new communities: the virtual physiological human use case stefan zasada university college london...
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New Communities: The Virtual Physiological Human Use
CaseStefan Zasada
University College London
Federating Infrastructures • 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
Community-oriented services
•Simple Data Acces and upload•Long term preservation•Shared workspaces•Execution and workflow (data mining, etc.)•Joint metadata and data visibility
Enabling services (making use of existing services where possible
•Persistent identifier service (EPIC, DataCite)•Federated AAI service•Network Services•Monitoring and accounting
EUDAT
http://eudat.eu/ 3
www.egi.euEGI-InSPIRE RI-261323
EGI• European
– Over 35 countries
• Grid– Secure sharing
• Infrastructure– Computers– Data– Instruments– …. and beyond!!
Established to & successful in finding the Higgs Boson
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
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
OrganismOrganTissue
CellOrganelleInteraction
ProteinCell Signals
TranscriptionGene
Molecule
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VPH DEISA Virtual Community established in collaboration with Hermann Lederer, MPS RZG
Virtual Physiological Human
• 42 projects: 1 NoE + IPs, STREPS + CAs.• New projects to be funded under Call 9
“a methodological and technological framework that, once established, will enable collaborative investigation of the human body as a single complex system ...”
Networking NoE
VPHShareVPHShare
7http://www.vph-noe.eu
September 18th-20th, 2012. London, UK
VIP for VPH - CNRS and UCL 8
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.
September 18th-20th, 2012. London, UK
VIP for VPH - CNRS and UCL 9
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
September 18th-20th, 2012. London, UK
VIP for VPH - CNRS and UCL 10
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
September 18th-20th, 2012. London, UK
VIP for VPH - CNRS and UCL 11
Interface with the VPH Toolkit
● 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.
The Application Hosting Environment http://www.realitygrid.org/AHE/
VIP for VPH - System Architecture
September 18th-20th, 2012. London, UK
VIP for VPH - CNRS and UCL 12
VIP for VPH in actionUse Case Scenario
● A heavy MRI simulation
ApplicationSoftware
SIMRI – 3D MRI simulator based on the Bloch equation.
Website http://www.simri.org
Main Algorithm
Solution to linear differential equation.(ODE solver).
VIP for VPH - System ArchitectureEach model is 50-100MB in size, and generates the same amount of output data
September 18th-20th, 2012. London, UK
VIP for VPH - CNRS and UCL 13
Use case scenario – EP9: VIP for VPH
● Data transfer from the EGI data storage system to the PRACE HPC resource.
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
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
Acknowledgements
Tristan GlatardWilliam RomeroGiuseppe FiameniTiziana Ferrari Johannes ReetzDerek Groen
+ many others…
VPHShareVPHShare
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