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scotch decomposition method
This commit is contained in:
mattijs
@ -2,7 +2,10 @@ decompositionMethod/decompositionMethod.C
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geomDecomp/geomDecomp.C
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simpleGeomDecomp/simpleGeomDecomp.C
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hierarchGeomDecomp/hierarchGeomDecomp.C
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metisDecomp/metisDecomp.C
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manualDecomp/manualDecomp.C
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scotchDecomp/scotchDecomp.C
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metisDecomp/metisDecomp.C
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LIB = $(FOAM_LIBBIN)/libdecompositionMethods
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@ -1,6 +1,8 @@
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EXE_INC = \
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-I$(WM_THIRD_PARTY_DIR)/scotch_5.1/src/libscotch/lnInclude \
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-I$(WM_THIRD_PARTY_DIR)/metis-5.0pre2/include
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LIB_LIBS = \
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-lscotch \
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-lmetis \
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-lGKlib
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@ -0,0 +1,425 @@
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/*---------------------------------------------------------------------------*\
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========= |
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\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
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\\ / O peration |
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\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
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\\/ M anipulation |
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-------------------------------------------------------------------------------
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License
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This file is part of OpenFOAM.
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||||
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OpenFOAM is free software; you can redistribute it and/or modify it
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under the terms of the GNU General Public License as published by the
|
||||
Free Software Foundation; either version 2 of the License, or (at your
|
||||
option) any later version.
|
||||
|
||||
OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
|
||||
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
|
||||
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
|
||||
for more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with OpenFOAM; if not, write to the Free Software Foundation,
|
||||
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
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S Strat=b{job=t,map=t,poli=S,sep=(m{asc=b{bnd=d{pass=40,dif=1,rem=1}f{move=80,pass=-1,bal=0.005},org=f{move=80,pass=-1,bal=0.005},width=3},low=h{pass=10}f{move=80,pass=-1,bal=0.0005},type=h,vert=80,rat=0.8}|m{asc=b{bnd=d{pass=40,dif=1,rem=1}f{move=80,pass=-1,bal=0.005},org=f{move=80,pass=-1,bal=0.005},width=3},low=h{pass=10}f{move=80,pass=-1,bal=0.0005},type=h,vert=80,rat=0.8})}
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\*---------------------------------------------------------------------------*/
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#include "scotchDecomp.H"
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#include "addToRunTimeSelectionTable.H"
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#include "floatScalar.H"
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#include "IFstream.H"
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#include "Time.H"
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#include "cyclicPolyPatch.H"
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extern "C"
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{
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#define OMPI_SKIP_MPICXX
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#include "module.h"
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#include "common.h"
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#include "scotch.h"
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}
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// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
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namespace Foam
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{
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defineTypeNameAndDebug(scotchDecomp, 0);
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addToRunTimeSelectionTable
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(
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decompositionMethod,
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scotchDecomp,
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dictionaryMesh
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);
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}
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// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
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void Foam::scotchDecomp::check(const int retVal, const char* str)
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{
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if (retVal)
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{
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FatalErrorIn("scotchDecomp::decompose(..)")
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<< "Called to scotch routine " << str << " failed."
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<< exit(FatalError);
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}
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}
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// Call Metis with options from dictionary.
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Foam::label Foam::scotchDecomp::decompose
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(
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const List<int>& adjncy,
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const List<int>& xadj,
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List<int>& finalDecomp
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)
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{
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// Strategy
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// ~~~~~~~~
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// Default.
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SCOTCH_Strat stradat;
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check(SCOTCH_stratInit(&stradat), "SCOTCH_stratInit");
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//SCOTCH_stratGraphMap(&stradat, &argv[i][2]);
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//fprintf(stdout, "S\tStrat=");
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//SCOTCH_stratSave(&stradat, stdout);
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//fprintf(stdout, "\n");
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// Graph
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// ~~~~~
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SCOTCH_Graph grafdat;
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check(SCOTCH_graphInit(&grafdat), "SCOTCH_graphInit");
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check
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(
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SCOTCH_graphBuild
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(
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&grafdat,
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0, // baseval, c-style numbering
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xadj.size()-1, // vertnbr, nCells
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xadj.begin(), // verttab, start index per cell into adjncy
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&xadj[1], // vendtab, end index ,,
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NULL, // velotab, vertex weights
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NULL, // vlbltab
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adjncy.size(), // edgenbr, number of arcs
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adjncy.begin(), // edgetab
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NULL // edlotab, edge weights
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),
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"SCOTCH_graphBuild"
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);
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check(SCOTCH_graphCheck(&grafdat), "SCOTCH_graphCheck");
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//// Architecture
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//// ~~~~~~~~~~~~
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//// (fully connected network topology since using switch)
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//
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//SCOTCH_Arch archdat;
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//check(SCOTCH_archInit(&archdat), "SCOTCH_archInit");
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//check
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//(
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// // SCOTCH_archCmpltw for weighted.
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// SCOTCH_archCmplt(&archdat, nProcessors_),
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// "SCOTCH_archCmplt"
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//);
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//SCOTCH_Mapping mapdat;
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//SCOTCH_graphMapInit(&grafdat, &mapdat, &archdat, NULL);
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//SCOTCH_graphMapCompute(&grafdat, &mapdat, &stradat); /* Perform mapping */
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finalDecomp.setSize(xadj.size()-1);
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check
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(
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SCOTCH_graphPart
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(
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&grafdat,
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nProcessors_, // partnbr
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&stradat, // const SCOTCH_Strat *
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finalDecomp.begin() // parttab
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),
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"SCOTCH_graphPart"
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);
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// Release storage for graph
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SCOTCH_graphExit(&grafdat);
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SCOTCH_stratExit(&stradat);
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//// Release storage for network topology
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//SCOTCH_archExit(&archdat);
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return 0;
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}
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// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
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Foam::scotchDecomp::scotchDecomp
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(
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const dictionary& decompositionDict,
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const polyMesh& mesh
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)
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:
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decompositionMethod(decompositionDict),
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mesh_(mesh)
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{}
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// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
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Foam::labelList Foam::scotchDecomp::decompose(const pointField& points)
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{
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if (points.size() != mesh_.nCells())
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{
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FatalErrorIn("scotchDecomp::decompose(const pointField&)")
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<< "Can use this decomposition method only for the whole mesh"
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<< endl
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<< "and supply one coordinate (cellCentre) for every cell." << endl
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<< "The number of coordinates " << points.size() << endl
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<< "The number of cells in the mesh " << mesh_.nCells()
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<< exit(FatalError);
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}
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// Make Metis CSR (Compressed Storage Format) storage
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// adjncy : contains neighbours (= edges in graph)
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// xadj(celli) : start of information in adjncy for celli
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List<int> xadj(mesh_.nCells()+1);
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// Initialise the number of internal faces of the cells to twice the
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// number of internal faces
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label nInternalFaces = 2*mesh_.nInternalFaces();
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// Check the boundary for coupled patches and add to the number of
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// internal faces
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const polyBoundaryMesh& pbm = mesh_.boundaryMesh();
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forAll(pbm, patchi)
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{
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if (isA<cyclicPolyPatch>(pbm[patchi]))
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{
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nInternalFaces += pbm[patchi].size();
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}
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}
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// Create the adjncy array the size of the total number of internal and
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// coupled faces
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List<int> adjncy(nInternalFaces);
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// Fill in xadj
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// ~~~~~~~~~~~~
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label freeAdj = 0;
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for (label cellI = 0; cellI < mesh_.nCells(); cellI++)
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{
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xadj[cellI] = freeAdj;
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const labelList& cFaces = mesh_.cells()[cellI];
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forAll(cFaces, i)
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{
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label faceI = cFaces[i];
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if
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(
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mesh_.isInternalFace(faceI)
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|| isA<cyclicPolyPatch>(pbm[pbm.whichPatch(faceI)])
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)
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{
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freeAdj++;
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}
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}
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}
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xadj[mesh_.nCells()] = freeAdj;
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// Fill in adjncy
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// ~~~~~~~~~~~~~~
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labelList nFacesPerCell(mesh_.nCells(), 0);
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// Internal faces
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for (label faceI = 0; faceI < mesh_.nInternalFaces(); faceI++)
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{
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label own = mesh_.faceOwner()[faceI];
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label nei = mesh_.faceNeighbour()[faceI];
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adjncy[xadj[own] + nFacesPerCell[own]++] = nei;
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adjncy[xadj[nei] + nFacesPerCell[nei]++] = own;
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}
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// Coupled faces. Only cyclics done.
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forAll(pbm, patchi)
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{
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if (isA<cyclicPolyPatch>(pbm[patchi]))
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{
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const unallocLabelList& faceCells = pbm[patchi].faceCells();
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label sizeby2 = faceCells.size()/2;
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for (label facei=0; facei<sizeby2; facei++)
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{
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label own = faceCells[facei];
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label nei = faceCells[facei + sizeby2];
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adjncy[xadj[own] + nFacesPerCell[own]++] = nei;
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adjncy[xadj[nei] + nFacesPerCell[nei]++] = own;
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}
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}
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}
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// Decompose using default weights
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List<int> finalDecomp;
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decompose(adjncy, xadj, finalDecomp);
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// Copy back to labelList
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labelList decomp(finalDecomp.size());
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forAll(decomp, i)
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{
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decomp[i] = finalDecomp[i];
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}
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return decomp;
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}
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// From cell-cell connections to Metis format (like CompactListList)
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void Foam::scotchDecomp::calcMetisCSR
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(
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const labelListList& cellCells,
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List<int>& adjncy,
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List<int>& xadj
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)
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{
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// Count number of internal faces
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label nConnections = 0;
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forAll(cellCells, coarseI)
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{
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nConnections += cellCells[coarseI].size();
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}
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// Create the adjncy array as twice the size of the total number of
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// internal faces
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adjncy.setSize(nConnections);
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xadj.setSize(cellCells.size()+1);
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// Fill in xadj
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// ~~~~~~~~~~~~
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label freeAdj = 0;
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forAll(cellCells, coarseI)
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{
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xadj[coarseI] = freeAdj;
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const labelList& cCells = cellCells[coarseI];
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forAll(cCells, i)
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{
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adjncy[freeAdj++] = cCells[i];
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}
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}
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xadj[cellCells.size()] = freeAdj;
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}
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|
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Foam::labelList Foam::scotchDecomp::decompose
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(
|
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const labelList& agglom,
|
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const pointField& agglomPoints
|
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)
|
||||
{
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if (agglom.size() != mesh_.nCells())
|
||||
{
|
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FatalErrorIn
|
||||
(
|
||||
"parMetisDecomp::decompose(const labelList&, const pointField&)"
|
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) << "Size of cell-to-coarse map " << agglom.size()
|
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<< " differs from number of cells in mesh " << mesh_.nCells()
|
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<< exit(FatalError);
|
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}
|
||||
|
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// Make Metis CSR (Compressed Storage Format) storage
|
||||
// adjncy : contains neighbours (= edges in graph)
|
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// xadj(celli) : start of information in adjncy for celli
|
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List<int> adjncy;
|
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List<int> xadj;
|
||||
{
|
||||
// Get cellCells on coarse mesh.
|
||||
labelListList cellCells;
|
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calcCellCells
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(
|
||||
mesh_,
|
||||
agglom,
|
||||
agglomPoints.size(),
|
||||
cellCells
|
||||
);
|
||||
|
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calcMetisCSR(cellCells, adjncy, xadj);
|
||||
}
|
||||
|
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// Decompose using default weights
|
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List<int> finalDecomp;
|
||||
decompose(adjncy, xadj, finalDecomp);
|
||||
|
||||
|
||||
// Rework back into decomposition for original mesh_
|
||||
labelList fineDistribution(agglom.size());
|
||||
|
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forAll(fineDistribution, i)
|
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{
|
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fineDistribution[i] = finalDecomp[agglom[i]];
|
||||
}
|
||||
|
||||
return fineDistribution;
|
||||
}
|
||||
|
||||
|
||||
Foam::labelList Foam::scotchDecomp::decompose
|
||||
(
|
||||
const labelListList& globalCellCells,
|
||||
const pointField& cellCentres
|
||||
)
|
||||
{
|
||||
if (cellCentres.size() != globalCellCells.size())
|
||||
{
|
||||
FatalErrorIn
|
||||
(
|
||||
"scotchDecomp::decompose(const pointField&, const labelListList&)"
|
||||
) << "Inconsistent number of cells (" << globalCellCells.size()
|
||||
<< ") and number of cell centres (" << cellCentres.size()
|
||||
<< ")." << exit(FatalError);
|
||||
}
|
||||
|
||||
|
||||
// Make Metis CSR (Compressed Storage Format) storage
|
||||
// adjncy : contains neighbours (= edges in graph)
|
||||
// xadj(celli) : start of information in adjncy for celli
|
||||
|
||||
List<int> adjncy;
|
||||
List<int> xadj;
|
||||
calcMetisCSR(globalCellCells, adjncy, xadj);
|
||||
|
||||
|
||||
// Decompose using default weights
|
||||
List<int> finalDecomp;
|
||||
decompose(adjncy, xadj, finalDecomp);
|
||||
|
||||
// Copy back to labelList
|
||||
labelList decomp(finalDecomp.size());
|
||||
forAll(decomp, i)
|
||||
{
|
||||
decomp[i] = finalDecomp[i];
|
||||
}
|
||||
return decomp;
|
||||
}
|
||||
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -0,0 +1,150 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
|
||||
\\/ M anipulation |
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
This file is part of OpenFOAM.
|
||||
|
||||
OpenFOAM is free software; you can redistribute it and/or modify it
|
||||
under the terms of the GNU General Public License as published by the
|
||||
Free Software Foundation; either version 2 of the License, or (at your
|
||||
option) any later version.
|
||||
|
||||
OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
|
||||
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
|
||||
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
|
||||
for more details.
|
||||
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with OpenFOAM; if not, write to the Free Software Foundation,
|
||||
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
|
||||
|
||||
Class
|
||||
Foam::scotchDecomp
|
||||
|
||||
Description
|
||||
Scotch domain decomposition
|
||||
|
||||
SourceFiles
|
||||
scotchDecomp.C
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
#ifndef scotchDecomp_H
|
||||
#define scotchDecomp_H
|
||||
|
||||
#include "decompositionMethod.H"
|
||||
|
||||
namespace Foam
|
||||
{
|
||||
|
||||
/*---------------------------------------------------------------------------*\
|
||||
Class scotchDecomp Declaration
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
class scotchDecomp
|
||||
:
|
||||
public decompositionMethod
|
||||
{
|
||||
// Private data
|
||||
|
||||
const polyMesh& mesh_;
|
||||
|
||||
|
||||
// Private Member Functions
|
||||
|
||||
//- Check and print error message
|
||||
static void check(const int, const char*);
|
||||
|
||||
label decompose
|
||||
(
|
||||
const List<int>& adjncy,
|
||||
const List<int>& xadj,
|
||||
List<int>& finalDecomp
|
||||
);
|
||||
|
||||
//- Disallow default bitwise copy construct and assignment
|
||||
void operator=(const scotchDecomp&);
|
||||
scotchDecomp(const scotchDecomp&);
|
||||
|
||||
|
||||
public:
|
||||
|
||||
//- Runtime type information
|
||||
TypeName("scotch");
|
||||
|
||||
|
||||
// Constructors
|
||||
|
||||
//- Construct given the decomposition dictionary and mesh
|
||||
scotchDecomp
|
||||
(
|
||||
const dictionary& decompositionDict,
|
||||
const polyMesh& mesh
|
||||
);
|
||||
|
||||
|
||||
// Destructor
|
||||
|
||||
virtual ~scotchDecomp()
|
||||
{}
|
||||
|
||||
|
||||
// Member Functions
|
||||
|
||||
virtual bool parallelAware() const
|
||||
{
|
||||
// Metis does not know about proc boundaries
|
||||
return false;
|
||||
}
|
||||
|
||||
//- Return for every coordinate the wanted processor number. Use the
|
||||
// mesh connectivity (if needed)
|
||||
virtual labelList decompose(const pointField&);
|
||||
|
||||
//- Return for every coordinate the wanted processor number. Gets
|
||||
// passed agglomeration map (from fine to coarse cells) and coarse cell
|
||||
// location. Can be overridden by decomposers that provide this
|
||||
// functionality natively.
|
||||
virtual labelList decompose
|
||||
(
|
||||
const labelList& agglom,
|
||||
const pointField&
|
||||
);
|
||||
|
||||
//- Return for every coordinate the wanted processor number. Explicitly
|
||||
// provided mesh connectivity.
|
||||
// The connectivity is equal to mesh.cellCells() except for
|
||||
// - in parallel the cell numbers are global cell numbers (starting
|
||||
// from 0 at processor0 and then incrementing all through the
|
||||
// processors)
|
||||
// - the connections are across coupled patches
|
||||
virtual labelList decompose
|
||||
(
|
||||
const labelListList& globalCellCells,
|
||||
const pointField& cc
|
||||
);
|
||||
|
||||
//- Helper to convert cellcells into compact row storage
|
||||
static void calcMetisCSR
|
||||
(
|
||||
const labelListList& globalCellCells,
|
||||
List<int>& adjncy,
|
||||
List<int>& xadj
|
||||
);
|
||||
|
||||
};
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
} // End namespace Foam
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
#endif
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -1,8 +1,8 @@
|
||||
.SUFFIXES: .y .Y
|
||||
|
||||
ytoo = bison -v $(YYPREFIX) -d $$SOURCE ; mv $$SOURCE_DIR/*.tab.c $*.c ; mv $$SOURCE_DIR/*.tab.h $*.h ; $(cc) $(cFLAGS) -c $*.c -o $@
|
||||
ytoo = bison -v -d -y $$SOURCE ; mv y.tab.c $*.c ; mv y.tab.h $*.h ; $(cc) $(cFLAGS) -c $*.c -o $@
|
||||
|
||||
Ytoo = bison -v $(YYPREFIX) -d $$SOURCE ; mv $$SOURCE_DIR/*.tab.c $*.C ; mv $$SOURCE_DIR/*.tab.h $*.H ; $(CC) $(c++FLAGS) -c $*.C -o $@
|
||||
Ytoo = bison -v -d -y $$SOURCE ; mv y.tab.c $*.C ; mv y.tab.h $*.H ; $(CC) $(c++FLAGS) -c $*.C -o $@
|
||||
|
||||
.y.dep:
|
||||
$(MAKE_DEP)
|
||||
|
||||
@ -5,6 +5,7 @@ include $(GENERAL_RULES)/sourceToDep
|
||||
include $(GENERAL_RULES)/java
|
||||
include $(GENERAL_RULES)/flex
|
||||
include $(GENERAL_RULES)/flex++
|
||||
include $(GENERAL_RULES)/byacc
|
||||
include $(GENERAL_RULES)/btyacc++
|
||||
#include $(GENERAL_RULES)/byacc
|
||||
#include $(GENERAL_RULES)/btyacc++
|
||||
include $(GENERAL_RULES)/bison
|
||||
include $(GENERAL_RULES)/moc
|
||||
|
||||
Reference in New Issue
Block a user