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New Communities: The Virtual Physiological Human Use Case

New Communities: The Virtual Physiological Human Use Case. Stefan Zasada University College London stefan.zasada@ucl.ac.uk. Many applications are now workflows of operations that require compute resources of different scales + data

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New Communities: The Virtual Physiological Human Use Case

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  1. New Communities: The Virtual Physiological Human Use Case Stefan Zasada University College London stefan.zasada@ucl.ac.uk

  2. Many applications are now workflows of operations that require compute resources of different scales + data • Workflow components of different sizes should be allocated to appropriate resources: clusters or supercomputers • We need to be able to transparently interoperate across EGI, PRACE, EUDAT & other infrastructures • A working group has been established to interoperate across EUDAT, EGI and PRACE • ++ • We’re working to bring a use cases from VPH to help develop this collaboration Federating Infrastructures

  3. EUDAT • Community-orientedservices • Simple Data Accesandupload • Long termpreservation • Sharedworkspaces • Executionandworkflow (datamining, etc.) • Joint metadataanddatavisibility • Enablingservices (makinguseofexistingserviceswherepossible • Persistent identifierservice (EPIC, DataCite) • Federated AAI service • Network Services • Monitoringandaccounting Core services arebuilding blocks ofEUDAT‘s Common Data Infrastructure mainlyincluded on bottomlayerofdataservices http://eudat.eu/

  4. EGI • European • Over 35 countries • Grid • Secure sharing • Infrastructure • Computers • Data • Instruments • …. and beyond!! Established to & successful in finding the Higgs Boson

  5. PRACE The Partnership for Advanced Computing in Europe is the European HPC Research Infrastructure PRACE enables world-class science through large scale simulations PRACE provides HPC services on leading edge capability systems on a diverse set of architectures PRACE operates up to six Tier-0 systems as a single entity including user and application support PRACE offers its resources through a single pan-European peer review process

  6. Virtual Physiological Human (VPH) • €207M initiative in EU-FP7 • Aims • Enable collaborative investigation of the human body across all relevant scales. • Introduce multiscale methodologies into medical and clinical research • The VPH framework is: • Descriptive • Integrative • Predictive Organism Organ Tissue Cell Organelle Interaction Protein Cell Signals Transcription Gene Molecule VPH DEISA Virtual Community established in collaboration with Hermann Lederer, MPS RZG

  7. Virtual Physiological Human “a methodological and technological framework that, once established, will enable collaborative investigation of the human body as a single complex system ...” • 42 projects: 1 NoE + IPs, STREPS + CAs. • New projects to be funded under Call 9 Networking NoE http://www.vph-noe.eu

  8. VIP for VPH - CNRS and UCL The Virtual Imaging Platform - VIP • Multi-modality medical image simulators:MRI, US, CT, and PET. • Simulators described as workflows. • Geometric definition and physical parameters such as proton density, echogenicity, radioactivity, chemical composition. • Ontologies (ongoing work by INRIA Rennes). • European Grid Infrastructure (EGI). • Biomed Virtual Organization.

  9. VIP for VPH - CNRS and UCL Exemplar Project – VIP for VPH • 250 registered users, from 25 countries. • Most used portal certificate in EGI. https://wiki.egi.eu/wiki/EGI_robot_certificate_users • Consummed 379 CPU years fromJanuary 2011 to August 2012.http://accounting.egi.eu VIP for VPH System Architecture

  10. VIP for VPH - CNRS and UCL Interface with the VPH Toolkit • Generic Application Service Wrapper (GASW) enables to access several Distributed Computing Infrastructures.http://vip.creatis.insa-lyon.fr:9002/projects/gasw • The GASW AHE plug-in enables GASW to access AHE resources.- Launch and monitor jobs.- Data transfer.http://vip.creatis.insa-lyon.fr:9002/projects/ahe MOTEUR http://modalis.i3s.unice.fr/softwares/moteur/ VIP for VPH - System Architecture

  11. VIP for VPH - CNRS and UCL Interface with the VPH Toolkit The Application Hosting Environment • Part of the VPH ToolKit, freely available to the VPH community. • Interfaces to back-end middlewares (i.e. Globus 2/4, Unicore 6) • Manages submission and monitoring of jobs as well as data transfer. http://www.realitygrid.org/AHE/ VIP for VPH - System Architecture

  12. VIP for VPH - CNRS and UCL VIP for VPH in action Use Case Scenario • A heavy MRI simulation Each model is 50-100MB in size, and generates the same amount of output data VIP for VPH - System Architecture

  13. VIP for VPH - CNRS and UCL Use case scenario – EP9: VIP for VPH • Data transfer from the EGI data storage system to the PRACE HPC resource.

  14. EUDAT/EGI/PRACE • VIP4VPH already makes use of EGI and PRACE resources • Uses MOTEUR workflow engine + other infrastructure components • Application Hosting Environment provides bridge into PRACE • We need to involve EUDAT: • Data should be moved from current VIP server to EUDAT when PRACE resources are used & resulting data ingested back • GridFTP interface a requirement to interoperated with existing infrastructure

  15. Proposed architecture • Authentication: 1 VO(MS) should be supported on EUDAT. Otherwise, application switches (VOMS) proxies (possible but not suitable). • Application could merge 3.a and 3.b in a 3rd-party transfer

  16. Acknowledgements • Tristan Glatard • William Romero • Giuseppe Fiameni • Tiziana Ferrari  • Johannes Reetz • Derek Groen + many others…

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