A worldwide e-Infrastructure for NMR and structural biology

Pooling EGI and OSG resources: WeNMR achieves full and transparent interoperability across the Atlantic

A.M.J.J. Bonvin1, M. Verlato2, R. Quick3

  1. Faculty of Science – Chemistry, Padualaan 8, 3584 CH Utrecht, the Netherlands, a.m.j.j.bonvin@uu.nl, www.wenmr.eu
  2. Istituto Nazionale di Fisica Nucleare, Sez. di Padova, 35131 Padova, Italy, Marco.Verlato@pd.infn.it, www.infn.it
  3. Open Science Grid Operations, Indiana University, 535 W Michigan Street, Indianapolis, IN 46202 rquick@iu.edu, www.opensciencegrid.org

November 4th, 2013

The WeNMR (www.wenmr.eu) Virtual Research Community (VRC) (an European FP7 e-Infrastructure project, grant no. 261572), supported by the European Grid Initiative (www.egi.eu), is the largest VRC within the life sciences, with over 575 VO members, a good fraction of which (>15%) corresponding to US users. WeNMR brings together complementary research teams in structural biology and life sciences into a worldwide virtual research community and provides them with a platform integrating and streamlining the computational approaches necessary for NMR and SAXS data analysis and structural modelling.

WeNMR has a long-standing collaboration in the US with SBGrid (www.sbgrid.org), a global consortium of over 220 structural biology groups making use of the Open Science Grid (OSG) (www.opensciencegrid.org) resources. In a joint SBGrid/OSG – WeNMR/EGI meeting held in March 2011, it was decided to implement interoperability between EGI and OSG in the domain of Structural Biology, aiming at a transparent integration of resources.

Following a number of pilots, full and transparent interoperability was achieved in October 2013. For this, the WeNMR VO (enmr.eu, mapped to enmr on OSG resources) was enabled on US sites, starting with the resources provided by Fermi National Accelerator Lab (fermigrid.fnal.gov). Further actions were undertaken to allow a transparent mapping of resources from OSG to EGI, in particular for the OSG sites to be discoverable under the EGI information system. The same was done for the accounting. With all this in place, grid jobs can now be submitted using standard EMI middleware and job description language (JDL) from a gLite-based user interface (UI). The software required by the WeNMR services was automatically deployed from the CVMFS system developed at RAL (www.gridpp.ac.uk/wiki/RALnonLHCCVMFS), which is duplicated on US sites through the OASIS system (oasis.opensciencegrid.org). In that way, all enmr software available on EGI resources through CVMFS becomes automatically available on OSG resources.

With all this in place, a number of WeNMR services, including the popular grid-enabled HADDOCK and CS-Rosetta web portals [Wassenaar et al. (2012) J Grid Comp 10:743-767], could be put in EGI/OSG production mode, sending jobs to grid resources in a transparent manner, without specifying a-priori on which side of the Atlantic these should run; it is the Workload Management System (WMS [Andreetto et al. (2012) J Phys: Conf Ser 396:032021]), which decides where to send the jobs based on site availability and rankings defined in the JDL files. Support of the WeNMR VO will be extended to more OSG sites in the coming weeks.

With this we have successfully achieved a transparent pooling of EGI and OSG resources in order to serve at best our worldwide user community in structural biology and life sciences.

Cite WeNMR/WestLife

 
Usage of the WeNMR/WestLife portals should be acknowledged in any publication:
 
"The FP7 WeNMR (project# 261572) and H2020 West-Life (project# 675858) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure and DIRAC4EGI service with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, RAL-LCG2, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan and the US Open Science Grid."
 
And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.

EGI-approved

The WeNMR Virtual Research Community has been the first to be officially recognized by the EGI.

European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858

West-Life