Multi-infrastructure workflow execution for medical simulation in the Virtual Imaging Platform

VIP
Virtual Imaging Platform

Multi-infrastructure workflow execution
for medical simulation in the

Rafael FERREIRA DA SILVA1, Sorina CAMARASU-POP1, Baptiste GRENIER3
Vanessa HAMAR2, David MANSET3, Johan MONTAGNAT4, Jérôme REVILLARD3
Javier ROJAS BALDERRAMA4, Andrei TSAREGORODTSEV2, Tristan GLATARD1

1 Université de Lyon, CNRS, INSERM, CREATIS
2 Centre de Physique des Particules de Marseille
3 maatG France
4 CNRS/UNS, I3S lab, MODALIS team

Bristol, HealthGrid 2011

VIP ANR-09-COSI-013-02 www.creatis.insa-lyon.fr/vip 1

VIP
Introduction

  Simulation
Computation: 16h

Example: 2D+t ultrasound simulation
[O. Bernard]

Example: Prostate traitement in protontherapy
Computation: 2 months
[L. Grevillot, D. Sarrut]

8.5 CPU
days

US MRI CT PET

VIP
Introduction

  European Grid Infrastructure (EGI)
  High throughput for computation and data transfers
  Challenges
  High latencies
  Low reliability


VIP
Our Goal

  Multi-infrastructure workflow execution
  Grid resources
  Personal clusters (non-grid resources)

  Improve data transfer reliability
  Local reliable storage


VIP
VIP Architecture


VIP
Workflows
  Virtual Imaging Platform (VIP)
  Workflow

Activities

Data sources

Data sinks

Simulated US image
of the heart
  Core Simulation Workflows
  MRI, US, CT and PET


VIP
Workflow Wrapping

  Simulations are described as workflows

  Workflows are interpreted and executed by MOTEUR
  Core engine workflow interpreter
  Data flow evaluation
  Production of computational tasks

  Workflow activities are described using jGASW
  Code wrapper for distributed platforms and local executions
  Grid jobs (bash scripts) are generated from processed data

  Each jGASW descriptor bundles a unique executable

http://modalis.i3s.unice.fr/softwares/moteur/start
http://modalis.i3s.unice.fr/jgasw

VIP
Pilot Jobs
  Pull mode
  Execution environment verification
  Worker node reservation

Moteur + jGASW

User Jobs

Pilot-jobs System

gLite WMS

X
Worker Nodes DIRAC Architecture


VIP
Multi-infrastructure Execution

  Design constraints
  No intervention from the cluster administrator
  No sharing or generic user accounts
  Minimal technical assumptions on the cluster architecture

  Setup
  The agent is launched by the user on his cluster(s) account(s)
  Download of a tar.gz bundle and run setup script
  Support to PBS, BQS and SLURM

  Execution
  Queries WMS for user’s waiting tasks Personal
cluster

  Submits pilots to the local cluster queue VIP cluster bundle

  Embedded data transfer client (VLET)

http://vip.creatis.insa-lyon.fr:9002/projects/dirac-cluster-agent/wiki/Wiki!


VIP
Multi-infrastructure Execution

  Conditions
  EGI
  134-node cluster limited to 67 pilots running concurrently
  3 executions of a PET workflow

  Results

  Conclusion
  Involving a small personal cluster in a simulation has a significant
impact on the execution


VIP
Reliable Data Management

  EGI three-tier data management
  Challenge: data availability between 80-95%
  Storage Elements (SE) – DPM, dCache, STORM, Castor
  Logical File Catalog (LFC) – single index space

  Current Data Management in VIP
  Critical input files are replicated
  Files are cached by pilot jobs
  Output files are stored on site SE
  Jobs error rate: 5-10%

  Local Data Manager
  Failover storage
  Available for users and grid jobs
  Overlay of DPM SE


VIP
Reliable Data Management
  Data Management use case

Input download

Output upload


Impact of the Data Manager
VIP
Virtual Imaging Platform on Job Reliability
  Conditions
  EGI, biomed VO (production infrastructure)
  Ultrasonic Simulation comprised of 128 jobs
  Each job has 5 input files + 1 output file
  Failure rate: 1%

  Results

  Conclusion
  Job data transfers failure rate can be significantly decreased in the
presence of a failover storage


VIP
Web Portal
  Workflow submission and management

  Workflow execution and monitoring


VIP
Web Portal

  Detailed performance information


VIP
Web Portal

  Authentication based on X.509 certificates


VIP
Web Portal

  File transfer operations

http://vip.creatis.insa-lyon.fr


VIP
Platform Usage Statistics

  484 workflows executions (Nov 2010 – Apr 2011)
  10 (real) users
  5 application classes


VIP
Conclusions

  VIP can execute workflows on multi-infrastructures
  Extension of jGASW application description
  Extension of DIRAC to support personal clusters with no administration
intervention and respecting common security rules
  Results show that a small personal cluster can significantly contribute to
a simulation running on EGI

  VIP Data Manager
  A first test shows that job failure rate was decreased from 7.7% to 1.5%

  Try it!
  Requires a certificate registered in the Biomed VO
  http://vip.creatis.insa-lyon.fr


VIP
Future Work

  Workflow Execution
  Scalability and Reliability
  Memory shortage
  Workflow checkpointing

  Provenance of simulated data


VIP
Future Work

  Simulators and Models
  Biological object model sharing for image simulation
  See poster FORESTIER et al. at CBMS 2011
  Semantic catalog of biological models
  3D visualization


VIP
Future Work

  Simulators and Models
  Multi-Modality Simulation Workflow
  See poster MARION et al. at CBMS 2011

SIMRI (MRI) Sindbad (CT)


VIP

Multi-infrastructure workflow execution for medical
simulation in the Virtual Imaging Platform

Questions?

http://www.creatis.insa-lyon.fr/vip!


VIP
References
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VIP
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applications with user-level scheduling on the grid. Future Generation Computer Systems, 25(1):28 – 34, 2009.
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VIP
Workflow Wrapping

  Multi-infrastructure code descriptor (jGASW extension)


Multi-infrastructure workflow execution for medical simulation in the Virtual Imaging Platform

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