Transcript VPH_use_case_EGI

New Communities: The Virtual
Physiological Human Use
Case
Stefan Zasada
University College London
[email protected]
Federating Infrastructures
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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
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We’re working to bring a use cases from VPH to help
develop this collaboration
EUDAT
Community-oriented services
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Simple Data Acces and upload
Long term preservation
Shared workspaces
Execution and workflow (data mining,
etc.)
• Joint metadata and data visibility
Core services are building blocks of EUDAT‘s
Common Data Infrastructure
mainly included on bottom layer of data services
Enabling services (making use of
existing services where possible
• Persistent identifier service (EPIC,
DataCite)
• Federated AAI service
• Network Services
• Monitoring and accounting
http://eudat.eu/
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EGI
• European
– Over 35 countries
• Grid
– Secure sharing
• Infrastructure
– Computers
– Data
– Instruments
– …. and beyond!!
Established to & successful in finding the Higgs Boson
EGI-InSPIRE RI-261323
www.egi.eu
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
Organism
Organ
Tissue
Cell
Organelle
Interaction
Protein
Cell Signals
Transcription
Gene
Molecule
VPH DEISA Virtual Community
established in collaboration with
Hermann Lederer, MPS RZG
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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 ...”
http://www.vph-noe.eu
CREST
CREST
CREST
CREST
epcc|cresta
Visual Identity Designs
Networking
NoE
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The Virtual Imaging Platform - VIP
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September 18th-20th,
2012. London, UK
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).
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European Grid Infrastructure (EGI).
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Biomed Virtual Organization.
VIP for VPH - CNRS and UCL
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Exemplar Project – VIP for VPH
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250 registered users, from 25 countries.
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Most used portal certificate in EGI.
https://wiki.egi.eu/wiki/EGI_robot_certificate_users
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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
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Interface with the VPH Toolkit
MOTEUR
http://modalis.i3s.unice.fr/softwares/moteu
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Generic Application Service Wrapper
(GASW) enables to access several
Distributed Computing
Infrastructures.
http://vip.creatis.insa-lyon.fr:9002/projects/gasw
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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
VIP for VPH - System Architecture
September 18th-20th,
2012. London, UK
VIP for VPH - CNRS and UCL
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Interface with the VPH Toolkit
The Application
Hosting Environment
http://www.realitygrid.org/AH
E/
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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.
VIP for VPH - System Architecture
September 18th-20th,
2012. London, UK
VIP for VPH - CNRS and UCL
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VIP for VPH in action
Use Case Scenario
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A heavy MRI simulation
Application SIMRI – 3D MRI simulator
Software based on the Bloch equation.
Website
http://www.simri.org
Main Solution to linear differential
Algorithm equation.
(ODE solver).
VIP for VPH - System Architecture
September 18th-20th,
2012. London, UK
Each model is 50-100MB in size, and
generates the same amount of
output data
VIP for VPH - CNRS and UCL
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Use case scenario – EP9: VIP for VPH
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Data transfer from the EGI data storage system to the
PRACE HPC resource.
September 18th-20th,
2012. London, UK
VIP for VPH - CNRS and UCL
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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
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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 Glatard
William Romero
Giuseppe Fiameni
Tiziana Ferrari
Johannes Reetz
Derek Groen
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+ many others…
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