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Polish Infrastructure for Supporting Computational Science in the European Research Space

Polish Infrastructure for Supporting Computational Science in the European Research Space. Jacek Kitowski, Kazimierz Wiatr, Marian Bubak Michał Turała , Łukasz Dutka and Zofia Mosurska ACK CYFRONET AGH, Cracow , Poland. CMS’09 Computer Methods and Systems Cracow , Nov . 26-27, 2009.

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Polish Infrastructure for Supporting Computational Science in the European Research Space

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  1. PolishInfrastructure for SupportingComputational Science intheEuropeanResearchSpace Jacek Kitowski, Kazimierz Wiatr, Marian BubakMichał Turała, Łukasz Dutka and Zofia Mosurska ACK CYFRONET AGH, Cracow, Poland CMS’09 Computer Methods and Systems Cracow, Nov. 26-27, 2009

  2. Outline • National Grid Initiative in Poland in a nutshell • Motivation – e-Science and Science 2.0 • Rationales and Foundations • Status • PL-Grid Project – Current Results • Summary • IntegrationActivityintheframework of EuropeanGridInitiative

  3. Demandfrom Community for e-Science Approachin spite of complexity: Computing, Storage, Infrastructure • E-Science: collaborative research supported by advanced distributed computations • Multi-disciplinary, Multi-Site and Multi-National • Building with and demanding advances in Computing/Computer Sciences • Goal: to enable better research in all disciplines • System-level Science: beyond individual phenomena, components interact and interrelate, experiments in silico • to generate, interpretand analyse rich data resources • From experiments, observations and simulations • Quality management, preservation and reliable evidence • to develop and explore models and simulations • Computation and data at all scales • Trustworthy, economic, timely and relevant results • to enable dynamic distributed collaboration • Facilitating collaboration with information and resource sharing • Security, trust, reliability, accountability, manageability and agility ACK: I. Foster, System Level Science and System Level Models, Snowmass, August 1-2, 2007 ACK: M. Atkinson, e-Science (...), Grid2006 & 2-nd Int.Conf.e-Social Science 2006, National e-Science Centre UK

  4. Science 2.0 ACK:David de Roure, http://www.soton.ac.uk/~dder/talks.html

  5. Users’ Requirements • Resources -- Services • Infrastructure • Data • Computational ACK: F. Gagliardi

  6. IntroducingtheGrid • Coordinates resources thatare NOT subject of centalizedcontrol, whichcan be used as a virtual computer / storage • Using standard, open, general-purposeprotocols and interfaces • Deliversnontrivalquality of services • Resources areshared by usersdue to VirtualOrganizations

  7. EGEE EGEE • Archeology • Astronomy • Astrophysics • Civil Protection • Comp. Chemistry • Earth Sciences • Finance • Fusion • Geophysics • High Energy Physics • Life Sciences • Multimedia • Material Sciences • … >250 sites 48 countries >100,000 CPUs >30 PetaBytes >10,000 users >150 VOs >150,000 jobs/day Mariusz Sterzel CGW'08 Kraków, 13 October 2008 7

  8. GEANT2 RationalesbehindPL-GridConsortium • TheConsortiumconsists of five High Performance ComputingPolishCentresrepresentingCommunities (coordinated by ACK CYFRONET) due to: • Participationin International and National Projects and Collaboration • ~35 international projects FP5, FP6, FP7 on Grids (50% common) • ~15 Polishprojects (50% common) • Needs by Polish Scientific Communities • ~75% publicationsin 5 Communities • Computational resources to date • Top500 list • European/Worldwide integrationActivities • EGEE I-III, EGI_DS, EGI, e-IRG, PRACE, DEISA, OMII, EU Unit F3 „ResearchInfrastructure” Experts • National Network Infrastructureready • (thanks to Pionier National Project)

  9. Partners’ Computing Resources TOP500 – November2008

  10. Motivation E-Science approach to research EGI initiativeongoingin Europe (http://web.eu-egi.eu) Formation of stablee-intrastucturein Europe CollaborationwithNGIs and coordination development activites PL-Grid Project (2009-2012) ApplicationinOperationalProgrammeInnovativeEconomy, Activity 2.3 (in Sept. 2008) Got fundedMarch 2, 2009 (via EuropeanStructuralFunds) PL-GridFoundations – Summary Polish Infrastructure for Supporting Computational Science in the European Research Space European Grid Initiative (EGI) National Grid Initiative (NGI) PL-Grid Response to the needs of Polish scientists and ongoing Grid activities in Poland, other European countries and all over the world

  11. AdvancedServicePlatforms Application Application Application Application DomainGrid DomainGrid DomainGrid DomainGrid Grid infrastructure (Grid services) PL-Grid Clusters High Performance Computers Data repositories National Computer Network PIONIER PL-GridAssumptions • Polish Grid is developing a common base infrastructure– compatible and interoperablewithEuropean and Worldwide Grids. • Specialized, domain Grid systems – including services and tools focused on specific types of applications. • Such an approach should enable efficient use of available financial resources. • Plans for HPC and ScalabilityComputingenabled. • Offer for theUsers • ComputingPower 215 Tflop/s • Storage 2500 TB • SupportfromPL-Gridstaffto usingadvancedGridtools • Support for portinglegacycodesto Grid environment • Support for designingapplicationsfor PL-Grid environment

  12. Users Grid Application Programming Interface Grid portals, development tools Virtual organizations and security systems Other Grids systems Grid services UNICORE (DEISA) LCG/gLite (EGEE) Basic Grid services Distributed computational resources Distributed data repositories National computer network Grid resources Elements and Functionality • PL-Grid softwarecomprises: • user tools (portals, systems for applications management and monitoring, result visualization and other purposes, compatible with the lower-layer software used in PL-Grid); • software libraries; • virtual organization systems: certificates, accounting, security, dynamic ; • data management systems: metadata catalogues, replica management, file transfer; • resource management systems: job management, applications, grid services and infrastructure monitoring, license management, local resource management, monitoring. • Three Grid structuresaremaintained: • production, • reseach, • development/testing.

  13. PROJECT MANAGEMENT P1 P2 PLANNING AND DEVELOPMENT OF INFRASTRUCTURE Coordination StructureOperation Rules Dissemination P3 OPERATIONS CENTER P6 P4 SECURITY CENTER GRID SOFTWARE AND USERS TOOLS DEVELOPMENT … . EGEE DEISA P5 SUPPORT FOR VARIOUS DOMAIN GRIDS Training Planned Realization of Aims The PL-Grid Project is split into several workpackages • Main Project Indicators: • PeakPerf.: 215 Tflops • DiskStorage: 2500 TB

  14. Operational Center: Tasks • Coordination of Operation • Management and accounting • EGI and DEISA collaboration(Scalability and HPC Computing) • Users’ requirementsanalysis for operationalissues • Runninginfrastructure for: • Production • Developers • Research • Futureconsideration: • Computational Cloud • Data Cloud • Internal and ExternalClouds • Virtualizationaspects EGI Group EGI Production Middleware EGI TestingMiddleware

  15. Operational Center: CurrentResults • PL-Grid VO (vo.plgrid.pl) fully operational • Virtual production resources for PL-Grid users in 4 centres (Gdańsk, Kraków, Poznań, Wrocław) • Infrastructure monitoring (failure detection) tools based on Nagios & EGEE SAM in place • Support teams, tools and EGEE/EGI-compliant operations procedures aimed at achieving high availability of resources established • Knowledge sharing tool for operations problems • Problem tracking tool to be released in November • Provisional user registration procedure • User registration portal in preparation (1st prototype released in October) • Accounting integrated with EGEE PCSS WCSS Cyfronet

  16. Operational Center: NextPlans User Registration access to any person registered as researcher in Poland - www.opi.org.pl portal being already developed (to be released end of October'09) access to resources based on grants – giving rights to use X CPUhours and TB of disk space access services – way of accessing resources in particular computing centre PL-Grid Research Infrastructure – “resources on demand” allows to request machines for different purposes install a grid middleware for testing purposes for developers to build a testing environment any other research requiring grid resources procedures are being defined Enable access to UNICORE resources small amount of dedicated UNICORE machines integrate UNICORE and gLite – make use of the same resources

  17. Software and Tools Development: CurrentResults • Establishment of eight groups of research developers, 20+ people from five Polish supercomputing centers, collaborating together to improve the quality of existing European grid infrastructure services, tools and applications • Research and development testbed available based on dedicated physical and virtual machines from supercomputing centers • Initial evaluation of new user tools, environments and grid applications developed and supported in Poland • Basic extensions and improvement procedures proposed to various functionalities provided by gLite, Unicore and QosCosGrid • Software reengineering, development and testing of useful user tools, such as Migrating Desktop, gEclipse, ViroLab/GridSpace, FIVO, Vine Toolkit, QCG-OpenMPI, QCG-ProActive, etc. • Software quality management for new services and tools to be deployed and maintained in the second phase of Pl-Grid • Active links to new user communities in Poland interested in advanced computing technologies in order to collect additional requirements and scenarios: www.plgrid.pl/ankieta

  18. Software and Tools Development: in numbers Research developers: 20+ Main research teams: 8 Supercomputing centers involved : 5 Dedicated physical / virtual machines: 30+ Tested infrastructures: EGEE, DEISA Software reengineering and tools testing: QosCosGrid, GridSpace, Migrating Desktop, gEclipse, Virolab/GridSpace, FiVO, Vine, QCG-OpenMPI/ProActive, etc. Software quality management:for new services and tools Current applications under integration and testing procedures: 10+ Current user tools under integration and testing procedures: 5+ Active links to new user communities in Poland:www.plgrid.pl/ankieta

  19. Software and Tools Development: Next Plans • Closer collaboration with user and developer communities representing various scientific domains (based on feedback received from our questionnaire) • Adaptation of virtualization techniques improving usability, fault tolerance, checkpointing and cluster management • Fancy web GUIs based on Liferay and Vine Toolkit accessing existing and extended e-Infrastructure services • Performance tests of various large scale cross-cluster parallel applications using co-allocation and advance reservation techniques • More analysis of grid management, monitoring and security solutions • Common software repository and deployment rules • Example services, tools and applications available as virtual boxes with different configurations • Main checkpoints and timeline: We are here VI 09 IX 09 IX 10 IV 11 I 12

  20. Users’ Support and Training • General task: • Running Help-Desk and users’ training and support tasks • Supporting how to effectively exploit developed infrastructure including selection of right applications for users’ problems and seamless running computation on the grid. • Pl-grid is an user oriented infrastructure, support and training team will be close to the users. • At the moment: • Support Team is organized • Internal training for support team already begun • Selection of licensed application required by the users’ community to be installed on the whole PL-Grid infrastructure • First training for the users delivered. • Plans: • Many, many trainings for beginners and advanced grid users

  21. PL-Grid Security Group:CurrentResults • Defined security guidelines for architecture planning • Defined security policy for local sites installations • Incident reporting systems review to choose best solution for PL-Grid • GGUS -  Global GridUser Support • RTIR - RequestTracking for IncidentResponse • DIHS - DistributedIncidentHandling System • Architecture and prototype version of on-line user mapping and credentials distribution system.

  22. PL-Grid Security Group: NextPlans • Establish NGI-wide CERT • Introduce security policies into local sites • Develop and deploy local sites security policy conformity monitoring system • check if software (kernel, services) is up to date • check listening ports, firewall rules • monitor suid/sgid lists and integrity • Develop distributed alert correlation system build on top of network and host sensors.

  23. How to become a User ? • Each Polish scientist can make use of PL+Grid resources • Just to register • For registration and other information see: http://www.plgrid.pl • Ask questions: m.sterzel@cyfronet.pl • For registration send an e-mail to: email: plgrid-rejestracja@rt.grid.cyfronet.pl ACK: M. Sterzel, Cyfronet

  24. Examples

  25. Example: VirtualLaboratoryGridSpace • Use of distributed computational resources and data repositories • High-level tools offered for the user for in-silico experiments ACK: EU Project Virolab, http://virolab.cyfronet.pl

  26. SampleexperimentinViroLab Environment • Patient’s data • Medical examination • HIV genetic sequence put into database • Experiment in-silico • Collect HIV genetic sequences from database • Perform sequence matching dopasowanie • Calculate virus resistance http://virolab.cyfronet.pl http://www.virolab.org

  27. t.szepieniec@cyfronet.pl Example: BiotechnologyinGrid Never Born Protein Folding ACK: Irena Roterman, Jagiellonian University, Tomasz Szepieniec, Cyfronet

  28. Contract-basedDynamicVirtualOrganizationsFiVO FiVO • Goal: • Allowendusers to definedtheirrequirements for theVirtualOrganization on a high level of abstraction • Semanticdescription of domain FiVO FiVO FiVO Overall system architecture • Results: • Automatic deployment of the VO • Security and monitoring • Optimization of data access • Replication and migration

  29. Summary – Activities • Achieved • Establish PL-Grid VO using Partners’ local and EGEE resources • In operation for Users’ Communities • Provide resources for covering operational costs • Provide resources for keeping international collaboration ongoing • Long term • Software and tools implementation • Users’ support and traning • Provide, keep and extend the necessary infrastructure • Work on approaching paradigms and integration development • HPCaaS and Scalable Computing (Capability and Capacity Computing) • Clouds Computing (internal-external, computing clouds, data clouds) • SOA paradigm, knowledge usage … • „Future Internet” as defined by EC in Workprogramme

  30. Acknowledgements • ACK Cyfronet AGH • Tomasz Szepieniec • Marcin Radecki • Mariusz Sterzel • Karol Krawentek • Agnieszka Szymańska • Andrzej Oziębło • Tadeusz Szymocha • Alex Kusznir • Teresa Ozga • Aleksandra Mazur • ICM • Piotr Bała • Maciej Filocha • PCSS • Norbert Meyer • Krzysztof Kurowski • Mirosław Kupczyk • WCSS • Józef Janyszek • Bartłomiej Balcerek • Paweł Dziekoński • TASK • Mścisław Nakonieczny • Jarosław Rybicki • Rafał Tylman Workperformedinthe Framework of Project POIG.02.03.00-00-007/08

  31. http://plgrid.pl Thankyou Visitourbooth

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