1. WeNMR Operations Report Marco Verlato INFN (National Institute of Nuclear Physics) Division of Padova Italy marco.verlato@pd.infn.it EGI Community Forum 2013 Manchester, UK, 08-12 April 2013

2. 4 Project Coordinator: Prof. Alexandre M.J.J. Bonvin, Utrecht University, NL Contract n°: RI-261572 Project type: CP-CSA Duration: 36 months (Oct.2013) Total budget: 2’434’000 € EC Funding: 2’150’000 € A Worldwide e-Infrastructure for NMR and structural biology 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, since 2012 The team The WeNMR Project www.wenmr.eu Linked with Bio-NMR and EAST-NMR EU projects and INSTRUCT ESFRI 1 st VRC recognized by EGI

3. # Number of dimensions 2 # INAME 1 1H # INAME 2 1H 12 2.137 2.387 1 T 0.000e+00 0.00e+00 - 0 2756 2760 0 14 2.387 4.140 1 T 0.000e+00 0.00e+00 - 0 2760 2752 0 32 1.849 4.432 1 T 0.000e+00 0.00e+00 - 0 2259 2257 0 36 1.849 3.143 1 T 0.000e+00 0.00e+00 - 0 2259 2587 0 39 1.760 4.432 1 T 0.000e+00 0.00e+00 - 0 2260 2257 0 40 1.760 1.849 1 T 0.000e+00 0.00e+00 - 0 2260 2259 0 43 1.760 3.143 1 T 0.000e+00 0.00e+00 - 0 2260 2587 0 46 1.649 4.432 1 T 1.035e+05 0.00e+00 r 0 2583 2257 0 47 1.649 1.849 1 T 0.000e+00 0.00e+00 - 0 2583 2259 0 assign ( resid 501 and name OO ) ( resid 501 and name Z ) ( resid 501 and name X ) ( resid 501 and name Y ) ( resid 2 and name CA ) -0.1400 0.15000 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 ) -0.0100 0.15000 Data interpretation Structure, dynamics & interactions  impact on research and health: - origin of disease - design of new experiments - drug design… - drug design… Exploiting GRID resources in structural biology… Computations NMR data collection and processing SAXS data analysis

4. Our policy is to shield as much as possible the end user from the grid and all middleware related issues and commands We chose to develop mainly web portal providing “protocolized” access to the grid To facilitate operation, we use when possible robot certificates 29 portals (5 developed by external teams) are currently embedded in the WeNMR gateway and provide services for NMR and SAXS spectroscopists 11 of these run calculations on the grid The WeNMR service portfolio

5. The VRC portal: www.wenmr.eu

6. The WeNMR VRCThe WeNMR VRC Knowledge 42 Help Centers 52 Tutorials 70 Wiki docs 20 Movies Consultancy Services Portals VRC Third-party aggregation Grid Exposure Marketplace Blogs, news, events… (often picked up from eScienceTalk/GridCast) Users New! SSO Facebook, Linkedin www.wenmr.eu

7. 7 Web portal to chemical shift-based structure calculations with Rosetta Rosetta is extremly CPU intensive and can perfectly make use of the grid resources One typical run would require between 1000 and 5000 CPU hours on a single processor! Only a few days on the GRID depending on the load Example: CS-ROSETTA

8. 8 Parts of the computations are done locally The most CPU demanding ones are done on the grid CS-ROSETTA Workflow

9. 9 Grid daemon beyond a portal

10. VO registered user distribution >500 users from 50 countries 30% outside Europe 10 users/month steady growth enmr.eu is the largest VO in Life Sciences

11. Resources distribution

12. Distribution and usage of resources Support from 7 European National Grid Initiatives: France, Germany, Italy, Netherlands, Portugal, Spain, UK Support from Africa, Asia and Latin America: South Africa (SAGrid), Taiwan (TWGrid), Brazil, Argentina, Venezuela (GISELA) ~50,000 CPU-cores (24 opportunistic sites) and 320 CPU-cores (3 owned sites) 24% of jobs (16% of CPU-time) provided by the owned sites NEW! 10 job/slots from BEIJING-LCG2 NEW! 48 job/slots from MY-BIRUNI

13. Distribution and usage of resources 153,000 jobs/month 1.8M jobs last year 353,000 CPU.hours/month 4.2M CPU.hours last year

14. Implemented by exploiting the granularity made available by the VOMS service: a VOMS group defined for each application e.g.: voms-proxy-init –voms enmr.eu:/enmr.eu/haddock the user proxy carries the VOMS group info Application accounting

15. Wide use of the EGI/NGIs monitoring tools: Operating a dedicated instance of Gstat 2.0 Operating a dedicated Nagios server with WeNMR specific Nagios probes Operating a dedicated WMSMonitor server Collaboration with EGI Operations team for integrating the dedicated services with:  EGI VO Admin Dashboard  EGI VO Operations Dashboard Grid operations monitoring Supported by the Italian NGI

16. We make wide use of the EGI Accounting Portal for our periodic reports, presentations etc. A few open issues about accounting: Decommissioned sites do not show anymore in the statistics (RT #4741 – GGUS #88525, Nov’12), i.e. historical data are lost  A: Yes, the site is registered as "closed". The portal does not show closed site historic data. When a site changes name the data can be associated with the new site name to preserve the old history. The old sites could be displayed in site aggregation views since the data is still there, but we cannot make the sites directly accessible on the production trees. In any case, there were requirements to implement a "decommissioned" flag on GOCDB for these cases, but there was not much discussion. Open issues

17. …continue for accounting Accessibility difficulties from some users (GGUS #86305, Sep’12) Q: I am no longer given access to the VO member view of the accounting portal. It used to work for me in the past (and I am managing the enmr.eu VO). And the error message I am getting is: "You are not a VO Member so you can not access to this page.“ Since I can still manage properly the enmr.eu VOMS, I am clearly still VO member. The problem occurs irrespective of the browser and even on my iPhone. All were working in the past. I renewed my certificate about a few weeks ago. Other sites requiring certificates are working fine. Issue is under investigation with a temporary Dutch X509 certificate NGIs publishing user-level accounting data to the authorised VO Resource Managers (RT # 3070 – GGUS #75762, Oct’11) – also related to RT #3446: Implementing per-site vo adm view A: The TSA1.5 Accounting team is following up with sites not publishing Users DN. Many more sites are now properly configured, but we are currently dealing with a tail of sites still publishing 'unknown' in the repositories. Other NGIs are not publishing userDN because they publish aggregated usage records (i.e. Italy and NDGF), this is not a configuration problem but it would require further developments. (Nov.12) Issue seems solved: from the 62% of unknown userDN of June’12 to 0% in Feb’13 and 4% in Mar’13. Open issues

18. About monitoning: Job slots availability properly published from sites (GGUS # 91733, Feb’13) Q: GStat does report the number of sites with the available CPUs for a given VO. This is however misleading since number of CPUs might not match the number of job slots allocated to a given VO (nor the priorities). It would be very nice and useful to have also an overview of the available job slots per site for a given VO. A: Sites generally don't allocate a fixed number of slots per VO, they use a fairshare algorithm. The target share for a VO is usually published in the CECapability attribute, e.g.GlueCECapability: Share=biomed:20 which means that biomed would get about 20% of the resources if all supported VOs submitted jobs continuously. About VOMS: Admin access from iPhone (GGUS #80613, Mar.12) Q: It appears that the VOMS server used to be accessible from an iPhone, but not anymore since a few months now. Other site that requests a certificate are accessible from the iPhone. Does anyone know why and if there is a fix? VOMS server from an iphone is actually quite useful when it comes to accept a new member. A: This looks like a trustmanager issue, so reassigning it to Joni. That said, you should check with your iDevice if EMI 3 VOMS (which does not rely on trustmanager anymore) solve the issue. Open issues Solved with EMI-3