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Introduction to Grid

Introduction to Grid. Eddie.Aronovich@cs.tau.ac.il. Acknowledgements. Presentation is based on slides from: Roberto Barbera, University of Catania and INFN (EGEE Tutorial Roma, 02.11.2005) Mike Mineter, Concepts of grid computing

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Introduction to Grid

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  1. Introduction to Grid Eddie.Aronovich@cs.tau.ac.il

  2. Acknowledgements • Presentation is based on slides from: • Roberto Barbera, University of Catania and INFN (EGEE Tutorial Roma, 02.11.2005) • Mike Mineter, Concepts of grid computing • Fabrizio Gagliardi, EGEE Project Director, CERN, Geneva, Switzerland (Naregi Symposium 2005 – Tokyo) • Fabrizio Gagliardi, EGEE Project Director, CERN, Geneva, Switzerland (APAC, 27 September 2005) • Guy Warner, NeSC Training Team (An Induction to EGEE for GOSC and the NGS NeSC, 8th December 2004 ) EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  3. EGEE project in 1K words https://goc.grid-support.ac.uk/gridsite/monitoring/ EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  4. From Phase I to II • From 1st EGEE EU Review in February 2005: • “The reviewers found the overall performance of the project very good.” • “… remarkable achievement to set up this consortium, to realize appropriate structures to provide the necessary leadership, and to cope with changing requirements.” • EGEE I • Large scale deployment of EGEE infrastructure to deliver production level Grid services with selected number of applications • EGEE II • Natural continuation of the project’s first phase • Emphasis on providing an infrastructure for e-Science  increased support for applications  increased multidisciplinary Grid infrastructure  more involvement from Industry • Extending the Grid infrastructure world-wide  increased international collaboration (Asia-Pacific is already a partner!) EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  5. What do we need more ? • Processing power • Storage • Security aware integrative infrastructure • Community aware environment Or what we may call…. EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  6. e-Science • What is e-Science? Collaborative science that is made possible by the sharing across the Internet of resources (data, instruments, computation, people’s expertise...) • Often very compute intensive • Often very data intensive (both creating new data and accessing very large data collections) – data deluges from new technologies • Crosses organisational boundaries • Examples…. EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  7. Mont Blanc (4810 m) Downtown Geneva A good example: Particle Physics • Large amount of data produced in a few places: CERN, FNAL, KEK… • Large worldwide organized collaborations (i.e. LHC CERN experiments) of computer-savvy scientists • Computing and data management resources distributed world-wide owned and managed by many different entities • Large Hadron Collider (LHC) at CERN in Geneva Switzerland: • One of the most powerfulinstruments ever built to investigate matter EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  8. The LHC Experiments • Large Hadron Collider (LHC): • four experiments: • ALICE • ATLAS • CMS • LHCb • 27 km tunnel • Start-up in 2007 EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  9. 10-15 Petabytes ˜20.000.000 CD-ROM 10 times the Eiffel Tower ˜3000 m Orders of magnitude… EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  10. EGEE is building a large-scale production grid service to: Underpin research, technology and public service Link with and build on national, regional and international initiatives Foster international cooperation both in the creation and the use of the e-infrastructure Collaboration Pan-European Grid Operations, Support and training Network infrastructure& Resource centres EGEE – building e-infrastructure EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  11. Grids and e-Infrastructure • “Campus grids”: internal to an institute / university: • “High throughput” – harvesting compute time • Not really ‘a grid’ unless crossing administrative domains • Can become a resource on a grid • Example: Condor • http://www.nesc.ac.uk/esi/events/556/ • Grids: cross administrative boundaries • National scale: in UK, NGS • Regional efforts: in China, EUMedGrid, CrossGrid, SeeGrid • International scale: in Europe, EGEE EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  12. e-Infrastructure • implementation blocks From a talk by Mario Campolargo, Brussels, 30 May 2005 EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  13. Contents • “The Grid” vision • What is “a grid” ? • Drivers of grid computing • Implementation samples • Grid Status & Standards • The basis: authentication, authorisation, security • So, What can it do ? EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  14. The Grid Metaphor Mobile Access G R I D M I D D L E W A R E Supercomputer, PC-Cluster Workstation Data-storage, Sensors, Experiments Visualising Internet, networks EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  15. The grid vision • The grid vision is of “Virtual computing” (+ information services to locate computation, storage resources) • Compare: The web: “virtual documents” (+ search engine to locate them) • MOTIVATION: collaboration through sharing resources (and expertise) to expand horizons of • Research • Commerce – engineering, … “the knowledge economy” • Public service – health, environment,… EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  16. Contents • “The Grid” vision • What is “a grid” ? • Drivers of grid computing • Implementation samples • Grid Status & Standards • The basis: authentication, authorisation, security • So, What can it do ? EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  17. Institute A Institute C Institute B Institute D “A grid” • The initial vision: “The Grid” • The present reality: Many “grids” • Each grid is an infrastructure enabling one or more “virtual organisations” to share computing resources • What’s a VO? • People in different organisations seeking to cooperate and share resources across their organisational boundaries • Why establish a Grid? • Share data • Pool computers • Collaborate VO EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  18. Application Software Operating System Disks, Processor, Memory, … The Single Computer • The Operating System enables easy use of • Input devices • Processor • Disks • Display • Any other attached devices EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  19. Application Software Middlewarefor sharing computers, servers, printers, … Operating System on each computer Resources connected by a LAN Resources on a Local Area Network User just perceives “shared resources”, with no regard to location in the organisation: - Authenticated by username / password - Authorised to use own files,… EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  20. Resources on a grid Application Software Interface between app. and grid Grid Middleware: “collective services” Grid Middleware on each resource Operating System on each resource Resources connected by internet EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  21. INTERNET A grid • Grid middleware runs on each shared resource • Data storage • (Usually) batch jobs on pools of processors • Users join VO’s • Virtual organisation negotiates with sites to agree access to resources • Distributed services (both people and middleware) enable the grid EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  22. What characterises a grid? • Co-ordinated resource sharing • No centralised point of control • Different administrative domains. • Standard, open, general-purpose protocols and interfaces • NOT specific to an application • EGEE, NGS support multiple VO’s • Delivering non-trivial qualities of service • Co-ordinated to deliver combined services, greater than sum of the individual components • http://www.gridtoday.com/02/0722/100136.html EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  23. The components of a Grid • Resources • networking, computers, storage, data, instruments, … • Grid Middleware • the “operating system of the grid” • Operations infrastructure • Run enabling services (people + software) • Virtual Organization management • Procedures for gaining access to resources EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  24. Key concepts • Virtual organisation: people and resources collaborating - across admin, organisational boundaries • Single sign-on • I connect to one machine – some sort of “digital credential” is passed on to any other resource I use, basis of: • Authentication: How do I identify myself to a resource without username/password for each resource I use? • Authorisation: what can I do? Determined by • My membership of VO • VO negotiations with resource providers • Grid middleware runs on each resource • User just perceives “shared resources” with no concern for location or owning organisation EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  25. Contents • “The Grid” vision • What is “a grid” ? • Drivers of grid computing • Implementation samples • Grid Status & Standards • The basis: authentication, authorisation, security • So, What can it do ? EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  26. Large Hadron Collider at CERN • Data Challenge: • 10Petabytes/year of data !!! • 20 million CDs each year! • Simulation, reconstruction, analysis: • LHC data handling requires computing power equivalent to ~100,000 of today's fastest PC processors! • Operational challenges • Reliable and scalable through project lifetime of decades Mont Blanc (4810 m) Downtown Geneva EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

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  28. DAME: Grid based tools and Infer-structure for Aero-Engine Diagnosis and Prognosis Engine flight data London Airport Airline office New York Airport Grid Diagnostics Centre Maintenance Centre American data center European data center “A Significant factor in the success of the Rolls-Royce campaign to power the Boeing 7E7 with the Trent 1000 was the emphasis on the new aftermarket support service for the engines provided via DS&S. Boeing personnel were shown DAME as an example of the new ways of gathering and processing the large amounts of data that could be retrieved from an advanced aircraft such as the 7E7, and they were very impressed”, DS&S 2004 XTO Companies: Rolls-Royce DS&S Cybula Universities: York, Leeds, Sheffield, Oxford Engine Model Case Based Reasoning EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  29. Contents • “The Grid” vision • What is “a grid” ? • Drivers of grid computing • Implementation samples • Grid Status & Standards • The basis: authentication, authorisation, security • So, What can it do ? EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  30. If “The Grid” vision leads us here… … then where are we now? EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  31. Grids: where are we now? • Many key concepts identified and known • Many grid projects have tested, and benefit from, these • Major efforts now on establishing: • Standards (a slow process) (e.g. Global Grid Forum, http://www.gridforum.org/ ) • Production Grids for multiple VO’s • “Production” = Reliable, sustainable, with commitments to quality of service • In Europe, EGEE • In UK, National Grid Service • In US, Teragrid • One stack of middleware that serves many research (and other!!!) communities • Operational procedures and services (people!, policy,..) • New user communities • … whilst research & development continues EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  32. The vision of 2001: convergence of Web Services and Grids Open Grid Services Architecture web developments “big Science” research OGSIGrid prototypes Web services World-wide web INTERNET High-end computing High throughput-computing Massively parallel computing EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  33. Contents • “The Grid” vision • What is “a grid” ? • Drivers of grid computing • Implementation samples • Grid Status & Standards • The basis: authentication, authorisation, security • So, What can it do ? EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  34. Approaches to Security: 1 The Poor Security House EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  35. Approaches to Security: 2 The Paranoid Security House EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  36. Approaches to Security: 3 The Realistic Security House EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  37. Grid security and trust -1 • Providers of resources (computers, databases,..) need risks to be controlled: they are asked to trust users they do not know • They trust a VO • The VO trusts its users • User’s need • single sign-on: to be able to logon to a machine that can pass the user’s identity to other resources • To trust owners of the resources they are using • Build middleware on layer providing: • Authentication: who wants to use/provide resource • Authorisation: what the user is allowed to do • Security: reduce vulnerability, e.g. from outside the firewall • Non-repudiation: knowing who did what • Digital credentials and the “Grid Security Infrastructure” middleware are the basis of production grids EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  38. Grid security and trust -2 • Currently, achieved by Certification: • User’s identity has to be certified by one of the national Certification Authorities (CAs) • mutually recognized http://www.gridpma.org/, for EU go via here to http://marianne.in2p3.fr/datagrid/ca/ca-table-ca.htmlto find your CA • E.g. In IL go to https://certificates.iucc.ac.il • Resources are also certified by CAs • User • User joins a VO • Digital certificate is basis of AA • Identity passed to other resources you use, where it is mapped to a local account – the mapping is maintained by the VO • Common agreed policies establish rights for a Virtual Organization to use resources EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  39. Grid security and trust -3 • Certification and GSI provides • Authentication • Resource can trust user • User can trust the resource provider • …. So long as certificates are protected – they are your grid identity • A basis for Authorisation • so a VO can manage access to resources • Resource providers trust the VO • The VO trusts the user • Mechanism for checking message integrity • Messages are passed between machines • Public/private key pairs protect message integrity as well as authentication • Not (usually) encrypted but message-integrity is checked EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  40. Cert Independent Scotland ID Certificate Request User send public key to CA along with proof of identity. User generatespublic/privatekey pair. CA confirms identity, signs certificate and sends back to user. CertificateRequest Public Key Public Certificate Authority Private Key encrypted on local disk slide based on presentation given by Carl Kesselman at GGF Summer School 2004 EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  41. Contents • “The Grid” vision • What is “a grid” ? • Drivers of grid computing • Implementation samples • Grid Status & Standards • The basis: authentication, authorisation, security • So, What can it do ? EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  42. PADOVA BARI 15 resource centres • 17 CEs • 16 SEs Number of jobs Month BioMed Overview • Infrastructure • ~3.000 CPUs • ~12 TB of disk • in 9 countries • >50 users in 7 countries working with 12 applications • 18 research labs EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  43. ~ 70 users, 9 countries • > 12 Applications (medical image processing, bioinformatics) • ~3000 CPUs, ~12 TB disk space • ~100 CPU years, ~ 500K jobs last 6 months Biomed Virtual Organisation EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  44. Bioinformatics • GPS@: Grid Protein Sequence Analysis • Gridified version of NPSA web portal • Offering proteins databases and sequence analysis algorithms to the bioinformaticians (3000 hits per day) • Need for large databases and big number of short jobs • Objective: increased computing power • Status: 9 bioinformatic softwares gridified • Grid added value: open to a wider community with larger bioinformatic computations • xmipp_MLrefine • 3D structure analysis of macromolecules • From (very noisy) electron microscopy images • Maximum likelihood approach to find the optimal model • Objective: study molecule interaction and chem. properties • Status: algorithm being optimised and ported to 3D • Grid added value: parallel computation on different resources of independent jobs EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  45. Target discovery Lead discovery Lead Optimization Target Identification Target Validation Lead Identification Clinical Phases (I-III) Database filtering QSAR Alignment Computer Aided Drug Design (CADD) ADMET Similarity analysis Biophores vHTS diversity selection Combinatorial libraries de novo design Duration: 12 – 15 years, Costs: 500 - 800 million US $ Drug Discovery • Demonstrate the relevance and the impact of the grid approach to address Drug Discovery for neglected diseases EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  46. UI Docking platform components • Predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure Grid infrastructure Targets family ~10 Compounds database ~millions Parameter / scoring settings Software methods ~10 EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  47. First biomedical data challenge: World-wide In Silico Docking On Malaria (WISDOM) • Significant biological parameters • two different molecular docking applications (Autodock and FlexX) • about one million virtual ligands selected • target proteins from the parasite responsible for malaria • Significant numbers • Total of about 46 million ligands docked in 6 weeks • 1TB of data produced • Up 1000 computers in 15 countries used simultaneously corresponding to about 80 CPU years WISDOM open day December 16th, 2005, Bonn (Germany) Discuss Data Challenge results Prepare next steps towards a malaria Grid (EGEE-II, Embrace, Bioinfogrid) Information: http://wisdom.eu-egee.fr EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  48. Medical imaging • GATE • Radiotherapy planning • Improvement of precision by Monte Carlo simulation • Processing of DICOM medical images • Objective: very short computation time compatible with clinical practice • Status: development and performance testing • Grid Added Value: parallelisation reduces computing time • CDSS • Clinical Decision Support System • Assembling knowledge databases • Using image classification engines • Objective: access to knowledge databases from hospitals • Status: from development to deployment, some medical end users • Grid Added Value: ubiquitous, managed access to distributed databases and engines EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  49. Medical imaging • SiMRI3D • 3D Magnetic Resonance Image Simulator • MRI physics simulation, parallel implementation • Very compute intensive • Objective: offering an image simulator service to the research community • Status: parallelised and now running on EGEE resources • Grid Added Value: enables simulation of high-res images • gPTM3D • Interactive tool to segment and analyse medical images • A non gridified version is distributed in several hospitals • Need for very fast scheduling of interactive tasks • Objectives: shorten computation time using the grid • Interactive reconstruction time: < 2min and scalable • Status: development of the gridified version being finalized • Grid Added Value: permanent availability of resources EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

  50. Generic Applications • EGEE Generic Applications Advisory Panel (EGAAP) • UNIQUE entry point for “external” applications • Reviews proposals and make recommendations to EGEE management • Deals with “scientific” aspects, not with technical details • Generic Applications group in charge of introducing selected applications to the EGEE infrastructure • 6 applications selected so far: • Earth sciences (earth observation, geophysics, hydrology, seismology) • MAGIC (astrophysics) • Computational Chemistry • PLANCK (astrophysics and cosmology) • Drug Discovery • E-GRID (e-finance and e-business) • GRACE (grid search engine, ended Feb 2005) EGEE tutorial, Seoul Biomed Grid Induction (Tel-Aviv Univ), Feb 2006

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