EGEE Newsletter
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pointer image Focus on Uppsala

BarcelonaIngmar Bergman walked its streets as a child. Linnaeus taught and worked at its botanical garden. It lays claim to the oldest university and largest cathedral in Scandinavia. In April it will host much of the European e-Infrastructure community at the last Enabling Grids for E-sciencE event.

The 5th EGEE User Forum will be held in collaboration with the European Grid Initiative and Nordic Data Grid Facility April 12-15, 2010. With the establishment of sustainable European and National e-Infrastructures, this be the place for users to meet, share experiences, and shape the future of European e-Infrastructures.

Please also note that registration for this important event is now open! Save money on VAT by signing up before 31st of December! now for the choicest spots. Note also, the Call for Abstracts deadline has been extended. The new deadline is Monday, December 14.

Learn more about Uppsala at the tourism website, which includes a .


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pointer image EGI - The End of the beginning?

- from Steven Newhouse, interim EGI Director

Five o’clock p.m. Tuesday 24th November represented an important checkpoint in the next phase of Distributed Computing Infrastructure (DCI) provision in Europe. It marked the close of the European Commission’s FP7 call for projects in DCI that will (we hope!) fund the projects that make up the European Grid Initiative (EGI).

Recall that EGI partitions the activity currently taking place within EGEE-III into three distinct areas: the infrastructure, the middleware and the development of the user communities. Groups across Europe, from both within the current EGEE-III consortium and many new partners that will be part of this exciting change in European DCI provision, have been active over the last few months in building the consortia and writing the project proposals for submission into these recently closed calls.

One of EGEE-III’s main goals for the second year of the project is to plan and implement an orderly transition to EGI. The submission of the project proposals represents a concrete target that we can now plan towards. The plans that have already been put in place around the EGI Design Study (EGI_DS) [PDF, 1.17 MB] and Functions documents for the second year in EGEE-III, will now be adapted. The modifications are small... but in the same way that no building is ever built exactly to its plans, the EGI_DS Blueprint has had to be adapted by practical and budgetary realities imposed on us. And of course the proposed activity may still be changed through the FP7 review and negotiation process!

The challenging issues around EGEE to EGI transition planning were accidentally summed up many years ago by United States Secretary of Defense Donald Rumsfeld (he was talking about an entirely different context):

There are known knowns. These are things we know that we know. There are known unknowns. That is to say, there are things that we now know we don’t know. But there are also unknown unknowns. These are things we do not know we don’t know.

The submission of the project proposals for EGI-InSPIRE (infrastructure), the European Middleware Initiative (for the middleware) and the ROSCOE and SAFE proposal (the user communities currently supported by EGEE-III) represent the conversion of a lot of known unknowns to known knowns.

All that remains over the next five months is to work on the remaining known unknowns and see what unknown unknowns appear!

From the . Image courtesy of .

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pointer image A challenge to improve Nuclear Magnetic Resonance for structural biology

(Press Release, Monday 30 November 2009)

In structural biology, the only technique available to predict the three dimensional structure of large complex molecules in solution, such as proteins and DNA, is NMR spectroscopy. To catalyze improvements in the techniques behind these predictions, the “eNMR” project has launched a new initiative. In September’s Nature Methods the project issued an invitation to the entire biomolecular Nuclear Magnetic Resonance community to participate in a large scale test of modern computing algorithms. This community-wide “contest” will potentially improve efficiency, reproducibility and reliability of NMR structure determination. eNMR will be using the Enabling Grids for E-sciencE infrastructure to power their analysis.

NMR spectroscopy is important in many different areas of science and is often used to determine the structure of complex molecules. The technique is particularly useful in biological sciences as it can predict the three dimensional structure of macromolecules in solution, including substances such as proteins and DNA that are key to understanding how the human body works. The analysis, however, is labour intensive and automation would accelerate the pace of research, helping scientists to identify molecules more quickly.

[PDF, 167 KB].

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pointer image EGEE and DEISA fuse through Kepler: achieving grid and HPC interoperation

Interested in a having a little supercomputer alongside your grid? Some applications in the fusion strategic discipline cluster can now run on grid and high performance computers. From on-going work with the EUFORIA and DEISA projects, these researchers can now run some tasks on both infrastructures.

At SuperComputing 09, held in November in Portland, Oregon, US, a group of grid researchers from Poland (PSNC) and Spain (CIEMAT) demonstrated how the Kepler workflow tool can handle jobs, farming them to DEISA, the Distributed European Infrastructure for Supercomputing Applications, (via UNICORE) and EGEE (via gLite) as part of the EUFORIA environment.

EUFORIA () supports fusion modelers in simulation work by providing tools to generate the range of codes needed for simulating the full fusion reactor (learn more at ).

EUFORIA collaborates with DEISA and EGEE to ensure a wide adoption of the tools developed and deployed by EUFORIA in the infrastructure of DEISA and EGEE. With these developments, users can now create and run complex workflows, with some components running in HPC, some components running in grid.

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pointer image Also on the Interoperation front: Reaching TeraGrid through SAGA

In other grid-HPC interoperations news (this time Westward facing) it is now possible with Ganga, the gLite connected job submission interface and DIANE, the job scheduler, as demonstrated at the EGEE’09 conference in Barcelona, to use TeraGrid resources.

“This is very exciting, not only to access more computing resources,” says Jakub Moscicki, who works with Ganga and DIANE, “but also, for certain applications you may need qualitatively different resources.

“For Lattice QCD simulations [see our previous news item on searching for new physics with Monte Carlo lattice QCD (quantum chromodynamics) calculations] we would like to increase the model size of the lattice. If we do that, you can no longer simulate it on one processor – it is too heavy. So if you can exploit multi-core and super computers such as those on TeraGrid then it is possible. Now we can used mixed resources.”

This was accomplished by connecting to – an Open Grid Forum specification that defines a simple application programming interface (API) for grid applications. This was a joint development of CERN-based Ganga team and the SAGA team from Louisiana State University. Plans to make SAGA interface with gLite, allowing SAGA and TeraGrid users access EGEE resources are also in the works.

Image courtesy of .

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pointer image Getting voted off the “EGEE Island”: enforcing the Service Level Agreement

Two grids sites were suspended from the production infrastructure in October as part of a new policy by the grid operations and management coordinators (SA1) to improve overall operations and performance.

SA1’s new policy of removing sites with a 50% or less availability rate enforces EGEE’s Service Level Agreement and comes on the heels of recommendations by EC-appointed reviewers. The “off the island” status is not irreversible. Excluded sites can rejoin the production system after successfully re-passing the certification process.

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pointer image Climate VO now running on EGEE’s Seed Resources

Since April 2009, about 60 users have joined the virtual organization “”. Most users are from the climate change domain. During the summer this VO was granted access to the EGEE Seed Resources. These resources are set aside by EGEE for the newly grid-interested. The project has allocated funds to support these resources so they are freely available to new users, and integrated them into its support process. (See our previous story “Seed Resources—up and ready for you!”)

“We identified a pilot application in September/October by contacting our users and finally in November we finalized the porting on the EGEE platform (we solved some application license issues as well),” says Giovanni Aloisio of the University of Salento, Italy. “In December we should start our first tests (exploiting the seed resources) running tens to hundreds of jobs related to the impacts of climate change on economy”.

The users belong to the institutions participating in the testbed:
 Euro-Mediterranean Centre for Climate Change (CMCC), Italy
Institut Pierre-Simon Laplace (IPSL), France
Rensselaer Polytechnic Institute (RPI) and High Altitude Observatory (HAO) at the National Center for Atmospheric Research (NCAR),USA
Fraunhofer-SCAI, Germany
University of Reading, UK
University of Salento, Italy
University of Cantabria, Spain 

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pointer image All the cool kids are doing it: Become an accredited trainer!

The EGEE Training group is preparing for the future by developing a database of skilled trainers able to assist with training in their respective countries. By accrediting trainers, the NA3 activity can recognise the valuable contribution made by the present group of trainers and provide incentive for new ones. Trainers are nominated for accreditation by a lightweight peer approval process ( full details of which can be found ). A map of the accredited trainers by country is maintained on the NA3 website.

“We look for people who have experience running EGEE training courses in the past,” says Robin McConnell, leader of the training activity. The status of being ‘accredited’ will likely take on more importance in the future.

“As we move towards the end of EGEE to EGI, there is no central training provision in EGI – only a coordinating position. So the NGIs must take training on themselves, it will be a national task. Due to the funding it is unlikely that they will get assistance from other countries. So accreditation will identify people who are appropriate for the training task within those countries.”

Within EGEE there are currently 133 accredited trainers, 29 of who have been accredited in the last 3 months. Are you interested in becoming accredited? NA3 runs “Train the trainers: courses which can enhance your skills. Keep up to date with all training events .

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pointer image New to using gLite? This resource is for you

screen-shotNeed help sorting through all these acronyms? Want to know how to get your grid certificate? Register your virtual organisation? Want to renew your proxy? Want to know what a proxy is?

Head to EGEE Use Cases Documentation, put together by EGEE’s Direct User Support team to aid new gLite users. Some documents will also be useful to more advanced users dealing with Message Passing Interface (MPI) jobs, AMGA and bioinformatics.

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EGEE Newsletter
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A newsletter produced by EGEE
EGEE: Enabling Grids for E-sciencE
Project Identifier: FP7-2008-INFSO-RI-222667