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ENH: support KaHIP decomposition
- refactor some common metis-like elements into the metisLikeDecomp abstract class.
This commit is contained in:
Mark Olesen
3
applications/test/checkDecomposePar/Make/files
Normal file
3
applications/test/checkDecomposePar/Make/files
Normal file
@ -0,0 +1,3 @@
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Test-checkDecomposePar.C
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EXE = $(FOAM_APPBIN)/Test-checkDecomposePar
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10
applications/test/checkDecomposePar/Make/options
Normal file
10
applications/test/checkDecomposePar/Make/options
Normal file
@ -0,0 +1,10 @@
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EXE_INC = \
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-I$(LIB_SRC)/parallel/decompose/decompose/lnInclude \
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-I$(LIB_SRC)/parallel/decompose/decompositionMethods/lnInclude \
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-I$(LIB_SRC)/finiteVolume/lnInclude \
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-I$(LIB_SRC)/meshTools/lnInclude \
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-I$(LIB_SRC)/regionModels/regionModel/lnInclude
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EXE_LIBS = \
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-ldecompositionMethods \
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-lregionModels
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193
applications/test/checkDecomposePar/Test-checkDecomposePar.C
Normal file
193
applications/test/checkDecomposePar/Test-checkDecomposePar.C
Normal file
@ -0,0 +1,193 @@
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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) 2017 OpenCFD Ltd.
|
||||
\\/ M anipulation |
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-------------------------------------------------------------------------------
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License
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||||
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 3 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, see <http://www.gnu.org/licenses/>.
|
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Application
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checkDecomposePar
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Group
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grpParallelUtilities
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Description
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Check decomposition from kaffpa (KaHIP) output.
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foamToMetisGraph was likely used for producing the kaffpa input.
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\*---------------------------------------------------------------------------*/
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#include "OSspecific.H"
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#include "fvCFD.H"
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#include "cpuTime.H"
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#include "IFstream.H"
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#include "regionProperties.H"
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#include "decompositionInformation.H"
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#include "decompositionModel.H"
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// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
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int main(int argc, char *argv[])
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{
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argList::addNote
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(
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"Check decomposition from kaffpa (KaHIP) output"
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);
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argList::noParallel();
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argList::noBanner();
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#include "addRegionOption.H"
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argList::addBoolOption
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(
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"allRegions",
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"operate on all regions in regionProperties"
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);
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argList::addBoolOption
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(
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"verbose",
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"more information about decomposition"
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);
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argList::validArgs.append("kaffpa-output-file");
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// Include explicit constant options, have zero from time range
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timeSelector::addOptions(true, false);
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#include "setRootCase.H"
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const fileName decompFile = args[1];
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const bool region = args.optionFound("region");
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const bool allRegions = args.optionFound("allRegions");
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const bool verbose = args.optionFound("verbose");
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// Set time from database
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#include "createTime.H"
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// Allow override of time
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instantList times = timeSelector::selectIfPresent(runTime, args);
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// Allow override of decomposeParDict location
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fileName decompDictFile;
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args.optionReadIfPresent("decomposeParDict", decompDictFile);
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wordList regionNames;
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wordList regionDirs;
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if (allRegions)
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{
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Info<< "Decomposing all regions in regionProperties" << nl << endl;
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regionProperties rp(runTime);
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forAllConstIters(rp, iter)
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{
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const wordList& regions = iter();
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forAll(regions, i)
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{
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if (findIndex(regionNames, regions[i]) == -1)
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{
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regionNames.append(regions[i]);
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}
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}
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}
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regionDirs = regionNames;
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}
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else
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{
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word regionName;
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if (args.optionReadIfPresent("region", regionName))
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{
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regionNames = wordList(1, regionName);
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regionDirs = regionNames;
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}
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else
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{
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regionNames = wordList(1, fvMesh::defaultRegion);
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regionDirs = wordList(1, word::null);
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}
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}
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labelList cellToProc;
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forAll(regionNames, regioni)
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{
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const word& regionName = regionNames[regioni];
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const word& regionDir = regionDirs[regioni];
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Info<< "\n\nDecomposing mesh " << regionName << nl << endl;
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Info<< "Create mesh..." << flush;
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fvMesh mesh
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(
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IOobject
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(
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regionName,
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runTime.timeName(),
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runTime,
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IOobject::MUST_READ,
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IOobject::NO_WRITE,
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false
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)
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);
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Info<< " nCells = " << mesh.nCells() << endl;
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// Expected format is a simple ASCII list
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cellToProc.setSize(mesh.nCells());
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{
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IFstream is(decompFile);
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forAll(cellToProc, celli)
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{
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cellToProc[celli] = readLabel(is);
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}
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}
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const label nDomains = max(cellToProc) + 1;
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CompactListList<label> cellCells;
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decompositionMethod::calcCellCells
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(
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mesh,
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identity(mesh.nCells()),
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mesh.nCells(),
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false,
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cellCells
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);
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decompositionInformation info
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(
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cellCells,
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cellToProc,
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nDomains
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);
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if (verbose)
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{
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info.printDetails(Info);
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Info<< nl;
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}
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info.printSummary(Info);
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}
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Info<< "\nEnd\n" << endl;
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return 0;
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}
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// ************************************************************************* //
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3
applications/test/decomposePar/Make/files
Normal file
3
applications/test/decomposePar/Make/files
Normal file
@ -0,0 +1,3 @@
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Test-decomposePar.C
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EXE = $(FOAM_APPBIN)/Test-decomposePar
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12
applications/test/decomposePar/Make/options
Normal file
12
applications/test/decomposePar/Make/options
Normal file
@ -0,0 +1,12 @@
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EXE_INC = \
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-I$(LIB_SRC)/parallel/decompose/decompose/lnInclude \
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-I$(LIB_SRC)/parallel/decompose/decompositionMethods/lnInclude \
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-I$(LIB_SRC)/finiteVolume/lnInclude \
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-I$(LIB_SRC)/meshTools/lnInclude \
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-I$(LIB_SRC)/regionModels/regionModel/lnInclude
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EXE_LIBS = \
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-ldecompose \
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-ldecompositionMethods \
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-L$(FOAM_LIBBIN)/dummy -lmetisDecomp -lscotchDecomp -lkahipDecomp \
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-lregionModels
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278
applications/test/decomposePar/Test-decomposePar.C
Normal file
278
applications/test/decomposePar/Test-decomposePar.C
Normal file
@ -0,0 +1,278 @@
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/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2017 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 3 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, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
Application
|
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decomposePar
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Group
|
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grpParallelUtilities
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Description
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Automatically decomposes a mesh and fields of a case for parallel
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execution of OpenFOAM.
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Usage
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\b decomposePar [OPTION]
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Options:
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- \par -region \<regionName\>
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Decompose named region. Does not check for existence of processor*.
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- \par -allRegions
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Decompose all regions in regionProperties. Does not check for
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existence of processor*.
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- \par -constant
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- \par -time xxx:yyy
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Override controlDict settings and decompose selected times. Does not
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re-decompose the mesh i.e. does not handle moving mesh or changing
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mesh cases.
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\*---------------------------------------------------------------------------*/
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#include "OSspecific.H"
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#include "fvCFD.H"
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#include "cpuTime.H"
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#include "IOobjectList.H"
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#include "regionProperties.H"
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#include "decompositionInformation.H"
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#include "decompositionModel.H"
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// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
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int main(int argc, char *argv[])
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{
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argList::addNote
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(
|
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"decompose a mesh and fields of a case for parallel execution"
|
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);
|
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|
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argList::noParallel();
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argList::addOption
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(
|
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"decomposeParDict",
|
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"file",
|
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"read decomposePar dictionary from specified location"
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);
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#include "addRegionOption.H"
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argList::addBoolOption
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(
|
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"allRegions",
|
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"operate on all regions in regionProperties"
|
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);
|
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argList::addBoolOption
|
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(
|
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"verbose",
|
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"more information about decomposition"
|
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);
|
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argList::addOption
|
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(
|
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"domains",
|
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"N"
|
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"override numberOfSubdomains"
|
||||
);
|
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|
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argList::addOption
|
||||
(
|
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"method",
|
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"name"
|
||||
"override method"
|
||||
);
|
||||
|
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// Include explicit constant options, have zero from time range
|
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timeSelector::addOptions(true, false);
|
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|
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#include "setRootCase.H"
|
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|
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const bool region = args.optionFound("region");
|
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const bool allRegions = args.optionFound("allRegions");
|
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const bool verbose = args.optionFound("verbose");
|
||||
|
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const label numSubdomains =
|
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args.optionLookupOrDefault<label>("domains", 0);
|
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|
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const word methodName =
|
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args.optionLookupOrDefault<word>("method", word::null);
|
||||
|
||||
|
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// Set time from database
|
||||
#include "createTime.H"
|
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// Allow override of time
|
||||
instantList times = timeSelector::selectIfPresent(runTime, args);
|
||||
|
||||
// Allow override of decomposeParDict location
|
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fileName decompDictFile;
|
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args.optionReadIfPresent("decomposeParDict", decompDictFile);
|
||||
|
||||
wordList regionNames;
|
||||
wordList regionDirs;
|
||||
if (allRegions)
|
||||
{
|
||||
Info<< "Decomposing all regions in regionProperties" << nl << endl;
|
||||
regionProperties rp(runTime);
|
||||
forAllConstIters(rp, iter)
|
||||
{
|
||||
const wordList& regions = iter();
|
||||
forAll(regions, i)
|
||||
{
|
||||
if (findIndex(regionNames, regions[i]) == -1)
|
||||
{
|
||||
regionNames.append(regions[i]);
|
||||
}
|
||||
}
|
||||
}
|
||||
regionDirs = regionNames;
|
||||
}
|
||||
else
|
||||
{
|
||||
word regionName;
|
||||
if (args.optionReadIfPresent("region", regionName))
|
||||
{
|
||||
regionNames = wordList(1, regionName);
|
||||
regionDirs = regionNames;
|
||||
}
|
||||
else
|
||||
{
|
||||
regionNames = wordList(1, fvMesh::defaultRegion);
|
||||
regionDirs = wordList(1, word::null);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
forAll(regionNames, regioni)
|
||||
{
|
||||
const word& regionName = regionNames[regioni];
|
||||
const word& regionDir = regionDirs[regioni];
|
||||
|
||||
Info<< "\n\nDecomposing mesh " << regionName << nl << endl;
|
||||
Info<< "Create mesh..." << flush;
|
||||
|
||||
fvMesh mesh
|
||||
(
|
||||
IOobject
|
||||
(
|
||||
regionName,
|
||||
runTime.timeName(),
|
||||
runTime,
|
||||
IOobject::MUST_READ,
|
||||
IOobject::NO_WRITE,
|
||||
false
|
||||
)
|
||||
);
|
||||
|
||||
Info<< " nCells = " << mesh.nCells() << endl;
|
||||
|
||||
Info<< "\nCalculating distribution of cells" << endl;
|
||||
cpuTime decompositionTime;
|
||||
|
||||
const decompositionModel& model = decompositionModel::New
|
||||
(
|
||||
mesh,
|
||||
decompDictFile
|
||||
);
|
||||
|
||||
// Allow command-line override for quick testing
|
||||
|
||||
dictionary& modelDict = const_cast<decompositionModel&>(model);
|
||||
|
||||
if (numSubdomains)
|
||||
{
|
||||
modelDict.add
|
||||
(
|
||||
word("numberOfSubdomains"),
|
||||
numSubdomains,
|
||||
true
|
||||
);
|
||||
}
|
||||
|
||||
if (!methodName.empty())
|
||||
{
|
||||
modelDict.add
|
||||
(
|
||||
word("method"),
|
||||
methodName,
|
||||
true
|
||||
);
|
||||
}
|
||||
|
||||
scalarField cellWeights;
|
||||
word weightName;
|
||||
if (model.readIfPresent("weightField", weightName))
|
||||
{
|
||||
volScalarField weights
|
||||
(
|
||||
IOobject
|
||||
(
|
||||
weightName,
|
||||
mesh.time().timeName(),
|
||||
mesh,
|
||||
IOobject::MUST_READ,
|
||||
IOobject::NO_WRITE
|
||||
),
|
||||
mesh
|
||||
);
|
||||
cellWeights = weights.primitiveField();
|
||||
}
|
||||
|
||||
decompositionMethod& method = model.decomposer();
|
||||
|
||||
CompactListList<label> cellCells;
|
||||
decompositionMethod::calcCellCells
|
||||
(
|
||||
mesh,
|
||||
identity(mesh.nCells()),
|
||||
mesh.nCells(),
|
||||
false,
|
||||
cellCells
|
||||
);
|
||||
|
||||
labelList cellToProc = method.decompose(mesh, cellWeights);
|
||||
|
||||
Info<< "\nFinished decomposition into "
|
||||
<< method.nDomains() << " domains in "
|
||||
<< decompositionTime.elapsedCpuTime()
|
||||
<< " s" << nl << endl;
|
||||
|
||||
decompositionInformation info
|
||||
(
|
||||
cellCells,
|
||||
cellToProc,
|
||||
method.nDomains()
|
||||
);
|
||||
|
||||
if (verbose)
|
||||
{
|
||||
info.printDetails(Info);
|
||||
Info<< nl;
|
||||
}
|
||||
info.printSummary(Info);
|
||||
}
|
||||
|
||||
Info<< "\nEnd\n" << endl;
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
// ************************************************************************* //
|
||||
3
applications/test/foamToMetisGraph/Make/files
Normal file
3
applications/test/foamToMetisGraph/Make/files
Normal file
@ -0,0 +1,3 @@
|
||||
foamToMetisGraph.C
|
||||
|
||||
EXE = $(FOAM_USER_APPBIN)/foamToMetisGraph
|
||||
3
applications/test/foamToMetisGraph/Make/options
Normal file
3
applications/test/foamToMetisGraph/Make/options
Normal file
@ -0,0 +1,3 @@
|
||||
EXE_INC =
|
||||
|
||||
EXE_LIBS =
|
||||
86
applications/test/foamToMetisGraph/foamToMetisGraph.C
Normal file
86
applications/test/foamToMetisGraph/foamToMetisGraph.C
Normal file
@ -0,0 +1,86 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2017 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 3 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, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
Description
|
||||
Create a metis graph file representation of an OpenFOAM mesh
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
#include "argList.H"
|
||||
#include "Time.H"
|
||||
#include "polyMesh.H"
|
||||
#include "OFstream.H"
|
||||
|
||||
using namespace Foam;
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
// Main program:
|
||||
|
||||
int main(int argc, char *argv[])
|
||||
{
|
||||
argList::noParallel();
|
||||
argList::noFunctionObjects();
|
||||
argList::addNote
|
||||
(
|
||||
"Create a metis graph file representation for an OpenFOAM mesh"
|
||||
);
|
||||
|
||||
#include "setRootCase.H"
|
||||
#include "createTime.H"
|
||||
#include "createPolyMesh.H"
|
||||
|
||||
const labelListList& cellCells = mesh.cellCells();
|
||||
|
||||
// No. of Nodes = nCells
|
||||
// No. of Edges connecting Nodes = nInternalFaces
|
||||
|
||||
OFstream os(args.caseName() + ".graph", IOstream::ASCII);
|
||||
|
||||
os << "%% metis graph file, of an OpenFOAM mesh %%" << nl
|
||||
<< "%% nCells=" << mesh.nCells()
|
||||
<< " nFaces=" << mesh.nFaces()
|
||||
<< " nInternalFaces=" << mesh.nInternalFaces() << nl;
|
||||
|
||||
os << cellCells.size() << " " << mesh.nInternalFaces() << nl;
|
||||
|
||||
for (const auto& edges : cellCells)
|
||||
{
|
||||
forAll(edges, i)
|
||||
{
|
||||
if (i) os << " ";
|
||||
os << edges[i] + 1; // index starts at 1.
|
||||
}
|
||||
os << nl;
|
||||
}
|
||||
|
||||
Info<<"Wrote graph with "
|
||||
<< mesh.nCells() << " nodes and "
|
||||
<< mesh.nInternalFaces() << " edges to "
|
||||
<< os.name() << nl;
|
||||
|
||||
Info<< nl << "End\n" << endl;
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -18,4 +18,4 @@ EXE_LIBS = \
|
||||
-lreconstruct \
|
||||
$(LINK_FLAGS) \
|
||||
-ldecompositionMethods \
|
||||
-L$(FOAM_LIBBIN)/dummy -lmetisDecomp -lscotchDecomp
|
||||
-L$(FOAM_LIBBIN)/dummy -lmetisDecomp -lscotchDecomp -lkahipDecomp
|
||||
|
||||
@ -11,7 +11,8 @@ EXE_LIBS = \
|
||||
-ldynamicMesh \
|
||||
-ldecompose \
|
||||
-lgenericPatchFields \
|
||||
-ldecompositionMethods -L$(FOAM_LIBBIN)/dummy -lmetisDecomp -lscotchDecomp \
|
||||
-ldecompositionMethods \
|
||||
-L$(FOAM_LIBBIN)/dummy -lmetisDecomp -lscotchDecomp -lkahipDecomp \
|
||||
-llagrangian \
|
||||
-ldynamicMesh \
|
||||
-lregionModels
|
||||
|
||||
59
etc/config.sh/kahip
Normal file
59
etc/config.sh/kahip
Normal file
@ -0,0 +1,59 @@
|
||||
#----------------------------------*-sh-*--------------------------------------
|
||||
# ========= |
|
||||
# \\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
# \\ / O peration |
|
||||
# \\ / A nd | Copyright (C) 2017 OpenCFD Ltd.
|
||||
# \\/ M anipulation |
|
||||
#------------------------------------------------------------------------------
|
||||
# This file is part of OpenFOAM, licensed under the GNU General Public License
|
||||
# <http://www.gnu.org/licenses/>.
|
||||
#
|
||||
# File
|
||||
# etc/config.sh/kahip
|
||||
#
|
||||
# Description
|
||||
# Setup for kahip include/libraries.
|
||||
# Sourced during wmake process only.
|
||||
#
|
||||
# Normally used to specify the kahip version and location for a
|
||||
# ThirdParty installation.
|
||||
#
|
||||
# If using system-wide installations, use the following setting:
|
||||
#
|
||||
# KAHIP_VERSION=kahip-system
|
||||
#
|
||||
# If the system kahip is unusable (eg, too old) and you don't
|
||||
# have or want a ThirdParty installation:
|
||||
#
|
||||
# KAHIP_VERSION=kahip-none
|
||||
#
|
||||
# If using a central installation, but not located under ThirdParty:
|
||||
# - specify kahip-system
|
||||
# - provide full path for KAHIP_ARCH_PATH
|
||||
#
|
||||
# Note
|
||||
# A csh version is not needed, since the values here are only sourced
|
||||
# during the wmake process.
|
||||
#
|
||||
# KaHIP can also be entirely disabled, by either renaming this file or
|
||||
# by creating an empty one with the same name at a user or site location.
|
||||
#
|
||||
# KaHIP is 32-bit precision only.
|
||||
# An Int64 OpenFOAM version can use it, but the mesh size is limited
|
||||
# accordingly.
|
||||
#
|
||||
# If KaHIP was compiled with openmp, you may need to add in additional
|
||||
# compile or link flags in KAHIP_COMP_FLAGS KAHIP_LINK_FLAGS
|
||||
#
|
||||
#------------------------------------------------------------------------------
|
||||
# USER EDITABLE PART: Changes made here may be lost with the next upgrade
|
||||
|
||||
KAHIP_VERSION=kahip-2.00
|
||||
export KAHIP_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/$KAHIP_VERSION
|
||||
|
||||
# Adjust as required
|
||||
# export KAHIP_COMP_FLAGS="-fopenmp"
|
||||
# export KAHIP_LINK_FLAGS="-lgomp"
|
||||
|
||||
# END OF (NORMAL) USER EDITABLE PART
|
||||
#------------------------------------------------------------------------------
|
||||
@ -134,6 +134,7 @@ unset GPERFTOOLS_ARCH_PATH
|
||||
unset GMP_ARCH_PATH
|
||||
unset MPFR_ARCH_PATH
|
||||
unset MESA_ARCH_PATH
|
||||
unset KAHIP_ARCH_PATH
|
||||
unset METIS_ARCH_PATH
|
||||
unset SCOTCH_ARCH_PATH
|
||||
|
||||
|
||||
1
src/dummyThirdParty/Allwmake
vendored
1
src/dummyThirdParty/Allwmake
vendored
@ -7,6 +7,7 @@ cd ${0%/*} || exit 1 # Run from this directory
|
||||
wmake $targetType scotchDecomp
|
||||
wmake $targetType ptscotchDecomp
|
||||
wmake $targetType metisDecomp
|
||||
wmake $targetType kahipDecomp
|
||||
wmake $targetType MGridGen
|
||||
|
||||
#------------------------------------------------------------------------------
|
||||
|
||||
3
src/dummyThirdParty/kahipDecomp/Make/files
vendored
Normal file
3
src/dummyThirdParty/kahipDecomp/Make/files
vendored
Normal file
@ -0,0 +1,3 @@
|
||||
dummyKahipDecomp.C
|
||||
|
||||
LIB = $(FOAM_LIBBIN)/dummy/libkahipDecomp
|
||||
5
src/dummyThirdParty/kahipDecomp/Make/options
vendored
Normal file
5
src/dummyThirdParty/kahipDecomp/Make/options
vendored
Normal file
@ -0,0 +1,5 @@
|
||||
EXE_INC = \
|
||||
-I$(LIB_SRC)/parallel/decompose/decompositionMethods/lnInclude \
|
||||
-I$(LIB_SRC)/parallel/decompose/kahipDecomp/lnInclude
|
||||
|
||||
LIB_LIBS =
|
||||
83
src/dummyThirdParty/kahipDecomp/dummyKahipDecomp.C
vendored
Normal file
83
src/dummyThirdParty/kahipDecomp/dummyKahipDecomp.C
vendored
Normal file
@ -0,0 +1,83 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2017 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 3 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, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
#include "kahipDecomp.H"
|
||||
#include "addToRunTimeSelectionTable.H"
|
||||
#include "Time.H"
|
||||
|
||||
static const char* notImplementedMessage =
|
||||
"You are trying to use kahip but do not have the kahipDecomp library loaded."
|
||||
"\nThis message is from the dummy kahipDecomp stub library instead.\n"
|
||||
"\n"
|
||||
"Please install kahip and make sure that libkahip.so is in your "
|
||||
"LD_LIBRARY_PATH.\n"
|
||||
"The kahipDecomp library can then be built from "
|
||||
"src/parallel/decompose/kahipDecomp and dynamically loading or linking"
|
||||
" this library will add kahip as a decomposition method.\n";
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
namespace Foam
|
||||
{
|
||||
defineTypeNameAndDebug(kahipDecomp, 0);
|
||||
|
||||
addToRunTimeSelectionTable
|
||||
(
|
||||
decompositionMethod,
|
||||
kahipDecomp,
|
||||
dictionary
|
||||
);
|
||||
}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
|
||||
|
||||
Foam::label Foam::kahipDecomp::decomposeSerial
|
||||
(
|
||||
const UList<label>& adjncy,
|
||||
const UList<label>& xadj,
|
||||
const UList<scalar>& cellWeights,
|
||||
List<label>& decomp
|
||||
)
|
||||
{
|
||||
FatalErrorInFunction
|
||||
<< notImplementedMessage << exit(FatalError);
|
||||
|
||||
return -1;
|
||||
}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
|
||||
|
||||
Foam::kahipDecomp::kahipDecomp
|
||||
(
|
||||
const dictionary& decompositionDict
|
||||
)
|
||||
:
|
||||
metisLikeDecomp(decompositionDict)
|
||||
{}
|
||||
|
||||
|
||||
// ************************************************************************* //
|
||||
37
src/dummyThirdParty/kahipDecomp/kaHIP_interface.h
vendored
Normal file
37
src/dummyThirdParty/kahipDecomp/kaHIP_interface.h
vendored
Normal file
@ -0,0 +1,37 @@
|
||||
#ifndef KAHIP_H
|
||||
#define KAHIP_H
|
||||
|
||||
/* *** DUMMY VERSION of kaHIP_interface.h - this file should not be included if you have KaHIP
|
||||
* installed in the correct position in $WM_THIRD_PARTY_DIR - see
|
||||
* decompositionMethods/kahipDecomp/Make/options
|
||||
*/
|
||||
|
||||
#warning "Dummy kahip.h - included since it cannot find KaHIP installation."
|
||||
|
||||
#ifdef __cplusplus
|
||||
extern "C" {
|
||||
#endif
|
||||
|
||||
void kaffpa
|
||||
(
|
||||
// [inputs]
|
||||
int* n,
|
||||
int* vwgt,
|
||||
int* xadj,
|
||||
int* adjcwgt,
|
||||
int* adjncy,
|
||||
int* nparts,
|
||||
double* imbalance,
|
||||
bool suppress_output,
|
||||
int seed,
|
||||
int mode,
|
||||
// [outputs]
|
||||
int* edgecut,
|
||||
int* part
|
||||
);
|
||||
|
||||
#ifdef __cplusplus
|
||||
}
|
||||
#endif
|
||||
|
||||
#endif
|
||||
@ -35,8 +35,7 @@ static const char* notImplementedMessage =
|
||||
"LD_LIBRARY_PATH.\n"
|
||||
"The metisDecomp library can then be built from "
|
||||
"src/parallel/decompose/metisDecomp and dynamically loading or linking"
|
||||
" this library will add metis as a decomposition method.\n"
|
||||
"Please be aware that there are license restrictions on using Metis.";
|
||||
" this library will add metis as a decomposition method.\n";
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
@ -55,12 +54,12 @@ namespace Foam
|
||||
|
||||
// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
|
||||
|
||||
Foam::label Foam::metisDecomp::decompose
|
||||
Foam::label Foam::metisDecomp::decomposeSerial
|
||||
(
|
||||
const List<label>& adjncy,
|
||||
const List<label>& xadj,
|
||||
const scalarField& cellWeights,
|
||||
List<label>& finalDecomp
|
||||
const UList<label>& adjncy,
|
||||
const UList<label>& xadj,
|
||||
const UList<scalar>& cellWeights,
|
||||
List<label>& decomp
|
||||
)
|
||||
{
|
||||
FatalErrorInFunction
|
||||
@ -77,53 +76,8 @@ Foam::metisDecomp::metisDecomp
|
||||
const dictionary& decompositionDict
|
||||
)
|
||||
:
|
||||
decompositionMethod(decompositionDict)
|
||||
metisLikeDecomp(decompositionDict)
|
||||
{}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
|
||||
|
||||
Foam::labelList Foam::metisDecomp::decompose
|
||||
(
|
||||
const polyMesh& mesh,
|
||||
const pointField& points,
|
||||
const scalarField& pointWeights
|
||||
)
|
||||
{
|
||||
FatalErrorInFunction
|
||||
<< notImplementedMessage << exit(FatalError);
|
||||
|
||||
return labelList();
|
||||
}
|
||||
|
||||
|
||||
Foam::labelList Foam::metisDecomp::decompose
|
||||
(
|
||||
const polyMesh& mesh,
|
||||
const labelList& agglom,
|
||||
const pointField& agglomPoints,
|
||||
const scalarField& agglomWeights
|
||||
)
|
||||
{
|
||||
FatalErrorInFunction
|
||||
<< notImplementedMessage << exit(FatalError);
|
||||
|
||||
return labelList();
|
||||
}
|
||||
|
||||
|
||||
Foam::labelList Foam::metisDecomp::decompose
|
||||
(
|
||||
const labelListList& globalCellCells,
|
||||
const pointField& cellCentres,
|
||||
const scalarField& cellWeights
|
||||
)
|
||||
{
|
||||
FatalErrorInFunction
|
||||
<< notImplementedMessage << exit(FatalError);
|
||||
|
||||
return labelList();
|
||||
}
|
||||
|
||||
|
||||
// ************************************************************************* //
|
||||
|
||||
@ -54,17 +54,19 @@ namespace Foam
|
||||
|
||||
// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
|
||||
|
||||
void Foam::ptscotchDecomp::graphPath(const polyMesh& unused)
|
||||
{}
|
||||
|
||||
|
||||
void Foam::ptscotchDecomp::check(const int retVal, const char* str)
|
||||
{}
|
||||
|
||||
|
||||
Foam::label Foam::ptscotchDecomp::decompose
|
||||
(
|
||||
const fileName& meshPath,
|
||||
const List<label>& initxadj,
|
||||
const List<label>& initadjncy,
|
||||
const scalarField& initcWeights,
|
||||
|
||||
const UList<label>& initxadj,
|
||||
const UList<label>& initadjncy,
|
||||
const UList<scalar>& initcWeights,
|
||||
List<label>& finalDecomp
|
||||
) const
|
||||
{
|
||||
@ -77,12 +79,11 @@ Foam::label Foam::ptscotchDecomp::decompose
|
||||
|
||||
Foam::label Foam::ptscotchDecomp::decompose
|
||||
(
|
||||
const fileName& meshPath,
|
||||
const label adjncySize,
|
||||
const label adjncy[],
|
||||
const label xadjSize,
|
||||
const label xadj[],
|
||||
const scalarField& cWeights,
|
||||
const UList<scalar>& cWeights,
|
||||
List<label>& finalDecomp
|
||||
) const
|
||||
{
|
||||
|
||||
@ -53,18 +53,20 @@ namespace Foam
|
||||
|
||||
// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
|
||||
|
||||
void Foam::scotchDecomp::graphPath(const polyMesh& unused)
|
||||
{}
|
||||
|
||||
|
||||
void Foam::scotchDecomp::check(const int retVal, const char* str)
|
||||
{}
|
||||
|
||||
|
||||
Foam::label Foam::scotchDecomp::decompose
|
||||
Foam::label Foam::scotchDecomp::decomposeSerial
|
||||
(
|
||||
const fileName& meshPath,
|
||||
const List<label>& adjncy,
|
||||
const List<label>& xadj,
|
||||
const scalarField& cWeights,
|
||||
|
||||
List<label>& finalDecomp
|
||||
const UList<label>& adjncy,
|
||||
const UList<label>& xadj,
|
||||
const UList<scalar>& cWeights,
|
||||
List<label>& decomp
|
||||
)
|
||||
{
|
||||
FatalErrorInFunction
|
||||
@ -81,7 +83,7 @@ Foam::scotchDecomp::scotchDecomp
|
||||
const dictionary& decompositionDict
|
||||
)
|
||||
:
|
||||
decompositionMethod(decompositionDict)
|
||||
metisLikeDecomp(decompositionDict)
|
||||
{}
|
||||
|
||||
|
||||
|
||||
@ -17,8 +17,9 @@ wcleanMpiLib()
|
||||
}
|
||||
|
||||
|
||||
wclean scotchDecomp
|
||||
wclean metisDecomp
|
||||
wclean kahipDecomp
|
||||
wclean scotchDecomp
|
||||
wclean decompositionMethods
|
||||
wclean decompose
|
||||
wcleanMpiLib ptscotchDecomp
|
||||
|
||||
@ -25,6 +25,54 @@ findFirstFile()
|
||||
}
|
||||
|
||||
|
||||
# Test for kahip.
|
||||
# - return 0 and export KAHIP_ARCH_PATH on success
|
||||
hasKahip()
|
||||
{
|
||||
local warning="==> skip kahip"
|
||||
local header label settings
|
||||
|
||||
unset KAHIP_ARCH_PATH KAHIP_VERSION
|
||||
unset KAHIP_COMP_FLAGS KAHIP_LINK_FLAGS
|
||||
settings=$($WM_PROJECT_DIR/bin/foamEtcFile config.sh/kahip) || {
|
||||
echo "$warning (no config.sh/kahip settings)"
|
||||
return 1
|
||||
}
|
||||
|
||||
. $settings
|
||||
if [ -z "$KAHIP_ARCH_PATH" -o "${KAHIP_ARCH_PATH##*-}" = none ]
|
||||
then
|
||||
echo "$warning (not available)"
|
||||
return 1
|
||||
fi
|
||||
|
||||
# Header
|
||||
header=$(findFirstFile \
|
||||
$KAHIP_ARCH_PATH/include/kaHIP_interface.h \
|
||||
/usr/include/kaHIP_interface.h \
|
||||
) || {
|
||||
echo "$warning (no header)"
|
||||
return 2 # file not found
|
||||
}
|
||||
|
||||
# Library
|
||||
[ "${KAHIP_ARCH_PATH##*-}" = system ] || \
|
||||
findFirstFile \
|
||||
$KAHIP_ARCH_PATH/lib/libkahip.a \
|
||||
$KAHIP_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/libkahip.a \
|
||||
> /dev/null || {
|
||||
echo "$warning (missing library)"
|
||||
return 2
|
||||
}
|
||||
|
||||
# kahip itself is 32-bit int, but our interface itself handles some
|
||||
# 64-bit conversion (mesh size).
|
||||
|
||||
export KAHIP_ARCH_PATH
|
||||
echo "kahip (label=32) - $KAHIP_ARCH_PATH"
|
||||
}
|
||||
|
||||
|
||||
# Test for metis.
|
||||
# - return 0 and export METIS_ARCH_PATH on success
|
||||
hasMetis()
|
||||
@ -208,6 +256,11 @@ then
|
||||
wmake $targetType metisDecomp
|
||||
fi
|
||||
|
||||
if hasKahip
|
||||
then
|
||||
wmake $targetType kahipDecomp
|
||||
fi
|
||||
|
||||
wmake $targetType decompositionMethods
|
||||
wmake $targetType decompose
|
||||
|
||||
|
||||
@ -1,3 +1,4 @@
|
||||
decompositionInformation.C
|
||||
decompositionModel.C
|
||||
fvFieldDecomposer.C
|
||||
|
||||
|
||||
236
src/parallel/decompose/decompose/decompositionInformation.C
Normal file
236
src/parallel/decompose/decompose/decompositionInformation.C
Normal file
@ -0,0 +1,236 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2017 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 3 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, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
#include "decompositionInformation.H"
|
||||
#include "ListOps.H"
|
||||
|
||||
// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
|
||||
|
||||
void Foam::decompositionInformation::populate
|
||||
(
|
||||
const labelUList& adjncy,
|
||||
const labelUList& xadj,
|
||||
const labelUList& decomp,
|
||||
const label nDomain
|
||||
)
|
||||
{
|
||||
nDomains_ = nDomain;
|
||||
|
||||
distrib_.clear();
|
||||
distrib_.setSize(nDomain);
|
||||
|
||||
for (labelList& subdist : distrib_)
|
||||
{
|
||||
subdist.clear();
|
||||
subdist.setSize(nDomain, Zero);
|
||||
}
|
||||
|
||||
const label nCells = xadj.size()-1;
|
||||
for (label celli = 0; celli < nCells; ++celli)
|
||||
{
|
||||
const label ownProc = decomp[celli];
|
||||
|
||||
labelList& subdist = distrib_[ownProc];
|
||||
|
||||
// Number of cells
|
||||
++subdist[ownProc];
|
||||
|
||||
for (label i = xadj[celli]; i < xadj[celli+1]; ++i)
|
||||
{
|
||||
const label neiProc = decomp[adjncy[i]];
|
||||
|
||||
if (neiProc != ownProc)
|
||||
{
|
||||
// Number of processor faces
|
||||
++subdist[neiProc];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// Build summary
|
||||
|
||||
labelList cellsCount(nDomains_, Zero);
|
||||
labelList neighCount(nDomains_, Zero);
|
||||
labelList facesCount(nDomains_, Zero);
|
||||
|
||||
forAll(distrib_, ownProc)
|
||||
{
|
||||
const labelList& subdist = distrib_[ownProc];
|
||||
|
||||
cellsCount[ownProc] = subdist[ownProc];
|
||||
|
||||
forAll(subdist, neiProc)
|
||||
{
|
||||
const label n = subdist[neiProc];
|
||||
|
||||
if (n && ownProc != neiProc)
|
||||
{
|
||||
++neighCount[ownProc];
|
||||
facesCount[ownProc] += n;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
const label n2 = (nDomains_ / 2);
|
||||
|
||||
sort(cellsCount);
|
||||
cellsInfo_.min = cellsCount.first();
|
||||
cellsInfo_.max = cellsCount.last();
|
||||
cellsInfo_.median = cellsCount[n2];
|
||||
|
||||
sort(neighCount);
|
||||
neighInfo_.min = neighCount.first();
|
||||
neighInfo_.max = neighCount.last();
|
||||
neighInfo_.median = neighCount[n2];
|
||||
|
||||
sort(facesCount);
|
||||
facesInfo_.min = facesCount.first();
|
||||
facesInfo_.max = facesCount.last();
|
||||
facesInfo_.median = facesCount[n2];
|
||||
}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
|
||||
|
||||
Foam::decompositionInformation::decompositionInformation
|
||||
(
|
||||
const labelUList& adjncy,
|
||||
const labelUList& xadj,
|
||||
const labelUList& decomp,
|
||||
const label nDomains
|
||||
)
|
||||
:
|
||||
distrib_(),
|
||||
nDomains_(0)
|
||||
{
|
||||
populate(adjncy, xadj, decomp, nDomains);
|
||||
}
|
||||
|
||||
|
||||
Foam::decompositionInformation::decompositionInformation
|
||||
(
|
||||
const CompactListList<label>& cellCells,
|
||||
const labelUList& decomp,
|
||||
const label nDomains
|
||||
)
|
||||
:
|
||||
distrib_(),
|
||||
nDomains_(0)
|
||||
{
|
||||
populate(cellCells.m(), cellCells.offsets(), decomp, nDomains);
|
||||
}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
|
||||
|
||||
void Foam::decompositionInformation::clear()
|
||||
{
|
||||
distrib_.clear();
|
||||
cellsInfo_.clear();
|
||||
neighInfo_.clear();
|
||||
facesInfo_.clear();
|
||||
}
|
||||
|
||||
|
||||
void Foam::decompositionInformation::printSummary(Ostream& os) const
|
||||
{
|
||||
os << "Cells "; cellsInfo_.print(os) << nl;
|
||||
os << "Neigh "; neighInfo_.print(os)<< nl;
|
||||
os << "Faces "; facesInfo_.print(os)<< nl;
|
||||
}
|
||||
|
||||
|
||||
void Foam::decompositionInformation::printDetails(Ostream& os) const
|
||||
{
|
||||
forAll(distrib_, ownProc)
|
||||
{
|
||||
const labelList& subdist = distrib_[ownProc];
|
||||
|
||||
// First pass:
|
||||
label neighCount = 0;
|
||||
label facesCount = 0;
|
||||
|
||||
forAll(subdist, neiProc)
|
||||
{
|
||||
const label n = subdist[neiProc];
|
||||
|
||||
if (n && ownProc != neiProc)
|
||||
{
|
||||
++neighCount;
|
||||
facesCount += n;
|
||||
}
|
||||
}
|
||||
|
||||
os << "Part[" << ownProc << "] cells:" << subdist[ownProc]
|
||||
<< " neigh:" << neighCount
|
||||
<< " faces:" << facesCount;
|
||||
|
||||
// Second pass with details:
|
||||
if (facesCount)
|
||||
{
|
||||
Info<< " ";
|
||||
|
||||
forAll(subdist, neiProc)
|
||||
{
|
||||
const label n = subdist[neiProc];
|
||||
|
||||
if (n && ownProc != neiProc)
|
||||
{
|
||||
os << " (" << neiProc << " " << n << ")";
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
os << nl;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
void Foam::decompositionInformation::printAll(Ostream& os) const
|
||||
{
|
||||
printDetails(os);
|
||||
printSummary(os);
|
||||
}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * Ostream Operator * * * * * * * * * * * * * //
|
||||
|
||||
|
||||
Foam::Ostream& Foam::decompositionInformation::stats::print(Ostream& os) const
|
||||
{
|
||||
os << "max/median/min: "
|
||||
<< this->max << " / " << this->median << " / " << this->min;
|
||||
|
||||
if (this->median)
|
||||
{
|
||||
const scalar ratio = scalar(100*this->max)/this->median;
|
||||
|
||||
os << " (" << ratio << "%)";
|
||||
}
|
||||
|
||||
return os;
|
||||
}
|
||||
|
||||
// ************************************************************************* //
|
||||
149
src/parallel/decompose/decompose/decompositionInformation.H
Normal file
149
src/parallel/decompose/decompose/decompositionInformation.H
Normal file
@ -0,0 +1,149 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2017 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 3 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, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
Class
|
||||
Foam::decompositionInformation
|
||||
|
||||
Description
|
||||
Abstract base class for decomposition
|
||||
|
||||
SourceFiles
|
||||
decompositionInformation.C
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
#ifndef decompositionInformation_H
|
||||
#define decompositionInformation_H
|
||||
|
||||
#include "polyMesh.H"
|
||||
#include "CompactListList.H"
|
||||
#include "IOstreams.H"
|
||||
|
||||
namespace Foam
|
||||
{
|
||||
|
||||
/*---------------------------------------------------------------------------*\
|
||||
Class decompositionInformation Declaration
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
class decompositionInformation
|
||||
{
|
||||
//- Simple storage for organizing min/max/median quantities
|
||||
struct stats
|
||||
{
|
||||
label min;
|
||||
label max;
|
||||
label median;
|
||||
|
||||
stats() : min(0), max(0), median(0) {}
|
||||
|
||||
void clear()
|
||||
{
|
||||
min = 0;
|
||||
max = 0;
|
||||
median = 0;
|
||||
}
|
||||
|
||||
Ostream& print(Ostream& os) const;
|
||||
};
|
||||
|
||||
// Private data
|
||||
|
||||
labelListList distrib_;
|
||||
label nDomains_;
|
||||
|
||||
stats cellsInfo_;
|
||||
stats neighInfo_;
|
||||
stats facesInfo_;
|
||||
|
||||
|
||||
// Private Member Functions
|
||||
|
||||
//- Populate from cell decomposition list
|
||||
void populate
|
||||
(
|
||||
const labelUList& adjncy,
|
||||
const labelUList& xadj,
|
||||
const labelUList& decomp,
|
||||
const label nDomains
|
||||
);
|
||||
|
||||
//- Disallow default bitwise copy construct and assignment
|
||||
decompositionInformation(const decompositionInformation&) = delete;
|
||||
void operator=(const decompositionInformation&) = delete;
|
||||
|
||||
|
||||
public:
|
||||
|
||||
// Constructors
|
||||
|
||||
//- Construct
|
||||
decompositionInformation
|
||||
(
|
||||
const labelUList& adjncy,
|
||||
const labelUList& xadj,
|
||||
const labelUList& decomp,
|
||||
const label nDomains
|
||||
);
|
||||
|
||||
//- Construct
|
||||
decompositionInformation
|
||||
(
|
||||
const CompactListList<label>& cellCells,
|
||||
const labelUList& decomp,
|
||||
const label nDomains
|
||||
);
|
||||
|
||||
|
||||
//- Destructor
|
||||
~decompositionInformation()
|
||||
{}
|
||||
|
||||
|
||||
// Member Functions
|
||||
|
||||
void clear();
|
||||
|
||||
label nDomains() const
|
||||
{
|
||||
return nDomains_;
|
||||
}
|
||||
|
||||
|
||||
void printSummary(Ostream& os) const;
|
||||
|
||||
void printDetails(Ostream& os) const;
|
||||
|
||||
void printAll(Ostream& os) const;
|
||||
};
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
} // End namespace Foam
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
#endif
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -4,6 +4,7 @@ simpleGeomDecomp/simpleGeomDecomp.C
|
||||
hierarchGeomDecomp/hierarchGeomDecomp.C
|
||||
manualDecomp/manualDecomp.C
|
||||
multiLevelDecomp/multiLevelDecomp.C
|
||||
metisLikeDecomp/metisLikeDecomp.C
|
||||
structuredDecomp/structuredDecomp.C
|
||||
noDecomp/noDecomp.C
|
||||
|
||||
|
||||
@ -21,9 +21,6 @@ License
|
||||
You should have received a copy of the GNU General Public License
|
||||
along with OpenFOAM. If not, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
InClass
|
||||
decompositionMethod
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
#include "decompositionMethod.H"
|
||||
@ -49,6 +46,7 @@ namespace Foam
|
||||
defineRunTimeSelectionTable(decompositionMethod, dictionary);
|
||||
}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
|
||||
|
||||
Foam::decompositionMethod::decompositionMethod
|
||||
@ -349,8 +347,8 @@ void Foam::decompositionMethod::calcCellCells
|
||||
|
||||
for (label facei = 0; facei < mesh.nInternalFaces(); facei++)
|
||||
{
|
||||
label own = agglom[faceOwner[facei]];
|
||||
label nei = agglom[faceNeighbour[facei]];
|
||||
const label own = agglom[faceOwner[facei]];
|
||||
const label nei = agglom[faceNeighbour[facei]];
|
||||
|
||||
nFacesPerCell[own]++;
|
||||
nFacesPerCell[nei]++;
|
||||
@ -367,7 +365,7 @@ void Foam::decompositionMethod::calcCellCells
|
||||
|
||||
forAll(pp, i)
|
||||
{
|
||||
label own = agglom[faceOwner[facei]];
|
||||
const label own = agglom[faceOwner[facei]];
|
||||
|
||||
label globalNei = globalNeighbour[bFacei];
|
||||
if
|
||||
@ -399,8 +397,8 @@ void Foam::decompositionMethod::calcCellCells
|
||||
// For internal faces is just offsetted owner and neighbour
|
||||
for (label facei = 0; facei < mesh.nInternalFaces(); facei++)
|
||||
{
|
||||
label own = agglom[faceOwner[facei]];
|
||||
label nei = agglom[faceNeighbour[facei]];
|
||||
const label own = agglom[faceOwner[facei]];
|
||||
const label nei = agglom[faceNeighbour[facei]];
|
||||
|
||||
m[offsets[own] + nFacesPerCell[own]++] = globalAgglom.toGlobal(nei);
|
||||
m[offsets[nei] + nFacesPerCell[nei]++] = globalAgglom.toGlobal(own);
|
||||
@ -418,9 +416,9 @@ void Foam::decompositionMethod::calcCellCells
|
||||
|
||||
forAll(pp, i)
|
||||
{
|
||||
label own = agglom[faceOwner[facei]];
|
||||
const label own = agglom[faceOwner[facei]];
|
||||
|
||||
label globalNei = globalNeighbour[bFacei];
|
||||
const label globalNei = globalNeighbour[bFacei];
|
||||
|
||||
if
|
||||
(
|
||||
@ -457,7 +455,7 @@ void Foam::decompositionMethod::calcCellCells
|
||||
nbrCells.clear();
|
||||
nbrCells.insert(globalAgglom.toGlobal(celli));
|
||||
|
||||
label endIndex = cellCells.offsets()[celli+1];
|
||||
const label endIndex = cellCells.offsets()[celli+1];
|
||||
|
||||
for (label i = startIndex; i < endIndex; i++)
|
||||
{
|
||||
@ -555,8 +553,8 @@ void Foam::decompositionMethod::calcCellCells
|
||||
|
||||
for (label faceI = 0; faceI < mesh.nInternalFaces(); faceI++)
|
||||
{
|
||||
label own = agglom[faceOwner[faceI]];
|
||||
label nei = agglom[faceNeighbour[faceI]];
|
||||
const label own = agglom[faceOwner[faceI]];
|
||||
const label nei = agglom[faceNeighbour[faceI]];
|
||||
|
||||
nFacesPerCell[own]++;
|
||||
nFacesPerCell[nei]++;
|
||||
@ -573,9 +571,9 @@ void Foam::decompositionMethod::calcCellCells
|
||||
|
||||
forAll(pp, i)
|
||||
{
|
||||
label own = agglom[faceOwner[faceI]];
|
||||
const label own = agglom[faceOwner[faceI]];
|
||||
|
||||
label globalNei = globalNeighbour[bFaceI];
|
||||
const label globalNei = globalNeighbour[bFaceI];
|
||||
if
|
||||
(
|
||||
!globalAgglom.isLocal(globalNei)
|
||||
@ -607,11 +605,11 @@ void Foam::decompositionMethod::calcCellCells
|
||||
// For internal faces is just offsetted owner and neighbour
|
||||
for (label faceI = 0; faceI < mesh.nInternalFaces(); faceI++)
|
||||
{
|
||||
label own = agglom[faceOwner[faceI]];
|
||||
label nei = agglom[faceNeighbour[faceI]];
|
||||
const label own = agglom[faceOwner[faceI]];
|
||||
const label nei = agglom[faceNeighbour[faceI]];
|
||||
|
||||
label ownIndex = offsets[own] + nFacesPerCell[own]++;
|
||||
label neiIndex = offsets[nei] + nFacesPerCell[nei]++;
|
||||
const label ownIndex = offsets[own] + nFacesPerCell[own]++;
|
||||
const label neiIndex = offsets[nei] + nFacesPerCell[nei]++;
|
||||
|
||||
m[ownIndex] = globalAgglom.toGlobal(nei);
|
||||
w[ownIndex] = mag(mesh.faceAreas()[faceI]);
|
||||
@ -631,9 +629,9 @@ void Foam::decompositionMethod::calcCellCells
|
||||
|
||||
forAll(pp, i)
|
||||
{
|
||||
label own = agglom[faceOwner[faceI]];
|
||||
const label own = agglom[faceOwner[faceI]];
|
||||
|
||||
label globalNei = globalNeighbour[bFaceI];
|
||||
const label globalNei = globalNeighbour[bFaceI];
|
||||
|
||||
if
|
||||
(
|
||||
@ -672,7 +670,7 @@ void Foam::decompositionMethod::calcCellCells
|
||||
nbrCells.clear();
|
||||
nbrCells.insert(globalAgglom.toGlobal(cellI));
|
||||
|
||||
label endIndex = cellCells.offsets()[cellI+1];
|
||||
const label endIndex = cellCells.offsets()[cellI+1];
|
||||
|
||||
for (label i = startIndex; i < endIndex; i++)
|
||||
{
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2011-2016 OpenFOAM Foundation
|
||||
\\/ M anipulation | Copyright (C) 2015 OpenCFD Ltd.
|
||||
\\/ M anipulation | Copyright (C) 2015-2017 OpenCFD Ltd.
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
This file is part of OpenFOAM.
|
||||
|
||||
@ -0,0 +1,264 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2017 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 3 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, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
#include "metisLikeDecomp.H"
|
||||
#include "Time.H"
|
||||
#include "globalIndex.H"
|
||||
|
||||
// * * * * * * * * * * * * Protected Member Functions * * * * * * * * * * * //
|
||||
|
||||
Foam::label Foam::metisLikeDecomp::decomposeGeneral
|
||||
(
|
||||
const UList<label>& adjncy,
|
||||
const UList<label>& xadj,
|
||||
const UList<scalar>& cWeights,
|
||||
List<label>& decomp
|
||||
)
|
||||
{
|
||||
if (!Pstream::parRun())
|
||||
{
|
||||
return decomposeSerial
|
||||
(
|
||||
adjncy,
|
||||
xadj,
|
||||
cWeights,
|
||||
decomp
|
||||
);
|
||||
}
|
||||
|
||||
if (debug)
|
||||
{
|
||||
Info<< type() << "Decomp : running in parallel."
|
||||
<< " Decomposing all of graph on master processor." << endl;
|
||||
}
|
||||
globalIndex globalCells(xadj.size()-1);
|
||||
label nTotalConnections = returnReduce(adjncy.size(), sumOp<label>());
|
||||
|
||||
// Send all to master. Use scheduled to save some storage.
|
||||
if (Pstream::master())
|
||||
{
|
||||
List<label> allAdjncy(nTotalConnections);
|
||||
List<label> allXadj(globalCells.size()+1);
|
||||
List<scalar> allWeights(globalCells.size());
|
||||
|
||||
// Insert my own
|
||||
label nTotalCells = 0;
|
||||
forAll(cWeights, celli)
|
||||
{
|
||||
allXadj[nTotalCells] = xadj[celli];
|
||||
allWeights[nTotalCells++] = cWeights[celli];
|
||||
}
|
||||
nTotalConnections = 0;
|
||||
forAll(adjncy, i)
|
||||
{
|
||||
allAdjncy[nTotalConnections++] = adjncy[i];
|
||||
}
|
||||
|
||||
for (int slave=1; slave<Pstream::nProcs(); ++slave)
|
||||
{
|
||||
IPstream fromSlave(Pstream::commsTypes::scheduled, slave);
|
||||
List<label> nbrAdjncy(fromSlave);
|
||||
List<label> nbrXadj(fromSlave);
|
||||
List<scalar> nbrWeights(fromSlave);
|
||||
|
||||
// Append.
|
||||
forAll(nbrXadj, celli)
|
||||
{
|
||||
allXadj[nTotalCells] = nTotalConnections+nbrXadj[celli];
|
||||
allWeights[nTotalCells++] = nbrWeights[celli];
|
||||
}
|
||||
// No need to renumber xadj since already global.
|
||||
forAll(nbrAdjncy, i)
|
||||
{
|
||||
allAdjncy[nTotalConnections++] = nbrAdjncy[i];
|
||||
}
|
||||
}
|
||||
allXadj[nTotalCells] = nTotalConnections;
|
||||
|
||||
labelList allDecomp;
|
||||
decomposeSerial
|
||||
(
|
||||
allAdjncy,
|
||||
allXadj,
|
||||
allWeights,
|
||||
allDecomp
|
||||
);
|
||||
|
||||
|
||||
// Send allFinalDecomp back
|
||||
for (int slave=1; slave<Pstream::nProcs(); ++slave)
|
||||
{
|
||||
OPstream toSlave(Pstream::commsTypes::scheduled, slave);
|
||||
toSlave << SubList<label>
|
||||
(
|
||||
allDecomp,
|
||||
globalCells.localSize(slave),
|
||||
globalCells.offset(slave)
|
||||
);
|
||||
}
|
||||
|
||||
// Get my own part (always first)
|
||||
decomp = SubList<label>(allDecomp, globalCells.localSize());
|
||||
}
|
||||
else
|
||||
{
|
||||
// Send my part of the graph (already in global numbering)
|
||||
{
|
||||
OPstream toMaster
|
||||
(
|
||||
Pstream::commsTypes::scheduled,
|
||||
Pstream::masterNo()
|
||||
);
|
||||
toMaster<< adjncy << SubList<label>(xadj, xadj.size()-1)
|
||||
<< cWeights;
|
||||
}
|
||||
|
||||
// Receive back decomposition
|
||||
IPstream fromMaster
|
||||
(
|
||||
Pstream::commsTypes::scheduled,
|
||||
Pstream::masterNo()
|
||||
);
|
||||
fromMaster >> decomp;
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
|
||||
|
||||
Foam::metisLikeDecomp::metisLikeDecomp(const dictionary& decompositionDict)
|
||||
:
|
||||
decompositionMethod(decompositionDict)
|
||||
{}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
|
||||
|
||||
Foam::labelList Foam::metisLikeDecomp::decompose
|
||||
(
|
||||
const polyMesh& mesh,
|
||||
const pointField& points,
|
||||
const scalarField& pointWeights
|
||||
)
|
||||
{
|
||||
if (points.size() != mesh.nCells())
|
||||
{
|
||||
FatalErrorInFunction
|
||||
<< "Can use this decomposition method only for entire mesh" << nl
|
||||
<< "and supply one coordinate (cellCentre) for every cell." << nl
|
||||
<< "The number of coordinates " << points.size() << nl
|
||||
<< "The number of cells in the mesh " << mesh.nCells()
|
||||
<< exit(FatalError);
|
||||
}
|
||||
|
||||
CompactListList<label> cellCells;
|
||||
calcCellCells
|
||||
(
|
||||
mesh,
|
||||
identity(mesh.nCells()),
|
||||
mesh.nCells(),
|
||||
false,
|
||||
cellCells
|
||||
);
|
||||
|
||||
// Decompose using default weights
|
||||
labelList decomp;
|
||||
decomposeGeneral(cellCells.m(), cellCells.offsets(), pointWeights, decomp);
|
||||
|
||||
return decomp;
|
||||
}
|
||||
|
||||
|
||||
Foam::labelList Foam::metisLikeDecomp::decompose
|
||||
(
|
||||
const polyMesh& mesh,
|
||||
const labelList& agglom,
|
||||
const pointField& agglomPoints,
|
||||
const scalarField& agglomWeights
|
||||
)
|
||||
{
|
||||
if (agglom.size() != mesh.nCells())
|
||||
{
|
||||
FatalErrorInFunction
|
||||
<< "Size of cell-to-coarse map " << agglom.size()
|
||||
<< " differs from number of cells in mesh " << mesh.nCells()
|
||||
<< exit(FatalError);
|
||||
}
|
||||
|
||||
// Make Metis CSR (Compressed Storage Format) storage
|
||||
// adjncy : contains neighbours (= edges in graph)
|
||||
// xadj(celli) : start of information in adjncy for celli
|
||||
|
||||
CompactListList<label> cellCells;
|
||||
calcCellCells(mesh, agglom, agglomPoints.size(), false, cellCells);
|
||||
|
||||
// Decompose using default weights
|
||||
labelList decomp;
|
||||
decomposeGeneral(cellCells.m(), cellCells.offsets(), agglomWeights, decomp);
|
||||
|
||||
|
||||
// Rework back into decomposition for original mesh
|
||||
labelList fineDistribution(agglom.size());
|
||||
|
||||
forAll(fineDistribution, i)
|
||||
{
|
||||
fineDistribution[i] = decomp[agglom[i]];
|
||||
}
|
||||
|
||||
return fineDistribution;
|
||||
}
|
||||
|
||||
|
||||
Foam::labelList Foam::metisLikeDecomp::decompose
|
||||
(
|
||||
const labelListList& globalCellCells,
|
||||
const pointField& cellCentres,
|
||||
const scalarField& cellWeights
|
||||
)
|
||||
{
|
||||
if (cellCentres.size() != globalCellCells.size())
|
||||
{
|
||||
FatalErrorInFunction
|
||||
<< "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
|
||||
|
||||
CompactListList<label> cellCells(globalCellCells);
|
||||
|
||||
// Decompose using default weights
|
||||
labelList decomp;
|
||||
decomposeGeneral(cellCells.m(), cellCells.offsets(), cellWeights, decomp);
|
||||
|
||||
return decomp;
|
||||
}
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -0,0 +1,151 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2017 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 3 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, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
Class
|
||||
Foam::metisLikeDecomp
|
||||
|
||||
Description
|
||||
Domain decomposition using METIS-like data structures.
|
||||
|
||||
When run in parallel will collect the entire graph on to the master,
|
||||
decompose and send back.
|
||||
|
||||
SourceFiles
|
||||
metisLikeDecomp.C
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
#ifndef metisLikeDecomp_H
|
||||
#define metisLikeDecomp_H
|
||||
|
||||
#include "decompositionMethod.H"
|
||||
|
||||
namespace Foam
|
||||
{
|
||||
|
||||
/*---------------------------------------------------------------------------*\
|
||||
Class metisLikeDecomp Declaration
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
class metisLikeDecomp
|
||||
:
|
||||
public decompositionMethod
|
||||
{
|
||||
// Private Member Functions
|
||||
|
||||
//- Disallow default bitwise copy construct and assignment
|
||||
void operator=(const metisLikeDecomp&) = delete;
|
||||
metisLikeDecomp(const metisLikeDecomp&) = delete;
|
||||
|
||||
|
||||
protected:
|
||||
|
||||
// Protected Member Functions
|
||||
|
||||
//- Serial and/or collect/distribute for parallel operation
|
||||
virtual label decomposeGeneral
|
||||
(
|
||||
const UList<label>& adjncy,
|
||||
const UList<label>& xadj,
|
||||
const UList<scalar>& cellWeights,
|
||||
List<label>& decomp
|
||||
);
|
||||
|
||||
//- Decomposition with metis-like parameters
|
||||
virtual label decomposeSerial
|
||||
(
|
||||
const UList<label>& adjncy,
|
||||
const UList<label>& xadj,
|
||||
const UList<scalar>& cellWeights,
|
||||
List<label>& decomp
|
||||
) = 0;
|
||||
|
||||
public:
|
||||
|
||||
// Constructors
|
||||
|
||||
//- Construct given the decomposition dictionary
|
||||
metisLikeDecomp(const dictionary& decompositionDict);
|
||||
|
||||
|
||||
//- Destructor
|
||||
virtual ~metisLikeDecomp()
|
||||
{}
|
||||
|
||||
|
||||
// Member Functions
|
||||
|
||||
//- Inherit decompose from decompositionMethod
|
||||
using decompositionMethod::decompose;
|
||||
|
||||
//- Return for every coordinate the wanted processor number.
|
||||
// Uses the mesh connectivity (if needed).
|
||||
// Weights get normalised so the minimum value is 1 before truncation
|
||||
// to an integer so the weights should be multiples of the minimum
|
||||
// value. The overall sum of weights might otherwise overflow.
|
||||
virtual labelList decompose
|
||||
(
|
||||
const polyMesh& mesh,
|
||||
const pointField& points,
|
||||
const scalarField& pointWeights
|
||||
);
|
||||
|
||||
//- 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.
|
||||
// See note on weights above.
|
||||
virtual labelList decompose
|
||||
(
|
||||
const polyMesh& mesh,
|
||||
const labelList& agglom,
|
||||
const pointField& regionPoints,
|
||||
const scalarField& regionWeights
|
||||
);
|
||||
|
||||
//- 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
|
||||
// See note on weights above.
|
||||
virtual labelList decompose
|
||||
(
|
||||
const labelListList& globalCellCells,
|
||||
const pointField& cellCentres,
|
||||
const scalarField& cellWeights
|
||||
);
|
||||
};
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
} // End namespace Foam
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
#endif
|
||||
|
||||
// ************************************************************************* //
|
||||
3
src/parallel/decompose/kahipDecomp/Make/files
Normal file
3
src/parallel/decompose/kahipDecomp/Make/files
Normal file
@ -0,0 +1,3 @@
|
||||
kahipDecomp.C
|
||||
|
||||
LIB = $(FOAM_LIBBIN)/libkahipDecomp
|
||||
13
src/parallel/decompose/kahipDecomp/Make/options
Normal file
13
src/parallel/decompose/kahipDecomp/Make/options
Normal file
@ -0,0 +1,13 @@
|
||||
EXE_INC = \
|
||||
-I$(KAHIP_ARCH_PATH)/include \
|
||||
-I../decompositionMethods/lnInclude \
|
||||
$(KAHIP_COMP_FLAGS)
|
||||
|
||||
/*
|
||||
* The $(KAHIP_ARCH_PATH)/lib$WM_COMPILER_LIB_ARCH path is provided
|
||||
* to support central, non-thirdparty installations
|
||||
*/
|
||||
LIB_LIBS = \
|
||||
-L$(KAHIP_ARCH_PATH)/lib \
|
||||
-L$(KAHIP_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
|
||||
-L$(FOAM_EXT_LIBBIN) $(KAHIP_LINK_FLAGS) -lkahip
|
||||
329
src/parallel/decompose/kahipDecomp/kahipDecomp.C
Normal file
329
src/parallel/decompose/kahipDecomp/kahipDecomp.C
Normal file
@ -0,0 +1,329 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2017 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 3 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, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
#include "kahipDecomp.H"
|
||||
#include "addToRunTimeSelectionTable.H"
|
||||
#include "Time.H"
|
||||
|
||||
#include "kaHIP_interface.h"
|
||||
|
||||
#include <string>
|
||||
#include <map>
|
||||
#include <vector>
|
||||
|
||||
// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
|
||||
|
||||
namespace Foam
|
||||
{
|
||||
defineTypeNameAndDebug(kahipDecomp, 0);
|
||||
addToRunTimeSelectionTable(decompositionMethod, kahipDecomp, dictionary);
|
||||
}
|
||||
|
||||
|
||||
const Foam::Enum
|
||||
<
|
||||
Foam::kahipDecomp::configs
|
||||
>
|
||||
Foam::kahipDecomp::configNames
|
||||
{
|
||||
{ kahipDecomp::configs::FAST, "fast" },
|
||||
{ kahipDecomp::configs::ECO, "eco" },
|
||||
{ kahipDecomp::configs::STRONG, "strong" },
|
||||
{ kahipDecomp::configs::FASTSOCIAL, "fast-social" },
|
||||
{ kahipDecomp::configs::ECOSOCIAL, "eco-social" },
|
||||
{ kahipDecomp::configs::STRONGSOCIAL, "strong-social" },
|
||||
};
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
|
||||
|
||||
Foam::label Foam::kahipDecomp::decomposeSerial
|
||||
(
|
||||
const UList<label>& adjncy,
|
||||
const UList<label>& xadj,
|
||||
const UList<scalar>& cWeights,
|
||||
List<label>& decomp
|
||||
)
|
||||
{
|
||||
// Default setup
|
||||
enum configs kahipConfig = configs::FAST;
|
||||
double imbalance = 0.01;
|
||||
int seed = 0;
|
||||
bool verbose = false;
|
||||
|
||||
const dictionary* coeffsDictPtr =
|
||||
decompositionDict_.subDictPtr("kahipCoeffs");
|
||||
|
||||
#if WM_LABEL_SIZE == 64
|
||||
if (xadj.size()-1 > INT_MAX)
|
||||
{
|
||||
FatalErrorInFunction
|
||||
<< "Cannot decompose " << (xadj.size()-1) << " cells," << nl
|
||||
<< "Exceeded integer limit of " << INT_MAX << nl
|
||||
<< exit(FatalError);
|
||||
}
|
||||
#endif
|
||||
|
||||
int numCells = xadj.size()-1;
|
||||
|
||||
// Cell weights (so on the vertices of the dual)
|
||||
List<int> cellWeights;
|
||||
|
||||
// Check for externally provided cellweights and if so initialise weights
|
||||
const scalar minWeights = gMin(cWeights);
|
||||
if (!cWeights.empty())
|
||||
{
|
||||
if (minWeights <= 0)
|
||||
{
|
||||
WarningInFunction
|
||||
<< "Illegal minimum weight " << minWeights
|
||||
<< endl;
|
||||
}
|
||||
|
||||
if (cWeights.size() != numCells)
|
||||
{
|
||||
FatalErrorInFunction
|
||||
<< "Number of cell weights " << cWeights.size()
|
||||
<< " does not equal number of cells " << numCells
|
||||
<< exit(FatalError);
|
||||
}
|
||||
|
||||
// Convert to integers.
|
||||
cellWeights.setSize(cWeights.size());
|
||||
forAll(cellWeights, i)
|
||||
{
|
||||
cellWeights[i] = int(cWeights[i]/minWeights);
|
||||
}
|
||||
}
|
||||
|
||||
// Additional sizing parameters (testing only)
|
||||
std::map<std::string, std::vector<int>> sizingParams;
|
||||
|
||||
// Check for user supplied weights and decomp options
|
||||
if (coeffsDictPtr)
|
||||
{
|
||||
const dictionary& coeffDict = *coeffsDictPtr;
|
||||
|
||||
//- Find the key in the dictionary and return the corresponding
|
||||
// enumeration element based on its name.
|
||||
// Return the default value if the key was not found in the dictionary.
|
||||
// Fatal if the enumerated name was incorrect.
|
||||
|
||||
kahipConfig =
|
||||
configNames.lookupOrDefault("config", coeffDict, kahipConfig);
|
||||
|
||||
coeffDict.readIfPresent("imbalance", imbalance);
|
||||
coeffDict.readIfPresent("verbose", verbose);
|
||||
|
||||
Info<< "kahipDecomp :"
|
||||
<< " config=" << configNames[kahipConfig]
|
||||
<< " imbalance=" << imbalance;
|
||||
|
||||
List<int> labels;
|
||||
if
|
||||
(
|
||||
coeffDict.readIfPresent("hierarchy", labels)
|
||||
&& !labels.empty()
|
||||
)
|
||||
{
|
||||
std::vector<int> vec;
|
||||
vec.reserve(labels.size()+1);
|
||||
|
||||
// Verify sizing
|
||||
|
||||
int n = 1;
|
||||
for (auto val : labels)
|
||||
{
|
||||
n *= val;
|
||||
vec.push_back(val);
|
||||
}
|
||||
|
||||
if (n != nProcessors_)
|
||||
{
|
||||
// Size mismatch. Try to correct.
|
||||
|
||||
if (nProcessors_ % n)
|
||||
{
|
||||
WarningInFunction
|
||||
<< "Mismatch in number of processors and "
|
||||
<< "hierarchy specified" << flatOutput(labels) << endl;
|
||||
|
||||
vec.clear();
|
||||
}
|
||||
else
|
||||
{
|
||||
// Evenly divisible, add extra hierarchy level
|
||||
vec.push_back(nProcessors_ / n);
|
||||
}
|
||||
}
|
||||
|
||||
if (!vec.empty())
|
||||
{
|
||||
sizingParams["hierarchy"] = std::move(vec);
|
||||
|
||||
Info<< " hierarchy=" << flatOutput(labels);
|
||||
}
|
||||
}
|
||||
|
||||
if
|
||||
(
|
||||
coeffDict.readIfPresent("distance", labels)
|
||||
&& !labels.empty()
|
||||
)
|
||||
{
|
||||
std::vector<int> vec(labels.size());
|
||||
|
||||
forAll(labels, i)
|
||||
{
|
||||
vec[i] = labels[i];
|
||||
}
|
||||
|
||||
sizingParams["distance"] = std::move(vec);
|
||||
|
||||
Info<< " distance=" << flatOutput(labels);
|
||||
}
|
||||
|
||||
if (coeffDict.readIfPresent("seed", seed))
|
||||
{
|
||||
Info<< " seed=" << seed;
|
||||
}
|
||||
|
||||
Info<< endl;
|
||||
}
|
||||
else
|
||||
{
|
||||
Info<< "kahipDecomp :"
|
||||
<< " config=" << configNames[kahipConfig]
|
||||
<< " imbalance=" << imbalance << endl;
|
||||
}
|
||||
|
||||
// Number of partitions
|
||||
int nParts = nProcessors_;
|
||||
|
||||
// Output: number of cut edges
|
||||
int edgeCut = 0;
|
||||
|
||||
#if WM_LABEL_SIZE == 32
|
||||
|
||||
// Input:
|
||||
int* xadjPtr = const_cast<UList<int>&>(xadj).begin();
|
||||
int* adjncyPtr = const_cast<UList<int>&>(adjncy).begin();
|
||||
|
||||
// Output: cell -> processor addressing
|
||||
decomp.setSize(numCells);
|
||||
int* decompPtr = decomp.begin();
|
||||
|
||||
#elif WM_LABEL_SIZE == 64
|
||||
|
||||
// input (copy)
|
||||
List<int> xadjCopy(xadj.size());
|
||||
List<int> adjncyCopy(adjncy.size());
|
||||
|
||||
forAll(xadj,i)
|
||||
{
|
||||
xadjCopy[i] = xadj[i];
|
||||
}
|
||||
forAll(adjncy,i)
|
||||
{
|
||||
adjncyCopy[i] = adjncy[i];
|
||||
}
|
||||
|
||||
int* xadjPtr = xadjCopy.begin();
|
||||
int* adjncyPtr = adjncyCopy.begin();
|
||||
|
||||
if (decomp.size() != numCells)
|
||||
{
|
||||
decomp.clear();
|
||||
}
|
||||
|
||||
// Output: cell -> processor addressing
|
||||
List<int> decompCopy(numCells);
|
||||
int* decompPtr = decompCopy.begin();
|
||||
#endif
|
||||
|
||||
#if 0 // WIP: #ifdef KAFFPA_CPP_INTERFACE
|
||||
kaffpa_cpp
|
||||
(
|
||||
&numCells, // num vertices in graph
|
||||
(cellWeights.size() ? cellWeights.begin() : nullptr), // vertex wts
|
||||
xadjPtr, // indexing into adjncy
|
||||
nullptr, // edge wts
|
||||
adjncyPtr, // neighbour info
|
||||
&nParts, // nparts
|
||||
&imbalance, // amount of imbalance allowed
|
||||
!verbose, // suppress output
|
||||
seed, // for random
|
||||
int(kahipConfig),
|
||||
&edgeCut, // [output]
|
||||
decompPtr, // [output]
|
||||
sizingParams
|
||||
);
|
||||
#else
|
||||
kaffpa
|
||||
(
|
||||
&numCells, // num vertices in graph
|
||||
(cellWeights.size() ? cellWeights.begin() : nullptr), // vertex wts
|
||||
xadjPtr, // indexing into adjncy
|
||||
nullptr, // edge wts
|
||||
adjncyPtr, // neighbour info
|
||||
&nParts, // nparts
|
||||
&imbalance, // amount of imbalance allowed
|
||||
!verbose, // suppress output
|
||||
seed, // for random
|
||||
int(kahipConfig),
|
||||
&edgeCut, // [output]
|
||||
decompPtr // [output]
|
||||
);
|
||||
#endif
|
||||
|
||||
#if WM_LABEL_SIZE == 64
|
||||
|
||||
// Drop input copy
|
||||
xadjCopy.clear();
|
||||
adjncyCopy.clear();
|
||||
|
||||
// Copy back to List<label>
|
||||
decomp.setSize(numCells);
|
||||
forAll(decompCopy, i)
|
||||
{
|
||||
decomp[i] = decompCopy[i];
|
||||
}
|
||||
|
||||
decompCopy.clear();
|
||||
#endif
|
||||
|
||||
return edgeCut;
|
||||
}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
|
||||
|
||||
Foam::kahipDecomp::kahipDecomp(const dictionary& decompositionDict)
|
||||
:
|
||||
metisLikeDecomp(decompositionDict)
|
||||
{}
|
||||
|
||||
|
||||
// ************************************************************************* //
|
||||
143
src/parallel/decompose/kahipDecomp/kahipDecomp.H
Normal file
143
src/parallel/decompose/kahipDecomp/kahipDecomp.H
Normal file
@ -0,0 +1,143 @@
|
||||
/*---------------------------------------------------------------------------*\
|
||||
========= |
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2017 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 3 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, see <http://www.gnu.org/licenses/>.
|
||||
|
||||
Class
|
||||
Foam::kahipDecomp
|
||||
|
||||
Description
|
||||
Domain decomposition using KaHIP
|
||||
http://algo2.iti.kit.edu/documents/kahip/
|
||||
|
||||
When run in parallel will collect the entire graph on to the master,
|
||||
decompose and send back.
|
||||
|
||||
\verbatim
|
||||
numberOfSubdomains N;
|
||||
method kahip;
|
||||
|
||||
kahipCoeffs
|
||||
{
|
||||
config fast;
|
||||
imbalance 0.01;
|
||||
}
|
||||
\endverbatim
|
||||
|
||||
Where the coefficients dictionary is optional, as are all its entries:
|
||||
\table
|
||||
Property | Description | Default value
|
||||
config | fast / eco / strong | fast
|
||||
imbalance | imbalance on cells between domains | 0.01
|
||||
seed | initial value for random number generator | 0
|
||||
\endtable
|
||||
|
||||
SourceFiles
|
||||
kahipDecomp.C
|
||||
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
#ifndef kahipDecomp_H
|
||||
#define kahipDecomp_H
|
||||
|
||||
#include "metisLikeDecomp.H"
|
||||
#include "Enum.H"
|
||||
|
||||
namespace Foam
|
||||
{
|
||||
|
||||
/*---------------------------------------------------------------------------*\
|
||||
Class kahipDecomp Declaration
|
||||
\*---------------------------------------------------------------------------*/
|
||||
|
||||
class kahipDecomp
|
||||
:
|
||||
public metisLikeDecomp
|
||||
{
|
||||
|
||||
// Private Member Functions
|
||||
|
||||
//- Call kahip with options from dictionary.
|
||||
virtual label decomposeSerial
|
||||
(
|
||||
const UList<label>& adjncy,
|
||||
const UList<label>& xadj,
|
||||
const UList<scalar>& cellWeights,
|
||||
List<label>& decomp
|
||||
);
|
||||
|
||||
//- Disallow default bitwise copy construct and assignment
|
||||
void operator=(const kahipDecomp&) = delete;
|
||||
kahipDecomp(const kahipDecomp&) = delete;
|
||||
|
||||
|
||||
public:
|
||||
|
||||
//- The predefined KaHIP configuration types
|
||||
enum class configs
|
||||
{
|
||||
FAST = 0, //!< default
|
||||
ECO = 1,
|
||||
STRONG = 2,
|
||||
FASTSOCIAL = 3,
|
||||
ECOSOCIAL = 4,
|
||||
STRONGSOCIAL = 5,
|
||||
};
|
||||
|
||||
|
||||
//- The selection names for predefined KaHIP configurations
|
||||
static const Enum<configs> configNames;
|
||||
|
||||
|
||||
//- Runtime type information
|
||||
TypeName("kahip");
|
||||
|
||||
|
||||
// Constructors
|
||||
|
||||
//- Construct given the decomposition dictionary
|
||||
kahipDecomp(const dictionary& decompositionDict);
|
||||
|
||||
|
||||
//- Destructor
|
||||
virtual ~kahipDecomp()
|
||||
{}
|
||||
|
||||
|
||||
// Member Functions
|
||||
|
||||
virtual bool parallelAware() const
|
||||
{
|
||||
return true;
|
||||
}
|
||||
|
||||
};
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
} // End namespace Foam
|
||||
|
||||
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
|
||||
|
||||
#endif
|
||||
|
||||
// ************************************************************************* //
|
||||
@ -45,13 +45,12 @@ namespace Foam
|
||||
|
||||
// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
|
||||
|
||||
Foam::label Foam::metisDecomp::decompose
|
||||
Foam::label Foam::metisDecomp::decomposeSerial
|
||||
(
|
||||
const List<label>& adjncy,
|
||||
const List<label>& xadj,
|
||||
const scalarField& cWeights,
|
||||
|
||||
List<label>& finalDecomp
|
||||
const UList<label>& adjncy,
|
||||
const UList<label>& xadj,
|
||||
const UList<scalar>& cWeights,
|
||||
List<label>& decomp
|
||||
)
|
||||
{
|
||||
// Method of decomposition
|
||||
@ -59,6 +58,9 @@ Foam::label Foam::metisDecomp::decompose
|
||||
// k-way: multi-level k-way
|
||||
word method("recursive");
|
||||
|
||||
const dictionary* coeffsDictPtr =
|
||||
decompositionDict_.subDictPtr("metisCoeffs");
|
||||
|
||||
label numCells = xadj.size()-1;
|
||||
|
||||
// Decomposition options
|
||||
@ -77,7 +79,7 @@ Foam::label Foam::metisDecomp::decompose
|
||||
|
||||
|
||||
// Check for externally provided cellweights and if so initialise weights
|
||||
scalar minWeights = gMin(cWeights);
|
||||
const scalar minWeights = gMin(cWeights);
|
||||
if (cWeights.size() > 0)
|
||||
{
|
||||
if (minWeights <= 0)
|
||||
@ -105,14 +107,13 @@ Foam::label Foam::metisDecomp::decompose
|
||||
|
||||
|
||||
// Check for user supplied weights and decomp options
|
||||
if (decompositionDict_.found("metisCoeffs"))
|
||||
if (coeffsDictPtr)
|
||||
{
|
||||
const dictionary& metisCoeffs =
|
||||
decompositionDict_.subDict("metisCoeffs");
|
||||
const dictionary& coeffDict = *coeffsDictPtr;
|
||||
|
||||
word weightsFile;
|
||||
|
||||
if (metisCoeffs.readIfPresent("method", method))
|
||||
if (coeffDict.readIfPresent("method", method))
|
||||
{
|
||||
if (method != "recursive" && method != "k-way")
|
||||
{
|
||||
@ -127,7 +128,7 @@ Foam::label Foam::metisDecomp::decompose
|
||||
<< nl << endl;
|
||||
}
|
||||
|
||||
if (metisCoeffs.readIfPresent("options", options))
|
||||
if (coeffDict.readIfPresent("options", options))
|
||||
{
|
||||
if (options.size() != METIS_NOPTIONS)
|
||||
{
|
||||
@ -142,7 +143,7 @@ Foam::label Foam::metisDecomp::decompose
|
||||
<< nl << endl;
|
||||
}
|
||||
|
||||
if (metisCoeffs.readIfPresent("processorWeights", processorWeights))
|
||||
if (coeffDict.readIfPresent("processorWeights", processorWeights))
|
||||
{
|
||||
processorWeights /= sum(processorWeights);
|
||||
|
||||
@ -161,7 +162,7 @@ Foam::label Foam::metisDecomp::decompose
|
||||
label nProcs = nProcessors_;
|
||||
|
||||
// Output: cell -> processor addressing
|
||||
finalDecomp.setSize(numCells);
|
||||
decomp.setSize(numCells);
|
||||
|
||||
// Output: number of cut edges
|
||||
label edgeCut = 0;
|
||||
@ -172,17 +173,17 @@ Foam::label Foam::metisDecomp::decompose
|
||||
(
|
||||
&numCells, // num vertices in graph
|
||||
&ncon, // num balancing constraints
|
||||
const_cast<List<label>&>(xadj).begin(), // indexing into adjncy
|
||||
const_cast<List<label>&>(adjncy).begin(), // neighbour info
|
||||
cellWeights.begin(),// vertexweights
|
||||
const_cast<UList<label>&>(xadj).begin(), // indexing into adjncy
|
||||
const_cast<UList<label>&>(adjncy).begin(), // neighbour info
|
||||
cellWeights.begin(),// vertex wts
|
||||
nullptr, // vsize: total communication vol
|
||||
faceWeights.begin(),// edgeweights
|
||||
faceWeights.begin(),// edge wts
|
||||
&nProcs, // nParts
|
||||
processorWeights.begin(), // tpwgts
|
||||
nullptr, // ubvec: processor imbalance (default)
|
||||
options.begin(),
|
||||
&edgeCut,
|
||||
finalDecomp.begin()
|
||||
decomp.begin()
|
||||
);
|
||||
}
|
||||
else
|
||||
@ -191,17 +192,17 @@ Foam::label Foam::metisDecomp::decompose
|
||||
(
|
||||
&numCells, // num vertices in graph
|
||||
&ncon, // num balancing constraints
|
||||
const_cast<List<label>&>(xadj).begin(), // indexing into adjncy
|
||||
const_cast<List<label>&>(adjncy).begin(), // neighbour info
|
||||
cellWeights.begin(),// vertexweights
|
||||
const_cast<UList<label>&>(xadj).begin(), // indexing into adjncy
|
||||
const_cast<UList<label>&>(adjncy).begin(), // neighbour info
|
||||
cellWeights.begin(),// vertex wts
|
||||
nullptr, // vsize: total communication vol
|
||||
faceWeights.begin(),// edgeweights
|
||||
faceWeights.begin(),// edge wts
|
||||
&nProcs, // nParts
|
||||
processorWeights.begin(), // tpwgts
|
||||
nullptr, // ubvec: processor imbalance (default)
|
||||
options.begin(),
|
||||
&edgeCut,
|
||||
finalDecomp.begin()
|
||||
decomp.begin()
|
||||
);
|
||||
}
|
||||
|
||||
@ -213,116 +214,8 @@ Foam::label Foam::metisDecomp::decompose
|
||||
|
||||
Foam::metisDecomp::metisDecomp(const dictionary& decompositionDict)
|
||||
:
|
||||
decompositionMethod(decompositionDict)
|
||||
metisLikeDecomp(decompositionDict)
|
||||
{}
|
||||
|
||||
|
||||
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
|
||||
|
||||
Foam::labelList Foam::metisDecomp::decompose
|
||||
(
|
||||
const polyMesh& mesh,
|
||||
const pointField& points,
|
||||
const scalarField& pointWeights
|
||||
)
|
||||
{
|
||||
if (points.size() != mesh.nCells())
|
||||
{
|
||||
FatalErrorInFunction
|
||||
<< "Can use this decomposition method only for the whole mesh"
|
||||
<< endl
|
||||
<< "and supply one coordinate (cellCentre) for every cell." << endl
|
||||
<< "The number of coordinates " << points.size() << endl
|
||||
<< "The number of cells in the mesh " << mesh.nCells()
|
||||
<< exit(FatalError);
|
||||
}
|
||||
|
||||
CompactListList<label> cellCells;
|
||||
calcCellCells
|
||||
(
|
||||
mesh,
|
||||
identity(mesh.nCells()),
|
||||
mesh.nCells(),
|
||||
false,
|
||||
cellCells
|
||||
);
|
||||
|
||||
// Decompose using default weights
|
||||
labelList decomp;
|
||||
decompose(cellCells.m(), cellCells.offsets(), pointWeights, decomp);
|
||||
|
||||
return decomp;
|
||||
}
|
||||
|
||||
|
||||
Foam::labelList Foam::metisDecomp::decompose
|
||||
(
|
||||
const polyMesh& mesh,
|
||||
const labelList& agglom,
|
||||
const pointField& agglomPoints,
|
||||
const scalarField& agglomWeights
|
||||
)
|
||||
{
|
||||
if (agglom.size() != mesh.nCells())
|
||||
{
|
||||
FatalErrorInFunction
|
||||
<< "Size of cell-to-coarse map " << agglom.size()
|
||||
<< " differs from number of cells in mesh " << mesh.nCells()
|
||||
<< exit(FatalError);
|
||||
}
|
||||
|
||||
// Make Metis CSR (Compressed Storage Format) storage
|
||||
// adjncy : contains neighbours (= edges in graph)
|
||||
// xadj(celli) : start of information in adjncy for celli
|
||||
|
||||
CompactListList<label> cellCells;
|
||||
calcCellCells(mesh, agglom, agglomPoints.size(), false, cellCells);
|
||||
|
||||
// Decompose using default weights
|
||||
labelList finalDecomp;
|
||||
decompose(cellCells.m(), cellCells.offsets(), agglomWeights, finalDecomp);
|
||||
|
||||
|
||||
// Rework back into decomposition for original mesh
|
||||
labelList fineDistribution(agglom.size());
|
||||
|
||||
forAll(fineDistribution, i)
|
||||
{
|
||||
fineDistribution[i] = finalDecomp[agglom[i]];
|
||||
}
|
||||
|
||||
return fineDistribution;
|
||||
}
|
||||
|
||||
|
||||
Foam::labelList Foam::metisDecomp::decompose
|
||||
(
|
||||
const labelListList& globalCellCells,
|
||||
const pointField& cellCentres,
|
||||
const scalarField& cellWeights
|
||||
)
|
||||
{
|
||||
if (cellCentres.size() != globalCellCells.size())
|
||||
{
|
||||
FatalErrorInFunction
|
||||
<< "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
|
||||
|
||||
CompactListList<label> cellCells(globalCellCells);
|
||||
|
||||
// Decompose using default weights
|
||||
labelList decomp;
|
||||
decompose(cellCells.m(), cellCells.offsets(), cellWeights, decomp);
|
||||
|
||||
return decomp;
|
||||
}
|
||||
|
||||
|
||||
// ************************************************************************* //
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2011-2015 OpenFOAM Foundation
|
||||
\\/ M anipulation |
|
||||
\\/ M anipulation | Copyright (C) 2017 OpenCFD Ltd.
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
This file is part of OpenFOAM.
|
||||
@ -27,6 +27,29 @@ Class
|
||||
Description
|
||||
Metis domain decomposition
|
||||
|
||||
When run in parallel will collect the entire graph on to the master,
|
||||
decompose and send back.
|
||||
|
||||
\verbatim
|
||||
numberOfSubdomains N;
|
||||
method metis;
|
||||
|
||||
metisCoeffs
|
||||
{
|
||||
method recursive; // k-way
|
||||
options ( ...);
|
||||
processorWeights ( ... );
|
||||
}
|
||||
\endverbatim
|
||||
|
||||
Where the coefficients dictionary is optional, as are all its entries:
|
||||
\table
|
||||
Property | Description | Default value
|
||||
method | recursive / k-way | recursive
|
||||
options | metis options |
|
||||
processorWeights | list of weighting per partition |
|
||||
\endtable
|
||||
|
||||
SourceFiles
|
||||
metisDecomp.C
|
||||
|
||||
@ -35,7 +58,7 @@ SourceFiles
|
||||
#ifndef metisDecomp_H
|
||||
#define metisDecomp_H
|
||||
|
||||
#include "decompositionMethod.H"
|
||||
#include "metisLikeDecomp.H"
|
||||
|
||||
namespace Foam
|
||||
{
|
||||
@ -46,23 +69,23 @@ namespace Foam
|
||||
|
||||
class metisDecomp
|
||||
:
|
||||
public decompositionMethod
|
||||
public metisLikeDecomp
|
||||
{
|
||||
|
||||
// Private Member Functions
|
||||
|
||||
//- Call Metis with options from dictionary.
|
||||
label decompose
|
||||
virtual label decomposeSerial
|
||||
(
|
||||
const List<label>& adjncy,
|
||||
const List<label>& xadj,
|
||||
const scalarField& cellWeights,
|
||||
List<label>& finalDecomp
|
||||
const UList<label>& adjncy,
|
||||
const UList<label>& xadj,
|
||||
const UList<scalar>& cellWeights,
|
||||
List<label>& decomp
|
||||
);
|
||||
|
||||
//- Disallow default bitwise copy construct and assignment
|
||||
void operator=(const metisDecomp&);
|
||||
metisDecomp(const metisDecomp&);
|
||||
void operator=(const metisDecomp&) = delete;
|
||||
metisDecomp(const metisDecomp&) = delete;
|
||||
|
||||
|
||||
public:
|
||||
@ -74,7 +97,7 @@ public:
|
||||
// Constructors
|
||||
|
||||
//- Construct given the decomposition dictionary
|
||||
metisDecomp(const dictionary&);
|
||||
metisDecomp(const dictionary& decompositionDict);
|
||||
|
||||
|
||||
//- Destructor
|
||||
@ -86,52 +109,9 @@ public:
|
||||
|
||||
virtual bool parallelAware() const
|
||||
{
|
||||
// Metis does not know about proc boundaries
|
||||
return false;
|
||||
return true;
|
||||
}
|
||||
|
||||
//- Inherit decompose from decompositionMethod
|
||||
using decompositionMethod::decompose;
|
||||
|
||||
//- Return for every coordinate the wanted processor number. Use the
|
||||
// mesh connectivity (if needed)
|
||||
// Weights get normalised so the minimum value is 1 before truncation
|
||||
// to an integer so the weights should be multiples of the minimum
|
||||
// value. The overall sum of weights might otherwise overflow.
|
||||
virtual labelList decompose
|
||||
(
|
||||
const polyMesh& mesh,
|
||||
const pointField& points,
|
||||
const scalarField& pointWeights
|
||||
);
|
||||
|
||||
//- 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.
|
||||
// See note on weights above.
|
||||
virtual labelList decompose
|
||||
(
|
||||
const polyMesh& mesh,
|
||||
const labelList& agglom,
|
||||
const pointField& regionPoints,
|
||||
const scalarField& regionWeights
|
||||
);
|
||||
|
||||
//- 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
|
||||
// See note on weights above.
|
||||
virtual labelList decompose
|
||||
(
|
||||
const labelListList& globalCellCells,
|
||||
const pointField& cc,
|
||||
const scalarField& cWeights
|
||||
);
|
||||
};
|
||||
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2011-2017 OpenFOAM Foundation
|
||||
\\/ M anipulation | Copyright (C) 2015 OpenCFD Ltd.
|
||||
\\/ M anipulation | Copyright (C) 2015-2017 OpenCFD Ltd.
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
This file is part of OpenFOAM.
|
||||
@ -228,12 +228,17 @@ License
|
||||
namespace Foam
|
||||
{
|
||||
defineTypeNameAndDebug(ptscotchDecomp, 0);
|
||||
|
||||
addToRunTimeSelectionTable(decompositionMethod, ptscotchDecomp, dictionary);
|
||||
}
|
||||
|
||||
// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
|
||||
|
||||
void Foam::ptscotchDecomp::graphPath(const polyMesh& mesh)
|
||||
{
|
||||
graphPath_ = mesh.time().path()/mesh.name();
|
||||
}
|
||||
|
||||
|
||||
void Foam::ptscotchDecomp::check(const int retVal, const char* str)
|
||||
{
|
||||
if (retVal)
|
||||
@ -248,11 +253,9 @@ void Foam::ptscotchDecomp::check(const int retVal, const char* str)
|
||||
////- Does prevention of 0 cell domains and calls ptscotch.
|
||||
//Foam::label Foam::ptscotchDecomp::decomposeZeroDomains
|
||||
//(
|
||||
// const fileName& meshPath,
|
||||
// const List<label>& initadjncy,
|
||||
// const List<label>& initxadj,
|
||||
// const scalarField& initcWeights,
|
||||
//
|
||||
// const UList<label>& initadjncy,
|
||||
// const UList<label>& initxadj,
|
||||
// const UList<scalar>& initcWeights,
|
||||
// List<label>& finalDecomp
|
||||
//) const
|
||||
//{
|
||||
@ -272,7 +275,6 @@ void Foam::ptscotchDecomp::check(const int retVal, const char* str)
|
||||
// {
|
||||
// return decompose
|
||||
// (
|
||||
// meshPath,
|
||||
// initadjncy,
|
||||
// initxadj,
|
||||
// initcWeights,
|
||||
@ -381,7 +383,7 @@ void Foam::ptscotchDecomp::check(const int retVal, const char* str)
|
||||
//
|
||||
//
|
||||
// // Do decomposition as normal. Sets finalDecomp.
|
||||
// label result = decompose(meshPath, adjncy, xadj, cWeights, finalDecomp);
|
||||
// label result = decompose(adjncy, xadj, cWeights, finalDecomp);
|
||||
//
|
||||
//
|
||||
// if (debug)
|
||||
@ -437,23 +439,19 @@ void Foam::ptscotchDecomp::check(const int retVal, const char* str)
|
||||
//}
|
||||
|
||||
|
||||
// Call scotch with options from dictionary.
|
||||
Foam::label Foam::ptscotchDecomp::decompose
|
||||
(
|
||||
const fileName& meshPath,
|
||||
const List<label>& adjncy,
|
||||
const List<label>& xadj,
|
||||
const scalarField& cWeights,
|
||||
const UList<label>& adjncy,
|
||||
const UList<label>& xadj,
|
||||
const UList<scalar>& cWeights,
|
||||
List<label>& finalDecomp
|
||||
) const
|
||||
{
|
||||
List<label> dummyAdjncy(1);
|
||||
List<label> dummyXadj(1);
|
||||
dummyXadj[0] = 0;
|
||||
List<label> dummyAdjncy { 0 };
|
||||
List<label> dummyXadj { 0 };
|
||||
|
||||
return decompose
|
||||
(
|
||||
meshPath,
|
||||
adjncy.size(),
|
||||
(adjncy.size() ? adjncy.begin() : dummyAdjncy.begin()),
|
||||
xadj.size(),
|
||||
@ -464,16 +462,13 @@ Foam::label Foam::ptscotchDecomp::decompose
|
||||
}
|
||||
|
||||
|
||||
// Call scotch with options from dictionary.
|
||||
Foam::label Foam::ptscotchDecomp::decompose
|
||||
(
|
||||
const fileName& meshPath,
|
||||
const label adjncySize,
|
||||
const label adjncy[],
|
||||
const label xadjSize,
|
||||
const label xadj[],
|
||||
const scalarField& cWeights,
|
||||
|
||||
const UList<scalar>& cWeights,
|
||||
List<label>& finalDecomp
|
||||
) const
|
||||
{
|
||||
@ -492,7 +487,7 @@ Foam::label Foam::ptscotchDecomp::decompose
|
||||
{
|
||||
OFstream str
|
||||
(
|
||||
meshPath + "_" + Foam::name(Pstream::myProcNo()) + ".dgr"
|
||||
graphPath_ + "_" + Foam::name(Pstream::myProcNo()) + ".dgr"
|
||||
);
|
||||
|
||||
Pout<< "Dumping Scotch graph file to " << str.name() << endl
|
||||
@ -572,8 +567,8 @@ Foam::label Foam::ptscotchDecomp::decompose
|
||||
|
||||
// Check for externally provided cellweights and if so initialise weights
|
||||
|
||||
scalar minWeights = gMin(cWeights);
|
||||
scalar maxWeights = gMax(cWeights);
|
||||
const scalar minWeights = gMin(cWeights);
|
||||
const scalar maxWeights = gMax(cWeights);
|
||||
|
||||
if (maxWeights > minWeights)
|
||||
{
|
||||
@ -719,7 +714,10 @@ Foam::label Foam::ptscotchDecomp::decompose
|
||||
}
|
||||
check
|
||||
(
|
||||
SCOTCH_archCmpltw(&archdat, nProcessors_, processorWeights.begin()),
|
||||
SCOTCH_archCmpltw
|
||||
(
|
||||
&archdat, nProcessors_, processorWeights.begin()
|
||||
),
|
||||
"SCOTCH_archCmpltw"
|
||||
);
|
||||
}
|
||||
@ -819,6 +817,9 @@ Foam::labelList Foam::ptscotchDecomp::decompose
|
||||
const scalarField& pointWeights
|
||||
)
|
||||
{
|
||||
// Where to write graph
|
||||
graphPath(mesh);
|
||||
|
||||
if (points.size() != mesh.nCells())
|
||||
{
|
||||
FatalErrorInFunction
|
||||
@ -835,7 +836,6 @@ Foam::labelList Foam::ptscotchDecomp::decompose
|
||||
// adjncy : contains neighbours (= edges in graph)
|
||||
// xadj(celli) : start of information in adjncy for celli
|
||||
|
||||
|
||||
CompactListList<label> cellCells;
|
||||
calcCellCells
|
||||
(
|
||||
@ -847,22 +847,15 @@ Foam::labelList Foam::ptscotchDecomp::decompose
|
||||
);
|
||||
|
||||
// Decompose using default weights
|
||||
List<label> finalDecomp;
|
||||
labelList decomp;
|
||||
decompose
|
||||
(
|
||||
mesh.time().path()/mesh.name(),
|
||||
cellCells.m(),
|
||||
cellCells.offsets(),
|
||||
pointWeights,
|
||||
finalDecomp
|
||||
decomp
|
||||
);
|
||||
|
||||
// Copy back to labelList
|
||||
labelList decomp(points.size());
|
||||
forAll(decomp, i)
|
||||
{
|
||||
decomp[i] = finalDecomp[i];
|
||||
}
|
||||
return decomp;
|
||||
}
|
||||
|
||||
@ -875,6 +868,9 @@ Foam::labelList Foam::ptscotchDecomp::decompose
|
||||
const scalarField& pointWeights
|
||||
)
|
||||
{
|
||||
// Where to write graph
|
||||
graphPath(mesh);
|
||||
|
||||
if (agglom.size() != mesh.nCells())
|
||||
{
|
||||
FatalErrorInFunction
|
||||
@ -898,14 +894,13 @@ Foam::labelList Foam::ptscotchDecomp::decompose
|
||||
);
|
||||
|
||||
// Decompose using weights
|
||||
List<label> finalDecomp;
|
||||
labelList decomp;
|
||||
decompose
|
||||
(
|
||||
mesh.time().path()/mesh.name(),
|
||||
cellCells.m(),
|
||||
cellCells.offsets(),
|
||||
pointWeights,
|
||||
finalDecomp
|
||||
decomp
|
||||
);
|
||||
|
||||
// Rework back into decomposition for original mesh
|
||||
@ -913,7 +908,7 @@ Foam::labelList Foam::ptscotchDecomp::decompose
|
||||
|
||||
forAll(fineDistribution, i)
|
||||
{
|
||||
fineDistribution[i] = finalDecomp[agglom[i]];
|
||||
fineDistribution[i] = decomp[agglom[i]];
|
||||
}
|
||||
|
||||
return fineDistribution;
|
||||
@ -927,6 +922,9 @@ Foam::labelList Foam::ptscotchDecomp::decompose
|
||||
const scalarField& cWeights
|
||||
)
|
||||
{
|
||||
// Where to write graph
|
||||
graphPath_ = "ptscotch";
|
||||
|
||||
if (cellCentres.size() != globalCellCells.size())
|
||||
{
|
||||
FatalErrorInFunction
|
||||
@ -943,22 +941,15 @@ Foam::labelList Foam::ptscotchDecomp::decompose
|
||||
CompactListList<label> cellCells(globalCellCells);
|
||||
|
||||
// Decompose using weights
|
||||
List<label> finalDecomp;
|
||||
labelList decomp;
|
||||
decompose
|
||||
(
|
||||
"ptscotch",
|
||||
cellCells.m(),
|
||||
cellCells.offsets(),
|
||||
cWeights,
|
||||
finalDecomp
|
||||
decomp
|
||||
);
|
||||
|
||||
// Copy back to labelList
|
||||
labelList decomp(cellCentres.size());
|
||||
forAll(decomp, i)
|
||||
{
|
||||
decomp[i] = finalDecomp[i];
|
||||
}
|
||||
return decomp;
|
||||
}
|
||||
|
||||
|
||||
@ -64,36 +64,43 @@ class ptscotchDecomp
|
||||
:
|
||||
public decompositionMethod
|
||||
{
|
||||
// Private data
|
||||
|
||||
//- Output path and name for optional grf file.
|
||||
fileName graphPath_;
|
||||
|
||||
|
||||
// Private Member Functions
|
||||
|
||||
//- Set graph path and name
|
||||
void graphPath(const polyMesh& mesh);
|
||||
|
||||
//- Check and print error message
|
||||
static void check(const int, const char*);
|
||||
|
||||
//- Decompose. Handles size 0 arrays
|
||||
label decompose
|
||||
(
|
||||
const fileName& meshPath,
|
||||
const List<label>& adjncy,
|
||||
const List<label>& xadj,
|
||||
const scalarField& cWeights,
|
||||
const UList<label>& adjncy,
|
||||
const UList<label>& xadj,
|
||||
const UList<scalar>& cWeights,
|
||||
List<label>& finalDecomp
|
||||
) const;
|
||||
|
||||
//- Low level decompose
|
||||
label decompose
|
||||
(
|
||||
const fileName& meshPath,
|
||||
const label adjncySize,
|
||||
const label adjncy[],
|
||||
const label xadjSize,
|
||||
const label xadj[],
|
||||
const scalarField& cWeights,
|
||||
const UList<scalar>& cWeights,
|
||||
List<label>& finalDecomp
|
||||
) const;
|
||||
|
||||
//- Disallow default bitwise copy construct and assignment
|
||||
void operator=(const ptscotchDecomp&);
|
||||
ptscotchDecomp(const ptscotchDecomp&);
|
||||
void operator=(const ptscotchDecomp&) = delete;
|
||||
ptscotchDecomp(const ptscotchDecomp&) = delete;
|
||||
|
||||
|
||||
public:
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2011-2017 OpenFOAM Foundation
|
||||
\\/ M anipulation | Copyright (C) 2015 OpenCFD Ltd.
|
||||
\\/ M anipulation | Copyright (C) 2015-2017 OpenCFD Ltd.
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
This file is part of OpenFOAM.
|
||||
@ -126,8 +126,6 @@ License
|
||||
#include "floatScalar.H"
|
||||
#include "Time.H"
|
||||
#include "OFstream.H"
|
||||
#include "globalIndex.H"
|
||||
#include "SubField.H"
|
||||
|
||||
extern "C"
|
||||
{
|
||||
@ -161,6 +159,12 @@ namespace Foam
|
||||
|
||||
// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
|
||||
|
||||
void Foam::scotchDecomp::graphPath(const polyMesh& mesh)
|
||||
{
|
||||
graphPath_ = mesh.time().path()/mesh.name() + ".grf";
|
||||
}
|
||||
|
||||
|
||||
void Foam::scotchDecomp::check(const int retVal, const char* str)
|
||||
{
|
||||
if (retVal)
|
||||
@ -172,186 +176,53 @@ void Foam::scotchDecomp::check(const int retVal, const char* str)
|
||||
}
|
||||
|
||||
|
||||
Foam::label Foam::scotchDecomp::decompose
|
||||
Foam::label Foam::scotchDecomp::decomposeSerial
|
||||
(
|
||||
const fileName& meshPath,
|
||||
const List<label>& adjncy,
|
||||
const List<label>& xadj,
|
||||
const scalarField& cWeights,
|
||||
|
||||
List<label>& finalDecomp
|
||||
const UList<label>& adjncy,
|
||||
const UList<label>& xadj,
|
||||
const UList<scalar>& cWeights,
|
||||
List<label>& decomp
|
||||
)
|
||||
{
|
||||
if (!Pstream::parRun())
|
||||
{
|
||||
decomposeOneProc
|
||||
(
|
||||
meshPath,
|
||||
adjncy,
|
||||
xadj,
|
||||
cWeights,
|
||||
finalDecomp
|
||||
);
|
||||
}
|
||||
else
|
||||
{
|
||||
if (debug)
|
||||
{
|
||||
Info<< "scotchDecomp : running in parallel."
|
||||
<< " Decomposing all of graph on master processor." << endl;
|
||||
}
|
||||
globalIndex globalCells(xadj.size()-1);
|
||||
label nTotalConnections = returnReduce(adjncy.size(), sumOp<label>());
|
||||
const dictionary* coeffsDictPtr =
|
||||
decompositionDict_.subDictPtr("scotchCoeffs");
|
||||
|
||||
// Send all to master. Use scheduled to save some storage.
|
||||
if (Pstream::master())
|
||||
{
|
||||
Field<label> allAdjncy(nTotalConnections);
|
||||
Field<label> allXadj(globalCells.size()+1);
|
||||
scalarField allWeights(globalCells.size());
|
||||
|
||||
// Insert my own
|
||||
label nTotalCells = 0;
|
||||
forAll(cWeights, celli)
|
||||
{
|
||||
allXadj[nTotalCells] = xadj[celli];
|
||||
allWeights[nTotalCells++] = cWeights[celli];
|
||||
}
|
||||
nTotalConnections = 0;
|
||||
forAll(adjncy, i)
|
||||
{
|
||||
allAdjncy[nTotalConnections++] = adjncy[i];
|
||||
}
|
||||
|
||||
for (int slave=1; slave<Pstream::nProcs(); slave++)
|
||||
{
|
||||
IPstream fromSlave(Pstream::commsTypes::scheduled, slave);
|
||||
Field<label> nbrAdjncy(fromSlave);
|
||||
Field<label> nbrXadj(fromSlave);
|
||||
scalarField nbrWeights(fromSlave);
|
||||
|
||||
// Append.
|
||||
//label procStart = nTotalCells;
|
||||
forAll(nbrXadj, celli)
|
||||
{
|
||||
allXadj[nTotalCells] = nTotalConnections+nbrXadj[celli];
|
||||
allWeights[nTotalCells++] = nbrWeights[celli];
|
||||
}
|
||||
// No need to renumber xadj since already global.
|
||||
forAll(nbrAdjncy, i)
|
||||
{
|
||||
allAdjncy[nTotalConnections++] = nbrAdjncy[i];
|
||||
}
|
||||
}
|
||||
allXadj[nTotalCells] = nTotalConnections;
|
||||
|
||||
|
||||
Field<label> allFinalDecomp;
|
||||
decomposeOneProc
|
||||
(
|
||||
meshPath,
|
||||
allAdjncy,
|
||||
allXadj,
|
||||
allWeights,
|
||||
allFinalDecomp
|
||||
);
|
||||
|
||||
|
||||
// Send allFinalDecomp back
|
||||
for (int slave=1; slave<Pstream::nProcs(); slave++)
|
||||
{
|
||||
OPstream toSlave(Pstream::commsTypes::scheduled, slave);
|
||||
toSlave << SubField<label>
|
||||
(
|
||||
allFinalDecomp,
|
||||
globalCells.localSize(slave),
|
||||
globalCells.offset(slave)
|
||||
);
|
||||
}
|
||||
// Get my own part (always first)
|
||||
finalDecomp = SubField<label>
|
||||
(
|
||||
allFinalDecomp,
|
||||
globalCells.localSize()
|
||||
);
|
||||
}
|
||||
else
|
||||
{
|
||||
// Send my part of the graph (already in global numbering)
|
||||
{
|
||||
OPstream toMaster
|
||||
(
|
||||
Pstream::commsTypes::scheduled,
|
||||
Pstream::masterNo()
|
||||
);
|
||||
toMaster<< adjncy << SubField<label>(xadj, xadj.size()-1)
|
||||
<< cWeights;
|
||||
}
|
||||
|
||||
// Receive back decomposition
|
||||
IPstream fromMaster
|
||||
(
|
||||
Pstream::commsTypes::scheduled,
|
||||
Pstream::masterNo()
|
||||
);
|
||||
fromMaster >> finalDecomp;
|
||||
}
|
||||
}
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
||||
// Call scotch with options from dictionary.
|
||||
Foam::label Foam::scotchDecomp::decomposeOneProc
|
||||
(
|
||||
const fileName& meshPath,
|
||||
const List<label>& adjncy,
|
||||
const List<label>& xadj,
|
||||
const scalarField& cWeights,
|
||||
|
||||
List<label>& finalDecomp
|
||||
)
|
||||
{
|
||||
// Dump graph
|
||||
if (decompositionDict_.found("scotchCoeffs"))
|
||||
if (coeffsDictPtr && coeffsDictPtr->lookupOrDefault("writeGraph", false))
|
||||
{
|
||||
const dictionary& scotchCoeffs =
|
||||
decompositionDict_.subDict("scotchCoeffs");
|
||||
OFstream str(graphPath_);
|
||||
|
||||
if (scotchCoeffs.lookupOrDefault("writeGraph", false))
|
||||
Info<< "Dumping Scotch graph file to " << str.name() << endl
|
||||
<< "Use this in combination with gpart." << endl;
|
||||
|
||||
const label version = 0;
|
||||
str << version << nl;
|
||||
// Numer of vertices
|
||||
str << xadj.size()-1 << ' ' << adjncy.size() << nl;
|
||||
|
||||
// Numbering starts from 0
|
||||
const label baseval = 0;
|
||||
// Has weights?
|
||||
const label hasEdgeWeights = 0;
|
||||
const label hasVertexWeights = 0;
|
||||
const label numericflag = 10*hasEdgeWeights+hasVertexWeights;
|
||||
str << baseval << ' ' << numericflag << nl;
|
||||
|
||||
for (label celli = 0; celli < xadj.size()-1; ++celli)
|
||||
{
|
||||
OFstream str(meshPath + ".grf");
|
||||
const label start = xadj[celli];
|
||||
const label end = xadj[celli+1];
|
||||
|
||||
Info<< "Dumping Scotch graph file to " << str.name() << endl
|
||||
<< "Use this in combination with gpart." << endl;
|
||||
str << end-start; // size
|
||||
|
||||
label version = 0;
|
||||
str << version << nl;
|
||||
// Numer of vertices
|
||||
str << xadj.size()-1 << ' ' << adjncy.size() << nl;
|
||||
// Numbering starts from 0
|
||||
label baseval = 0;
|
||||
// Has weights?
|
||||
label hasEdgeWeights = 0;
|
||||
label hasVertexWeights = 0;
|
||||
label numericflag = 10*hasEdgeWeights+hasVertexWeights;
|
||||
str << baseval << ' ' << numericflag << nl;
|
||||
for (label celli = 0; celli < xadj.size()-1; celli++)
|
||||
for (label i = start; i < end; ++i)
|
||||
{
|
||||
label start = xadj[celli];
|
||||
label end = xadj[celli+1];
|
||||
str << end-start;
|
||||
|
||||
for (label i = start; i < end; i++)
|
||||
{
|
||||
str << ' ' << adjncy[i];
|
||||
}
|
||||
str << nl;
|
||||
str << ' ' << adjncy[i];
|
||||
}
|
||||
str << nl;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
// Strategy
|
||||
// ~~~~~~~~
|
||||
|
||||
@ -359,13 +230,10 @@ Foam::label Foam::scotchDecomp::decomposeOneProc
|
||||
SCOTCH_Strat stradat;
|
||||
check(SCOTCH_stratInit(&stradat), "SCOTCH_stratInit");
|
||||
|
||||
if (decompositionDict_.found("scotchCoeffs"))
|
||||
if (coeffsDictPtr)
|
||||
{
|
||||
const dictionary& scotchCoeffs =
|
||||
decompositionDict_.subDict("scotchCoeffs");
|
||||
|
||||
string strategy;
|
||||
if (scotchCoeffs.readIfPresent("strategy", strategy))
|
||||
if (coeffsDictPtr->readIfPresent("strategy", strategy))
|
||||
{
|
||||
if (debug)
|
||||
{
|
||||
@ -384,10 +252,9 @@ Foam::label Foam::scotchDecomp::decomposeOneProc
|
||||
|
||||
List<label> velotab;
|
||||
|
||||
|
||||
// Check for externally provided cellweights and if so initialise weights
|
||||
// Note: min, not gMin since routine runs on master only.
|
||||
scalar minWeights = min(cWeights);
|
||||
const scalar minWeights = min(cWeights);
|
||||
if (!cWeights.empty())
|
||||
{
|
||||
if (minWeights <= 0)
|
||||
@ -431,7 +298,6 @@ Foam::label Foam::scotchDecomp::decomposeOneProc
|
||||
}
|
||||
|
||||
|
||||
|
||||
SCOTCH_Graph grafdat;
|
||||
check(SCOTCH_graphInit(&grafdat), "SCOTCH_graphInit");
|
||||
check
|
||||
@ -462,14 +328,12 @@ Foam::label Foam::scotchDecomp::decomposeOneProc
|
||||
check(SCOTCH_archInit(&archdat), "SCOTCH_archInit");
|
||||
|
||||
List<label> processorWeights;
|
||||
if (decompositionDict_.found("scotchCoeffs"))
|
||||
{
|
||||
const dictionary& scotchCoeffs =
|
||||
decompositionDict_.subDict("scotchCoeffs");
|
||||
|
||||
scotchCoeffs.readIfPresent("processorWeights", processorWeights);
|
||||
}
|
||||
if (processorWeights.size())
|
||||
if
|
||||
(
|
||||
coeffsDictPtr
|
||||
&& coeffsDictPtr->readIfPresent("processorWeights", processorWeights)
|
||||
&& processorWeights.size()
|
||||
)
|
||||
{
|
||||
if (debug)
|
||||
{
|
||||
@ -478,7 +342,10 @@ Foam::label Foam::scotchDecomp::decomposeOneProc
|
||||
}
|
||||
check
|
||||
(
|
||||
SCOTCH_archCmpltw(&archdat, nProcessors_, processorWeights.begin()),
|
||||
SCOTCH_archCmpltw
|
||||
(
|
||||
&archdat, nProcessors_, processorWeights.begin()
|
||||
),
|
||||
"SCOTCH_archCmpltw"
|
||||
);
|
||||
}
|
||||
@ -491,7 +358,7 @@ Foam::label Foam::scotchDecomp::decomposeOneProc
|
||||
);
|
||||
|
||||
|
||||
//- Hack to test clustering. Note that finalDecomp is non-compact
|
||||
//- Hack to test clustering. Note that decomp is non-compact
|
||||
// numbers!
|
||||
//
|
||||
////- Set up variable sizes architecture
|
||||
@ -542,16 +409,16 @@ Foam::label Foam::scotchDecomp::decomposeOneProc
|
||||
);
|
||||
#endif
|
||||
|
||||
finalDecomp.setSize(xadj.size()-1);
|
||||
finalDecomp = 0;
|
||||
decomp.setSize(xadj.size()-1);
|
||||
decomp = 0;
|
||||
check
|
||||
(
|
||||
SCOTCH_graphMap
|
||||
(
|
||||
&grafdat,
|
||||
&archdat,
|
||||
&stradat, // const SCOTCH_Strat *
|
||||
finalDecomp.begin() // parttab
|
||||
&stradat, // const SCOTCH_Strat *
|
||||
decomp.begin() // parttab
|
||||
),
|
||||
"SCOTCH_graphMap"
|
||||
);
|
||||
@ -560,17 +427,15 @@ Foam::label Foam::scotchDecomp::decomposeOneProc
|
||||
feenableexcept(oldExcepts);
|
||||
#endif
|
||||
|
||||
|
||||
|
||||
//finalDecomp.setSize(xadj.size()-1);
|
||||
//decomp.setSize(xadj.size()-1);
|
||||
//check
|
||||
//(
|
||||
// SCOTCH_graphPart
|
||||
// (
|
||||
// &grafdat,
|
||||
// nProcessors_, // partnbr
|
||||
// &stradat, // const SCOTCH_Strat *
|
||||
// finalDecomp.begin() // parttab
|
||||
// nProcessors_, // partnbr
|
||||
// &stradat, // const SCOTCH_Strat *
|
||||
// decomp.begin() // parttab
|
||||
// ),
|
||||
// "SCOTCH_graphPart"
|
||||
//);
|
||||
@ -590,7 +455,7 @@ Foam::label Foam::scotchDecomp::decomposeOneProc
|
||||
|
||||
Foam::scotchDecomp::scotchDecomp(const dictionary& decompositionDict)
|
||||
:
|
||||
decompositionMethod(decompositionDict)
|
||||
metisLikeDecomp(decompositionDict)
|
||||
{}
|
||||
|
||||
|
||||
@ -603,46 +468,15 @@ Foam::labelList Foam::scotchDecomp::decompose
|
||||
const scalarField& pointWeights
|
||||
)
|
||||
{
|
||||
if (points.size() != mesh.nCells())
|
||||
{
|
||||
FatalErrorInFunction
|
||||
<< "Can use this decomposition method only for the whole mesh"
|
||||
<< endl
|
||||
<< "and supply one coordinate (cellCentre) for every cell." << endl
|
||||
<< "The number of coordinates " << points.size() << endl
|
||||
<< "The number of cells in the mesh " << mesh.nCells()
|
||||
<< exit(FatalError);
|
||||
}
|
||||
// Where to write graph
|
||||
graphPath(mesh);
|
||||
|
||||
// Calculate local or global (if Pstream::parRun()) connectivity
|
||||
CompactListList<label> cellCells;
|
||||
calcCellCells
|
||||
return metisLikeDecomp::decompose
|
||||
(
|
||||
mesh,
|
||||
identity(mesh.nCells()),
|
||||
mesh.nCells(),
|
||||
true,
|
||||
cellCells
|
||||
points,
|
||||
pointWeights
|
||||
);
|
||||
|
||||
// Decompose using default weights
|
||||
List<label> finalDecomp;
|
||||
decompose
|
||||
(
|
||||
mesh.time().path()/mesh.name(),
|
||||
cellCells.m(),
|
||||
cellCells.offsets(),
|
||||
pointWeights,
|
||||
finalDecomp
|
||||
);
|
||||
|
||||
// Copy back to labelList
|
||||
labelList decomp(finalDecomp.size());
|
||||
forAll(decomp, i)
|
||||
{
|
||||
decomp[i] = finalDecomp[i];
|
||||
}
|
||||
return decomp;
|
||||
}
|
||||
|
||||
|
||||
@ -654,45 +488,16 @@ Foam::labelList Foam::scotchDecomp::decompose
|
||||
const scalarField& pointWeights
|
||||
)
|
||||
{
|
||||
if (agglom.size() != mesh.nCells())
|
||||
{
|
||||
FatalErrorInFunction
|
||||
<< "Size of cell-to-coarse map " << agglom.size()
|
||||
<< " differs from number of cells in mesh " << mesh.nCells()
|
||||
<< exit(FatalError);
|
||||
}
|
||||
// Where to write graph
|
||||
graphPath(mesh);
|
||||
|
||||
// Calculate local or global (if Pstream::parRun()) connectivity
|
||||
CompactListList<label> cellCells;
|
||||
calcCellCells
|
||||
return metisLikeDecomp::decompose
|
||||
(
|
||||
mesh,
|
||||
agglom,
|
||||
agglomPoints.size(),
|
||||
true,
|
||||
cellCells
|
||||
agglomPoints,
|
||||
pointWeights
|
||||
);
|
||||
|
||||
// Decompose using weights
|
||||
List<label> finalDecomp;
|
||||
decompose
|
||||
(
|
||||
mesh.time().path()/mesh.name(),
|
||||
cellCells.m(),
|
||||
cellCells.offsets(),
|
||||
pointWeights,
|
||||
finalDecomp
|
||||
);
|
||||
|
||||
// Rework back into decomposition for original mesh_
|
||||
labelList fineDistribution(agglom.size());
|
||||
|
||||
forAll(fineDistribution, i)
|
||||
{
|
||||
fineDistribution[i] = finalDecomp[agglom[i]];
|
||||
}
|
||||
|
||||
return fineDistribution;
|
||||
}
|
||||
|
||||
|
||||
@ -703,39 +508,15 @@ Foam::labelList Foam::scotchDecomp::decompose
|
||||
const scalarField& cWeights
|
||||
)
|
||||
{
|
||||
if (cellCentres.size() != globalCellCells.size())
|
||||
{
|
||||
FatalErrorInFunction
|
||||
<< "Inconsistent number of cells (" << globalCellCells.size()
|
||||
<< ") and number of cell centres (" << cellCentres.size()
|
||||
<< ")." << exit(FatalError);
|
||||
}
|
||||
// Where to write graph
|
||||
graphPath_ = "scotch.grf";
|
||||
|
||||
|
||||
// Make Metis CSR (Compressed Storage Format) storage
|
||||
// adjncy : contains neighbours (= edges in graph)
|
||||
// xadj(celli) : start of information in adjncy for celli
|
||||
|
||||
CompactListList<label> cellCells(globalCellCells);
|
||||
|
||||
// Decompose using weights
|
||||
List<label> finalDecomp;
|
||||
decompose
|
||||
return metisLikeDecomp::decompose
|
||||
(
|
||||
"scotch",
|
||||
cellCells.m(),
|
||||
cellCells.offsets(),
|
||||
cWeights,
|
||||
finalDecomp
|
||||
globalCellCells,
|
||||
cellCentres,
|
||||
cWeights
|
||||
);
|
||||
|
||||
// Copy back to labelList
|
||||
labelList decomp(finalDecomp.size());
|
||||
forAll(decomp, i)
|
||||
{
|
||||
decomp[i] = finalDecomp[i];
|
||||
}
|
||||
return decomp;
|
||||
}
|
||||
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
|
||||
\\ / O peration |
|
||||
\\ / A nd | Copyright (C) 2011-2016 OpenFOAM Foundation
|
||||
\\/ M anipulation |
|
||||
\\/ M anipulation | Copyright (C) 2017 OpenCFD Ltd.
|
||||
-------------------------------------------------------------------------------
|
||||
License
|
||||
This file is part of OpenFOAM.
|
||||
@ -213,7 +213,7 @@ SourceFiles
|
||||
#ifndef scotchDecomp_H
|
||||
#define scotchDecomp_H
|
||||
|
||||
#include "decompositionMethod.H"
|
||||
#include "metisLikeDecomp.H"
|
||||
|
||||
namespace Foam
|
||||
{
|
||||
@ -224,35 +224,34 @@ namespace Foam
|
||||
|
||||
class scotchDecomp
|
||||
:
|
||||
public decompositionMethod
|
||||
public metisLikeDecomp
|
||||
{
|
||||
// Private data
|
||||
|
||||
//- Output path and name for optional grf file.
|
||||
fileName graphPath_;
|
||||
|
||||
|
||||
// Private Member Functions
|
||||
|
||||
//- Set graph path and name
|
||||
void graphPath(const polyMesh& mesh);
|
||||
|
||||
//- Check and print error message
|
||||
static void check(const int, const char*);
|
||||
|
||||
label decompose
|
||||
(
|
||||
const fileName& meshPath,
|
||||
const List<label>& adjncy,
|
||||
const List<label>& xadj,
|
||||
const scalarField& cWeights,
|
||||
List<label>& finalDecomp
|
||||
);
|
||||
|
||||
//- Decompose non-parallel
|
||||
label decomposeOneProc
|
||||
virtual label decomposeSerial
|
||||
(
|
||||
const fileName& meshPath,
|
||||
const List<label>& adjncy,
|
||||
const List<label>& xadj,
|
||||
const scalarField& cWeights,
|
||||
List<label>& finalDecomp
|
||||
const UList<label>& adjncy,
|
||||
const UList<label>& xadj,
|
||||
const UList<scalar>& cWeights,
|
||||
List<label>& decomp
|
||||
);
|
||||
|
||||
//- Disallow default bitwise copy construct and assignment
|
||||
void operator=(const scotchDecomp&);
|
||||
scotchDecomp(const scotchDecomp&);
|
||||
void operator=(const scotchDecomp&) = delete;
|
||||
scotchDecomp(const scotchDecomp&) = delete;
|
||||
|
||||
|
||||
public:
|
||||
@ -280,14 +279,10 @@ public:
|
||||
return true;
|
||||
}
|
||||
|
||||
//- Inherit decompose from decompositionMethod
|
||||
//- Inherit all decompose methods
|
||||
using decompositionMethod::decompose;
|
||||
|
||||
//- Return for every coordinate the wanted processor number. Use the
|
||||
// mesh connectivity (if needed)
|
||||
// Weights get normalised with minimum weight and truncated to
|
||||
// convert into integer so e.g. 3.5 is seen as 3. The overall sum
|
||||
// of weights might otherwise overflow.
|
||||
//- Return for every coordinate the wanted processor number.
|
||||
virtual labelList decompose
|
||||
(
|
||||
const polyMesh& mesh,
|
||||
@ -295,11 +290,7 @@ public:
|
||||
const scalarField& pointWeights
|
||||
);
|
||||
|
||||
//- 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.
|
||||
// See note on weights above.
|
||||
//- Return for every coordinate the wanted processor number.
|
||||
virtual labelList decompose
|
||||
(
|
||||
const polyMesh& mesh,
|
||||
@ -308,14 +299,7 @@ public:
|
||||
const scalarField& regionWeights
|
||||
);
|
||||
|
||||
//- 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
|
||||
// See note on weights above.
|
||||
//- Return for every coordinate the wanted processor number.
|
||||
virtual labelList decompose
|
||||
(
|
||||
const labelListList& globalCellCells,
|
||||
|
||||
Reference in New Issue
Block a user