Inspired - EGI · 2016-08-03 · Inspired // Issue #14 January 2014 4 A new science gateway for the...

news from the EGI communityISSUE 14JANUARY 2014

(Fab

ien1

309

/wik

icom

mon

s)

TOP STORIES

page 2

MORE

09 Futures and trends for e-infrastructures & life sciences

10 CSC - The Finnish HPC Centre

European GridInfrastructure

www.egi.eu

Asking for resources with e-GRANTpage 3

WeNMR's solution for ID managementpage 5

Inspired

The Distributed Competence Centre

07 What to expect from H2020 ICT work programmes?

08 Fusion devices on the grid

DIRAC for EGI pilotpage 6

11 TERENA: drawing researchers and networkers together

01 Bienvenue Yannick and toodle pip Catherine

A gateway for condensed matter physics

> Nuno Ferreira and Gergely Sipos introduce theDistributed Competence Centre, a new mechanism tofederate technical support to new user communities

> Antun Balaz tells us how a SCI-BUS based sciencegateway is making a difference for the condensedmatter physics community

> Paul van Dijk writes about the WeNMR’s solution forfederated identity management

> Ricardo Graciani describes the plans to set up a DIRACpilot

> ...and I write about the e-GRANT - the new EGI resourceallocation tool

Plus we have stories about:> What to expect from H2020 ICT work programmes?> Fusion devices on the grid> Futures and trends for e-infrastructures & life sciences> CSC - The Finnish HPC Centre> TERENA: drawing researchers and networkers together

Please send your comments, feedback and suggestionsto: [email protected] Thanks!

This Issue

This issue's cover image is a view of theFrench city of Clermont-Ferrand.

(Illustration: Fabien1309 / wikicommons)

1Inspired // Issue #14 January 2014

Bienvenue Yannick and toodle pip CatherineNeasan O'Neill welcomes EGI.eu's new director

Yannick Legré has beenappointed EGI.eu director andhe will take the reins inAmsterdam from the start ofFebruary. At the same time theinterim director Catherine Gaterwill be leaving the organisationto take up an opportunity withthe Europeana project in London.Yannick has been involved in theEuropean grid since the veryearly days with the EuropeanDataGrid project in 2001. He nowjoins EGI.eu as it enters its fifthyear and one that could definethe European grid, he also knowshe has some big shoes to fill.“I watched EGI.eu grow andflourish when Steven Newhousewas director, what he and therest of the staff have achievedhas been phenomenal, but we

now have to look to the futureand the Horizon2020 programme,”explains Yannick. “I am lookingforward to working with thewhole collaboration, and theEGI.eu staff, to ensure that wecan guarantee the future of theEuropean grid for years to come.”Yannick’s appointment is not theonly change at EGI.eu. CatherineGater, who has been the actingEGI.eu director, will be tacklingnew challenges as projectmanager for the EuropeanaSounds project coordinated bythe British Library.“It wasn’t the easiest decision, asI have been working with the gridcommunity for several years nowand it has been an exciting andvaried time,” says Catherine.“But I know that I am leaving

EGI.eu in excellent hands andhopefully I can continue tocollaborate with the fantasticpeople I have met over the lastfive years.”Tiziana Ferrari will continue asthe EGI-InSPIRE project directorto work with Yannick on the up-coming Horizon 2020 proposals.

Yannick Legré is the newEGI.eu director


The Distributed Competence Centre

Nuno Ferreira and Gergely Sipos introduce a new mechanism to federate technicalsupport to new user communities

One of EGI’s most importantassets is the experienceacquired through years oftesting, integrating and usingdistributed federated services.This knowledge base is diverseand distributed, and is providedby experts from NGIs, ResourceCentres, Technology Providersand user communities.The Distributed CompetenceCentre (DCC) is a new mechanism,set up to make the most of thisexpertise and make it moreeasily available. The DCCstrengthens technical support tonew user communities andResearch Infrastructures, whichis one of EGI’s strategic objectivesfor 2014.

The Distributed CompetenceCentreThe DCC federates EGI’sdistributed technical supportskills to help internationalresearch communities facingdata handling and processingchallenges.The DCC pools the technicalknowhow from the National GridInfrastructures and ResourceCentres which are part of EGIand offers expertise on:1) core e-Infrastructure servicesthat provide the foundations forcommunity-specific services,such as authentication,authorisation, accounting andinformation discovery;2) grid and cloud platformtechnology,

3) community-specific platforms,such as compute-intensiveparallel applications, visualisation,science gateways and workflows.

How does it work? The DCCin actionThe process starts when aresearch infrastructure or a usercommunity approaches EGI witha specific storage or computechallenge. The problem ispassed on to experts in the DCCappointed to help capture,refine and document thetechnical requirements.Depending on the nature of theproblem, the DCC experts canrecommend an implementationplan directly, or forward thescoped problem to a VirtualTeam (VT). The VT will define ajoin technical work programmethat supports users from theinitial requirement analysisphase, to integration,prototyping and testing.

Any user community canbenefit from the DCCexpertiseStarting from the first quarter of2014, calls will be openedperiodically for participation inuser porting projects which willsee the involvement of the DCC.The calls will also provide theopportunity to apply forcompute and storage resourcesavailable through the Europeangrid and the federated cloudplatform.

More information

The DCC wikipages:http://go.egi.eu/DCC

Contact: [email protected]

DCC, Distributed Competence Centre;NGI, National Grid Infrastructure; RC, Resource Centre;

TP, Technology Provider; VT,Virtual Team


The e-GRANT portal is anallocation tool that sets 5,000job slots and 170 TB of storageaside for new and existing usercommunities. To access theresources, researchers just needto fill an online form and ask forwhat they need and for howlong they need it.The compute and storageresources available through thee-GRANT portal are contributedby five EGI members (Belarus,Croatia, Greece, Poland andTurkey), as well as the Interna-tional Desktop Grid Federation.“This is an opportunity forscientists to try out what wehave to offer them,” explainsPeter Solagna, OperationsManager at EGI.eu.“It gives new and existing usercommunities simplified accessto the resources needed to

perform their work, allowingpilot projects or the ability toreserve resources for specificactivities.”To streamline the process,applicants are not required tohave a grid certificate or to bepart of a Virtual Organisationregistered in EGI. Applicants justneed to give information aboutthe user community or projectthat they represent, the use casethat they want to run, and anassessment of the resourcesneeded. They will then becontacted by the EGI OperationsTeam to discuss the proposaland allocation of resources tobest match needs and availableresources.During this initial phaseapplications will be processedon a ‘first come, first served’basis and will need to be

How to submit a request?

> Go to the e-GRANT page:http://e-grant.egi.eu

> Log in with SSO(get a free account at:http://egi.eu/sso/email)

> Fill the e-GRANT form

> [email protected]

The organisers of the CommunityForum 2014 invite the Europeandistributed computing communityand the researchers with aninterest in e-infrastructures toregister for the event.The forum will take place inHelsinki, Finland from 19-23 May2014. The event will be hostedby EGI.eu in partnership with theUniversity of Helsinki and CSC -IT Centre for Science Ltd.The leading theme of the eventis Advancing excellent science. Theconference programme willinclude user-orientated tracksdesigned to give new and existinguser communities an opportunityto present their requirements,report on success stories, get

support in porting applicationsand network with technicalproviders and other partners.The Call for Participation is openand abstracts may be submittedvia the conference website until16 February.The programme committeewelcomes proposals for net-working sessions to connect theresearch and technical commu-nities, and hands-on hackathonsto tackle software porting andother technical issues.Submission deadlines> Presentations, networkingsessions, hackathons: 16 February> Posters and demos: 16 March> Early-bird registration: 31 March

http://cf2014.egi.eu

approved by both the EGIOperations Team and theresource providers.In the event that a request forresources does not match withthe pool availability, users will beinvited to submit a revisedrequest.

EGI Community Forum: registration is open!Helsinki, Finland - 19-23 May 2014

More information

> Registration:http://go.egi.eu/CF2014-reg

> Indico pages:http://go.egi.eu/CF2014

How to ask for resources with the new e-GRANT portal?Sara Coelho writes about the new EGI resource allocation tool


A new science gateway for the condensed matterphysics communityAntun Balaz on how a SCI-BUS based science gateway is making the difference

Condensed matter physics andmaterials science addressproblems highly relevant tofundamental research, as well asto society. The development ofhigh-impact materials or researchon quantum information, forexample, depends on condensedmatter physics and contribute tothe IT and smartphone industry,semiconductor technology, andthe energy sector, amongothers.Typical research problems in thisarea involve calculating theproperties and dynamics ofcomplex quantum physicalsystems. Parallel large-scalenumerical simulations are widelyused, and deploy a broad rangeof algorithms to solve nonlinearpartial differential equations, orto apply classical and quantumMonte Carlo techniques, forinstance.The Serbian condensed matterphysics community uses scientificcomputing resources to run threemain applications: GP-SCL,SPEEDUP and QSPEEDUP.GP-SCL is a set of parallel codesfor calculating the dynamics andground states of quantum fluids(e.g. Bose-Einstein condensatesand superfluids). These representmacroscopic quantumphenomena where millions ofatoms or molecules behavecoherently, allowing specialproperties to emerge.SPEEDUP and QSPEEDUP codesuse, respectively, Monte Carlo-and quasi-Monte Carlo-basedpath integral algorithms tocalculate quantum mechanicaltransition amplitudes. Thesecalculations are the building

blocks in the study of manyquantum physics problems.These applications are developedby scientists from the ScientificComputing Laboratory of theInstitute of Physics Belgrade andare used by an increasingnumber of collaborators fromwithin Serbia, Europe, Brazil,India and China. The applicationsare deployed on the computinginfrastructure provided by theAcademic and Educational GridInitiative of Serbia, part of EGI.To increase the potential userbase of the applications, wecreated the AEGIS CMPC sciencegateway to provide seamlessaccess to the software and thedata obtained from thecalculations. The sciencegateway hides the complexity ofthe grid, which was a barrier formany scientists.The science gateway wasdeveloped within the frameworkof the SCI-BUS project, using theAEGIS infrastructure and relyingon the widely-used Liferay-basedWS-PGRADE/gUSE portal. Wehave extended the portal withapplication-specific workflows,as well as a set of modules, thatenables specification of thephysical system to be studiednumerically, and export ofsimulation results.Generic architecture behind thisscience gateway provides a user-oriented interface that visuallyunifies SPEEDUP, QSPEEDUP andGP-SCL portlets. The interfaceportal is developed in the GoogleWeb Toolkit environment. Theportal is a workflow developer-oriented interface that allowscreation, modification and

testing of new and existingworkflows. The final element is adocument-oriented databasethat stores configurations andnumerical results from all appli-cations supported by the sciencegateway. We have developed itbased on CouchDB technology,as this RESTful web-service isextended with three additionallayers responsible forauthentication /authorisation,tracking, and merging.The science gateway is inproduction and is used byscientists in their everydayresearch. We have organizedseveral in-house trainingsessions, and as a result severalPhD students are now regularlyusing the science gateway. So fara number of papers have beenpublished using the resultsobtained from the AEGIS sciencegateway, and we plan to extendit with additional applications,currently being developed byscientists from several researchgroups.

More information

AEGIS CMPC:http://sci-bus.ipb.ac.rs/

AEGIS: http://www.aegis.rs/

Scientific Computing Lab:http://www.scl.rs/

Institute of Physics Belgrade:http://www.ipb.ac.rs/

SCI-BUS:http://www.sci-bus.eu/


WeNMR’s solution for identity managementPaul van Dijk on how WeNMR and SURFnet established a Single Sign-On access todistributed services

The management of identities,especially in the context of adistributed service infrastructure,is generally regarded as a majorburden.This burden, however, caneasily be reduced becauseidentity is already managed,processed and handled by theuser’s home institution. By re-using institutional identities,research groups andresearchers in virtualcommunities can focus on thoseissues they should really focuson. In addition, users in thecommunity will be able to usetheir trusted institutionalaccount to obtain easy and SingleSign-On (SSO) access to sharedresources.

SURFconext and eduGAINmiddleware infrastructureWeNMR was able to apply SAML2.0 based technology andexisting identity federationinfrastructure to manage andsimplify access to sharedresources. In the Netherlandsthe identity federation for higher

education and research isoperated by SURFnet and isknown as SURFconext. Thisinfrastructure allows users frommany institutions to access awide range of services frommany different commercial andnon-commercial serviceproviders.Thanks to the eduGAINinfrastructure, WeNMR was ableto extend the coverage area ofidentity providers and add thehome institutions of WeNMRusers from Italy, Germany andFrance.

WeNMR Drupal Portal, acentral management andentry pointThe SSO support for web(-based)applications was built using theSAML 2.0 Web SSO profile.High-end distributed computinge-infrastructures such asWeNMR and EGI usually lack thesupport for web authenticationprotocols. To circumvent thisproblem, WeNMR created aDrupal module for SSO forexternal Services (SSOXS).

This SSOXS module successfullyextends Drupal to serve as aSSO authentication, central usermanagement and accountingportal for the external webservers or services of the project.At the same time the Drupalportal acts as a central entrypoint and virtual collaborationenvironment for the WeNMRcommunity. In collaboration withSURFnet, the SSOXS module hasnow been connected to eduGAINthrough SURFconext, effectivelyenabling institutional login intothe VRC.The successful WeNMRexperience provides an excellentblueprint of how virtual researchcommunities can share resourcesin a user-friendly and sustainableway.In 2014 WeNMR, EGI, SURFnetand other partners will furtherexplore possible models tomanage group memberships,attributes and certificates inorder to simplify the manage-ment of virtual communities andaccess to shared resources.

WeNMR Virtual Research Community

WeNMR is a FP7 funded project and a Virtual Research Community(VRC) supported by EGI. It has been set up to optimize and extendthe use of high-end solutions to determine the structure andproperties of proteins and other medically important molecules.The ability to easily manage and share these solutions acrossinstitutional and country borders is an important common goal.

The WeNMR federated identity management solution was developedin collaboration with Marc van Dijk, Niels van Dijk and AlexandreBonvin.


DIRAC for EGI: e-connecting scientistsRicardo Graciani on the plans to set up a DIRAC pilot

DIRAC is an open source softwareframework that includes all thenecessary components to buildcomplete distributed computingsystems. DIRAC allows connectionto most grid services, to commonlyused cloud managers, to stand-alone clusters and to otherdistributed data storage andcomputing solutions.This integration of differentresource paradigms into a singlevirtual system is seamless to theend user, which means thatDIRAC provides interconnectionand de facto interoperability witha single entry point and a richuser interface.DIRAC Pilot for EGIDIRAC, EGI.eu and several NGIsare setting up a pilot serviceproviding a single entry point toEGI’s distributed grid and cloude-Infrastructure.The aim of the pilot is to developa prototype of a full-scale DIRACservice for EGI. This experiencewill be used to develop Horizon2020 proposals for the deploy-ment, operation, and dissemina-tion of a global DIRAC service

connecting researchers to the e-Infrastructure. The service willconnect existing science gatewaysolutions and application/domainspecific VREs, as well as fromDIRAC interactive portals.The purpose is to demonstratehow DIRAC can help large well-established communities, as wellas small research groups andindividual scientists, to exploitthe existing e-Infrastructure andboost their scientific output.The ultimate vision is to lowertechnical entry barriers and togive scientists transparentaccess to distributed computingand storage resources. This willbridge the technological gap andpromote innovation with ameasurable positive impact onscientific output and on societyas a whole.The pilot begins in February 2014,with the contributions from thePolish and French NGIs. A numberof communities from differentresearch fields have been conta-cted to join, including WeNMR,the Pierre Auger collaborationand the EISCAT research

infrastructure, amongst others.i-Marine, an e-Infrastructure setup to develop VREs for fisheriesmanagement and conservationof marine resources, is alsointerested and the Greek NGI isevaluating DIRAC to ease themigration of grid users to theOkeanos IaaS. Furthermore,several enginee-ring groupsrequiring extra computing powerfor their appli-cations connectedto industrial and medical usecases will be served.The DIRAC pilot will be presentedat the upcoming EGI CommunityForum in Helsinki, where aDIRAC tutorial will also takeplace. An interim report on thisactivity will be presented duringISGC 2014 in Taipei, including ahands-on tutorial session.

The DIRAC project

The DIRAC Project is a collaboration set up tomaintain, develop and promote the usage ofthe DIRAC open source software frameworkfor distributed computing, on a best effortbasis.The main contributors and founders of theDIRAC Consortium are France’s CNRS, theUniversity of Barcelona in Spain and CERN. Theconsortium is open to new institutionsinterested in ensuring the steady developmentand continuous support of the DIRAC software.

[email protected] / http://diracgrid.org

EGI - DIRAC collaboration

Initial bootstrap meetings took place in Decemberand January, a work plan has been definedwith the support from EGI.eu, and monthlyfollow up meetings are foreseen. Slides andminutes are available online: go.egi.eu/DIRAC

Call for participationThis is mostly an unfunded effort. NGIs,technology providers and other interestedparties are invited to join and contribute to theDIRAC 4 EGI initiative.

[email protected]

"DIRAC can help large well-established communities, as

well as small researchgroups and individual

scientists, to exploit theexisting e-Infrastructure andboost their scientific output."


What to expect from the Horizon 2020 ICT WorkProgrammes?Sergio Andreozzi reports back from a European Commission Information Day

On 15 January, I attended anInformation Day where ECrepresentatives provided insighton Big Data and Open Datarelated challenges under the ICTWork Programme of Horizon2020. In the opening presentation,it was made clear that Horizon2020 is a very different programthan FP7. This is no longer“business as usual”. Besidessome change of terminology(e.g., project is now referred asaction), the main shift is from‘Research & Development’ to‘Research & Innovation’, with thegoal of bringing great ideas fromthe laboratories to the market.The following topics wereaddressed:> ICT 15 (Big Data and Open DataInnovation and Take-up) with abudget of €50 million and callfor proposals by 23 April 2014.> ICT 16 (Big Data - Research)with a budget of €39 million andcall for proposals by 15 April2015.ICT 15 aims to developtechnologies to increase theefficiency of all EU companies

and organisations that managevast amounts of data, and toboost the competitiveness of EUenterprises. Its two types ofaction are: an innovation action(ICT-15.a, €39 million) and acoordination and support action(ICT-15.b, €11 million).For ICT-15a, proposals shouldcontain focused activities toimprove existing businessesprocesses or open newopportunities. Instead of usecase they should be structuredaround clear businessrequirements from SMEs thatcan be validated in the market.ICT-15a aims to:1) Establish a European dataincubator for integration andreuse of open data for SMEs, tofoster the development of opendata supply chains, and toeducate and assist new users;2) Launch collaboration projectsfocused on innovation andtechnology transfer in multilingualdata harvesting and analyticssolutions and services.ICT-15b will maximise the valueof the European data economy

What is Horizon 2020?

Horizon 2020 is the financial instrument implementing theInnovation Union, a Europe 2020 flagship initiative aimedat securing Europe's global competitiveness. A number ofwork programmes detailing activities for 2014-2015 havebeen published. The EC is organising several Informationand Networking Days to provide insights on specific topicsand enable interested participants to network and developproposals for collaborative action.

by stimulating reuse of datasets, developing skills for bigdata analytics, and creating bigdata integrator platforms.ICT 16 follows a research andinnovation action. Proposalsshould focus on user-definedchallenges addressing ’big’dataset, such as: Volume (e.g.,PB), Variety, Velocity. Challengesmay be related to data structures,algorithms, and visualizationtools tackling complex conceptssuch as energy consciousness inreversible computing. Theindustry relevance andsustainability strategy are alsosignificant. The target data setsmust be European, e.g. from theEuropean Open Data portal, orthe Copernicus project. Datasources such as Twitter shouldonly be used as secondarysources.For a truly digital market inmultilingual Europe, it wasrecommended that languagebarriers should be removed byachieving automatic languagetranslation, not by adopting onemain language. It has beenreported that less than half ofEuropean citizens speak English.Dedicated backgrounddocuments are available onlineand contain extra informationand questions focusing on thekey aspects the evaluators willuse to assess the quality of theproposals.EGI is interested in participatingin project proposals with SMEsto offer its infrastructureservices and network of experts.


Optimization of fusion devices on the gridFrancisco Castejón and Antonio Gómez on the added value of the gridinfrastructure for fusion research

Clean and efficient, magneticconfinement fusion could be thesocially and environmentallyacceptable energy source of thefuture. Fusion power does notemit greenhouse gases, andrelies on deuterium and lithium,two cheap and abundant fuels.Yet there are still some problemsto solve before achievingcommercial fusion. The premisebehind fusion power is to createa ‘magnetic bottle’ to confine theplasma, a fluid fuel superheatedto temperatures of hundreds ofmillions of degrees Celsius.An important topic is the designof the magnetic bottles requiredto confine the plasma efficientlyand prevent power escapingfrom the fusion device.Because it's possible to buildthem in very different shapes,the number of potential fusiondevices is huge. The first keypoint is to define a reliablegauge to measure the quality ofthe confinement and then tolook for designs that couldimprove this.Every fusion device is characte-rised by a set of parameterscalled a magnetic configuration.The optimization criteria that aretaken into account includereducing the transport ofparticles and power from theinner to the outer parts of thedevice, and the stability of theplasma when high pressures arereached. As the evaluations ofthe different devices areindependent, this is a problemsuitable to be solved using thegrid. The European grid has

provided the large CPU timeneeded to evaluate tens ofthousands of magnetic bottles,thoroughly exploring theconfiguration space.The strategy we have adopted isbased on metaheuristics. Wegenerate new magnetic configu-rations in a ’master’ machineand evaluate the differentoptimization criteria on theworker nodes of the grid. Westore the new configurations onthe storage elements. Thestrategy we have adopted tosearch for and create new confi-gurations uses two processes:exploration and exploitation ofthe found optimal configurations(i.e., the search for a set of para-meters that obey the optimizationcriteria) and the variation ofthese parameters to improvethe magnetic configurations. Thealgorithm follows the behaviourof bees in nature. Because of

this, and because of thedistributed paradigm of the grid,our algorithm is calledDistributed Asynchronous Bees(DAB).The result of this new algorithmis the generation of newconfigurations on the grid. Thesenew devices improve the plasmaconfinement, hence are moresuitable concepts for building afusion reactor. We started withan especially complex type ofconfiguration called stellarators,which are characterised by beingmore stable, but are difficult todesign and build. An example ofoptimised configuration isshown in the figure. The nextstep will be to include the coilsthat confine the plasma in theoptimization loop, in order tolook for a balance betweenobtaining a good confinementand developing coils that are nottoo complex to be built.

The DAB algorithm has run on the grid to produce this optimized three-period stellarator. The plasma shape is shown together with the confining

magnetic coils. The colours correspond to the different intensities of themagnetic fields (red is more intense and blue is weaker).

9

Future opportunities and trends for e-infrastructuresand life sciencesAfonso Duarte and Fotis Psomopoulos on why e-infrastructures matter

Inspired // Issue #14 January 2014

The goal in science, as thecomputer scientist Jim Gray said,is not to have the biggest, fastestsingle computer, but rather “tohave a world in which all of thescience literature is online, all ofthe science data is online, andthey interoperate with eachother”. Though we are not quitethere yet, life sciences arerapidly transitioning towards anew era of Big Data, where data,algorithms and knowledge arebecoming increasingly availableto all. Ever since 2007, whengenetic sequencing began torelease flurries of data, lifesciences have been steadilymoving towards the analysis ofmassive data setsthis, i.e., the'Forth Paradigm'.EGI has been a key factor in thistransition, and will play a criticalrole in the shape of futureresearch within the life sciences.A good example is the complexnetwork that defines how bio-molecules interact with eachother. Understanding thedifferences between interactionsin healthy and unhealthyorganisms provides insight intothe genesis of disease and howto prevent it. As in many complexproblems, multidisciplinaryapproaches are behind thediscovery of such connectionsand the development of newdrugs. Among those approaches,structural biology andbioinformatics are key players incomprehending interactions atthe atomic level. However, therapid expansion of available dataon the structure and dynamicsof bio-molecules poses new

computational challenges.Currently we are trying to siftthrough all data in a fast andefficient way, bringing computa-tional methods and techniquesinto the spotlight of cutting edgeresearch. E-infrastructuresprovide access to these toolsand applications, allowing thesynergies between life sciencesand ICT researchers which arefundamental in moving researchforward.Attempting to quantify thisconclusion, we searched thePubMed database for relevantarticles and tried to reconstructthe story so far. Starting with thenumber of published articles,the underlying trend is ratherobvious: until 2011 combinedstructural biology and Big Dataprocesses were few and mainlyaiming towards high throughputmethods and visualisation tools.Recently, however, new toolsand e-infrastructures such asEGI gave way to a substantialnumber of publications ranging

from large-scale simulations todisease-oriented structuralmodels in proteomics. Althoughthese results are far from new,they do point out a criticalchange - research has shiftedradically from hypothesis-drivenstudies to data-drivensimulations of whole systems.Besides the development of newapplications and the improvementof the existing ones, it is evidentthat the life sciences and ICTcommunities need to capitaliseon their synergies to strengthenevery discipline.To this end, we will host adiscussion of the expectedtrends, applications and needsof the communities at theupcoming EGI Community forumin Helsinki. This will take place inthe form of a dedicatedworkshop and a networkingsession to showcase the role ofe-infrastructures and promotediscussion towards concretecollaborations and sustainablesynergies.

Number of articles in PubMed related to Structural Biology and Big Data(using a high, exclusive threshold). The word-cloud in the background has

been produced from the corresponding abstracts.


CSC – The Finnish HPC CenterAnni Jakobsson profiles the Finnish host of the EGI Community Forum

CSC — IT Center for Science Ltd.is a state-owned non-profitcompany providing services tothe Ministry of Education,Science and Culture. CSCprovides IT support andresources for academia,research institutes andcompanies, including modelling,computing and informationservices. CSC provides Finland’swidest selection of scientificsoftware and databases and itsmost powerful supercomputingenvironment, which researchersuse via the Finnish Universityand Research Network (FUNET).CSC is one of the hosts of theEGI Community Forum 2014,together with the University ofHelsinki and EGI.eu. For morethan 40 years, CSC has providedthe Finnish research communitywith an open access competitiveICT infrastructure for research.With continuous growth since itsestablishment in 1971, theorganisation has today over 250employees and an annualturnover of around 30 millioneuros. CSC is a limited companyowned by the FinnishGovernment and isadministrated by the Ministry ofEducation and Culture. AllFinnish research relies on CSCthrough one or several of itsservices, including: FUNET,supercomputer and computingclusters, storage and dataservices, software and tools, andtraining and technical support.

With a vision to “pioneer in thesustainable development of ICTservices” CSC has a further roleto introduce new technologiesand advances within ICT and itsapplications to benefit Finnishresearch. Over the years, thishas been accomplished by, forexample: connecting Finland tothe internet in 1988, introducingthe Cray T3E parallel computerin 1996, establishing an opticalresearch data network allowinglink speeds of up to 100 Gbps in2009, building a modular free-cooling energy-efficient datacentre in 2012, and piloting ahigh density supercomputerprototype with many-coreaccelerators in 2013. Thecapabilities of CSC have enableda number of advancements forFinnish research. These rangefrom galactic dynamo processes,fundamental aspects of goldclusters and particles, aerosoleffects on global warming,analysis of genetic variation inFinland and the Nordic countries,resolving 3D structures of

viruses, and more.CSC represents Finland in EGIand ensures that the gridinfrastructure being built isuseful for Finnish research andthat resources are accessible. Allresources provided by EGI areavailable for Finnish researchersthrough the EGI-InSPIRE projectand the Finnish GridInfrastructure (FGI).

More information

url: http://www.csc.fi/english

Anni Jakobsson is acommunications officer at CSC

The new Cray XC30 system located in thenew CSC data centre in Kajaani, Finland © CSC


Researchers and networkers draw closer throughTERENA and TNCLaura Durnford on TERENA's success stories of 2013

Research and education hasbenefited greatly from thedevelopment of networkedtechnologies, infrastructure andservices that enable internationalcollaboration and access to dataand resources in a secureenvironment.TERENA, the Trans-EuropeanResearch and EducationNetworking Association, helps tofurther such developments byfostering collaboration among awide range of researchers andexperts in IT, telecommunications,network technologies and more.With almost 1,000 attendees atits workshops, training eventsand the TERENA NetworkingConference (TNC), and around800 at its open meetings ofvolunteer Task Forces, 2013 wasa good year for 'networking thenetworkers'.The gap between the TERENAcommunity and its beneficiarieshas been narrowing thanks to agrowing collaboration inactivities related to accessingonline services and resourcesthrough ‘federations’ that verifyuser identity. A wide range ofapplications is in use in variousresearch communities, includingmany that do not have a simpleweb-browser front-end. Thisshows the importance of non-browser-based federated accessto allow machine-machineinteractions in secured workflows.The Federated Identity Manage-ment for Research group (FIM4R)also recommended, in a 2012paper, managing federatedaccess in a user-friendly waythat also takes into accountopen standards, compatibilitywith licenses, different levels of

assurance, and community-controlled authorisation.As a response to this paper,TERENA’s REFEDS (Research andEducation Federations)community mobilised to define aroadmap addressing perceivedrisks and barriers to researcherswho use federated access.REFEDS also worked with theGÉANT project’s eduGAIN inter-federation service team, which isled by TERENA, to solicit infor-mation about specific areas towork on, three of which are nowbeing supported by eduGAIN.This work is set to developfurther in 2014.TERENA’s other focus areas in2013 related to computer andnetwork security and certification,network architecture and opera-tions, media and e-learning andsupport for collaborativeperforming arts. TERENA alsoworked on eduroam® mobileaccess for students andresearchers NRENum.net andnumber mapping to allowseamless interconnectionbetween multiple technologies.It also published the ASPIRE 5-year foresight study and the2013 NREN Compendium - areference document regardingthe development of researchand education networking inEurope.Wide-ranging communitycollaborationThe focal point of the widerresearch and educationnetworking community was theTERENA Networking Conference– TNC2013 in Maastricht.TNC2013 drew a record 650participants and included talkson how the networking

community can help meet thedemands of ‘big data’, the use ofdynamic Bandwidth-on-Demandto transfer radio-astronomydata, large distance human-robot interaction, improvementsto large file transfers betweendata centres; analysis of medicaldata and more.The next TNC will be held inDublin, 19-22 May 2014, with thetheme ‘Networking with theworld’. Keynote speakers includeTracy Futhey, Barend Mons,Claire Boonstra, Stephen Farrell,David Puttnam and MartynDade-Robertson. Early birdregistration is available until 24February. Opportunities are stillopen to show demonstrations orexhibits, to provide sponsorship,to present lightning talks orposters, and for students toapply for free-of-chargeattendance.

More information

TNC 2014:https://tnc2014.terena.org

TERENA: www.terena.org

REFEDS: https://refeds.org/

® eduroam is a registeredtrademark of TERENA

Laura Durnford is TERENA'ssenior communications officer


When in Rome … do computational chemistry

Cloudscape VI is being held inBrussels on the 24th and 25th ofFebruary. The meeting focuseson the strategic role of cloudadoption and its socio-economicbenefitsCloudscape VI has a compellingtwo-day agenda covering topicsfrom security and dataregulations to cost efficiency andclouds for a smart economy. Themeeting will have talks by SteveMcGibbon of Microsoft, JoeWeinman of Telx and otherkeynote speakers, as well as a

series of practical parallelsessions on how to make thetransition to the cloud andovercome barriers.The event is for both public andprivate sector IT professionalsproviding a unique opportunityto learn from influential cloudexperts. Over the two days therewill be talks from companies andinstitutions at the forefront ofthe cloud computing industryand research, including Microsoft,EGI, Mobicloud, CERN, VMWareand the European Commission.

More information

http://www.cloudscapeseries.eu/

As part of their 'Circle ofFriends' the Cloudscapeprogramme organisers areoffering reduced registrationto EGI community members.More details on the specialrate are available online.

Upcoming event: Cloudscape VI, Brussels

Daniele Cesini reports on the first training workshop on grid porting ofcomputational chemistry applications

On the 20th and 21st of Januarythe COMPCHEM VirtualOrganisation and the Italian NGIUser Support and Training unitran a hands-on trainingworkshop for computationalchemistry researchers. Thecourse attracted 22 researchersfrom 12 different departmentsincluding a remote participantfrom the Spanish NationalResearch Council in Madrid.Hosted by the Italian NREN,GARR, the workshop was thefinal phase of a course that hadbegun with two online meetingsto introduce the participants toaccessing distributed resources.Over the two days the workshopfocused on porting specific usecases that the students hadresearched in advance. Theseuse cases were based on threedifferent commonly usedcomputational chemistryapplications: VENUS, a classicaltrajectory direct dynamics

computer program, CRYSTAL, acomputational tool for solidstate physics and chemistry andQuantum Espresso, an open-source software for electronic-structure calculations andmaterials modeling at thenanoscale. The porting wasimplemented starting with acommand line interface, to finishwith the creation of basic graphicinterfaces relying on the ItalianGrid Portal.The training was well receivedwith one attendee noting that ithad been “very useful toexchange information and shareexperiences with users belongingto different fields of thechemistry realm.”A follow up to improve themodule and a special issue ofthe VIRT&L-COMM electronicjournal containing the eventmaterial will be released.The organisers would like torecognize the support of the

National InteruniversityConsortium of Materials Scienceand Technology who fundedthree students to attend thecourse.

More information

COMPCHEM VO -https://www3.compchem.unipg.it/compchem/

Italian Grid Portal -http://portal.italiangrid.it

The applications mentionedin the text are available viathe EGI AppDB -http://appdb.egi.eu

Daniele Cesini is the ItalianNGI International Liaison

Inspired - EGI · 2016-08-03 · Inspired // Issue #14 January 2014 4 A new science gateway for the...

Documents

Transcript of Inspired - EGI · 2016-08-03 · Inspired // Issue #14 January 2014 4 A new science gateway for the...