Gmsh and GetDP in Academia and Industry - GNU...

GmshandGetDPinAcademiaandIndustry

C.GeuzaineUniversityofLiège,Belgium

OctConf2015-Darmstadt,September232015

• IamaprofessorofElectricalEngineeringandComputerScienceattheUniversityofLiègeinBelgium,whereIleadtheACEresearchgroup

• Ourresearchinterests:modeling,analysis,algorithmdevelopment,andsimulaNonforproblemsarisinginvariousareasofengineeringandscience

• Wewritequitealotofcodes,mostlyPDEsolversinC++/Python

• TwocodesreleasedunderGNUGPL:

• Gmshmeshgenerator:hVp://gmsh.info

• GetDPfiniteelementsolver:hVp://getdp.info

• Thesearelongtermefforts(bothstartedin1997)

SomeBackground

http://gmsh.info

http://getdp.info

SomeBackground

Today,GmshandGetDPrepresent

• halfamillionlinesof(mostlyC++)code

• sNllonly3coredevs;butabout100withrepowriteaccess

• about1000peopleonmailinglists

• about5000binarydownloadsperweek(80%Windows)

• about400(googlescholar)citaNonsperyear

SomeBackground

Today,GmshandGetDPrepresent

• halfamillionlinesof(mostlyC++)code

• sNllonly3coredevs;butabout100withrepowriteaccess

• about1000peopleonmailinglists

• about5000binarydownloadsperweek(80%Windows)

• about400(googlescholar)citaNonsperyear

Let’shavealook!

QuickoverviewofGmsh

• Gmshisbasedaroundfourmodules:Geometry,Mesh,SolverandPost-processing;3levelsofuse:

• Developper:throughthe(undocumented…)C++orPythonAPI

• Advanceduser:throughthededicated“.geo”language

• Noviceuser:throughtheGUI(whichtranslatesmostacNonsinto“.geo”filecommands)

• MaincharacterisNc:allalgorithmsarewriVenintermsofabstractCADenNNes,usinga“BoundaryREPresentaNon”approach

T2:InterfaceCAO/maillage

6

T2:InterfaceCAO/maillage

8

10 E. MARCHANDISE

10

51

50

60

61 62

41

00@T1

30

12

11

u00(x)

20

3140

Figure 5. Multiscale Laplace partitioning method of an aorta(G = 0, NB = 13, ⌘ = 17). In thisexample there are n = 6 di↵erent levels on which harmonic maps are computed. The red line showsthe partition line that recursively splits the mesh into two area balanced mesh partitions (see the

resulting mesh partition in Fig.6 ).

Copyright c� 2010 John Wiley & Sons, Ltd. Int. J. Numer. Meth. Engng 2010; 00:1–6Prepared using nmeauth.cls

Basic concepts

Any 3-D model can be defined using its Boundary Representation

(BRep): a volume is bounded by a set of surfaces, and a surface is

bounded by a series of curves; a curve is bounded by two end points.

Therefore, four kinds of model entities are defined:

1. Model Vertices G

0i

that are topological entities of dimension 0,

2. Model Edges G

1i


3. Model Faces G

2i


4. Model Regions G

3i

that are topological entities of dimension 3.

11

QuickoverviewofGmsh

Model entities are topological entities, i.e., they only deal with adja-

cencies in the model, and we use a bi-directional data structure for

representing the graph of adjacencies.

Schematically, we have

G

0i

⌦ G

1i

⌦ G

2i

⌦ G

3i

.

Any model entity is able to build its list of adjacencies using local

operations.

12

QuickoverviewofGmsh

The geometry of a model entity depends on the solid modeler for its

underlying representation. Solid modelers usually provide a parametriza-

tion of the shapes, i.e., a mapping p 2 R

d 7! x 2 R

3:

1. The geometry of a model vertex G

0i

is simply its 3-D location

x

i

= (xi

, y

i

, z

i

).

2. The geometry of a model edge G

1i

is its underlying curve Ci

with

its parametrization p(t) 2 Ci

, t 2 [t1, t2].

3. The geometry of a model face G

2i

is its underlying surface Si

with

its parametrization p(u, v) 2 Si

.

4. The geometry associated to a model region is R

3.

13

QuickoverviewofGmsh

u = u(t), v = v(t)

S

p(u, v)

C

v

u

x

x = x(t), y = y(t), z = z(t)

v = v(x, y, z)

C

S

p(x, y, z)

t1 p(t)tt2

C

u = u(x, y, z)

z

y

Point p located on the curve C that is itself embedded in surface S

14

QuickoverviewofGmsh

CAD kernel idiosyncrasies: seam edges and degenerated edges

15

QuickoverviewofGmsh

CAD kernel idiosyncrasies: seam edges and degenerated edges

15

QuickoverviewofGmsh

C.#Geuzaine#+#Onera#Scien0fic#Day#+#Oct.#3#2012 2

Surface&meshes

Surface#triangula?ons#can#be#generated

• either#directly#in#the#embedding#3MD#Euclidean#space

• or#in#the#parametric#plane#of#the#surface,#which#is#far#more#robust#(Delaunay#and#variants)

Surface mesh generation techniques

Surface meshes can be1 generated directly in the “real” 3D space; or2 generated in the parametric plane of the surface.

Several algorithms implemented: Delaunay, “Frontal Delaunay”, localmesh modifications (collapse and splits only)

C. Geuzaine WIAS, December 4th, 2008

Surface mesh generation techniques

When a decent parametrization of the surface exists, building themesh in the parametric plane is more robustIssues like seam and/or degenerated edges have to be taken intoaccount,Need ability to generate (highly) anisotropic meshes.

C. Geuzaine WIAS, December 4th, 2008

Abstract interface

• For the geometry:

GModel

GVertex

GEdge

GFace

GRegion

Concrete implementation for each CAD kernel (e.g. gmshFace, OCCFace,

parasolidFace, fourierFace, levelsetFace, discreteFace).

Direct access via CAD kernel APIs: never translate/convert formats!

16

QuickoverviewofGmsh

class GEdge : public GEntity {//bi-directional data structure

GVertex *v1, *v2;

std::list<GFace*> faces;

public:

//pure virtual functions that have to be overloaded for every

//solid modeler

virtual std::pair<double> parRange() = 0;

virtual Point3 point(double t) = 0;

virtual Vector3 firstDer(double t) = 0;

virtual Point2 reparam(GFace *f, double t, int dir) = 0;

virtual bool isSeam(GFace *f) = 0;

//other functions of the class are non pure virtual

//..

};

17

QuickoverviewofGmsh

class GFace : public GEntity {//bi-directional data structure

GRegion *r1, *r2;

std::list<GEdge*> edges;

public:

//pure virtual functions that have to be overloaded for every

//solid modeler

virtual std::pair<double> parRange(int dir) const = 0;

virtual Point3 point(double u, double v) const = 0;

virtual std::pair<Vector3> firstDer(double u, double v) const = 0;

//other functions of the class are non pure virtual

virtual double curvature(double u, double v) const;

//...

};

18

QuickoverviewofGmsh

Abstract interface (cont’d)

• For the mesh:

MElement

MVertex

Each GEntity stores its “internal” vertices. Parallel I/O through GModel.

Minimal storage:

- 44 bytes per vertex, 28 bytes per tetrahedron (12 Mtets/Gb)

- Enriched for specific algorithms

- MEdge and MFace created on demand

MElement provides access to mapping, Jacobian and integration

Library can be compiled with mesh generation algorithms built-in

19

QuickoverviewofGmsh

Recentfeatures:

• ReparameterizaNonofsurfaces(“STLremeshing”)

• Coarsegrained(distributed,viaMPI)andfine-grained(sharedmemory,viaOpenMP)parallel3DDelaunaymeshingalgorithm

• AutomaNcquadandhex-dominantmeshing

• Anisotropicmeshesandboundarylayers

• Homologyandcohomologysolver

QuickoverviewofGmsh

QuickoverviewofGetDP

• GetDPlanguage(“.pro”files)forthenaturalexpressionoffiniteelementproblems(explicitfuncNonspacesandweakforms,…)

• Solvingondomaintranslatesinto:

i.e.aquitedirecttranscripNonoftheweakformoftheproblem:Findsuchthat,

r · (aru) = f ⌦

Formulation{{NameF;TypeFemEquation;Quantity{{Nameu;TypeLocal;NameOfSpaceH1_0;}}Equation{Galerkin{[a[]*Dof{du},{du}];InOmega;…}Galerkin{[f[],{u}];InOmega;…}}}}

u 2 H10 (⌦)

Z

⌦aru ·ru0 d⌦+

Z

⌦f u0 d⌦ = 0

8u0 2 H10 (⌦)


• NodisNncNonbetween1D,2Dor3D;staNc,transient,Nme-(mulN-)harmonic,eigenproblems

• EasycouplingoffieldsandformulaNons(physics),staggeredormonolithic,e.g.forexplicitJacobianmatrices/sensiNvityanalysisofstronglycouplednonlinearproblems

• Naturalhandlingofnon-local(global,integral)quanNNes,e.g.forcircuitcoupling

• LinearalgebrathroughPETSc/SLEPcand/orSparksit/Arpack


• Recentdevelopments:

• UseofGmshlibraryforIO,post-processing,mesh-to-meshinterpolaNon

• LargescalecalculaNonsthroughdomaindecomposiNonmethods(>1billionDoFson10,000CPUsforNme-harmonicwavescaVering)

• High-ordereigenvalueproblems

• Built-inOctaveandPythoninterpreters

GmshandGetDPinacademiaandinindustry

Actualuseisdifficulttoassess,buttodayweesNmatethat

• Gmshisprobablythemostpopularopensourcemeshgenerator;itisusedinhundredsofuniversiNes,researchcentersandcommercialcompaniesaroundtheworld

• GetDPisusedintensivelyinafewdozensuniversiNesandcompanies

Severalcommercialtoolsuseorintegrate(withduallicensing)thecodes,e.g.hVp://www.nxmagneNcs.de

http://www.geuz.org/analog/downloads.html

http://www.nxmagnetics.de

GmshandGetDPinacademiaandinindustry

Actualuseisdifficulttoassess,buttodayweesNmatethat

• Gmshisprobablythemostpopularopensourcemeshgenerator;itisusedinhundredsofuniversiNes,researchcentersandcommercialcompaniesaroundtheworld

• GetDPisusedintensivelyinafewdozensuniversiNesandcompanies

Severalcommercialtoolsuseorintegrate(withduallicensing)thecodes,e.g.hVp://www.nxmagneNcs.de

Wheredowegofromhere?TheONELABproject:hVp://onelab.info

http://www.geuz.org/analog/downloads.html

http://www.nxmagnetics.de

http://onelab.info

• Economic• GrowingimportanceofnumericalsimulaNonineducaNonandindustry

• ProhibiNvecostofcommercialpackagesforasignificantsubsetofpotenNalusers(SMEs,educaNon,occasionaluse)

• ScienIfic• Highqualityoffree/open-sourcesoowaredevelopedinuniversiNesandresearchcenters

• SomeNmesaheadofcommercialequivalents

• PracIcal• Nouser-friendlyinterfaceand/orpoordocumentaNonformostopensourceFiniteElementAnalysis(FEA)codes

ContextoftheONELABproject

DevelopaplapormforintegraIngfreeFiniteElementAnalysis(FEA)sooware:

• allowingtheintegraNon(byco-simultaNon)ofanyopen-sourcecode,whatevertheircharacterisNcs

• withanintuiNveGUIallowingnewbieuserstogetstartedandguidedintotheworldofFEmodeling—butwiththepossibilitytoconstructsophis1cated,upgradable,mul1-code,mul1-pla8ormscriptsforthespecializeduser

• andwiththepossibilitytoconstructbotheducaNon-andbusiness-specifictools

GeneralgoaloftheONELABproject

ThesoluNonshouldovercometwodifficulNesassociatedwithfreeFEAsooware:

(1) Theheterogeneityofthetools

(2) Themissing“expertlayer”,top-downvalidaIonanddocumentaIonfoundincommercialofferings

GeneralgoaloftheONELABproject

• Manyclosed,commercialtools(COMSOL,AnsysWorkbench,…)

• Moreopentools,e.g.GiD(hVp://gid.cimne.upc.es),butnotfree

• Closestfreesooware:SALOME(hVp://salome-plaporm.org),butverylargeproject,notwellsuitedforbuilding“fastandlight”domain-specificapplicaNons

• Otheropensourceprojects:“mulN-physic”codes(Elmer,etc.)sNllmainlyfocusedonasingledomain(CFD,solids,E-M);theimplementaNonofnewphysicsleadstobare-bonesfeatures,farfromtherefinementofspecializedcodes;noeasy-to-useinterfaceandnodrivingofothercodes

Stateoftheart

http://salome-platform.org

http://salome-platform.org

• Don’treimplement,interfacetheexisNng!

• Makeitassmall,lightweightandaseasytomaintainaspossible(nosolver-dependentcodeintheinterface)

• Makeiteasytoprovidetemplates,withinteracNveparametermodificaNon

• ONELABrole=datacentralizaIon,(opNonal)modificaIonandredispatching

ONELABguidingprinciples

• Don’treimplement,interfacetheexisNng!

• Makeitassmall,lightweightandaseasytomaintainaspossible(nosolver-dependentcodeintheinterface)

• Makeiteasytoprovidetemplates,withinteracNveparametermodificaNon

• ONELABrole=datacentralizaIon,(opNonal)modificaIonandredispatching

Issuesofcompletenessandconsistencyoftheparametersetarecompletelydealtwithonthesolverside

ONELABguidingprinciples

(1)Heterogeneityofthetools

(2)Missing“expert”layer,top-downvalidaIonanddocumentaIon

ONELABfeatures

(1)AbstractinterfacetoFEAcodes

ONELABfeatures


• CAD&meshing;physicalproperNes,constraints&codedrivers;post-processing

ONELABfeatures



• ImplementedinGmsh:

ONELABfeatures




• Parameterexchangelibrary

ONELABfeatures





• NaNveC++andPythonclients;Parserfornon-naNveclients

ONELABfeatures






(2)DevelopmentanddocumentaIonoftemplates(“meta-models”)

ONELABfeatures







• Model:blackbox,parameterizableviaabstractinterface

ONELABfeatures







• Model:blackbox,parameterizableviaabstractinterface

• Meta-model:setofmodels+selecNonlogic

ONELABfeatures

Client-server:

• Clients:CADkernels,meshers,solvers,post-processors

• Server:Gmsh(currently)+database

Abstractinterface:

• Theserverhasnoaprioriknowledgeoftheclients(nometa-languageorexchangefileformat)

• Theserverdoesnotwriteinputfilesfor(naIve)clients:theclientcommunicateswiththeservertodefinewhatinformaNonshouldbeexchanged

ONELABimplementaIon

AbstractinterfacetophysicalproperNes,constraints&codedrivers:

• Libraryforparameterexchange:

• ReferenceserverinC++forportability,e.g.oniOS/Android(onelab::server)

• ClientsinC++(onelab::client)orPython

• Exchangeparameters(onelab::parameter)throughTCP/IPorUnixsockets,orin-memory

ONELABimplementaIon

AbstractinterfacetophysicalproperNes,constraints&codedrivers:

• Libraryforparameterexchange:

• ReferenceserverinC++forportability,e.g.oniOS/Android(onelab::server)

• ClientsinC++(onelab::client)orPython

• Exchangeparameters(onelab::parameter)throughTCP/IPorUnixsockets,orin-memory

• “NaNve”clientsuseC++orPythondirectly

• “Non-naNve”clientsusePython,byinstrumenNngtheirinputfiles

• Currently:Elmer,OpenFOAM,Code_Aster,Abaqus,Gnuplot

ONELABimplementaIon

ONELABimplementaIon

NaNveclient:overloadingofexisNngfuncNons(GetDP)...DefineConstant[Numstep={50,Name"Elmer/Numberoftimesteps"}];DefineConstant[TimeStep={0.1,Name"Elmer/Timestep"}];...

Non-naNveclients:instrumentaNontheinputfilesoftheclient(Elmer)...OL.lineNumStep.number(50,Elmer/,Numberoftimesteps);OL.lineTimeStep.number(0.1,Elmer/,Timestep);SimulationSimulationType=TransientTimestepsizes=OL.get(TimeStep)TimestepIntervals=OL.get(NumStep)...

Preprocessing:conversionintoavalidinputfilefortheclient(Elmer)...SimulationSimulationType=TransientTimestepsizes=0.1TimestepIntervals=50...

onelab::parameter

• nameas‘/’-separatedpath

• dynamicdependencylistofclientsandstatuschange

• decoraNons(help,bounds,choices,...)

• serializaNonanddeserializaNon

ONELABimplementaIon

onelab::parameter





ExamplefornaNveGmsh&GetDPclients(in.geoor.profiles):DefineConstant[N={32,Name“Numberofslices”}];

ExampleforPythonclient:c=onelab.client()

N=c.defineNumber('Numberofslices',value=32)

ONELABimplementaIon

onelab::parameter





ExamplefornaNveGmsh&GetDPclients(in.geoor.profiles):DefineConstant[N={32,Name“Numberofslices”}];

ExampleforPythonclient:c=onelab.client()

N=c.defineNumber('Numberofslices',value=32)

ONELABimplementaIon

Let’shaveanotherlook!

• GrowinguseofGmshandGetDPinacademiaandindustry

• “VulgarizaNon”requiresquiteabitofwork,hencetheONELABproject:

• Asimple(trivial?)waytointerfaceFEAsolvers

• InteracNve,basedonGmsh,andfree

• AndnowavailableoniOSandAndroid

• Giveitatry:

• Wishlist:wewantanOctaveserver(andclient)!

hVp://onelab.info

Conclusion

http://onelab.info

CommentaboutGmshonhVp://www.fltk.org(sic): >From Anonymous, 20:33 May 18, 2004 (score=1) Je suis outre du programme pour des intellectuels vous devrez avoir plus d’imagination vous faite onte au genie informatique

PS:Doingopensourceisrewarding!

http://www.fltk.org

CommentaboutGmshonhVp://www.fltk.org(sic): >From Anonymous, 20:33 May 18, 2004 (score=1) Je suis outre du programme pour des intellectuels vous devrez avoir plus d’imagination vous faite onte au genie informatique

TranslaNon(includingmisspellings!)forthenon-frenchspeaking:

>From Anonymous, 20:33 May 18, 2004 (score=1) I am ashamed of the program for intelectuals you should have more imagination you are the schame of computer science

PS:Doingopensourceisrewarding!

http://www.fltk.org

ThanksforyouraVenNon!

[email protected]

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