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PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw
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PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw

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Presentation PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw at the AMD Developer Summit (APU13) November 11-13, 2013.

Presentation PG-4036, Computational Fluid Dynamics of the blood flow in the cloud, by Jakub Pola and Lukasz Miroslaw at the AMD Developer Summit (APU13) November 11-13, 2013.

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  • 1. VITRTUS   CFD  OF  THE  BLOOD  FLOW  IN  THE  CLOUD   JAKUB  POLA   SOFTWARE  DEVELOPER,  VRATIS  LTD.    
  • 2. HEART  DIAGNOSIS   !  Non-­‐invasive:   ‒  X-­‐Ray  Computer  Tomography.   ‒  MagneMc  Resonance  Imaging.   ‒  Electrocardiography.   !  Invasive:   ‒  Angiography.   ‒  FracMonal  Flow  Reserve.   2   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL  
  • 3. HEART  DIAGNOSIS   FRACTIONAL  FLOW  RESERVE  EXAMPLE   !  COURAGE,  FAME2:   FFR  VALUE   Stent   implantaMon   Drug   therapy   !  DeFACTO  (2012):   FFR   3   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL   FFR  CT  
  • 4. COMPUTATIONAL  FLUID  DYNAMICS   FRAMEWORK   !  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?   4   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL  
  • 5. 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   5   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL  
  • 6. VIRTUS:  OVERVIEW   Mesh  storage  format   User  Interface   Database   PACS   SoQware  as  a  Service   AcHve  Mesh   6   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL   CalculaHons  
  • 7. VIRTUS:  WORKFLOW   CT  /  MRI  Scanning   SegmentaMon   CFD  SimulaMon   7   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL   Meshing   Post-­‐processing  /  VisualisaMon  
  • 8. VIRTUS:  ARCHITECTURE   STL   SegmentaMon   CT/MRI   V  Mesh   Surface  representaMon   of  volumetric  mesh   SimulaMon     4  txt  config  files   Set  boundary  condiMons   VisualizaMon     8   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL   GeneraMon  of  Volumetric   Mesh   (NETGEN)   surface  &  U,  p,  WSS   SimulaMon  
  • 9. VIRTUS:  GRAPHIC  USER  INTERFACE   9   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL  
  • 10. VIRTUS:  ARCHITECTURE   STL   SegmentaMon   CT/MRI   V  Mesh   Surface  representaMon   of  volumetric  mesh   SimulaMon     4  txt  config  files   Set  boundary  condiMons   VisualizaMon     10   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL   GeneraMon  of  Volumetric   Mesh   (NETGEN)   surface  &  U,  p,  WSS   SimulaMon  
  • 11. 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   11   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL  
  • 12. VIRTUS:  SEGMENTATION   ACTIVE  MESH   !  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)   12   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL  
  • 13. VIRTUS:  MESHING  MODULE   13   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL  
  • 14. VIRTUS:  ARCHITECTURE   STL   SegmentaMon   CT/MRI   V  Mesh   Surface  representaMon   of  volumetric  mesh   SimulaMon     4  txt  config  files   Set  boundary  condiMons   VisualizaMon     14   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL   GeneraMon  of  Volumetric   Mesh   (NETGEN)   surface  &  U,  p,  WSS   SimulaMon  
  • 15. VIRTUS:  SIMULATION  MODULE   USER  SIDE   !  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   15   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL  
  • 16. VIRTUS:  SIMULATION  MODULE   USER  SIDE   16   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL  
  • 17. VIRTUS:  SIMULATION  MODULE   SERVER  SIDE   !  Three  ways  to  execute  simulaMon:   ‒  Using  CPU  in  parallel  mode.   ‒  Using  CPU  +  GPU  in  parallel  mode.   ‒  Using  GPU  only.     17   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL  
  • 18. VIRTUS:  SIMULATION  MODULE   SERVER  SIDE:  CPU   CPU   Read  mesh   No   Assembly  matrices   Ax=b   ~33%   Conv erged ?   Yes   Finalize   18   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL   Solve   Ax=b   ~66%  
  • 19. VIRTUS:  SIMULATION  MODULE   SERVER  SIDE:  CPU  +  GPU   CPU   PCI   GPU   Ax=b   Solve   Ax=b   Read  mesh   Assembly  matrices   Ax=b   No   Conv erged ?   Yes   Finalize   19   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL   x  
  • 20. 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.   20   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL  
  • 21. VIRTUS:  SIMULATION  MODULE   SERVER  SIDE:  CPU  +  GPU   CPU   PCI   GPU   Ax=b   Solve   Ax=b   Read  mesh   Assembly  matrices   Ax=b   No   Conv erged ?   Yes   Finalize   21   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL   x  
  • 22. VIRTUS:  SIMULATION  MODULE   SERVER  SIDE:  GPU   CPU   Read  mesh   PCI   GPU   Mesh   Assembly  matrices   Ax=b   No   Finalize   22   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL   x   Solve   Ax=b   Conv erged ?   Yes  
  • 23. 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   23   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL  
  • 24. SPEEDIT  FLOW   TEST  CASES   !  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   24   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL  
  • 25. SPEEDIT  FLOW:  U-­‐SHAPED  PIPE   SIMULATION  EXECUTION  TIME   25   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL  
  • 26. SPEEDIT  FLOW:  U-­‐SHAPED  PIPE   ACCELERATION  RATIO   26   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL  
  • 27. SPEEDIT  FLOW:  BASILAR  ARTERY   SIMULATION  EXECUTION  TIME   27   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL  
  • 28. SPEEDIT  FLOW:  BASILAR  ARTERY   ACCELERATION  RATIO   28   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL  
  • 29. VIRTUS:  ARCHITECTURE   STL   SegmentaMon   CT/MRI   V  Mesh   Surface  representaMon   of  volumetric  mesh   SimulaMon     4  txt  config  files   Set  boundary  condiMons   VisualizaMon     29   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL   GeneraMon  of  Volumetric   Mesh   (NETGEN)   surface  &  U,  p,  WSS   SimulaMon  
  • 30. VRATIS:  VISUALIZATION  MODULE   30   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL  
  • 31. SUMMARY     !  VIRTUS  is  a  pla]orm  for  personalized  medicine  and  CFD  based  diagnosis.   !  Cloud-­‐based  approach  simplifies  the  usage.   !  GPU  reduces  Mme-­‐to-­‐soluMon.   31   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL  
  • 32. ! QuesMons?   ! Comments?   Jakub  Pola   jakub.pola@vraMs.com   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     32   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL  
  • 33. DISCLAIMER  &  ATTRIBUTION   The  informaMon  presented  in  this  document  is  for  informaMonal  purposes  only  and  may  contain  technical  inaccuracies,  omissions  and  typographical  errors.     The  informaMon  contained  herein  is  subject  to  change  and  may  be  rendered  inaccurate  for  many  reasons,  including  but  not  limited  to  product  and  roadmap   changes,  component  and  motherboard  version  changes,  new  model  and/or  product  releases,  product  differences  between  differing  manufacturers,  socware   changes,  BIOS  flashes,  firmware  upgrades,  or  the  like.  AMD  assumes  no  obligaMon  to  update  or  otherwise  correct  or  revise  this  informaMon.  However,  AMD   reserves  the  right  to  revise  this  informaMon  and  to  make  changes  from  Mme  to  Mme  to  the  content  hereof  without  obligaMon  of  AMD  to  noMfy  any  person  of   such  revisions  or  changes.     AMD  MAKES  NO  REPRESENTATIONS  OR  WARRANTIES  WITH  RESPECT  TO  THE  CONTENTS  HEREOF  AND  ASSUMES  NO  RESPONSIBILITY  FOR  ANY   INACCURACIES,  ERRORS  OR  OMISSIONS  THAT  MAY  APPEAR  IN  THIS  INFORMATION.     AMD  SPECIFICALLY  DISCLAIMS  ANY  IMPLIED  WARRANTIES  OF  MERCHANTABILITY  OR  FITNESS  FOR  ANY  PARTICULAR  PURPOSE.  IN  NO  EVENT  WILL  AMD  BE   LIABLE  TO  ANY  PERSON  FOR  ANY  DIRECT,  INDIRECT,  SPECIAL  OR  OTHER  CONSEQUENTIAL  DAMAGES  ARISING  FROM  THE  USE  OF  ANY  INFORMATION   CONTAINED  HEREIN,  EVEN  IF  AMD  IS  EXPRESSLY  ADVISED  OF  THE  POSSIBILITY  OF  SUCH  DAMAGES.     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.   33   |      PRESENTATION  TITLE      |      NOVEMBER  19,  2013      |      CONFIDENTIAL  

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