Merge branch 'master' of ssh://dm/home/dm4/OpenFOAM/OpenFOAM-dev

applications/utilities/mesh/manipulation/renumberMesh/Allwmake

@@ -1,12 +1,20 @@
 #!/bin/sh
 cd ${0%/*} || exit 1    # run from this directory
 
-export SLOAN_LINK_FLAGS=''
+export COMPILE_FLAGS=''
+export LINK_FLAGS=''
 
 if [ -f "${FOAM_LIBBIN}/libSloanRenumber.so" ]
 then
     echo "Found libSloanRenumber.so  --  enabling Sloan renumbering support."
-    export SLOAN_LINK_FLAGS="-lSloanRenumber"
+    export LINK_FLAGS="${LINK_FLAGS} -lSloanRenumber"
+fi
+
+if [ "${ZOLTAN_ARCH_PATH}/lib/libzoltan.a" -a -f "${FOAM_LIBBIN}/libzoltanRenumber.so" ]
+then
+    echo "Found libzoltanRenumber.so  --  enabling zoltan renumbering support."
+    export COMPILE_FLAGS="-DFOAM_USE_ZOLTAN"
+    export LINK_FLAGS="${LINK_FLAGS} -lzoltanRenumber -L${ZOLTAN_ARCH_PATH}/lib -lzoltan"
 fi
 
 wmake

applications/utilities/mesh/manipulation/renumberMesh/Make/options

@@ -1,9 +1,11 @@
 EXE_INC = \
     /* -DFULLDEBUG -g -O0 */ \
+    ${COMPILE_FLAGS} \
     -I$(LIB_SRC)/meshTools/lnInclude \
     -I$(LIB_SRC)/dynamicMesh/lnInclude \
     -I$(LIB_SRC)/finiteVolume/lnInclude \
     -I$(LIB_SRC)/renumber/renumberMethods/lnInclude \
+    -I$(LIB_SRC)/renumber/zoltanRenumber/lnInclude \
     -I$(LIB_SRC)/parallel/decompose/decompositionMethods/lnInclude
 
 EXE_LIBS = \
@@ -12,5 +14,5 @@ EXE_LIBS = \
     -lfiniteVolume \
     -lgenericPatchFields \
     -lrenumberMethods \
-    $(SLOAN_LINK_FLAGS) \
+    $(LINK_FLAGS) \
     -ldecompositionMethods -L$(FOAM_LIBBIN)/dummy -lmetisDecomp -lscotchDecomp

applications/utilities/mesh/manipulation/renumberMesh/renumberMesh.C

@@ -47,6 +47,11 @@ Description
 #include "CuthillMcKeeRenumber.H"
 #include "fvMeshSubset.H"
 
+#ifdef FOAM_USE_ZOLTAN
+#   include "zoltanRenumber.H"
+#endif
+
+
 using namespace Foam;
 
 
@@ -577,6 +582,15 @@ int main(int argc, char *argv[])
         "calculate the rms of the frontwidth"
     );
 
+
+// Force linker to include zoltan symbols. This section is only needed since
+// Zoltan is a static library
+#ifdef FOAM_USE_ZOLTAN
+    Info<< "renumberMesh built with zoltan support." << nl << endl;
+    (void)zoltanRenumber::typeName;
+#endif
+
+
 #   include "setRootCase.H"
 #   include "createTime.H"
     runTime.functionObjects().off();

applications/utilities/mesh/manipulation/renumberMesh/renumberMeshDict

@@ -42,6 +42,7 @@ method          CuthillMcKee;
 //method          random;
 //method          spring;
 //method          boundaryFirst;
+//method          zoltan;             // only if compiled with zoltan support
 
 //CuthillMcKeeCoeffs
 //{
@@ -83,4 +84,10 @@ blockCoeffs
 }
 
 
+zoltanCoeffs
+{
+    ORDER_METHOD    LOCAL_HSFC;
+}
+
+
 // ************************************************************************* //

etc/config/settings.csh

@@ -205,9 +205,9 @@ case ThirdParty:
     case Gcc++0x:
     case Gcc46:
     case Gcc46++0x:
-        set gcc_version=gcc-4.6.1
-        set gmp_version=gmp-5.0.2
-        set mpfr_version=mpfr-3.0.1
+        set gcc_version=gcc-4.6.2
+        set gmp_version=gmp-5.0.4
+        set mpfr_version=mpfr-3.1.0
         set mpc_version=mpc-0.9
         breaksw
     case Gcc45:

etc/config/settings.sh

@@ -233,11 +233,10 @@ case "${foamCompiler}" in
 OpenFOAM | ThirdParty)
     case "$WM_COMPILER" in
     Gcc | Gcc++0x | Gcc46 | Gcc46++0x)
-        gcc_version=gcc-4.6.1
-        gmp_version=gmp-5.0.2
-        mpfr_version=mpfr-3.0.1
+        gcc_version=gcc-4.6.2
+        gmp_version=gmp-5.0.4
+        mpfr_version=mpfr-3.1.0
         mpc_version=mpc-0.9
-        gmpPACKAGE=gmp-5.0.2
         ;;
     Gcc45 | Gcc45++0x)
         gcc_version=gcc-4.5.2

src/renumber/Allwmake

@@ -28,13 +28,13 @@ else
 fi
 
 
-#if [ -n "$ZOLTAN_ARCH_PATH" ]
-#then
-#    wmake $makeType zoltanRenumber
-#else
-#    echo
-#    echo "Skipping zoltanRenumber"
-#    echo
-#fi
+if [ -n "$ZOLTAN_ARCH_PATH" ]
+then
+    wmake $makeType zoltanRenumber
+else
+    echo
+    echo "Skipping zoltanRenumber"
+    echo
+fi
 
 # ----------------------------------------------------------------- end-of-file

src/renumber/zoltanRenumber/Make/files

@@ -0,0 +1,3 @@
+zoltanRenumber.C
+
+LIB = $(FOAM_LIBBIN)/libzoltanRenumber

src/renumber/zoltanRenumber/Make/options

@@ -0,0 +1,13 @@
+sinclude $(GENERAL_RULES)/mplib$(WM_MPLIB)
+sinclude $(RULES)/mplib$(WM_MPLIB)
+
+EXE_INC = \
+    /* -DFULLDEBUG -g -O0 */ \
+    $(PFLAGS) $(PINC) \
+    -I$(FOAM_SRC)/renumber/renumberMethods/lnInclude \
+    -I$(ZOLTAN_ARCH_PATH)/include/ \
+    -I$(LIB_SRC)/meshTools/lnInclude
+
+LIB_LIBS = \
+    -L$(ZOLTAN_ARCH_PATH)/lib -lzoltan \
+    -lmeshTools

src/renumber/zoltanRenumber/zoltanRenumber.C

@@ -0,0 +1,373 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2011-2012 OpenFOAM Foundation
+     \\/     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::zoltanRenumber
+
+Description
+    Renumber using Zoltan
+
+    Zoltan install:
+    - in your ~/.bashrc:
+            export ZOLTAN_ARCH_DIR=\
+                $WM_THIRD_PARTY_DIR/platforms/linux64Gcc/Zoltan_XXX
+    - unpack into $WM_THIRD_PARTY_DIR
+    - cd Zoltan_XXX
+    - mkdir build
+    - cd build
+    - export CCFLAGS="-fPIC"
+    - export CXXFLAGS="-fPIC"
+    - export CFLAGS="-fPIC"
+    - export LDFLAGS="-shared"
+    - ../configure \
+        --prefix=$ZOLTAN_ARCH_DIR \
+        --with-ccflags=-fPIC --with-cxxflags=-fPIC --with-ldflags=-shared
+
+SourceFiles
+    zoltanRenumber.C
+
+\*---------------------------------------------------------------------------*/
+
+#include "zoltanRenumber.H"
+#include "addToRunTimeSelectionTable.H"
+#include "IFstream.H"
+#include "labelIOList.H"
+#include "polyMesh.H"
+#include "globalMeshData.H"
+#include "globalIndex.H"
+#include "uint.H"
+
+#include "zoltan.h"
+#include <mpi.h>
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+    defineTypeNameAndDebug(zoltanRenumber, 0);
+
+    addToRunTimeSelectionTable
+    (
+        renumberMethod,
+        zoltanRenumber,
+        dictionary
+    );
+}
+
+
+static int get_number_of_vertices(void *data, int *ierr)
+{
+    const Foam::polyMesh& mesh = *static_cast<const Foam::polyMesh*>(data);
+    *ierr = ZOLTAN_OK;
+    return mesh.nCells();
+}
+
+
+static void get_vertex_list(void *data, int sizeGID, int sizeLID,
+            ZOLTAN_ID_PTR globalID, ZOLTAN_ID_PTR localID,
+                  int wgt_dim, float *obj_wgts, int *ierr)
+{
+    const Foam::polyMesh& mesh = *static_cast<const Foam::polyMesh*>(data);
+
+    *ierr = ZOLTAN_OK;
+
+  /* In this example, return the IDs of our vertices, but no weights.
+   * Zoltan will assume equally weighted vertices.
+   */
+
+    wgt_dim = 0;
+    obj_wgts = NULL;
+
+    for (Foam::label i=0; i<mesh.nCells(); i++)
+    {
+        globalID[i] = i;        // should be global
+        localID[i] = i;
+    }
+}
+
+
+static void get_num_edges_list(void *data, int sizeGID, int sizeLID,
+                      int num_obj,
+             ZOLTAN_ID_PTR globalID, ZOLTAN_ID_PTR localID,
+             int *numEdges, int *ierr)
+{
+  const Foam::polyMesh& mesh = *static_cast<const Foam::polyMesh*>(data);
+
+    if ((sizeGID != 1) || (sizeLID != 1) || (num_obj != mesh.nCells()))
+    {
+        *ierr = ZOLTAN_FATAL;
+        return;
+    }
+
+    for (Foam::label i=0; i < num_obj ;i++)
+    {
+        Foam::label cellI = localID[i];
+        const Foam::cell& cFaces = mesh.cells()[cellI];
+        forAll(cFaces, cFaceI)
+        {
+            Foam::label n = 0;
+            if (mesh.isInternalFace(cFaces[cFaceI]))
+            {
+                n++;
+            }
+            numEdges[i] = n;
+        }
+    }
+
+    *ierr = ZOLTAN_OK;
+}
+
+
+static void get_edge_list(void *data, int sizeGID, int sizeLID,
+        int num_obj, ZOLTAN_ID_PTR globalID, ZOLTAN_ID_PTR localID,
+        int *num_edges,
+        ZOLTAN_ID_PTR nborGID, int *nborProc,
+        int wgt_dim, float *ewgts, int *ierr)
+{
+    const Foam::polyMesh& mesh = *static_cast<const Foam::polyMesh*>(data);
+
+    if
+    (
+        (sizeGID != 1)
+     || (sizeLID != 1)
+     || (num_obj != mesh.nCells())
+     || (wgt_dim != 1)
+    )
+    {
+        *ierr = ZOLTAN_FATAL;
+        return;
+    }
+
+    ZOLTAN_ID_TYPE* nextNbor = nborGID;
+    int* nextProc = nborProc;
+    float* nextWgt = ewgts;
+
+    for (Foam::label i=0; i < num_obj; i++)
+    {
+        Foam::label cellI = localID[i];
+
+        const Foam::cell& cFaces = mesh.cells()[cellI];
+        forAll(cFaces, cFaceI)
+        {
+            Foam::label n = 0;
+
+            Foam::label faceI = cFaces[cFaceI];
+            if (mesh.isInternalFace(faceI))
+            {
+                Foam::label nbr = mesh.faceOwner()[faceI];
+                if (nbr == cellI)
+                {
+                    nbr = mesh.faceNeighbour()[faceI];
+                }
+
+                // Note: global index
+                *nextNbor++ = nbr;
+                *nextProc++ = 0;
+                *nextWgt++ = 1.0;
+
+                n++;
+            }
+            if (n != num_edges[i])
+            {
+                *ierr = ZOLTAN_FATAL;
+                return;
+            }
+        }
+    }
+    *ierr = ZOLTAN_OK;
+}
+
+
+static int get_mesh_dim(void *data, int *ierr)
+{
+    const Foam::polyMesh& mesh = *static_cast<const Foam::polyMesh*>(data);
+
+    return mesh.nSolutionD();
+}
+
+
+static void get_geom_list
+(
+    void *data,
+    int num_gid_entries,
+    int num_lid_entries,
+    int num_obj,
+    ZOLTAN_ID_PTR global_ids,
+    ZOLTAN_ID_PTR local_ids,
+    int num_dim,
+    double *geom_vec,
+    int *ierr
+)
+{
+    const Foam::polyMesh& mesh = *static_cast<const Foam::polyMesh*>(data);
+
+    if
+    (
+        (num_gid_entries != 1)
+     || (num_lid_entries != 1)
+     || (num_obj != mesh.nCells())
+     || (num_dim != mesh.nSolutionD())
+    )
+    {
+        *ierr = ZOLTAN_FATAL;
+        return;
+    }
+
+    double* p = geom_vec;
+
+
+    const Foam::Vector<Foam::label>& sol = mesh.solutionD();
+
+    const Foam::pointField& cc = mesh.cellCentres();
+
+    for (Foam::label cellI = 0; cellI < num_obj; cellI++)
+    {
+        const Foam::point& pt = cc[cellI];
+
+        for (Foam::direction cmpt = 0; cmpt < Foam::vector::nComponents; cmpt++)
+        {
+            if (sol[cmpt] == 1)
+            {
+                *p++ = pt[cmpt];
+            }
+        }
+    }
+    *ierr = ZOLTAN_OK;
+}
+
+
+// * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
+
+Foam::zoltanRenumber::zoltanRenumber(const dictionary& renumberDict)
+:
+    renumberMethod(renumberDict),
+    coeffsDict_(renumberDict.subDict(typeName+"Coeffs"))
+{}
+
+
+// * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
+
+Foam::labelList Foam::zoltanRenumber::renumber
+(
+    const polyMesh& pMesh,
+    const pointField& points
+) const
+{
+    stringList args(1);
+    args[0] = "zoltanRenumber";
+
+    int argc = args.size();
+    char* argv[argc];
+    for (label i = 0; i < argc; i++)
+    {
+        argv[i] = strdup(args[i].c_str());
+    }
+
+    float ver;
+    int rc = Zoltan_Initialize(argc, argv, &ver);
+
+    Foam::Pout<< "Initialised to " << ver << Foam::endl;
+
+    if (rc != ZOLTAN_OK)
+    {
+        FatalErrorIn("zoltanRenumber::renumber(..)")
+            << "Failed initialising Zoltan" << exit(FatalError);
+    }
+
+    struct Zoltan_Struct *zz = Zoltan_Create(MPI_COMM_WORLD);
+
+    polyMesh& mesh = const_cast<polyMesh&>(pMesh);
+
+
+    forAllConstIter(IDLList<entry>, coeffsDict_, iter)
+    {
+        if (!iter().isDict())
+        {
+            const word& key = iter().keyword();
+            const word value(iter().stream());
+
+            Info<< typeName << " : setting parameter " << key
+                << " to " << value << endl;
+
+            Zoltan_Set_Param(zz, key.c_str(), value.c_str());
+        }
+    }
+
+
+    Zoltan_Set_Num_Obj_Fn(zz, get_number_of_vertices, &mesh);
+    Zoltan_Set_Obj_List_Fn(zz, get_vertex_list, &mesh);
+
+    // Callbacks for geometry
+    Zoltan_Set_Num_Geom_Fn(zz, get_mesh_dim, &mesh);
+    Zoltan_Set_Geom_Multi_Fn(zz, get_geom_list, &mesh);
+
+    // Callbacks for connectivity
+    Zoltan_Set_Num_Edges_Multi_Fn(zz, get_num_edges_list, &mesh);
+    Zoltan_Set_Edge_List_Multi_Fn(zz, get_edge_list, &mesh);
+
+
+
+    //Note: !global indices
+    List<ZOLTAN_ID_TYPE> wantedCells(mesh.nCells());
+
+    globalIndex globalCells(mesh.nCells());
+    forAll(wantedCells, i)
+    {
+        //wantedCells[i] = i;
+        wantedCells[i] = globalCells.toGlobal(i);
+    }
+
+    List<ZOLTAN_ID_TYPE> oldToNew(mesh.nCells());
+
+    int err = Zoltan_Order
+    (
+        zz,
+        1,                                //int num_gid_entries,
+        mesh.globalData().nTotalCells(),  //int num_obj,
+        wantedCells.begin(),
+        oldToNew.begin()
+    );
+
+    if (err != ZOLTAN_OK)
+    {
+        FatalErrorIn("zoltanRenumber::renumber(..)")
+            << "Failed Zoltan_Order" << exit(FatalError);
+    }
+
+
+    for (label i = 0; i < argc; i++)
+    {
+        free(argv[i]);
+    }
+
+
+    labelList order(oldToNew.size());
+    forAll(order, i)
+    {
+        order[i] = oldToNew[i];
+    }
+    return order;
+}
+
+
+// ************************************************************************* //

src/renumber/zoltanRenumber/zoltanRenumber.H

@@ -0,0 +1,130 @@
+/*---------------------------------------------------------------------------*\
+  =========                 |
+  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+   \\    /   O peration     |
+    \\  /    A nd           | Copyright (C) 2011-2012 OpenFOAM Foundation
+     \\/     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::zoltanRenumber
+
+Description
+    Use Zoltan
+
+SourceFiles
+    zoltanRenumber.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef zoltanRenumber_H
+#define zoltanRenumber_H
+
+#include "renumberMethod.H"
+
+namespace Foam
+{
+
+/*---------------------------------------------------------------------------*\
+                      Class zoltanRenumber Declaration
+\*---------------------------------------------------------------------------*/
+
+class zoltanRenumber
+:
+    public renumberMethod
+{
+    // Private data
+
+        const dictionary coeffsDict_;
+
+
+
+    // Private Member Functions
+
+        //- Disallow default bitwise copy construct and assignment
+        void operator=(const zoltanRenumber&);
+        zoltanRenumber(const zoltanRenumber&);
+
+
+public:
+
+    //- Runtime type information
+    TypeName("zoltan");
+
+
+    // Constructors
+
+        //- Construct given the renumber dictionary
+        zoltanRenumber(const dictionary& renumberDict);
+
+
+    //- Destructor
+    virtual ~zoltanRenumber()
+    {}
+
+
+    // Member Functions
+
+        //- Return the order in which cells need to be visited, i.e.
+        //  from ordered back to original cell label.
+        //  This is only defined for geometric renumberMethods.
+        virtual labelList renumber(const pointField&) const
+        {
+            notImplemented("zoltanRenumber::renumber(const pointField&)");
+            return labelList(0);
+        }
+
+        //- Return the order in which cells need to be visited, i.e.
+        //  from ordered back to original cell label.
+        //  Use the mesh connectivity (if needed)
+        virtual labelList renumber
+        (
+            const polyMesh& mesh,
+            const pointField& cc
+        ) const;
+
+        //- Return the order in which cells need to be visited, i.e.
+        //  from ordered back to original cell label.
+        //  The connectivity is equal to mesh.cellCells() except
+        //  - the connections are across coupled patches
+        virtual labelList renumber
+        (
+            const labelListList& cellCells,
+            const pointField& cc
+        ) const
+        {
+            notImplemented
+            (
+                "zoltanRenumber::renumber"
+                "(const labelListList& cellCellsconst pointField&)"
+            );
+            return labelList(0);
+        }
+
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //