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December 3, 2008

Feature -  How to run a million jobs Image courtesy of David Abramson. At SC08, several experts organized an informal session to share information on up-and-coming solutions for expressing, managing, and executing “megajobs.” They also discussed ways of repackaging work to avoid megajobs altogether. Here iSGTW shares the latest ideas and developments about megajobs with its readers, and plans to follow up with articles on various mentioned technologies and trends in the coming months. Contributions are welcome.Biting off a megajob—it's a lot to chewAs large systems surpass 200,000 processors, more scientists are running “megajobs”, thousands to millions of identical or very similar, but independent, jobs executed on separate processors.  From biology, physics, chemistry and mathematics to genetics, mechanical engineering, economics and computational finance, researchers want an easy way to specify and manage many jobs, arrange inputs, and aggregate outputs. They want to readily identify

November 5, 2008

Announcement - NVIDIA to host CUDA tutorial at SC08 Image courtesy of NVIDIA  What: Full Day Tutorial: High Performance Computing with CUDA  CUDA is a C language environment that enables programmers to write software for GPUs, graphics rendering devices whose highly parallel structure makes them quite effective for many complex algorithms. Where: SC08 @ Austin Convention Center, Austin, TXWhen: Monday, Nov. 17, 2008, 8:30 a.m. - 5:00 p.m.Last year′s CUDA tutorial at SC07 was a standing-room only event. NVIDIA is pleased to announce that members of its CUDA engineering team are back this year and will be holding another full day tutorial, designed to give attendees a thorough introduction to the CUDA programming model. NVIDIA engineers will partner with academic and industrial researchers to present CUDA and discuss its advanced use for science and engineering domains. The morning session will introduce CUDA programming and the execution and memory models, and explore the uses of CUDA with many brief examples from

October 22, 2008

Link of the week - Cloud and grid: complementary technologies Image courtesy of dsa-research.org Ignacio Martín Llorente of the DSA (Distributed Systems Architecture) Research Group at the Universidad Complutense de Madrid discusses the relationship between cloud and grid computing in the group's blog.  A couple of excerpts follow.Grid is as an interoperability technology, enabling the integration and management of services and resources in a distributed, heterogeneous environment. The technology provides support for the deployment of different kinds of infrastructures joining resources which belong to different administrative domains. In the special case of a compute grid infrastructure, such as EGEE or TeraGrid, grid technology is used to federate computing resources spanning multiple sites for job execution and data processing. On the other hand, I do not think there is a single definition for cloud computing. From my view, the only new feature offered by cloud systems is the provision of virt

September 17, 2008

Announcement - Second European summit on interoperability in iGovernment Consiliazione Auditorium in Rome. Image courtesy of ESIIG 2.   ESIIG 2, the Second European Summit on Interoperability in the iGovernment, represents an unprecedented occasion to develop new synergies and create contacts with representatives of the European Commission, of the national and regional governments of Europe, of the research field, the Academia and experts of the ICT sector.Dates: 20-22 October 2008Location: Conciliazione Auditorium, Rome, ItalyOrganized by: LAit S.p.A. ESIIG 2 Web siteRegistration Goals:Promote interoperability as the key enabler for the development of iGovernment among European regionsAnalyze the state of the art of interoperability in Europe and regional best practicesInvolve international, national and European stakeholders active in the field interoperability in defining new priorities and more innovative and efficient eServices.  The event is organized under the patronage of  Mme Viviane Reding, member of

September 3, 2008
iSGTW Feature - Mega grid for mega science

Feature - Mega grid for mega science From left, Ian Foster, Carl Kesselman and Steve Tuecke who together created the Globus software for grid computing.Image courtesy of ANL. An editorial chronicling the development of grid computing and its relationship to the Large Hadron Collider, which originally appeared in the October 2006 print issue of R&D Magazine and ran again at rdmag.com last Friday (29 August), has been adapted and reprinted with permission. In 1995, Ian Foster at Argonne National Laboratory and the Univ. of Chicago, Ill., and Carl Kesselman in the Information Sciences Institute at the Univ. of Southern California, Los Angeles, known as the fathers of grid computing, looked at ways of using network technology to build very large, powerful systems, getting machines in different locations to work on parts of a problem and then combine for the result. Ultimately, these ideas together formed I-WAY, which enlisted high-speed networks to connect end resources at 17 sites across North America, marking the start of

August 20, 2008
iSGTW - Image of the Week: One view of the LHC

  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
iSGTW Feature - BNL takes a cue

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 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
iSGTW Feature - STAR of the show

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

July 23, 2008
iSGTW Announcement - Call for Papers: 2008 Microsoft eScience Workshop

Announcement - Call for Papers: 2008 Microsoft eScience Workshop, 7-9 Dec, Indianapolis Image courtesy of Microsoft  Accelerating Time to Scientific DiscoveryThe use of computers in scientific research creates challenges even as it expands the realm of the possible. Many of these challenges are common across research disciplines and areas of endeavor. Insights gained in one area of science can act as a catalyst for change and accelerate discovery in many others.This cross-disciplinary workshop will bring together scientists from diverse research disciplines and give them the opportunity to share their experiences of how computing is shaping their work. The goal is to discover new insights into facilitating scientific discovery. The focus will be on discussion of the computing technologies that enable scalable solutions that address scientific grand challenges. The event is being held in conjunction with the Fourth Annual IEEE eScience Conference.Important DatesPaper submission opens: July 1st, 2008Paper submission closes: Aug

July 23, 2008
iSGTW Announcement - NSF funds UIC to build new virtual reality display

Announcement -NSF Funds UIC to build new virtual reality display OmegaTable is the next generation of EVL tabletops, after the LambdaTable (pictured) that wowed visitors to the joint SDSC/Calit2/EVL booth at Supercomputing 07. . Image courtesy of Calit2.  Electronic Visualization Laboratory to Build a Multi-Sensory Touch Tabletop for 2D/3D Data The National Science Foundation (NSF) recently awarded a Major Research Instrumentation grant in the amount of $450,000 to University of Illinois at Chicago’s Electronic Visualization Laboratory (EVL) to build OmegaTable, a modular multi-sensory touch tabletop for interactive 2D and 3D visual data exploration. This powerful virtual-reality device will enable scientific communities to view, share and interact with large-scale 2D and 3D data at the same time, and will enable computer scientists to study the integration of multi-sensory touch and gestural interaction techniques for seamlessly manipulating both 2D and 3D data. “Integrated visualization instruments wi

July 23, 2008
iSGTW Feature - Electron microscopy via the grid

Feature - Electron tomography without the headaches Image courtesy of Belin Czechowicz, sxc.hu Seeing is understanding For biologists, seeing a structure's shape is the all-important step to understanding how it works. Just as in the architecture of a well-designed building, form follows function. So, when a 17th century Dutch draper who enjoyed grinding lenses as a hobby invented the microscope, Anton van Leeuwenhoek revolutionized biology. Microbiologists today may find their next tool coming from a source just as unlikely—academic computing.By using the grid and a number of super-slim electron scans of an object taken at a variety of angles, researchers can create 3-D views up to 2 million times real size. In spite of its usefulness for the field of microbiology, this process, known as electron tomography, has long remained unpractical for many researchers, as it is too computationally expensive.But a project called EGEETomo, centered at University of Almería, in Spain, is building a tool to make

July 2, 2008
iSGTW Announcement - e-Research in the Arts submission deadline, 15 July, Australia

  Announcement - e-Research in the Arts submission deadline, 15 July, Australia Image courtesy of eResearch Australasia  Submission deadline, 15 July, eResearch AustralasiaThe workshop at eResearch Australasia (e-Research in the Arts, Humanities and Cultural Heritage) aims to stimulate discussion between the UK and the Australasian arts, humanities and cultural heritage communities about the use of e-Research infrastructures, services, technologies and methodologies. To this end, it is soliciting presentations and papers on topics relevant to e-Research in an arts, humanities and cultural heritage context.Early adopters are experimenting and systematically investigating what e-Research could mean for practitioners as diverse as musicologists, archaeologists or archivists of cultural heritage data. The workshop will compare, explore links and develop synergies between these activities and the emerging agenda for arts, humanities and cultural heritage e-Research in Australasia.Call for Contributions We invite contributions

July 2, 2008
iSGTW Feature - Multiple middleware

Feature - Multiple middleware The National Institute of Nuclear Physics, or INFN, is dedicated to the study of the fundamental constituents of matter, and conducts theoretical and experimental research in the fields of subnuclear, nuclear and astroparticle physics. Image courtesy of INFN. Coexistence Since the birth of computational and data grids, a variety of middleware has been developed, deployed and used in a multitude of isolated e-infrastructures, and concern over middleware interoperability is growing. Recently, three researchers in Italy—Roberto Barbera of the University of Catania, Marco Fargetta of Consorzio COMETA, and Emidio Giorgio of INFN Catania—found a new approach to grid interoperation, based on “middleware co-existence.” In this approach, different middleware is deployed on the same infrastructure, allowing users to access and share resources within a single, well-defined policy, regardless of the middleware used, and with a common authentication and authorization scheme.Their appro

June 18, 2008

Feature - Optical network key to next-generation e-research Larry Smarr at TeraGrid 2008. Image courtesy of Shandra Williams, Pittsburgh Supercomputing Center. At the TeraGrid '08 conference, UC San Diego’s Larry Smarr urges university campuses to remove network bottlenecks to supercomputer users.“All the pieces are in place for a revolution in the usability of remote high-performance computers to advance science across many disciplines,” says Larry Smarr, director of the California Institute for Telecommunications and Information Technology (Calit2). Imagine scientists all over the world analyzing a complex dataset while interacting as if they were physically in the same room—it’s coming.“The last ten years have established the state, regional, national and global optical networks needed for this revolution, but the bottleneck is on the user’s campus,” says Smarr. He urges campuses to invest in local ‘data freeway’ systems —switche

June 18, 2008
iSGTW Link of the week - W3C eGovernment activity to help empower citizens

Link of the week - W3C eGovernment activity to help empower citizens Image courtesy of W3C W3C launched a new forum for governments, citizens, researchers, and other stakeholders to investigate how best to use Web technology for good governance and citizen participation.“I encourage people from government agencies to join this W3C forum to make the Web better serve the people,” says Tim Berners-Lee, W3C Director.  “Open Standards, and in particular Semantic Web Standards, can help lower the cost of government, make it easier for independent agencies to work together, and increase flexibility in the face of change. Publishing Linked Data on the Web enables creative re-use of it — citizen mashups, and commercial mashups, which combine the data from many sources to stunning new uses,” Berners-Lee adds. “By joining this forum, you can learn good eGovernance and how to build an Open Standards platform on top of your existing tools and services.” eGovernment refers to the use of the Web or

May 14, 2008
iSGTW Feature - Einstein at Home

  Feature - Hello, Einstein residence … Why yes, he’s home! Albert Einstein (c) Camera Press, K. of Ottawa In 1916 Albert Einstein postulated that our universe is pulsing with gravitational waves created by the gyrations of black holes, neutron stars and other cosmic colossi. Nearly a century later, these waves’ existence has yet to be confirmed.The Laser Interferometer Gravitational-Wave Observatory, LIGO, will detect the ripples in space-time using controlled laser light to precisely measure the time it takes light to travel between suspended mirrors. In celebration of the World Year of Physics 2005 honoring this great scientist, and with the support of the American Physical Society and international organizations, LIGO launched Einstein@home, modeled after SETI@home, to attract CPU power to their data-intensive search. Volunteers all over the world have been downloading Einstein@home and collectively processing about one terabyte per day of LIGO’s data on their home computers. Th

April 30, 2008

  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

March 26, 2008
iSGTW Feature - Our powers combined: gLite, Globus and Unicore play ball

i  Feature - Our powers combined: gLite, Globus and Unicore play ball The OMII-Europe team will celebrate the close of the project’s first phase in late April by releasing five interoperable software components that will give scientists the ability to combine the middleware powers of gLite, Globus and Unicore. Images courtesy of Sergio Andreozzi Connectivity and sharing lie at the heart of grid technology, yet ironically, the grid world can be a lonely place for a scientist. Researchers are limited to the storage, databases and processing power made available by their own particular grid middleware. This means each grid platform becomes the equivalent of an independent city-state. If you’ve ever felt the need to tunnel under your own city to visit other middleware dominions, then you’ll be interested in some new software that can let you do just that. In late April, OMII-Europe will celebrate the close of its first phase by releasing five interoperable software components that allow grid users to work acros

March 19, 2008
iSGTW Feature - EnVision: from data to discoveries

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

March 19, 2008
iSGTW Opinion - Opinion: Distributed computing and the Singularity

  Opinion - Distributed computing and the Singularity The Singularity—that moment in time where exponential progress progresses exponentially—has stirred much debate and captured the imagination.   Image courtesy of The Alieness GiselaGiardino23 Humans naturally see progress advancing along a linear path, when in fact this is often not the case.Historical progress in key areas is exponential, not linear: Moore’s law, for example, describes exponential growth in the complexity of integrated circuits. The shrinking time periods between key events in human history, the growing number of nodes on the Internet, and the mass use of inventions can also be measured in this manner.What will happen when this exponential growth reaches a critical point? Massive, unparalleled, incredible change. Called the Singularity, this describes a hypothesized point in the future where unprecedented acceleration of technological progress will trigger colossal change.From supercomputing to superintelligenceOne prediction of the

February 27, 2008
iSGTW Feature - Evolving towards the future of science: genetic algorithms and grid computing

  Feature - Evolving towards the future of science: genetic algorithms and grid computing Computer engineers are mimicking biological genetics to create algorithms able to optimize solutions to computing problems. These “genetic algorithms” are possible thanks to the recent advent of cheap, readily available computing power, such as that available from computing grids. Stock image from sxc.hu Great innovations are not rare—we are surrounded by them. For inspiration, look not at buildings and machinery, but at plants and animals. Some of our best synthetic technologies copy what we see in nature: think of seed-styled Velcro, mollusk-inspired epoxy, air conditioning based on termite mounds and solar panels that imitate insect eyes. Now, a relatively new type of biomimicry is helping researchers find great ideas.Mutating the way to perfection  “Genetic algorithms” are search functions that “evolve” towards the optimum solution to a problem. Imitating life’s genetic evolu

February 20, 2008

  Feature - New bridge over muddled waters of grid storage Interoperability between the two islands of SRM and SRB opens up opportunities for different grids to share data; for example, scientists using the Worldwide LHC Computing Grid could now process data from the U.S. TeraGrid. Image courtesy of The Gentle Two islands of storage technology have been joined, according to a presentation at the EGEE User Forum in Clermont-Ferrand, France, last week. Jens Jensen, of Rutherford Appleton Laboratory in the UK, told attendees how his team have successfully bridged two key grid technologies: the Storage Resource Broker (SRB) and Storage Resource Management (SRM). A demonstration of the bridging was first run at SC07 in Reno, Nevada, on behalf of the GridPP-led team.Two storage islands SRM and SRB are both ways of accessing the storage available on a grid—either using tapes, disks or disk arrays. Usually, storage elements running SRB can’t be seen by a grid running SRM, and vice versa. Most grids run one o

February 13, 2008

  Technology - Taming the data deluge: the new open source iRODS data grid system The iRODS team is working with a number of partners, including the U.S. National Archives. This image from the National Archives is a self-portrait of political cartoonist Clifford Berryman, who is credited with introducing the teddy bear into American vernacular after President Theodore Roosevelt famously refused to shoot an old, haggard bear during a hunting trip. Images courtesy of the National Archives The digital data we all love is growing explosively. In 2006, humanity produced 161 exabytes of digital data—that’s 161 billion billion bytes. This deluge of data is bringing with it unprecedented challenges in organizing and accessing digital information. To meet these challenges, the Data-Intensive Computing Environments group at the San Diego Supercomputer Center has released version 1.0 of iRODS, the Integrated Rule-Oriented Data System, a powerful new open-source approach to managing digital data. “iRODS is an innovati

February 13, 2008
iSGTW Technology - YAIM: herding gLite configuration

  Technology - YAIM: herding gLite configuration And why a yak? The yak logo was provided by David O’Callaghan, in reference to the concept of “shaving the yak.” This was subsequently adopted as part of YAIM’s motto.Images courtesy of YAIM Setting up a grid site can present a pretty steep learning curve, and with more than 250 EGEE sites and new administrators arriving all the time, anything that eases the transition to becoming a fully fledged grid administrator is a big plus. That’s where YAIM comes in. EGEE’s gLite middleware takes its components from a number of different sources, each of which has its own configuration paradigm. To save administrators from having to learn the details of each service, the YAIM configuration utility does all the hard work, providing simple and separable installation and configuration methods. Built on basic Unix technology, YAIM offers administrators a familiar and uniform interface, also adding transparency to the process. YAIM is installed on every