1 / 18

WeNMR Update Report: Workshop in Taipei, Taiwan on February 27th, 2012

This report provides an update on the WeNMR project, a worldwide e-infrastructure for NMR and structural biology. It includes information on project numbers, portals, users, resources, usage, and future plans.

eherrington
Download Presentation

WeNMR Update Report: Workshop in Taipei, Taiwan on February 27th, 2012

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Update report CHAIN Workshop, Taipei, Taiwan, February 27th 2012 Marco Verlato INFN (National Institute of Nuclear Physics) Division of Padova Italy marco.verlato@pd.infn.it

  2. The Project A Worldwide e-Infrastructure for NMR and structural biology Contract n°: RI-261572 Project type: CP-CSA Duration: 36 months (Oct.2013) Total budget: 2’434’000 € EC Funding: 2’150’000 € Project Coordinator: Prof. Alexandre M.J.J. Bonvin, Utrecht University, NL 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 www.wenmr.eu 1st VRC recognized by EGI MoUs/links with EMI, CHAIN, EUMEDGRID, Gisela, SAGrid, OSG/SBGrid and the INSTRUCT ESFRI project 4

  3. Update of numbers (portals, users, resources, usage) Focus for 2012: Planning for sustainability: defining the WeNMR “products” and its potential market Developing portals for SAXS spectroscopists Implementing the Workflow and Data Management System Recruitment of ASGC partner within the budget Implementing SSO mechanism for unified access to portals Progressing on interoperability with SBGrid/OSG News from the last CHAIN workshop

  4. Portals available from the WeNMR gateway • 19 portalsare currentlyembedded in the WeNMR gateway and provideservicesfor NMR spectroscopists • 10oftheseruncalculations on the Grid • 7 portals have been developed and released during 2011 • PortalsdedicatedtoSAXSspectroscopistswillbereleased 2012; however, the MaxOccportalalreadyallows the combineduseof NMR and SAXS data • Continue to expand the number and diversity of services, also increasing/strengthening the collaborations with teams outside the WeNMR partnership

  5. Worldwide user distribution • #382 VO registered users at Jan 2012 in 41 countries • #86 users (22%) in 11 countries outside EU (#54 in USA) • Steady growing rate ~ 10 users/month

  6. Worldwide resource distribution 35k 2k 40 central grid services in EU 0.3k 0.2k • 27 resource centres in Europe, ~35k CPU-cores • 4 resource centres outside Europe • TW-eScience (2k CPU-cores), Taiwan • UNLP+UFRJ+ULA (0.3k CPU-cores), GISELA • UJ (0.2k CPU-cores), SAGrid Countries with users Countries with users & resources

  7. Grid operations • Keeping aligned with EGI monitoring/accounting tools: • Operation of a dedicated instance of Gstat 2.0 • Operation of a dedicated Nagios server • Operation of a dedicated WMSMonitor server • Operation of dedicated DGAS servers to complement APEL • Collaboration with EGI-InSPIRE NA3 and EGI.eu UCST teams for integration with the EGI VO Dashboards

  8. Resource usage (last six months) • ~1 Million Normalized CPU-hours (kSI2K)/month on average • it was ~0.6M in the previous 6 months (+55%) • 75% by Dutch NGI, 2% for outside EU sites • ~160k jobs/month on average • it was ~140k in the previous 6 months (+13%) • 55% by Dutch NGI, 6% from outside EU sites lsgrid 10% enmr.eu 43% 46% biomed enmr.eu biomed

  9. Academia Sinica of Taiwan joins WeNMR Institute of Biological Chemistry Institute of Physics and ASGC Detailed program defined for contributing to all activities: Networking, dissemination and outreach Translating documentation/pub. abstracts into Chinese Covering major NMR, Biophysics and Struct. Biology events in AP area Services activities Allocate and operate ASGC resources for WeNMR VO Dedicated queues for MD simulation with multi-threaded GROMACS Training material/FAQ/User support in Chinese Joint Research activities Developing protocols for joint usage of SAXS and NMR with docking Enhancing the working capacity of the SAXS beamline at the National Synchrotron Radiation Research Centre (NSRRC) in Taiwan New partner in Asia-Pacific

  10. SSO has to be implemented before the end of 2012 So far 10 portals submitting jobs to grid with 8 different authentications Three portals developed at CIRMMP already handles SSO using a simple PostgreSQL DB storing usr/pwd, DN, VOMS roles and cert. expiration date Other more standard solutions evaluated: Umbrella system by the EuroFEL ESFRI project for the photon/neutron facilities user community based on Shibboleth/SAML, photon/neutron user federation, unique EU-wide identification Enabling support to Identity Federations as adopted in several Science Gateways e.g. EUMEDGRID, DECIDE, INDICATE, GISELA, CHAIN, etc. Single Sign On access to WeNMR portals

  11. Worldwide grid extension • WeNMR planned a grid interoperability activity to start in its second year • Built on Network Activities aimed at involving worldwide grids and e-Science projects in its first year • Goal: worldwidegridextensionoutsideEurope • Towards UMD based infrastructures • South Africa gLite√ • Latin America gLite√ • Asia-Pacific gLite√ • DEISA/PRACE  UNICORE • Towards non-UMD based infrastructures • OSG/SBGrid in USA  VDT (Globus, Condor, etc.) • Asian grids • Garuda in India  Globus • CNGrid in China  GOS

  12. Building on Network Activities • Collaborations (MoU) relevant for this activity already established with the following projects: • CHAIN(Co-ordination and Harmonisation of Advanced e-Infrastructures) • EUMEDGRID-Support (Sustainability of e-Infrastructures across the Mediterranean) • GISELA(Grid Initiatives for e-Science virtual communities in Europe and Latin America) • EU-IndiaGrid2 (Sustainable e-Infrastructures across Europe and India) • EMI and EGI • SBGrid (Software Consortium for Structural Biology) and OSG (Open Science Grid) in US • Attended networking events in 2010 and 2011: • WeNMR at CHAIN KoM (Roma, 13-14 December) • WeNMR at EU-IndiaGrid2 Workshop (Delhi, 13-16 December) • WeNMR at OSG All Hands (Boston, 7-11 March) • WeNMR at ISGC 2011 / OGF31 (Taipei, 21-25 March) • WeNMR at GISELA & CHAIN Workshop (Vilnius in April, Lyon in September ) • WeNMR at SC11 Exposition (Seattle, 14-17 November)

  13. Collaboration with EMI • MoU with EMI signed in 2011 • Crucial for testing EMI-ES component (and UNICORE resources through it) on the EMI Testing Infrastructure • Open the possibility to exploit DEISA/PRACE HPC resources (if required by NMR/SAXS applications) • EMI-ES to be released with EMI-2 in April 2012, tests planned to start in March with the devel. instance of WeNMR portal

  14. Collaboration with SBGrid/OSG • Collaboration with SBGrid Consortium well established • WeNMR access provided as option to users registering with SBGrid Science Portal since one year • 54 US users (DOEGridsCA) currently registered with enmr.eu VO (14%) • SBGrid is also a VO of OSG • supported by 26 OSG sites, >60k CPU-cores • gLite clients available on WNs • Interoperability effort started in March 2011 • joint team with OSG, SBGrid and WeNMR experts • use of SBGrid VO group /SBGrid/WeNMR to access OSG resources • two options for submitting WeNMR jobs to OSG: • using gLite UI / WMS / SE / LFC enabled with SBGrid VO • using the SBGridglideinWMS submission system • GlideinWMS is the OSG recommended pilot-based job submission system

  15. Using SBGridglideinWMS/1 • Condor submit node installed on a gLite UI at INFN • CS-Rosetta test jobs successfully submitted in two ways: • direct condor_submit (JDLcondor submit file translation needed) • via SAGA Python API implemented by LSU (www.saga-project.org)

  16. Using SBGridglideinWMS/2 • WeNMRsw installed from remote on $OSG_APP area • via condor job or globus-job-run on the CE head node • Glideins are submitted with SBGrid VO proxy • WeNMR jobs can be submitted with enmr.eu VO proxy • allows interaction with WeNMR existing LFC and SEs services • Job statistics provided by SBGrid Science Portal • Condor View • Gratia

  17. Next steps • Need of a SAGA implementation with both Condor and gLite/EMI-WMS adaptors • SAGA-LSU has a Condor adaptor and a MoU with EMI • JSAGA has the gLite adaptor but not the Condor one • Testing massive job submission with the devel. portal • Put the stuff in production • starting from the most demanding applications (Amber, CS-Rosetta, Haddock, …) or the most popular among US users • same robot proxy and same SAGA based script behind the portal for handling job submission to both gLite-WMS and Condor • Project milestone “Extension to SBGrid implemented” to be achieved by October 2012

More Related