SlideShare a Scribd company logo
Weighted Decomposition
Are some lattice sites more
equal than others?
Derek Groen
David Abou Chacra
Jiri Jaros
Rupert Nash
Miguel Bernabeu
Peter Coveney
Overview
● Cerebrovascular bloodflow and HemeLB.
● What type performance matters.
● Weighted decomposition
● Tests & results
● Discussion / Future work
Cerebrovascular diseases
● Stroke is the main cause of about 1.1M deaths per year
in Europe.
● ~15% are caused by bleeding in the brain.
● We aim to accurately model cerebral bloodflow, and to
eventually provide assistance with cerebrovascular
surgery.
Features in HemeLB
1. Generation of computational models from medical
images.
2. A wide range of collision kernels and boundary
conditions.
3. Sparse geometries with negligible overhead (using
ParMETIS).
4. Streaming visualization and steering of the simulation.
5. Coupling to external models.
Decomposition
Domain decomposition
current
1. read in blocks
2. pass the geometry
to ParMETIS
3. ParMETIS uses k-
way partitioning.
proposed changes
differ the weights on
lattice sites,
use a space filling
curve (z-ordering)
prior to partitioning.
Obtaining weights
Site type Weights Intel SandyBridge Weights AMD Bulldozer
Bulk 10.0 10.0
Wall 18.708 20.226
In/outlet 40.037 37..398
Wall+ in/outlet (22.700) (34.577)
We ran 5 test simulations with cylinders of different aspect ratios to obtain an
estimate of the calculation cost of each site type.
ParMETIS tends to perform worse when weight values are large.
4 4 4
4 4 4
16
16
16 8
8 8
8 8
8 8
8
8
8 8
8 8 8
88
16
16
16
Test setup
650,492
lattice sites
10% fluid
5,667,778
lattice sites
1.5% fluid
D3Q19
BFL boundaries
Bifurcation geometry
HECToR XE6
Aneurysm geometry
HECToR XT6 and ARCHER XC30
HECToR
ARCHER
HECToR
ARCHER
HECToR
ARCHER
Observations/Future work
● Some lattice sites are more equal than
others.
● Getting a load-balanced decomposition is a
major challenge.
Full Paper
A full paper will be available in the proceedings
of EASC 2014.
If you would like a preprint version, please
contact me at djgroennl@gmail.com
Thank you!
UKCOMES
UK Consortium On Mesoscale
Engineering and Science.

More Related Content

Similar to HemeLB weighted decomposition EASC 2014 slides

Multiscale modelling of brain bloodflow using HemeLB and Python Navier Stokes...
Multiscale modelling of brain bloodflow using HemeLB and Python Navier Stokes...Multiscale modelling of brain bloodflow using HemeLB and Python Navier Stokes...
Multiscale modelling of brain bloodflow using HemeLB and Python Navier Stokes...
Derek Groen
 
Andrew Williams Thesis Defense
Andrew Williams Thesis DefenseAndrew Williams Thesis Defense
Andrew Williams Thesis Defense
Andrew Robert
 
Parallelization of Yeast Diode and Implementation of a Concentration Gradient
Parallelization of Yeast Diode and Implementation of a Concentration GradientParallelization of Yeast Diode and Implementation of a Concentration Gradient
Parallelization of Yeast Diode and Implementation of a Concentration Gradient
Douglas Cohen
 
DTIP2016
DTIP2016DTIP2016
DTIP2016
Aissa Foughalia
 
Iom during carotid endarterectomy 2008
Iom during carotid endarterectomy  2008Iom during carotid endarterectomy  2008
Iom during carotid endarterectomy 2008
Tuan Le
 
C017651114
C017651114C017651114
C017651114
IOSR Journals
 
Design and Implementation of Thresholding Algorithm based on MFR for Retinal ...
Design and Implementation of Thresholding Algorithm based on MFR for Retinal ...Design and Implementation of Thresholding Algorithm based on MFR for Retinal ...
Design and Implementation of Thresholding Algorithm based on MFR for Retinal ...
iosrjce
 
DESIGN AND IMPLEMENTATON OF THRESHOLDNG ALGORITHM BASED ON MFR FOR RETINAL FU...
DESIGN AND IMPLEMENTATON OF THRESHOLDNG ALGORITHM BASED ON MFR FOR RETINAL FU...DESIGN AND IMPLEMENTATON OF THRESHOLDNG ALGORITHM BASED ON MFR FOR RETINAL FU...
DESIGN AND IMPLEMENTATON OF THRESHOLDNG ALGORITHM BASED ON MFR FOR RETINAL FU...
jamal mohamed college
 
Kotsalos PhD Defense : Presentation
Kotsalos PhD Defense : PresentationKotsalos PhD Defense : Presentation
Kotsalos PhD Defense : Presentation
Christos Kotsalos
 
Angiography of Head and Neck
Angiography of Head and NeckAngiography of Head and Neck
Angiography of Head and Neck
SharmaRajan4
 
MINIATURIZATION OF BRANCH-LINE COUPLERS USING OPEN STUBS AND STEPPED IMPEDANC...
MINIATURIZATION OF BRANCH-LINE COUPLERS USING OPEN STUBS AND STEPPED IMPEDANC...MINIATURIZATION OF BRANCH-LINE COUPLERS USING OPEN STUBS AND STEPPED IMPEDANC...
MINIATURIZATION OF BRANCH-LINE COUPLERS USING OPEN STUBS AND STEPPED IMPEDANC...
csijjournal
 
3D CFD simulation of intracranial aneurysm
3D CFD simulation of intracranial aneurysm3D CFD simulation of intracranial aneurysm
3D CFD simulation of intracranial aneurysm
walshb88
 
Basic_Layout_Techniques.pdf
Basic_Layout_Techniques.pdfBasic_Layout_Techniques.pdf
Basic_Layout_Techniques.pdf
Seenivasanphd
 
Detection of eye disorders through retinal image analysis
Detection of eye disorders through retinal image analysisDetection of eye disorders through retinal image analysis
Detection of eye disorders through retinal image analysis
Rahul Dey
 
Physical organization of parallel platforms
Physical organization of parallel platformsPhysical organization of parallel platforms
Physical organization of parallel platforms
Syed Zaid Irshad
 
Semi automatic vortex extraction in 4 d pc-mri cardiac blood flow data using ...
Semi automatic vortex extraction in 4 d pc-mri cardiac blood flow data using ...Semi automatic vortex extraction in 4 d pc-mri cardiac blood flow data using ...
Semi automatic vortex extraction in 4 d pc-mri cardiac blood flow data using ...
Subhashis Hazarika
 
A1 Project Poster 2016-General Template
A1 Project Poster 2016-General TemplateA1 Project Poster 2016-General Template
A1 Project Poster 2016-General Template
Xianqi Yuan
 
Conformer review
Conformer reviewConformer review
Conformer review
June-Woo Kim
 
Mitigation of Cross-Talk in Memory Arrays
Mitigation of Cross-Talk in Memory ArraysMitigation of Cross-Talk in Memory Arrays
Mitigation of Cross-Talk in Memory Arrays
Bruce Morton
 
Making effective use of graphics processing units (GPUs) in computations
Making effective use of graphics processing units (GPUs) in computationsMaking effective use of graphics processing units (GPUs) in computations
Making effective use of graphics processing units (GPUs) in computations
Oregon State University
 

Similar to HemeLB weighted decomposition EASC 2014 slides (20)

Multiscale modelling of brain bloodflow using HemeLB and Python Navier Stokes...
Multiscale modelling of brain bloodflow using HemeLB and Python Navier Stokes...Multiscale modelling of brain bloodflow using HemeLB and Python Navier Stokes...
Multiscale modelling of brain bloodflow using HemeLB and Python Navier Stokes...
 
Andrew Williams Thesis Defense
Andrew Williams Thesis DefenseAndrew Williams Thesis Defense
Andrew Williams Thesis Defense
 
Parallelization of Yeast Diode and Implementation of a Concentration Gradient
Parallelization of Yeast Diode and Implementation of a Concentration GradientParallelization of Yeast Diode and Implementation of a Concentration Gradient
Parallelization of Yeast Diode and Implementation of a Concentration Gradient
 
DTIP2016
DTIP2016DTIP2016
DTIP2016
 
Iom during carotid endarterectomy 2008
Iom during carotid endarterectomy  2008Iom during carotid endarterectomy  2008
Iom during carotid endarterectomy 2008
 
C017651114
C017651114C017651114
C017651114
 
Design and Implementation of Thresholding Algorithm based on MFR for Retinal ...
Design and Implementation of Thresholding Algorithm based on MFR for Retinal ...Design and Implementation of Thresholding Algorithm based on MFR for Retinal ...
Design and Implementation of Thresholding Algorithm based on MFR for Retinal ...
 
DESIGN AND IMPLEMENTATON OF THRESHOLDNG ALGORITHM BASED ON MFR FOR RETINAL FU...
DESIGN AND IMPLEMENTATON OF THRESHOLDNG ALGORITHM BASED ON MFR FOR RETINAL FU...DESIGN AND IMPLEMENTATON OF THRESHOLDNG ALGORITHM BASED ON MFR FOR RETINAL FU...
DESIGN AND IMPLEMENTATON OF THRESHOLDNG ALGORITHM BASED ON MFR FOR RETINAL FU...
 
Kotsalos PhD Defense : Presentation
Kotsalos PhD Defense : PresentationKotsalos PhD Defense : Presentation
Kotsalos PhD Defense : Presentation
 
Angiography of Head and Neck
Angiography of Head and NeckAngiography of Head and Neck
Angiography of Head and Neck
 
MINIATURIZATION OF BRANCH-LINE COUPLERS USING OPEN STUBS AND STEPPED IMPEDANC...
MINIATURIZATION OF BRANCH-LINE COUPLERS USING OPEN STUBS AND STEPPED IMPEDANC...MINIATURIZATION OF BRANCH-LINE COUPLERS USING OPEN STUBS AND STEPPED IMPEDANC...
MINIATURIZATION OF BRANCH-LINE COUPLERS USING OPEN STUBS AND STEPPED IMPEDANC...
 
3D CFD simulation of intracranial aneurysm
3D CFD simulation of intracranial aneurysm3D CFD simulation of intracranial aneurysm
3D CFD simulation of intracranial aneurysm
 
Basic_Layout_Techniques.pdf
Basic_Layout_Techniques.pdfBasic_Layout_Techniques.pdf
Basic_Layout_Techniques.pdf
 
Detection of eye disorders through retinal image analysis
Detection of eye disorders through retinal image analysisDetection of eye disorders through retinal image analysis
Detection of eye disorders through retinal image analysis
 
Physical organization of parallel platforms
Physical organization of parallel platformsPhysical organization of parallel platforms
Physical organization of parallel platforms
 
Semi automatic vortex extraction in 4 d pc-mri cardiac blood flow data using ...
Semi automatic vortex extraction in 4 d pc-mri cardiac blood flow data using ...Semi automatic vortex extraction in 4 d pc-mri cardiac blood flow data using ...
Semi automatic vortex extraction in 4 d pc-mri cardiac blood flow data using ...
 
A1 Project Poster 2016-General Template
A1 Project Poster 2016-General TemplateA1 Project Poster 2016-General Template
A1 Project Poster 2016-General Template
 
Conformer review
Conformer reviewConformer review
Conformer review
 
Mitigation of Cross-Talk in Memory Arrays
Mitigation of Cross-Talk in Memory ArraysMitigation of Cross-Talk in Memory Arrays
Mitigation of Cross-Talk in Memory Arrays
 
Making effective use of graphics processing units (GPUs) in computations
Making effective use of graphics processing units (GPUs) in computationsMaking effective use of graphics processing units (GPUs) in computations
Making effective use of graphics processing units (GPUs) in computations
 

Recently uploaded

UI5con 2024 - Keynote: Latest News about UI5 and it’s Ecosystem
UI5con 2024 - Keynote: Latest News about UI5 and it’s EcosystemUI5con 2024 - Keynote: Latest News about UI5 and it’s Ecosystem
UI5con 2024 - Keynote: Latest News about UI5 and it’s Ecosystem
Peter Muessig
 
Need for Speed: Removing speed bumps from your Symfony projects ⚡️
Need for Speed: Removing speed bumps from your Symfony projects ⚡️Need for Speed: Removing speed bumps from your Symfony projects ⚡️
Need for Speed: Removing speed bumps from your Symfony projects ⚡️
Łukasz Chruściel
 
SWEBOK and Education at FUSE Okinawa 2024
SWEBOK and Education at FUSE Okinawa 2024SWEBOK and Education at FUSE Okinawa 2024
SWEBOK and Education at FUSE Okinawa 2024
Hironori Washizaki
 
Fundamentals of Programming and Language Processors
Fundamentals of Programming and Language ProcessorsFundamentals of Programming and Language Processors
Fundamentals of Programming and Language Processors
Rakesh Kumar R
 
What is Master Data Management by PiLog Group
What is Master Data Management by PiLog GroupWhat is Master Data Management by PiLog Group
What is Master Data Management by PiLog Group
aymanquadri279
 
E-commerce Development Services- Hornet Dynamics
E-commerce Development Services- Hornet DynamicsE-commerce Development Services- Hornet Dynamics
E-commerce Development Services- Hornet Dynamics
Hornet Dynamics
 
ALGIT - Assembly Line for Green IT - Numbers, Data, Facts
ALGIT - Assembly Line for Green IT - Numbers, Data, FactsALGIT - Assembly Line for Green IT - Numbers, Data, Facts
ALGIT - Assembly Line for Green IT - Numbers, Data, Facts
Green Software Development
 
UI5con 2024 - Boost Your Development Experience with UI5 Tooling Extensions
UI5con 2024 - Boost Your Development Experience with UI5 Tooling ExtensionsUI5con 2024 - Boost Your Development Experience with UI5 Tooling Extensions
UI5con 2024 - Boost Your Development Experience with UI5 Tooling Extensions
Peter Muessig
 
Graspan: A Big Data System for Big Code Analysis
Graspan: A Big Data System for Big Code AnalysisGraspan: A Big Data System for Big Code Analysis
Graspan: A Big Data System for Big Code Analysis
Aftab Hussain
 
Neo4j - Product Vision and Knowledge Graphs - GraphSummit Paris
Neo4j - Product Vision and Knowledge Graphs - GraphSummit ParisNeo4j - Product Vision and Knowledge Graphs - GraphSummit Paris
Neo4j - Product Vision and Knowledge Graphs - GraphSummit Paris
Neo4j
 
A Study of Variable-Role-based Feature Enrichment in Neural Models of Code
A Study of Variable-Role-based Feature Enrichment in Neural Models of CodeA Study of Variable-Role-based Feature Enrichment in Neural Models of Code
A Study of Variable-Role-based Feature Enrichment in Neural Models of Code
Aftab Hussain
 
Oracle Database 19c New Features for DBAs and Developers.pptx
Oracle Database 19c New Features for DBAs and Developers.pptxOracle Database 19c New Features for DBAs and Developers.pptx
Oracle Database 19c New Features for DBAs and Developers.pptx
Remote DBA Services
 
LORRAINE ANDREI_LEQUIGAN_HOW TO USE ZOOM
LORRAINE ANDREI_LEQUIGAN_HOW TO USE ZOOMLORRAINE ANDREI_LEQUIGAN_HOW TO USE ZOOM
LORRAINE ANDREI_LEQUIGAN_HOW TO USE ZOOM
lorraineandreiamcidl
 
2024 eCommerceDays Toulouse - Sylius 2.0.pdf
2024 eCommerceDays Toulouse - Sylius 2.0.pdf2024 eCommerceDays Toulouse - Sylius 2.0.pdf
2024 eCommerceDays Toulouse - Sylius 2.0.pdf
Łukasz Chruściel
 
Webinar On-Demand: Using Flutter for Embedded
Webinar On-Demand: Using Flutter for EmbeddedWebinar On-Demand: Using Flutter for Embedded
Webinar On-Demand: Using Flutter for Embedded
ICS
 
AI Fusion Buddy Review: Brand New, Groundbreaking Gemini-Powered AI App
AI Fusion Buddy Review: Brand New, Groundbreaking Gemini-Powered AI AppAI Fusion Buddy Review: Brand New, Groundbreaking Gemini-Powered AI App
AI Fusion Buddy Review: Brand New, Groundbreaking Gemini-Powered AI App
Google
 
Transform Your Communication with Cloud-Based IVR Solutions
Transform Your Communication with Cloud-Based IVR SolutionsTransform Your Communication with Cloud-Based IVR Solutions
Transform Your Communication with Cloud-Based IVR Solutions
TheSMSPoint
 
Measures in SQL (SIGMOD 2024, Santiago, Chile)
Measures in SQL (SIGMOD 2024, Santiago, Chile)Measures in SQL (SIGMOD 2024, Santiago, Chile)
Measures in SQL (SIGMOD 2024, Santiago, Chile)
Julian Hyde
 
Hand Rolled Applicative User Validation Code Kata
Hand Rolled Applicative User ValidationCode KataHand Rolled Applicative User ValidationCode Kata
Hand Rolled Applicative User Validation Code Kata
Philip Schwarz
 
Using Xen Hypervisor for Functional Safety
Using Xen Hypervisor for Functional SafetyUsing Xen Hypervisor for Functional Safety
Using Xen Hypervisor for Functional Safety
Ayan Halder
 

Recently uploaded (20)

UI5con 2024 - Keynote: Latest News about UI5 and it’s Ecosystem
UI5con 2024 - Keynote: Latest News about UI5 and it’s EcosystemUI5con 2024 - Keynote: Latest News about UI5 and it’s Ecosystem
UI5con 2024 - Keynote: Latest News about UI5 and it’s Ecosystem
 
Need for Speed: Removing speed bumps from your Symfony projects ⚡️
Need for Speed: Removing speed bumps from your Symfony projects ⚡️Need for Speed: Removing speed bumps from your Symfony projects ⚡️
Need for Speed: Removing speed bumps from your Symfony projects ⚡️
 
SWEBOK and Education at FUSE Okinawa 2024
SWEBOK and Education at FUSE Okinawa 2024SWEBOK and Education at FUSE Okinawa 2024
SWEBOK and Education at FUSE Okinawa 2024
 
Fundamentals of Programming and Language Processors
Fundamentals of Programming and Language ProcessorsFundamentals of Programming and Language Processors
Fundamentals of Programming and Language Processors
 
What is Master Data Management by PiLog Group
What is Master Data Management by PiLog GroupWhat is Master Data Management by PiLog Group
What is Master Data Management by PiLog Group
 
E-commerce Development Services- Hornet Dynamics
E-commerce Development Services- Hornet DynamicsE-commerce Development Services- Hornet Dynamics
E-commerce Development Services- Hornet Dynamics
 
ALGIT - Assembly Line for Green IT - Numbers, Data, Facts
ALGIT - Assembly Line for Green IT - Numbers, Data, FactsALGIT - Assembly Line for Green IT - Numbers, Data, Facts
ALGIT - Assembly Line for Green IT - Numbers, Data, Facts
 
UI5con 2024 - Boost Your Development Experience with UI5 Tooling Extensions
UI5con 2024 - Boost Your Development Experience with UI5 Tooling ExtensionsUI5con 2024 - Boost Your Development Experience with UI5 Tooling Extensions
UI5con 2024 - Boost Your Development Experience with UI5 Tooling Extensions
 
Graspan: A Big Data System for Big Code Analysis
Graspan: A Big Data System for Big Code AnalysisGraspan: A Big Data System for Big Code Analysis
Graspan: A Big Data System for Big Code Analysis
 
Neo4j - Product Vision and Knowledge Graphs - GraphSummit Paris
Neo4j - Product Vision and Knowledge Graphs - GraphSummit ParisNeo4j - Product Vision and Knowledge Graphs - GraphSummit Paris
Neo4j - Product Vision and Knowledge Graphs - GraphSummit Paris
 
A Study of Variable-Role-based Feature Enrichment in Neural Models of Code
A Study of Variable-Role-based Feature Enrichment in Neural Models of CodeA Study of Variable-Role-based Feature Enrichment in Neural Models of Code
A Study of Variable-Role-based Feature Enrichment in Neural Models of Code
 
Oracle Database 19c New Features for DBAs and Developers.pptx
Oracle Database 19c New Features for DBAs and Developers.pptxOracle Database 19c New Features for DBAs and Developers.pptx
Oracle Database 19c New Features for DBAs and Developers.pptx
 
LORRAINE ANDREI_LEQUIGAN_HOW TO USE ZOOM
LORRAINE ANDREI_LEQUIGAN_HOW TO USE ZOOMLORRAINE ANDREI_LEQUIGAN_HOW TO USE ZOOM
LORRAINE ANDREI_LEQUIGAN_HOW TO USE ZOOM
 
2024 eCommerceDays Toulouse - Sylius 2.0.pdf
2024 eCommerceDays Toulouse - Sylius 2.0.pdf2024 eCommerceDays Toulouse - Sylius 2.0.pdf
2024 eCommerceDays Toulouse - Sylius 2.0.pdf
 
Webinar On-Demand: Using Flutter for Embedded
Webinar On-Demand: Using Flutter for EmbeddedWebinar On-Demand: Using Flutter for Embedded
Webinar On-Demand: Using Flutter for Embedded
 
AI Fusion Buddy Review: Brand New, Groundbreaking Gemini-Powered AI App
AI Fusion Buddy Review: Brand New, Groundbreaking Gemini-Powered AI AppAI Fusion Buddy Review: Brand New, Groundbreaking Gemini-Powered AI App
AI Fusion Buddy Review: Brand New, Groundbreaking Gemini-Powered AI App
 
Transform Your Communication with Cloud-Based IVR Solutions
Transform Your Communication with Cloud-Based IVR SolutionsTransform Your Communication with Cloud-Based IVR Solutions
Transform Your Communication with Cloud-Based IVR Solutions
 
Measures in SQL (SIGMOD 2024, Santiago, Chile)
Measures in SQL (SIGMOD 2024, Santiago, Chile)Measures in SQL (SIGMOD 2024, Santiago, Chile)
Measures in SQL (SIGMOD 2024, Santiago, Chile)
 
Hand Rolled Applicative User Validation Code Kata
Hand Rolled Applicative User ValidationCode KataHand Rolled Applicative User ValidationCode Kata
Hand Rolled Applicative User Validation Code Kata
 
Using Xen Hypervisor for Functional Safety
Using Xen Hypervisor for Functional SafetyUsing Xen Hypervisor for Functional Safety
Using Xen Hypervisor for Functional Safety
 

HemeLB weighted decomposition EASC 2014 slides

  • 1. Weighted Decomposition Are some lattice sites more equal than others? Derek Groen David Abou Chacra Jiri Jaros Rupert Nash Miguel Bernabeu Peter Coveney
  • 2. Overview ● Cerebrovascular bloodflow and HemeLB. ● What type performance matters. ● Weighted decomposition ● Tests & results ● Discussion / Future work
  • 3. Cerebrovascular diseases ● Stroke is the main cause of about 1.1M deaths per year in Europe. ● ~15% are caused by bleeding in the brain. ● We aim to accurately model cerebral bloodflow, and to eventually provide assistance with cerebrovascular surgery.
  • 4. Features in HemeLB 1. Generation of computational models from medical images. 2. A wide range of collision kernels and boundary conditions. 3. Sparse geometries with negligible overhead (using ParMETIS). 4. Streaming visualization and steering of the simulation. 5. Coupling to external models.
  • 5.
  • 6.
  • 8.
  • 9.
  • 10. Domain decomposition current 1. read in blocks 2. pass the geometry to ParMETIS 3. ParMETIS uses k- way partitioning. proposed changes differ the weights on lattice sites, use a space filling curve (z-ordering) prior to partitioning.
  • 11. Obtaining weights Site type Weights Intel SandyBridge Weights AMD Bulldozer Bulk 10.0 10.0 Wall 18.708 20.226 In/outlet 40.037 37..398 Wall+ in/outlet (22.700) (34.577) We ran 5 test simulations with cylinders of different aspect ratios to obtain an estimate of the calculation cost of each site type. ParMETIS tends to perform worse when weight values are large.
  • 12. 4 4 4 4 4 4 16 16 16 8 8 8 8 8 8 8 8 8 8 8 8 8 8 88 16 16 16
  • 13. Test setup 650,492 lattice sites 10% fluid 5,667,778 lattice sites 1.5% fluid D3Q19 BFL boundaries
  • 15.
  • 16.
  • 17.
  • 18. Aneurysm geometry HECToR XT6 and ARCHER XC30
  • 25.
  • 26. Observations/Future work ● Some lattice sites are more equal than others. ● Getting a load-balanced decomposition is a major challenge.
  • 27. Full Paper A full paper will be available in the proceedings of EASC 2014. If you would like a preprint version, please contact me at djgroennl@gmail.com
  • 28. Thank you! UKCOMES UK Consortium On Mesoscale Engineering and Science.