PhD Defense - HAL archive ouverte · 2014. 10. 5. · PhD Defense C´edric Lachat Design and validation of distributed-memory, parallel remeshing algorithms based on a sequential

Université de Nice - Sophia-Antipolis December 13, 2013

PhD DefenseCédric Lachat

Design and validation of distributed-memory,parallel remeshing algorithms based on asequential remesher

SUMMARY

Introduction

Data structures for parallel remeshing

Parallel remeshing

Experiments

Conclusion

Cédric Lachat- PhD Defense December 13, 2013- 2/55

1Introduction

Introduction

ContextI Numerical simulations are

needed in multiple domainsincluding:

I thermonuclear fusionI aeronauticsI meteorology, . . .

I Problems become bigger andmore and more complex:numerical simulations cannot berun on a single workstation→ Want of parallelizedcomputations→ Need to distribute dataacross the processors: domaindecomposition


Introduction

Numerical simulation

I Space discretization:I mesh

I Finite number of points onwhich values of theproblem are computed,e.g.:

I temperatureI pressureI speed,. . .

I Solution precision dependson mesh quality:

I need for remeshing


Introduction

Aim of this PhD thesis

I Achieve parallel remeshing based on a sequential remesherI Devise a scalable method→ distributed memory paradigm→ communication across subdomain boundaries

I Since distributed meshes are considered, need to devise acomplete framework for handling distributed meshes andrelated computations

I Parallel remeshing requires:I to iterate on mesh components to perform local computationsI to associate values with components

→ made available to users through an APII Improve locality of accesses in memory hierarchy:

I proper renumbering of entities on each subdomain


Introduction

State of the art (1/2)

I Parallel partitioningI spectral [Pothen et al., 1990], combinatorial [Kernighan and

Lin, 1970, Fiduccia and Mattheyses, 1982],evolutionist [Dongarra et al., 1988]

I only multi-level [Chevalier, 2007, Chevalier and Safro, 2009]provides good efficiency and quality on big graph

I Parallel dynamic load balancingI many tools: DRAMA [Maerten et al., 1999], Zoltan [Devine

et al., 1999, 2002], PLUM [Oliker et al., 2000],ParFUM [Lawlor et al., 2006]. . .


Introduction


I Parallel remeshingI parallelize remeshing techniques [Castanos and Savage, 1996,

Laemmer, 1997, Oliker et al., 2000, Chrisochoides and Nave,2003, Casagrande et al., 2005, Lawlor et al., 2006]

I re-use of sequential algorithms [Coupez et al., 2000, Cavalloet al., 2005, Dobrzynski and Remacle, 2007, Tremel et al.,2007, Digonnet et al., 2007, Ramadan et al., 2009]

I Renumbering [Löhner, 1993, Burgess and Giles, 1997, Löhner,1998, Amenta et al., 2003, Isenburg et al., 2006, Loseille andAlauzet, 2009]


2Data structures


Definitions

I Mesh:

I NodeI EdgeI Element

I Mesh representation:

I VertexI Entity

I main entity

I RelationI Enriched graph



Definitions

I Mesh:I Node

I EdgeI Element


I VertexI Entity

I main entity




Definitions

I Mesh:I NodeI Edge

I Element


I VertexI Entity

I main entity




Definitions

I Mesh:I NodeI EdgeI Element


I VertexI Entity

I main entity




Definitions


I Mesh representation:I Vertex

I Entity

I main entity




Definitions


I Mesh representation:I VertexI Entity

I main entityI RelationI Enriched graph



Definitions



I main entity




Definitions



I main entityI Relation

I Enriched graph



Definitions



I main entityI RelationI Enriched graph



Examples

I The same mesh can lead to different enriched graphsI Depending on the requirements of the numerical schemes



Distributed mesh

I On three processors

P0 P21P



Definitions

I Vertices, locally on P1:I LocalI HaloI Overlap

I Vertices, between P0and P1:

I FrontierI Vertices, globally:

I Internal

P0 P21P



Global numbering

I Necessary to describe the mesh in its entirety

P0 P21P

5

1

2 9

7

4

3 6 8

10



Local numbering

I Local indices are mandatory to address local data arrays

I For all local vertices onevery subdomain, verticesare indexed per entity

P0 P21P

1

1 1

122

1

1

1

2

I Local indices are extendedto index halo vertices aswell, e.g. with respect toprocessor P1:

P0 P21P

23

1

1

2 1 3


3Parallel remeshing

Parallel remeshing


I First class of parallel remeshing techniques:I Parallelization of existing sequential remeshing techniques

I introduced in 1996 [Castanos and Savage, 1996] for 2Dmeshes

I 3D remeshing in 2000 for homogeneous meshes [Oliker et al.,2000]

I Delaunay triangulation in 2003 [Chrisochoides and Nave, 2003]I 3D remeshing for mixed meshes [Lawlor et al., 2006]

I Problems:I Difficulties to parallelize each operator of the remesherI Remeshing some element requires neighborhood informationI Too much communication between subdomains is required to

achieve quality as high as in sequential processing→ This class of parallel remeshing methods cannot handlelarge-size meshes distributed across a large number ofprocessors


Parallel remeshing


I Second class of parallel remeshing:I Re-use sequential remeshers in a parallel framework:

I introduced in 2000 [Coupez et al., 2000, Dobrzynski andRemacle, 2007]

I 3D remeshing for mixed meshes [Cavallo et al., 2005]I remeshing with hierarchical transport [Digonnet et al., 2007]I multi-grid remeshing [Ramadan et al., 2009]

→ Our approach is to generalize this class of parallelremeshing techniques so as to allow for plugging-in anysequential remesher


Parallel remeshing

Requirements (1/2)

I How to remesh in parallel on distributed meshes?I Subdomain size could be greater than mesh size allowed by the

sequential remesher→ Need to identify in parallel non-overlapping zones ofprescribed size / workload

I Zone frontiers must be left unmodified so as to easereintegration of remeshed zones into the distributed mesh


Parallel remeshing

Global scheme:Iterative process until all tagged elements are remeshed

1b Tagging

2 Identification

3 Extraction 4 Remeshing

5 Reintegration

1a Tagging
