Eun_bo _shim by liwenting

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PRAGMA – San Diego, March 11-12

Distributed computing for the hemodynamics of the Korean artificial heart under APII-Testbed/STAR-TAP

Eun Bo Shim*, Chan Hyun Youn**, Hyun Chan Seong*, Sang Jin Jung**, Georgy Moody***, Roger G. Mark***
*: Mechanical Engineering, Kumoh National Univ. of Tech. (Korea) ** : Information and Communications University (Korea) *** : Harvard-MIT, Health Science and Technology (U.S.A.)

KNUT University of Technology

Kumoh National

Fluid & Biomedical Engineering Lab

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Objectives
 To present an effective way to simulate the hemodynamics of the KTAH(Korean total artificial heart)  To develop a distributed computing technique to compute hemodynamic problems  To construct the Globus-based information infrastructure for international collaboration

KNUT University of Technology

Kumoh National

Fluid & Biomedical Engineering Lab

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Schematic of the blood sac in the KTAH
Inlet:RA

Blood sac Inlet:LA

Outlet:PA

Actuator

Outlet:Ao

KNUT University of Technology

Kumoh National

Fluid & Biomedical Engineering Lab

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Hemodynamics of the KTAH

KNUT University of Technology

Kumoh National

Fluid & Biomedical Engineering Lab

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Computational aspect

Computer simulation
Physiology -? Physiology
Biomedical Eng., Clinical Exp. Biomedical Clinical Exp.

Computer Method FEM Method Method

Mechanics Fluid, solid, biophysics Fluid, solid, bio-physics -

Information Tech.Metacomputing, 차세대 인터넷 Distributed-computing ,

KNUT University of Technology

Kumoh National

Fluid & Biomedical Engineering Lab

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Schematic of cardiovascular model

1. 2. 3. 4. 5.

12 compartment model Time varying capacitance model for TAH Hemodynamic model Auto-regulation model Control system: Baroreflex model Cardiopulmonary model

KNUT University of Technology

Kumoh National

Fluid & Biomedical Engineering Lab

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Cardiovascular simulator - KTAH
1. 2. 3. 4. 5. B.C. for the hemodynamic computation Heart pulasation information JAVA Code Physiological modeling Lumped system model

 Click to run the program

KNUT University of Technology

Kumoh National

Fluid & Biomedical Engineering Lab

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Results of cardiovascular siumulation

KNUT University of Technology

Kumoh National

Fluid & Biomedical Engineering Lab

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Finite element algorithm
- Viscous Incompressible flow : Navier-Stokes Equations
- Governing Eq. : Navier-Stokes Equations

- FEM Discretization
- Numerical Scheme : PISO Type FEM Proposed by Shim & Chang (1994) Operator Splitting Algorithm (Treatment of Incompressibility) One Predictor Step + Two Corrector Steps Matrix Solver : Iteration Methods ICCG (Pressure Poisson Equation) PCGS (Momentum Equation) - Two Dimensional Flow Model Used Element : Bilinear Quadlirateral

KNUT University of Technology

Kumoh National

Fluid & Biomedical Engineering Lab

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Development of parallel computing program
Domain decomposition MPI_INIT Finite element formulation Excution at each processor Assembling over total domain Matrix problem MPI_END MPI_RECEIVE Application of boundary condition Matrix solution MPI_FINAL End Start Grid Generation (element)

KNUT University of Technology

Kumoh National

Fluid & Biomedical Engineering Lab

Testing of the effectiveness of parallel computing
Parallel Segregated Finite Element Model
2D Cavity problem MPI Programming
60 Single Parallel

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Grid No. vs. Solving Time

50

Relative Computational Time

40

30

20

10

0

-10

0

20

40

60

80

100

No. of Grids in x-dir

KNUT University of Technology

Kumoh National

Fluid & Biomedical Engineering Lab

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Globus/MPICH-G2 Test Platform
STAR-TAP / Abilene Globus / MPICH-G2 Platform
MIT

APII Testbed KOREN/KREONET2

KTAH model (ICU)

KTAH model(KNUT) Fluid & Biomedical Engineering Lab

KNUT University ofofTechnology University Technology

Kumoh National Kumoh National

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Globus/MPICH-G2 Structure
MPI Application MPICH-G2
User interface for MPI

 Globus 2.0 and MPICH-G2 1.2.3 Version  OS system - Unix, Linux  Use of Linux system

Globus Toolkit
Scheduling, Resource allocation

Network Fabric
Linux Solaris TCP

KNUT University of Technology

Kumoh National

Fluid & Biomedical Engineering Lab

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APII testbed based Globus platform
 Globus platform
ICU (3 systems), KNUT (1 system), MIT (1 system) 1st step : Installation and ICU STAR Certificate application TAP 2단계 : Test rose lilly lilac APII Testbed
(KOREN KREONET2)

Abilene

 Issues in the platform construction
Bandwidth problem for QoS – 2Mbps between ICU-KOREN -KREONET2-STAR TAP (no reservation policy) Time zone limitation and firewall
 proxy server expire over 12 hours

KNUT
fluid001

MIT

penelope

KNUT University of Technology

Kumoh National

Fluid & Biomedical Engineering Lab

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MPI application test using MPICH-G2
Velocity plot in 2D cavity problem

(Subjob 1)
system 1

(Subjob N)
system N

MPI Start

User MPI
MPICH-G2

User MPI
MPICH-G2

MPI Execution

Job

Globus

Globus

Approval of job

Network & Fabric
MPICH-G2 based distributed processing

KNUT University of Technology

Kumoh National

Fluid & Biomedical Engineering Lab

2D simualtion of the blood sac in the KTAH
Visualization

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Pressure contour KNUT University of Technology
Kumoh National

Velocity magnitude contour
Fluid & Biomedical Engineering Lab

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MPICH-G2 network test

Short Message test KNUT University of Technology
Kumoh National

Long Message test
Fluid & Biomedical Engineering Lab

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Future works
 Objective
Extension of the 2D distributed program to 3D simulation under APII testbed/Globus based platform

 Details of future works
Development of 3D distributed simulation code for the hemodynamics of the KTAH Real time visualization using OpenGL Performance test of APII testbed/Globus based platform Optimization of Globus based middleware using QoS technique  GARA QoS technique High performance message passing technique and MPICHG2 KNUT University of Technology
Kumoh National

Fluid & Biomedical Engineering Lab

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(KNUT-ICU-MIT)
KNUT

ICU

MIT

KNUT University of Technology

Kumoh National

Fluid & Biomedical Engineering Lab


								
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