pg-4036, computational fluid dynamics of the blood flow in the cloud, by jakub pola and lukasz...

VITRTUS CFD OF THE BLOOD FLOW IN THE CLOUD

JAKUB POLA SOFTWARE DEVELOPER, VRATIS LTD.

2 | PRESENTATION TITLE | NOVEMBER 19, 2013 | CONFIDENTIAL

HEART DIAGNOSIS

!  Non-‐invasive: ‒ X-‐Ray Computer Tomography. ‒ MagneMc Resonance Imaging. ‒ Electrocardiography.

!  Invasive: ‒ Angiography. ‒  FracMonal Flow Reserve.


HEART DIAGNOSIS

!  COURAGE, FAME2:

!  DeFACTO (2012):

FRACTIONAL FLOW RESERVE EXAMPLE

Stent implantaMon

Drug therapy

FFR VALUE

FFR FFR CT


COMPUTATIONAL FLUID DYNAMICS

!  Solve Navier – Stokes equaMons !  Procedure:

‒ Preprocessing: ‒ DefiniMon of the geometry. ‒ GeneraMon of volumetric mesh. ‒ DefiniMon of physical model. ‒ DefiniMon of boundary condiMons.

‒  SimulaMon: iteraMve solvers. ‒ Post-‐processing:

‒  Analysis ‒  VisualisaMon

!  How to obtain geometry and create a mesh?

!  How to solve the problem fast and efficiently?

FRAMEWORK


CFD IN MEDICINE

!  Stent grac design: ‒ DeterminaMon of proper shape of the stent grac

!  Design of heart valves: ‒ DeterminaMon of shape and biological and mechanical properMes

!  Drug delivery: ‒ DeterminaMon of the delivery device ‒ DeterminaMon of the drug state


VIRTUS: OVERVIEW

PACS

AcHve Mesh

Mesh storage format User Interface

Database

CalculaHons SoQware as a Service


VIRTUS: WORKFLOW

CT / MRI Scanning SegmentaMon

CFD SimulaMon Post-‐processing / VisualisaMon

Meshing


VIRTUS: ARCHITECTURE

GeneraMon of Volumetric Mesh

(NETGEN)

STL

SimulaMon

Surface representaMon of volumetric mesh

SimulaMon

VisualizaMon surface & U, p, WSS

CT/MRI

Set boundary condiMons

4 txt config files

V Mesh

SegmentaMon


VIRTUS: GRAPHIC USER INTERFACE




(NETGEN)

STL

SimulaMon


SimulaMon


CT/MRI


4 txt config files

V Mesh

SegmentaMon


VIRTUS: SEGMENTATION

! Create 3D model from series of images.

! Very Mme consuming task.

! Require mesh modeling to: ‒ fix the errors in the mesh ‒ prepare mesh to generate volumetric mesh


VIRTUS: SEGMENTATION

!  Input: ‒ CT or MRI scans in DICOM format.

!  Outputs: ‒  Surface mesh in STL format. ‒ Volumetric mesh in OpenFOAM format.

!  Real-‐Mme procedure.

!  Fasat algorithm.

!  Many mesh ediMng tools: ‒ Global/local mesh smoothing. ‒ Cut Mesh. ‒  Freeze Mesh. ‒ Push Mesh. ‒ Define Flow Inlets and Outlets ‒ Automated determinaMon of artery centerline(s)

ACTIVE MESH


VIRTUS: MESHING MODULE




(NETGEN)

STL

SimulaMon


SimulaMon


CT/MRI


4 txt config files

V Mesh

SegmentaMon


VIRTUS: SIMULATION MODULE

!  Just two steps: ‒ Type of simulaMon:

‒  Transient flows. ‒  Steady-‐state flows.

‒  Inlet boundary condiMon: ‒  Inlet velocity. ‒  Inlet pressure. ‒  Point and click procedure

!  ConfiguraMon ‒  Just four txt files

USER SIDE


VIRTUS: SIMULATION MODULE USER SIDE


VIRTUS: SIMULATION MODULE

!  Three ways to execute simulaMon: ‒ Using CPU in parallel mode. ‒ Using CPU + GPU in parallel mode. ‒ Using GPU only.

SERVER SIDE


VIRTUS: SIMULATION MODULE SERVER SIDE: CPU

Read mesh

CPU

Converged?

No

Finalize

Yes

Assembly matrices Ax=b

~33%

Solve Ax=b

~66%


VIRTUS: SIMULATION MODULE SERVER SIDE: CPU + GPU

Read mesh

CPU

Converged?

No

Finalize

Yes


Solve Ax=b

PCI GPU

Ax=b

x


VIRTUS: SPEEDIT TOOLKIT

!  Solvers: ‒ Conjugate Gradient. ‒ Bi-‐Conjugate Gradient.

!  PrecondiMoners: ‒ Diagonal. ‒ Approximate Inverse. ‒ Algebraic MulMgrid with Smoothed AggregaMon (CUSP).

!  Support for MulM-‐GPU.

!  Plaqorms: ‒ OpenCL. ‒ CUDA.


VIRTUS: SIMULATION MODULE SERVER SIDE: CPU + GPU

Read mesh

CPU

Converged?

No

Finalize

Yes


Solve Ax=b

PCI GPU

Ax=b

x


VIRTUS: SIMULATION MODULE SERVER SIDE: GPU

Read mesh

CPU

Converged?

No

Finalize Yes


Solve Ax=b

PCI GPU

x

Mesh


VIRTUS: SPEEDIT FLOW

!  Full GPU implementaMon of: ‒ PISO (Pressure Implicit with Split Operator) – transient solver for incompressible flows. ‒  SIMPLE (Semi-‐implicit Method for Pressure Linked EquaMons): Steady-‐state solver for incompressible flows.

!  Boundary CondiMons: ‒  Zero Gradient ‒ Time dependent and Fixed value.

!  Adjustable Mme step.

!  Roadmap: ‒  Support for OpenCL ‒ Turbulence (RANS, kOmegaSST model) ‒  Support for MulM-‐GPU


SPEEDIT FLOW

!  U-‐shaped pipe ‒ Radius – 1in ‒ 4M hex cells ‒ Transient flow simulaMon:

‒ U(t) = Asin(ωt) + B ‒  Steady-‐state simulaMon

‒  Re = 100 ‒  Re = 1000

!  Basilar artery*: ‒ 2M hex cells ‒ Transient flow. ‒ Two heart cycles.

* Geometry obtained from AneuriskWeb project. Emory University, Department of Math&CS, 2012

TEST CASES


SPEEDIT FLOW: U-‐SHAPED PIPE SIMULATION EXECUTION TIME


SPEEDIT FLOW: U-‐SHAPED PIPE ACCELERATION RATIO


SPEEDIT FLOW: BASILAR ARTERY SIMULATION EXECUTION TIME


SPEEDIT FLOW: BASILAR ARTERY ACCELERATION RATIO




(NETGEN)

STL

SimulaMon


SimulaMon


CT/MRI


4 txt config files

V Mesh

SegmentaMon


VRATIS: VISUALIZATION MODULE


SUMMARY

! VIRTUS is a pla]orm for personalized medicine and CFD based diagnosis.

! Cloud-‐based approach simplifies the usage.

! GPU reduces Mme-‐to-‐soluMon.


! QuesMons? ! Comments?

Jakub Pola [email protected]

virtus.vraMs.com Acknowledemnents: VraHs: Wojciech Tarnawski, Lukasz Miroslaw, Pawel Czubinski

Wroclaw Uni.: Zbigniew Koza, Piotr Olkiewicz

Wroclaw Uni. of Technology: Tadeusz Tomczak, Andrzej Kosior


DISCLAIMER & ATTRIBUTION

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ATTRIBUTION

© 2013 Advanced Micro Devices, Inc. All rights reserved. AMD, the AMD Arrow logo and combinaMons thereof are trademarks of Advanced Micro Devices, Inc. in the United States and/or other jurisdicMons. SPEC is a registered trademark of the Standard Performance EvaluaMon CorporaMon (SPEC). Other names are for informaMonal purposes only and may be trademarks of their respecMve owners.