submit papers and abstracts for the Science, Technology, Gateways, and Education tracks, and abstracts for all other parts of the TeraGrid’10 conference.
The conference, which will take place 2-5 August 2010 at the Sheraton Station Square Hotel in Pittsburgh, Pennsylvania, will showcase the capabilities and achievements of the nation’s largest open-access scientific discovery infrastructure.
Science, Technology, Gateways, Education Track Submissions Work for all Science, Technology, Gateways, and Education tracks not previously published in another venue, presented, or currently under consideration at another conference may be submitted as a paper or abstract. Papers should be no more than eight pages; abstracts should be no more than one page in length. Work previously published in another venue, presented, or currently under consideration at another conference may be submitted as a one-page abstract

February 3, 2010
Feature - Cosmic simulation

Feature - Cosmic simulation

This video simulates Governato’s new model of the formation of a dwarf galaxy over time. It is the first such simulation to match observations in terms of the mass of stars and dark matter in the galactic core. Video courtesy of Fabio Governato.

Cosmic structure formation theory has passed test after test, predicting how many galaxies will form, where they will form, and what type of galaxy they will be. But for almost 20 years, its predictions about the central mass of dwarf galaxies have been wrong.
“Potentially, this is a very big problem for the model,” said Fabio Governato, a researcher at the University of Washington in Seattle. “It might imply that the dark matter particle that we think is the correct one is not the correct one, or maybe that gravity works differently than we think it does. So this is a very fundamental problem for physics.”
Now, a simulation running on computer resources at NASA Advanced Supercomput

January 13, 2010
Announcement - Last chance to apply for computational time on TeraGrid

Announcement - Last chance to apply for computational time on TeraGrid, (midnight January 15, submitter’s local time)

Scientists, engineers, and other U.S. researchers may apply until January 15, 2010 (12:00 midnight local time) for the next quarterly review of requests for free allocations of high-performance computer time, advanced user support, and storage resources that are available through the National Science Foundation (NSF) Office of Cyberinfrastructure’s (OCI) TeraGrid. To apply for an allocation of any size, please visit TeraGrid’s online submission system.
Each quarter, a panel of computational experts known as the TeraGrid Resource Allocations Committee (TRAC) evaluates requests primarily on the appropriateness and technical aspects of using TeraGrid resources. Applications received by the January 15 deadline will be considered at the March 2010 TRAC meeting, and awards will be available for the one-year period from April 1, 2010 through March 31, 2011. TeraGri

November 11, 2009
Feature - iPlant: a new paradigm for a scientific field

Feature - iPlant: A new paradigm for a scientific field

Image courtesy of Asif Akbar.

iPlant is going to solve the grand challenges of plant biology. It’s a big bite to chew, but the creators of iPlant think big.
“One of the really neat things about this project is that it was funded to exist by, for, and of the community,” said Dan Stanzione, co-director of the iPlant project. “The idea was to be collaborative from square one, and not to take the ‘if you build it’ approach.”
That’s why the developers behind iPlant didn’t propose specific tools or structures. Instead, they created a process whereby the plant biology community could come together and decide what the field’s grand challenges are.
Stanzione estimates that over 100 faculty members from forty different institutions worldwide participated in the grand challenge process. “Most everything was done remotely,” said Stanzione. The tools used included telecon

October 28, 2009
Feature - Dash heralds new form of supercomputing

Feature - Dash heralds new form of supercomputing

Dash, pictured here, is an element of the Triton Resource, an integrated data-intensive resource primarily designed to support UC San Diego and UC researchers. Image courtesy of San Diego Supercomputer Center, UC San Diego.

The first of a new breed of supercomputers was born this fall when computer experts combined flash memory with supercomputer architecture to create Dash.
Normally supercomputers are measured by how many floating point operations, also known as “flops,” they can complete per second. And at a peak speed of 5.2 teraflops, Dash wouldn’t even make the top 500 list, where the slowest speed is about 17 teraflops.
“But if you look at other metrics, such as the ability to do input/output operations, it would potentially be one of the fastest machines,” said Allan Snavely, the project leader for Dash. “Dash is going after what we call data-intensive computing, which is quite different from

October 28, 2009
Feature - In case of emergency, call SPRUCE

Feature - In case of emergency, call SPRUCE

A part of the complete synthetic social contact network of Chicago obtained by integrating diverse data sources and methods based on social theories. This sort of simulation can bring insight into how a virus will transmit through a population. Check out this SciDac Review article for more information about this research. Image courtesy of Madhav Marathe and SDSC.

When disaster strikes, simulations could give authorities the information they need to save lives. But simulations are computationally intensive, and during a crisis, there’s no time to wait in line for access to computer resources. That’s where urgent computing comes in.
“What you really want is to be able to hook together or have access to all the supercomputers that you need, wherever they are,” said Pete Beckman, project lead for TeraGrid’s Special PRiority and Urgent Computing Environment, or SPRUCE. “The purpose of this sort of urgent com

October 21, 2009
Feature - Here to help: embedded cyberinfrastructure experts

Feature - Here to help: embedded cyberinfrastructure experts

It isn’t easy designing software that can run on a cluster like Fermilab's Grid Computing Center. That’s why advanced technical support is so essential. Photo by Reidar Hahn, Fermilab Visual Media Services.

Although much of today’s scientific research relies on advanced computing, for many researchers learning how to adapt and optimize applications to run on supercomputers, grids, clouds, or clusters can be daunting.
To help newcomers, many cyberinfrastructure providers offer in-depth support tailored to fit each user’s needs. This is much more than the typical technical support that helps users write scripts to enable their jobs to run. Instead, cyberinfrastructure experts are embedded directly into a user team to provide longer-term assistance.
One example is TeraGrid User Support and Services, led by director Sergiu Sanielevici.
“The designation of a supercomputer is that it’s basicall

October 14, 2009
Feature - A new test bed for future cyberinfrastructure

Feature - A new test bed for future cyberinfrastructure

Image courtesy of jaylopez at stock.xchng.

Grid, cluster, and cloud developers will have somewhere new to test their software before letting it loose on the world, thanks to a new initiative called FutureGrid.
“I think people found that it was pretty hard to test early grid software on the machines that were available, because the machines that were available didn’t like being experimented on,” said Geoffrey Fox, principle investigator for FutureGrid. “FutureGrid is trying to support the development of new applications and new system software, which are both rapidly changing.”
The FutureGrid collaboration, which will be headquartered at Indiana University, had its first all-hands meeting 2-3 October.
“We will have early users throughout the first year,” said Fox. A small number of users are already signed up, but there remains room for more on the FutureGrid roster.
“We would like