A worldwide e-infrastructure for NMR and structural biology

Transcription

1 A worldwide e-infrastructure for NMR and structural biology CHAIN Taipei, March 18, 2013 Alexandre M.J.J. Bonvin Project coordinator Bijvoet Center for Biomolecular Research Faculty of Science, Utrecht University the Netherlands

2 The Project A Worldwide e-infrastructure for NMR and structural biology Project Coordinator: Prof. Alexandre M.J.J. Bonvin, Utrecht University, NL Contract n : RI Project type: CP-CSA Duration: 36 months (Oct.2013) Total budget: EC Funding: The team: Utrecht University, Bijvoet Center for Biomolecular Research, NL Johann Wolfgang Goethe Universität Frankfurt a.m., Center for Biomolecular Magnetic Resonance DE University of Florence, Magnetic Resonance Center, IT Istituto Nazionale di Fisica Nucleare, Padova, IT Raboud University, Nijmegen, NL University of Cambridge UK European Molecular Biology Laboratory, Hamburg, DE Spronk NMR Consultancy, LT Academia Sinica, TW

3 Exploiting GRID resources in structural biology NMR data collection and processing SAXS data analysis Data interpretation # Number of dimensions 2 # INAME 1 1H # INAME 2 1H T 0.000e e T 0.000e e T 0.000e e T 0.000e e assign ( resid and name OO 1 T ) 0.000e e ( resid 501 and 40 name Z ) 1 T 0.000e e ( resid 501 and 43 name X ) 1 T 0.000e e ( resid 501 and 46 name Y ) 1 T 1.035e e+00 r T 0.000e e ( resid 2 and name CA ) assign ( resid 501 and name OO ) ( resid 501 and name Z ) ( resid 501 and name X ) ( resid 501 and name Y ) ( resid 3 and name CA ) Computations Structure, dynamics & interactions impact on research and health: - origin of disease - design of new experiments - drug design

4 The WeNMR philosophy for interacting with the Grid Our policy is to shield as much as possible the end user from the Grid and all middleware related issues and commands For this, we chose to develop mainly application web portals providing protocolized access to the Grid To facilitate operation, we use when possible robot certificates Experienced users can still interact directly with the Grid via UI and we provide ready-to-go customized UI distributions (MILU) for download

5 WeNMR platform (February 2013) Largest VO in the life sciences > 500 registered users (29% outside the EU) ~ CPU cores > 330 CPU years over the last 12 months > 1.25 million jobs over the last 12 months User-friendly access to Grid via web portals

6 The Virtual Research Community

7 The WeNMR VRC escience hub for NMR and structural biology

8 The WeNMR VRC Consultancy Third-party aggregation Tutorials, Wiki Knowledge Grid Help Center VRC Services Marketplace NEW! SSO Portals Blogs, news, events.. Exposure Facebook User

9 The WeNMR VRC Consultancy Tutorials, Wiki Help Center Knowledge VRC Third-party aggregation 42 help center requests Consultancy remote or on location 52 tutorials, 70 wiki Services documents, 20 movies Grid Marketplace NEW! SSO Portals Blogs, news, events.. Exposure Facebook User

10 The WeNMR VRC Consultancy Third-party aggregation 26 web portals of which 17 by partners Uniform access through the new Single Sign On functionality RPC access Help Center available for some portals Tutorials, Wiki Knowledge VRC Services Grid Marketplace NEW! SSO Portals Blogs, news, events.. Exposure Facebook User

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12 The WeNMR VRC Consultancy Third-party aggregation Tutorials, Wiki Knowledge Grid Help Center Marketplace VRC Services NEW! SSO Portals Blogs, news, events.. Exposure Facebook User

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20 The WeNMR services portfolio

21 Toward Federated Identity support Working with SURFnet in the Netherlands to provide user-friendly federated identity login

22 Toward Federated Identity support Working with SURFnet in the Netherlands to provide user-friendly federated identity login

23 Usage & Resources

24 GRID resource centers worldwide

25 GRID resource centers supporting the enmr.eu VO

26 CPU usage distribution Nov Oct. 2013

27 CPU usage distribution NGI-NL 43% Feb Mar. 2013

28 CPU usage distribution NGI-NL 43% Nov Oct. 2013

29 CPU usage distribution NGI-NL 43% Feb Mar. 2013

30 Comparison with other VOs bbmri.nl 71% 26% 42% biomed enmr.eu vo.neugrid.eu vo.renabi.fr lsgrid 1% 0% 0% 0% 0% 2% 0% 12% 0% 1% Cumulative CPU time Jan Dec % 1% 2% 1% 2% 1% 2% 2% 12% 3% 6% Number of users 13 Feb vlemed vo.eu-decide.eu life.vo.ibergrid.eu vo.sim-e-child.org vo.aginfra.eu libi Within Life Sciences LS vs. Other disciplines (excluding HEP) LS share is stable w/r to last year Astrophysics Comput. chemistry CS and Mathematics Earth Sciences Fusion Infrastructure Life Sciences Multidis. VOs Other Dis. 14,15% 43,74% 6,19% 19,4% 9,96% 2,64% 0% 3,24% 0,68%

31 Output from users of the gateway 36 publications in 2012 (19 in 2011) acknowledging WeNMR (or enmr) Users only 22% Methods development 47% Applica on of WeNMR Services 31% Application of WeNMR services = collaborations between WeNMR staff and users

32 Going worldwide...

33 Why going worldwide? Example: HADDOCK world map > 2800 registered users (150 with grid access) > served runs since June 2008 > 13% on the GRID All potential users of the Grid! Currently only if registered with the enmr.eu VO

34 VO registered user distribution

35 VO registered user distribution (Nov. 1 st 2012)

36 Extension towards EMI/UMD based e- Infrastrucures CPU capacity distribution (49k CPU-cores) Not negligible contribution from Taiwan and GISELA grid sites! Job distribution (780k, May-Oct.2012)

37 Extension towards Open Science Grid A good collaboration with SBGrid Consortium and its VO already established during the previous e-nmr project 67 US users (+49% in last year) already registered with enmr.eu VO (15% or the total) SBGrid VO enabled on >20 RCs and >40,000 CPU-cores Joint OSG-SBGrid-WeNMR-EGI interoperability task force set up and active from March 11 Results presented at EGI CF 2012 in March 12 and published in its proceedings PoS(EGICF12-EMITC2)040 Two steps implementation: Using EMI/gLite services (UI, WMS, LFC) via SBGrid VO Using GlideinWMS service, via enmr.eu and SBGrid VOs (recommended by OSG)

38 Extension towards Open Science Grid WeNMR application software installed from remote on OSG CEs WeNMR jobs are properly accounted on Gratia, the OSG accounting service, under the enmr.eu VO Job submission from UI by using both Condor CLI and SAGA API

39 Extension towards Asian grids Leveraging on the collaboration with EU PF7 CHAIN Project (and now its follow-up CHAIN-REDS) CHAIN promoted the Science Gateway approach to implement interoperability among several different middleware flavors, including: GARUDA (adopted by GARUDA, the Indian National Grid) GOS (adopted by CNGrid, the China National Grid) WeNMR is one of the VRCs selected by CHAIN to validate their interoperability model Official worldwide standards adopted: JSR 168 and JSR 286 (aka portlet 1.0 and 2.0 standards) OASIS SAML (security Assertion Markup Language) OGF (Open Grid Forum) SAGA (Simple API for Grid Applications) and its JSAGA implementation

40 Extension towards Asian grids WeNMR participated to the CHAIN Task to deliver the CHAIN Interoperability Demonstration at the EGI TF 2012 in September In particular we have been working on: defining the interoperability architecture with GARUDA deploying and testing Gromacs application on GARUDA resources also thanks to its past experience with EU-IndiaGrid project

41 Perspectives for the WeNMR Science Gateway The CHAIN Science Gateway approach could be adopted JSAGA components could be re-used... BUT we need a saga component working at the shell level since our portals as complex...! JSAGA Condor adaptor under development Negotiation with Resource Providers needed

42 What is happening behind the scene?

43 Acknowledgments The team Alexandre M.J.J. Bonvin Andrea Giachetti Antonio Rosato Anurag Bagaria Christophe Schmitz Eric Frizziero Gijs van der Schot Harald Schwalbe Hendrik R. A. Jonker Ivano Bertini Johan van der Zwan Lucio Ferella Marc van Dijk Marco Verlato Mikael Trellet Mirco Mazzucato Nuno Loureiro-Ferreira Peter Güntert Rolf Boelens Sjoerd J. de Vries Stefano Dal Pra Torsten Herrmann Tsjerk A. Wassenaar Victor Jaravine Wim F. Vranken Danny Hsu Simon Lin The partners Utrecht University, Bijvoet Center for Biomolecular Research, NL Johann Wolfgang Goethe Universität Frankfurt a.m., Center for Biomolecular Magnetic Resonance DE University of Florence, Magnetic Resonance Center, IT Istituto Nazionale di Fisica Nucleare, Padova, IT Raboud University, Nijmegen, NL University of Cambridge UK European Molecular Biology Laboratory, Hamburg, DE Spronk NMR Consultancy, LT Academia Sinica Contract n : RI Project type: CP-CSA

44 wordle.net

45 MoU with EMI established in 2011 Collaboration with EMI Crucial for testing EMI-ES component (and UNICORE resources through it) on the EMI Testing Infrastructure Would open the possibility to exploit DEISA/PRACE HPC resources (if required by NMR/SAXS applications) Unfortunately EMI-ES not released with EMI-2 in April 2012 as expected, ready for EMI-3? Positive feedback from EMI-UNICORE team obtained in Jan. 13, testing being tracked in GGUS ticket #89884 Use of EMI-2 component WNoDeS demonstrated at EGI TF in September 2012: VirtualCing Cloud demo on WNoDeS - cloud-demo-on-wnodes/