Grid Enabled Neurosurgical Grid Enabled Neurosurgical Imaging Using Simulation g g g http://wiki realitygrid org/wiki/GENIUS http://wiki.realitygrid.org/wiki/GENIUS
Introduction The GENIUS project aims to model large scale patient specific cerebral blood flow in clinically relevant time frames specific cerebral blood flow in clinically relevant time frames Objectives : Objectives : • To study cerebral blood flow using patient-specific image-based models. • To provide insights into the cerebral blood flow & anomalies. p g • To develop tools and policies by means of which users can better exploit the ability to reserve and co-reserve HPC resources. • To develop interfaces which permit users to easily deploy and monitor simulations across multiple computational resources. • To visualize and steer the results of distributed simulations in real time • To visualize and steer the results of distributed simulations in real time
H HemeLB LB Efficient fluid solver for modelling brain bloodflow called HemeLB: HemeLB: •Uses the lattice-Boltzmann method •Efficient algorithms for sparse geometries g p g •Topology-aware graph growing partitioning technique •Optimized inter and intra machine communications •Optimized inter- and intra-machine communications •Full checkpoint capabilities.
Getting the Patient Specific Data Getting the Patient Specific Data Data is generated by MRA scanners at the National scanners at the National Hospital for Neurosurgery and Neurology trilinear trilinear interpolation 512 2 pixels x 100 slices, p res: 0.46875 2 mm x 0.8 mm Our graphical-editing tool 2048 2 x 682 cubic voxels, 2048 2 682 bi l res: 0.469 mm
Cross-site Runs with MPI-g GENIUS has been designed to run across multiple machines using MPI-g • Some problems won’t fit on a single machine, and require the RAM/processors of multiple machines on the grid. • MPI-g allows for jobs to be turned around faster by using small numbers of processors on several machines - essential for clinician • HemeLB performs well on cross site runs, and makes use of overlapping communication in MPI-g
H HemeLB/MPI-g Requires LB/MPI R i Co-Allocation Co-Allocation • We can reserve multiple resources for We can reserve multiple resources for specified time periods • Co-allocation is useful for meta-computing C ll ti i f l f t ti jobs like HemeLB, viz and for workflow applications. • We use HARC - Highly Available Robust We use HARC Highly Available Robust Co-scheduler (developed by Jon Maclaren at LSU) at LSU). Slide courtesy Jon Maclaren
HARC HARC • HARC provides a secure co-allocation service C p o des a secu e co a ocat o se ce – Multiple Acceptors are used – Works well provided a majority of Acceptors stay alive – Paxos Commit keeps everything in sync – Gives the (distributed) service high availability – Deployment of 7 acceptors --> Mean Time To Failure ~ years Deployment of 7 acceptors > Mean Time To Failure years – Transport-level security using X.509 certificates • HARC is a good platform on which to build portals/other services – XML over HTTPS - simpler than SOAP services – Easy to interoperate with – Very easy to use with the Java Client API
Real Time Visualisation and Steering Real Time Visualisation and Steering • A way to let HemeLB know the parameters to be A t l t H LB k th t t b steered --> we use the RealityGrid steering system to steer the input data on the fly system to steer the input data on the fly. • One aim is to do all this for distributed (cross- O i i t d ll thi f di t ib t d ( site) simulations • For medical applications, need may be urgent
Application Hosting Environment • Need to utilize resources from globally distributed Need to utilize resources from globally distributed grids – Administratively distinct Administratively distinct – Running different middleware stacks • Wrestling with middleware can't be a limiting step • Wrestling with middleware can t be a limiting step for scientists • Need tools to hide complexity of underlying grids Need tools to hide comple it of nderl ing grids
PDA/Cellphone Visualisation and Steering PDA/Cellphone Visualisation and Steering • RealityGrid: a tool for modelling and y g simulating very large or complex condensed matter structures… • • Human Factors issues key Human Factors issues key • Large-scale applications, scheduling when resources become available, ‘around the clock’ computation… • AHE application launching built in to client c e t • User interaction/workflo w: not necessarily y 9:00am – 5:00pm, from the ‘desk’ environment
AHE AHE - HARC integration HARC integration • Users can co-reserve resources from the U f th AHE GUI client using HARC • When submitting a job, users can either run their jobs in normal queues, or use one of j q , their reservations • AHE passes reservation through to the • AHE passes reservation through to the Globus GRAM • AHE client uses HARC Java client API to AHE client ses HARC Ja a client API to manage reservations
AHE R G & WS GRAM I t AHE ReG & WS GRAM Integration ti • For steerable applications, AHE server starts up a ReG Steering Web Service (SWS) for the application, & sets the end point reference in the li ti & t th d i t f i th job’s environment • AHE can submit jobs to GridSAM (described in JSDL) JSDL) or WS GRAM (described in JDD) by WS GRAM (d ib d i JDD) b applying a XSL Transform to the job specific WS- ResourceProperties document ResourceProperties document • AHE --> WS GRAM can launch single or multisite AHE > WS GRAM l h i l lti it MPIg jobs
Conclusions • We have developed computationally efficient tools to manipulate, simulate and visualize patient specific i l t i l t d i li ti t ifi vascular systems • Goal is to better comprehend blood flow behavior of Goal is to better comprehend blood flow behavior of normal and anomalous cerebral systems and provide patient specific models for clinical guidance in surgical patient specific models for clinical guidance in surgical operations • Application Hosting Environment extended to launch pp g MPI-g cross site runs, integrate ReG steering and visualisation, as well as making HARC cross site reservations ti
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