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September 24, 2008

Feature - JobGrid connects Chinese graduates with employers Schematic of JobGrid workflow.Image courtesy of Feng Zhou, HUST. Graduates from over 75 universities in China and their potential employers have a new tool to help them find each other: JobGrid.Developed by researchers at Huazhong University of Science and Technology (HUST) and Beihang University (BUAA) on a grant from the Ministry of Education of China, JobGrid is the first data grid to provide an authentic, secure, user-friendly communication and decision support platform linking universities, graduates, companies and the government in China. It runs on the China Education and Research Network (CERNET).JobGrid integrates students’ records and relevant personal information from participating Chinese colleges and universities. It converts the dissimilar data to a uniform format, creating a comprehensive, authoritative database with privacy controls. The database supports data storage, extraction and export. Centralized transaction processing handled by a distribute

September 10, 2008

  Image of the week - ATLAS (Click on this link or the photo above to get the rotating, 360-degree, panoramic view, with natural sound.)ATLAS In a continuing series, Peter McCready has been creating panoramic views of all the large experiments of the LHC. ATLAS (A Toroidal LHC ApparatuS) was shot using a Nikon professional digital, single lens reflex camera, attached to a tripod that allows for a 360-degree, rotating view. For each image, 102 separate, individual photos were shot,  then stitched together into one seamless 40MP spherical image. Each image takes as much as four weeks to complete in the his digital darkroom. When coupled with ambient sound that he recorded at the site, the user gets what McCready calls a  “Virtual Reality” experience. Image courtesy of Peter McCready    

September 10, 2008

Editorial - Beam Day Simulation of the detection of a Higgs Boson.  Image courtesy of CERN Today, after more than a decade of meticulous preparation in the high-energy physics world—in theoretical frameworks, detector research and development, site construction, data simulations, analysis software, distributed computing infrastructures, networks and more—CERN’s Large Hadron Collider proton beam turns on and will begin circulating through its entire 27-km length.International Science Grid This Week congratulates the scientists, engineers, technicians, software developers, managers, coordinators, students, secretaries and all the other hard-working, talented and dedicated participants whose effort made this happen. The sheer volume of data that the LHC experiments will need to process became the driving force for developing the World-wide LHC Grid (wLCG), and hence Enabling Grids for E-SciencE (EGEE) in Europe and Open Science Grid in the United States. iSGTW celebrates with them, and thanks them, as

September 10, 2008

Profile - People behind the LHC grid: Wesley Smith The trigger makes the first decision, on whether to keep an event . . . or throw it out.  Image courtesy of CERN iSGTW: What do you do?Wesley Smith: I work at the Compact Muon Solenoid (CMS), where my job is to throw away 99.999 percent of the data we record.What we’re hoping to do is like looking for a needle in a haystack, only with multiple haystacks. I want to remove as much hay as possible, without losing any needles.iSGTW: How did you become interested in physics?Wesley Smith: I grew up in San Francisco, where we lived one block away from Mel Schwartz of Stanford University, who won the Nobel Prize in Particle Physics. I knew his son, we went to elementary school together, and our parents spent a lot of time together. It was a connection that stayed almost 40 years, and a powerful influence. Then when I was in college at Harvard, I studied under Carlo Rubbia (former Director General of CERN,1989-1994, and Nobel prize-winner in physics) and Larry Sulak.My first s

September 10, 2008

Podcasting from beam day In the control room of ATLAS, where there was a champagne toast shortly after the first beam successfully completed its 27 kilometer circuit.Image courtesy of iSGTW, GridTalk and GridCast. Today is the big day for all the sites involved in the superconducting supercollider. Click here, on the image at right, or on the GridCast page, to see the final moments in the control rooms, as the clock ticks away toward the startup.  (All times in the subtitles are approximate.)

August 20, 2008

  Image of the week - One view of the LHC (Click on this link or the photo above to get the rotating, 360-degree, panoramic view, with natural sound.)One view of the Large Hadron Collider To give an idea of the enormity of the project at CERN, Peter McCready took a series of panoramic views of each of the  experiments. Last week, we showed ALICE, here's a view of one portion of the LHC. McCready creates these images using digital cameras mounted atop a customized tripod apparatus that allows him to take wrap-around images of up to a complete 360 rotation. Each image requires more than one hundred separate, individual photoraphs to be shot, which are then stitched together to form one seamless spherical image. The completed photo takes up 40MP. Image courtesy of Peter McCready    

August 20, 2008

Feature - BNL takes a cue from nuclear physics Deep in the bowels of Brookhaven's RACF. Image courtesy of BNL Even though real data from the Large Hadron Collider (LHC) has yet to touch the Grid, scientists at Brookhaven National Laboratory’s ATLAS Tier-1 center already have their hands dirty. Working on a daily basis with the Relativistic Heavy Ion Collider (RHIC) – a massive particle accelerator that smashes together beams of gold atoms to explore the complex world of nuclear physics – the almost 40 staff members at Brookhaven’s RHIC and ATLAS Computing Facility (RACF) are no strangers to storing and distributing large amounts of data. “The benefit of an integrated facility like this is the ability to move around highly skilled and experienced IT experts from one project to the other, depending on what’s needed at the moment,” said RACF Director Michael Ernst. “There are many different flavors of physics computing, but the requirements for these two facilities are very sim

August 20, 2008

Feature - People behind the LHC grid: Jamie Shiers Some of the different projects involved, from across the globe. Image courtesy of Jamie Shiers Jamie Shiers is part of grid support for the Large Hadron Collider, and has been working on the LHC for 16 of his 25 years at CERN. Dressed in sneakers and jeans, and looking tan after a recent grid conference in Brazil, he talked with iSGTW at CERN’s Restaurant 1.  iSGTW: What first got you interested in physics? JS: It could be something in the genes, I suppose. I and two of my three brothers  became physicists—and we’ve all passed through CERN.  For me, what helped to get me hooked was a book about physics, called “Mister Tompkins in Wonderland,” that I read at age 14 or 15, by George Gamow—a Russian physicist who worked with Niels Bohr. He wrote about a world in which light was slowed down enough that you could see the effects of relativity. It was a great book that turned me on to physics . . . that, and the old c

August 13, 2008

Link of the Week - LHC at home Image courtesy of LHC@home Analyzing the 15 million gigabytes of data from the Large Hadron Collider is not just for the big guys. The public can participate too, by using a screen-saver program that uses your computer's idle time to work on a piece of the project. By downloading LHC@ home, you are simulating a particle traveling round-and-round the 27-kilometer ring. It’s done using a program called SixTrack, which not only simulates the particle’s travel but studies the stability of its orbits—thus producing information essential to verifying the long-term stability of the high energy particles in the LHC. SixTrack was developed by Frank Schmidt of the CERN Accelerators and Beams Department. Lyn Evans, head of the LHC project, says that the results “are really making a difference, providing us with new insights into how the LHC will perform.”Typically SixTrack simulates 60 particles at a time as they travel around the ring, and runs the simulation for as man

August 13, 2008

Feature - (Almost) starting up the LHC: a view from the front lines A welder works on the interconnection between two of the LHC's superconducting magnet systems, in the LHC tunnel, earlier this year. Image courtesy of CERN On Thursday, 8 August, CERN announced that it would make the first attempt to circulate a beam in the Large Hadron Collider (LHC) on 10 September, with the first test scheduled for the weekend of 9 August.To find out what it is like from the point of view of those actually building the LHC and installing the equipment, iSGTW caught up with Mike Lamont of LHC Machine Operations for a few minutes, just  before workers were about to start the initial steps of a preliminary, low-energy, “pre-startup.” iSGTW: What are your feelings, after all this time and effort?Lamont: “At the moment, my general feeling is an overwhelming one of relief, actually. We’ve pulled all the bits together; we’ve got the ring more or less cooled now; we’re underway.”“We’re up t

August 13, 2008

Feature - STAR  of the show The world made smaller, with the help of a new Tier-2 site in Prague. Image courtesy of EPSRC Without the need to connect remotely to Brookhaven National Laboratory (BNL) from all the way across the world to get analysis data, collaborating scientists in Prague can now do their analysis at lightning speed, thanks to their new local Tier2 site. In an experiment called STAR, researchers aim to recreate the quark-gluon plasma (a soup-like state of the matter) that permeated the universe less than a second after the Big Bang. To do this, they analyze data from BNL’s high-energy heavy nuclei collisions. Before installation of the Tier2 site at the Nuclear Physics Institute of the Academy of Sciences of the Czech Republic (NPI ASCR) in Prague, STAR collaborators had to connect to BNL remotely each time they needed to retrieve analysis data, and network latencies made this a tedious task.For the Prague collaborators to analyze data more efficiently, the datasets from BNL needed to be brought onsite

August 13, 2008

  Image of the week - Go ask ALICE (Click on this link or the photo above to get the rotating, 360-degree, panoramic view, with natural sound.)GO ASK ALICE Peter McCready created panoramic views of ALICE (above), ATLAS, CMS and the LHC using Nikon professional digital, single lens reflex cameras attached to a custom rig that allows for views of up to 360 degrees atop a carbon-fiber tripod. For each image, exactly 102 separate, individual photos are shot at varying exposures (some a little under- and some a little over-exposed) to capture the full dynamic range of the lighting during the shoot. They were then stitched together into one seamless 40MP spherical image using a MacBook Pro and Photoshop over the course of as many as four weeks of post-production digital darkroom work. Sound was recorded using Marantz broadcast quality solid state recorders,  with ambient audio loop isolation and extraction using Peak Pro.When asked why he loves to do what he terms “Virtual Reality photographs&r

August 6, 2008

Feature - Anthrax and the grid Researchers used Taverna to model molecules such as the anthrax bacillum. Image courtesy of EPSRC Bacillus anthracis, the bug that causes anthrax, is a peculiar creature.Even though it resembles a soil-growing bacterium, it just hibernates when in the ground, in some cases lying dormant for hundreds of years until ingested by a suitable animal host. Then it springs to life, often causing rapid, even fatal, illness. For years, scientists have wondered how and why this occurs. Now, using Taverna workflow technology developed under myGrid—an e-Science project funded by the Engineering and Physical Sciences Research Council (EPSRC)—researchers Anil Wipat, Colin Harwood and colleagues at the North East Regional e-Science Center in Newcastle, UK, think that they have puzzled out the answer, by sequencing its genome and thus characterizing the proteins it secretes Proteins equip a bacterium to survive in its environment and reveal much about its lifestyle.  A soil-living bacterium, for exa

August 6, 2008

Feature - Chronopolis By storing data digitally on Chronopolis, the equivalent of 2.5 million trees' worth of paper will be saved. Image courtesy of Roly Powderhill, sxc.hu How do you store 50 terabytes of archived data across a wide range of domains, and save 2.5 million trees worth of paper to boot?Digitally, with Chronopolis.Formally called the Chronopolis Digital Preservation Demonstration Project and funded by the Library of Congress , the project is being run by The San Diego Supercomputing Center (SDSC) at the University of California, San Diego, and partner institutions, which includes the UC San Diego Libraries, the National Center for Atmospheric Research in Colorado, and the University of Maryland’s Institute for Advanced Computer Studies. Together, they are building a scalable nationwide grid infrastructure that can be expanded at any time to meet the needs of the data providers. The system uses data scattered across the country.  Image courtesy of Chronopolis   Long-term preservation M

July 16, 2008

Feature - Virtual infrastructure With origins tracing back to 1293, the Universidad Complutense de Madrid is one of the oldest universities in the world, and home of OpenNebula. A problem of scale (and motley software) Grid site administrators have numerous problems to deal with when configuring and scaling their infrastructure, including a large number of users with different software components, and physical resources that cannot be isolated or partitioned. Together, these can make for limited service and reliability, along with inflexibility.To overcome these challenges, Ignacio M. Llorente and his colleagues of the dsa-research group at the Universidad Complutense de Madrid developed a new, open-source technology which acts as a virtualization layer between the service and the physical infrastructure layers, integrating existing grid and cluster middleware stacks. It extends the benefits of  Virtual Machine Monitors (VMMs) from a single physical resource to a cluster of resources, decoupling the server not only from

July 9, 2008

Feature - In this case, it is brain surgery New, grid-based imaging technology has the potential to change neurosurgery. Image courtesy of Phil Beard, sxc.hu To the edge Branching through your brain, a complex system of arteries, capillaries and veins feeds the organ that allows you to think. While the shape of each person’s network is similar in the basics to everyone else’s, it is unique in the particulars. This presents a challenge for neurosurgeons. A new type of three-dimensional imaging and processing tool, based upon grid-computing, stands ready to change the way doctors perform neurosurgery. Called HemeLB, it won the Transformational Science Challenge Award at TeraGrid ’08 in Las Vegas, US, last month. The current technology neurologists use allows for a patient’s vasculature to mapped by the processing of MRI scans. These scans, created with magnetic resonance imaging, use magnetic fields and radio waves to create pictures of bodily tissues. Typically these are two-dimensional images:

July 9, 2008

Feature - World Community Grid to Tackle Rice Crisis IBM and researchers at the University of Washington launched a new programon World Community Grid, a humanitarian research effort,  to developstronger strains of rice that could produce crops with larger and morenutritious yields. Image courtesy of the University of Washington. As concerns of a global hunger crisis mount, researchers at the University of Washington, Seattle, have launched a new program on IBM’s World Community Grid to develop stronger strains of rice that could produce crops with larger, more nutritious yields and greater resistance to changing weather patterns. Jumpstarted by a $2.5 million grant from the National Science Foundation, the “Nutritious Rice for the World” program will harness over 160 teraflops of the grid’s volunteer-donated processing power to study rice at the atomic level.  Researchers expect the results to transfer to other cereal crops such as corn, wheat, and barley and to have a major impact on global hea

July 2, 2008

Image of the week - Fun factoids “We report, you decide.”Image courtesy of YouTube“Developers of the grid say the net will be obsolete . . . ” “You'll be able to download a full-length feature film in seconds.” “The first test (of the grid) is this gigantic atom-smasher. Assuming it won’t blow up the world, which there is some talk it will do . . .”These were just some of the things said about the grid in a 2-minute story on a well-known cable news channel whose motto is “Fair and Balanced.”However, it is fun to watch what feels like a physics version of the spoof ‘news’ program The Daily Show.But we shouldn’t pick on any one media outlet. engadget summed up some of the more outrageous coverage with the headline “CERN creates a new super-fast internet, invites tons of people to a deathmatch.”In an effort to set the record straight—and give at least some credit wher

June 25, 2008

Grid computing walks the standard line: thinking inside the box With many projects involved, truly seamlesss interoperability can be a challenge.Image courtesy of NorduGrid and Vicky White“Standard” is often equated with “average” or “boring.” How can you innovate or invent when you’re bound by standards and regulations? How can you push the boundaries when you’re stuck inside a box?Yet how can you create something on a grand scale—something that can slot into place with other grand things—unless you create something interoperable. Something . . . standard.In this special feature, former iSGTW editor (and now GridTalk editor) Cristy Burne reports on this easily overlooked aspect of grid computing. Why should we care? Standardizing grids: the current landscape Challenges for the future The way forward A standard in action: GridFTP A “de facto” standard: VOMSBONUS FEATURE: What does the grid community have to say about standards? (See what people from inst

June 4, 2008

Feature - Friendly but fierce competition for the Higgs This diagram plots the limit (at 95% confidence level) of Higgs production (y-axis) for different possible Higgs masses (x-axis). Each mark along the y-axis is a multiple of the Standard Model rate of Higgs production, and this rate is shown as a straight line at "1." The more data Fermilab scientists collect, the closer their observed limits will get to the Standard Model rate.  Notice that the "observed" line comes vertically closest to 1, the Standard Model rate, at 160 on the x-axis. Fermilab physicists have amassed nearly enough data to make a statement about whether the Higgs exists at the mass value 160 GeV/c2.Image courtesy of the  Tevatron New Phenomena & Higgs Working Group on behalf of CDF and D0. The two Tevatron experiments at Fermilab, CDF and D0, have nearly ruled out the hoped-for mass value for the Higgs boson—the particle regarded by some as one of the last big mysteries of the universe. Its disc

May 21, 2008

Feature - CMS readies network links for LHC data CMS data transfer rate in MB/s during the data transer debugging task, from September through November 2007.Image courtesy of CMS. Transfer 300 thousand million bytes (300 Gigabytes) per day for six out of seven consecutive days and move a total of 2.3 Terabytes during that same seven-day period—that’s 2.3 million million bytes—these are the criteria that each major network link in the Compact Muon Solenoid’s computing structure must satisfy when the Large Hadron Collider turns on this summer. Together they will transfer tens of Terabytes a day.The CMS computing structure comprises an internationally distributed system of services and resources that interact over the network through the Worldwide LHC Computing Grid (WLCG). The three-tiered architecture, fetchingly illustrated in a Flash animation from the GridCafe, functions as a single coherent system. Data collected at CERN, the top tier (dubbed Tier-0), is distributed to a set of seven

May 7, 2008

  Feature - WISDOM unplugged: malaria drug-leads graduate to the wet lab The WISDOM project screened one million molecules for their potential to bind to and inhibit “plasmepsin,” a protein essential for survival of the malaria parasite. The parasite can be transferred to a human host via the mosquito vector.Image courtesy of PD-USGOV Hot on the heels of their initial success, WISDOM collaborators have high hopes as their anti-malaria drug-leads move from computer processers to petri dishes.“We’re excited to be at this stage,” says Ana Lucia Da Costa, WISDOM researcher at CNRS, France. “I can’t wait till we get the next set of results back.”The WISDOM project, a collaboration of eight core institutions in five countries, began searching for anti-malaria drugs in 2005. Rather than go straight to the lab, the team used a grid-powered software program to screen for potential drug-leads, searching for small molecules—called ligands—that could bind to and disable the mal

April 30, 2008

  Announcement - UK e-Science centers win continued funding Climateprediction.net, a project funded by the Natural Environment Research Council and run out of the South-East Regional e-Research Consortium, has engaged the spare computing power of more than 300,000 home computers to run models of future climate.Image courtesy of Climateprediction.net Four UK e-science centers have been awarded grants totaling just under £4 million to continue developing new e-science technologies and promote their adoption in academia and industry over the next five years.The centers are: National e-Science Centre (based at the universities of Edinburgh and Glasgow); the Belfast e-Science Centre (based at Queen’s University Belfast); the South-East Regional e-Research Consortium (based at Oxford, Reading and Southampton universities); the White Rose Grid e-Science Centre (based at the universities of Leeds, Sheffield and York).The grants have been awarded by the UK e-Science Core Programme, which is funded and managed by the Eng

April 30, 2008

  Feature - The new Nimbus: first steps in the clouds Cloud computing services provide users with flexible compute capacity, allowing each user to lease a portion of the greater “cloud” of resources.Image courtesy of exper While grids are composed of many diverse resources, their applications usually require a very specific, validated environment. As a result, applications that work on a developer’s desktop may only function “out of the box” on a small fraction of the total number of compute resources potentially available to scientists on the grid. This is one of the primary obstacles users face in grid computing.A grid of your virtual machinesOne solution is to take the developer’s desktop and scale it to hundreds of nodes by mapping the desktop onto hundreds of virtual machines and deploying them onto grid resources. To facilitate this mode of using the grid, researchers at the Computation Institute at the University of Chicago recently announced the availability of

April 30, 2008

Image of the week - Shave hundreds of years off your research life The villin protein is presented here in two superimposed forms: the first predicted using BEMusE on EU-IndiaGrid, and the second measured experimentally. The similarity demonstrates the algorithm’s accuracy.Image courtesy of Stefano Cozzini, EU-IndiaGrid BEMusE— or the Bias-Exchange Metadynamics Submission Environment—is a grid-enabled tool able to fold a 36-residue protein in less than a year of single CPU time: a vast improvement on the hundreds or thousands of CPU years required by other grid-based techniques.Bedazzling researchers with its accuracy and speed, BEMusE scooped the poster prize at December’s eScience 2007 conference.Biased towards gridBEMusE evolved from the Bias-Exchange Metadynamics algorithm, developed by Alessandro Laio and Stefano Piana, which folds proteins with increased accuracy. “It was immediately clear how much the algorithm would benefit from the grid,” says BEMusE researcher Stefano Cozzini, of Democ