Date: 2013-07-02T14:52:51+00:00

Actual source code: Partitioner.hh
petsc-3.4.2 2013-07-02

      1: #ifndef included_ALE_Partitioner_hh
      2: #define included_ALE_Partitioner_hh

      4: #ifndef  included_ALE_Completion_hh
      5: #include <sieve/Completion.hh>
      6: #endif

      8: #ifdef PETSC_HAVE_ZOLTAN
      9: #include <zoltan.h>

     11: extern "C" {
     12:   // Inputs
     13:   extern int  nvtxs_Zoltan;   // The number of vertices
     14:   extern int  nhedges_Zoltan; // The number of hyperedges
     15:   extern int *eptr_Zoltan;    // The offsets of each hyperedge
     16:   extern int *eind_Zoltan;    // The vertices in each hyperedge, indexed by eptr

     18:   int getNumVertices_Zoltan(void *, int *);

     20:   void getLocalElements_Zoltan(void *, int, int, ZOLTAN_ID_PTR, ZOLTAN_ID_PTR, int, float *, int *);

     22:   void getHgSizes_Zoltan(void *, int *, int *, int *, int *);

     24:   void getHg_Zoltan(void *, int, int, int, int, ZOLTAN_ID_PTR, int *, ZOLTAN_ID_PTR, int *);
     25: }

     27: #endif

     29: #ifdef PETSC_HAVE_CHACO
     30: #ifdef PETSC_HAVE_UNISTD_H
     31: #include <unistd.h>
     32: #endif
     33: /* Chaco does not have an include file */
     34: extern "C" {
     35:   extern int interface(int nvtxs, int *start, int *adjacency, int *vwgts,
     36:                        float *ewgts, float *x, float *y, float *z, char *outassignname,
     37:                        char *outfilename, short *assignment, int architecture, int ndims_tot,
     38:                        int mesh_dims[3], double *goal, int global_method, int local_method,
     39:                        int rqi_flag, int vmax, int ndims, double eigtol, long seed);

     41:   extern int FREE_GRAPH;
     42: }
     43: #endif
     44: #ifdef PETSC_HAVE_PARMETIS
     45:   #include <parmetis.h>
     46: #endif
     47: #ifdef PETSC_HAVE_HMETIS
     48: extern "C" {
     49:   extern void HMETIS_PartKway(int nvtxs, int nhedges, int *vwgts, int *eptr, int *eind, int *hewgts, int nparts, int ubfactor, int *options, int *part, int *edgeCut);
     50: }
     51: #endif

     53: namespace ALE {
     54: #if 1
     55: #ifdef PETSC_HAVE_CHACO
     56:   namespace Chaco {
     57:     template<typename Alloc_ = malloc_allocator<short int> >
     58:     class Partitioner {
     59:     public:
     60:       typedef short int part_type;
     61:       typedef Alloc_    alloc_type;
     62:       enum {DEFAULT_METHOD = 1, INERTIAL_METHOD = 3};
     63:     protected:
     64:       const int  logSize;
     65:       char      *msgLog;
     66:       int        fd_stdout, fd_pipe[2];
     67:       alloc_type _allocator;
     68:     public:
     69:       Partitioner(): logSize(10000) {};
     70:       ~Partitioner() {};
     71:     protected:
     72:       // Chaco outputs to stdout. We redirect this to a buffer.
     73:       // TODO: check error codes for UNIX calls
     74:       void startStdoutRedirect() {
     75: #ifdef PETSC_HAVE_UNISTD_H
     76:         this->fd_stdout = dup(1);
     77:         pipe(this->fd_pipe);
     78:         close(1);
     79:         dup2(this->fd_pipe[1], 1);
     80: #endif
     81:       };
     82:       void stopStdoutRedirect() {
     83: #ifdef PETSC_HAVE_UNISTD_H
     84:         int count;

     86:         fflush(stdout);
     87:         this->msgLog = new char[this->logSize];
     88:         count = read(this->fd_pipe[0], this->msgLog, (this->logSize-1)*sizeof(char));
     89:         if (count < 0) count = 0;
     90:         this->msgLog[count] = 0;
     91:         close(1);
     92:         dup2(this->fd_stdout, 1);
     93:         close(this->fd_stdout);
     94:         close(this->fd_pipe[0]);
     95:         close(this->fd_pipe[1]);
     96:         //std::cout << this->msgLog << std::endl;
     97:         delete [] this->msgLog;
     98: #endif
     99:       };
    100:     public:
    101:       static bool zeroBase() {return false;}
    102:       // This method returns the partition section mapping sieve points (here cells) to partitions
    103:       //   start:     start of edge list for each vertex
    104:       //   adjacency: adj[start[v]] is edge list data for vertex v
    105:       //   partition: this section is over the partitions and takes points as values
    106:       // TODO: Read global and local methods from options
    107:       template<typename Section, typename MeshManager>
    108:       void partition(const int numVertices, const int start[], const int adjacency[], const Obj<Section>& partition, const MeshManager& manager) {
    109:         FREE_GRAPH = 0;                         /* Do not let Chaco free my memory */
    110:         int nvtxs = numVertices;                /* number of vertices in full graph */
    111:         int *vwgts = NULL;                      /* weights for all vertices */
    112:         float *ewgts = NULL;                    /* weights for all edges */
    113:         float *x = NULL, *y = NULL, *z = NULL;  /* coordinates for inertial method */
    114:         char *outassignname = NULL;             /*  name of assignment output file */
    115:         char *outfilename = NULL;               /* output file name */
    116:         int architecture = 1;                   /* 0 => hypercube, d => d-dimensional mesh */
    117:         int ndims_tot = 0;                      /* total number of cube dimensions to divide */
    118:         int mesh_dims[3];                       /* dimensions of mesh of processors */
    119:         double *goal = NULL;                    /* desired set sizes for each set */
    120:         int global_method = 1;                  /* global partitioning algorithm */
    121:         int local_method = 1;                   /* local partitioning algorithm */
    122:         int rqi_flag = 0;                       /* should I use RQI/Symmlq eigensolver? */
    123:         int vmax = 200;                         /* how many vertices to coarsen down to? */
    124:         int ndims = 1;                          /* number of eigenvectors (2^d sets) */
    125:         double eigtol = 0.001;                  /* tolerance on eigenvectors */
    126:         long seed = 123636512;                  /* for random graph mutations */
    127:         int maxSize = 0;

    129:         if (global_method == INERTIAL_METHOD) {manager.createCellCoordinates(nvtxs, &x, &y, &z);}
    130:         mesh_dims[0] = partition->commSize(); mesh_dims[1] = 1; mesh_dims[2] = 1;
    131:         part_type *assignment = this->_allocator.allocate(nvtxs);
    132:         for(int i = 0; i < nvtxs; ++i) {this->_allocator.construct(assignment+i, 0);}

    134:         this->startStdoutRedirect();
    135:         interface(nvtxs, (int *) start, (int *) adjacency, vwgts, ewgts, x, y, z, outassignname, outfilename,
    136:                   assignment, architecture, ndims_tot, mesh_dims, goal, global_method, local_method, rqi_flag,
    137:                   vmax, ndims, eigtol, seed);
    138:         this->stopStdoutRedirect();

    140:         for(int v = 0; v < nvtxs; ++v) {partition->addFiberDimension(assignment[v], 1);}
    141:         partition->allocatePoint();
    142:         for(int p = 0; p < partition->commSize(); ++p) {
    143:           maxSize = std::max(maxSize, partition->getFiberDimension(p));
    144:         }
    145:         typename Section::value_type *values = new typename Section::value_type[maxSize];

    147:         for(int p = 0; p < partition->commSize(); ++p) {
    148:           int k = 0;

    150:           for(int v = 0; v < nvtxs; ++v) {
    151:             if (assignment[v] == p) values[k++] = manager.getCell(v);
    152:           }
    153:           if (k != partition->getFiberDimension(p)) throw ALE::Exception("Invalid partition");
    154:           partition->updatePoint(p, values);
    155:         }
    156:         delete [] values;

    158:         if (global_method == INERTIAL_METHOD) {manager.destroyCellCoordinates(nvtxs, &x, &y, &z);}
    159:         for(int i = 0; i < nvtxs; ++i) {this->_allocator.destroy(assignment+i);}
    160:         this->_allocator.deallocate(assignment, nvtxs);
    161:       };
    162:     };
    163:   }
    164: #endif
    165: #ifdef PETSC_HAVE_PARMETIS
    166:   namespace ParMetis {
    167:     template<typename Alloc_ = malloc_allocator<int> >
    168:     class Partitioner {
    169:     public:
    170:       typedef int    part_type;
    171:       typedef Alloc_ alloc_type;
    172:     protected:
    173:       alloc_type _allocator;
    174:     public:
    175:       static bool zeroBase() {return true;}
    176:       // This method returns the partition section mapping sieve points (here cells) to partitions
    177:       //   start:     start of edge list for each vertex
    178:       //   adjacency: adj[start[v]] is edge list data for vertex v
    179:       //   partition: this section is over the partitions and takes points as values
    180:       // TODO: Read parameters from options
    181:       template<typename Section, typename MeshManager>
    182:       void partition(const PetscInt numVertices, const PetscInt start[], const PetscInt adjacency[], const Obj<Section>& partition, const MeshManager& manager) {
    183:         //static part_type *partitionSieve(const Obj<bundle_type>& bundle, const int dim) {
    184:         PetscInt   nvtxs      = numVertices; // The number of vertices in full graph
    185:         PetscInt  *vtxdist;                  // Distribution of vertices across processes
    186:         PetscInt  *xadj       = const_cast<PetscInt*>(start);       // Start of edge list for each vertex
    187:         PetscInt  *adjncy     = const_cast<PetscInt*>(adjacency);   // Edge lists for all vertices
    188:         PetscInt  *vwgt       = NULL;        // Vertex weights
    189:         PetscInt  *adjwgt     = NULL;        // Edge weights
    190:         PetscInt   wgtflag    = 0;           // Indicates which weights are present
    191:         PetscInt   numflag    = 0;           // Indicates initial offset (0 or 1)
    192:         PetscInt   ncon       = 1;           // The number of weights per vertex
    193:         PetscInt   nparts     = partition->commSize(); // The number of partitions
    194:         PetscReal *tpwgts;                   // The fraction of vertex weights assigned to each partition
    195:         PetscReal *ubvec;                    // The balance intolerance for vertex weights
    196:         PetscInt   options[5];               // Options
    197:         PetscInt   maxSize    = 0;
    198:         // Outputs
    199:         PetscInt   edgeCut;                  // The number of edges cut by the partition
    200:         part_type *assignment;

    202:         options[0] = 0; // Use all defaults
    203:         // Calculate vertex distribution
    204:         //   Not sure this still works in parallel
    205:         vtxdist    = new PetscInt[nparts+1];
    206:         vtxdist[0] = 0;
    207:         MPI_Allgather(&nvtxs, 1, MPIU_INT, &vtxdist[1], 1, MPIU_INT, partition->comm());
    208:         for(PetscInt p = 2; p <= nparts; ++p) {
    209:           vtxdist[p] += vtxdist[p-1];
    210:         }
    211:         // Calculate weights
    212:         tpwgts     = new PetscReal[ncon*nparts];
    213:         for(int p = 0; p < nparts; ++p) {
    214:           tpwgts[p] = 1.0/nparts;
    215:         }
    216:         ubvec      = new PetscReal[ncon];
    217:         ubvec[0]   = 1.05;

    219:         assignment = this->_allocator.allocate(nvtxs);
    220:         for(PetscInt i = 0; i < nvtxs; ++i) {this->_allocator.construct(assignment+i, 0);}

    222:         if (partition->commSize() == 1) {
    223:           PetscMemzero(assignment, nvtxs * sizeof(part_type));
    224:         } else {
    225:           if (partition->debug() && nvtxs) {
    226:             for(int p = 0; p <= nvtxs; ++p) {
    227:               std::cout << "["<<partition->commRank()<<"]xadj["<<p<<"] = " << xadj[p] << std::endl;
    228:             }
    229:             for(int i = 0; i < xadj[nvtxs]; ++i) {
    230:               std::cout << "["<<partition->commRank()<<"]adjncy["<<i<<"] = " << adjncy[i] << std::endl;
    231:             }
    232:           }
    233:           if (vtxdist[1] == vtxdist[nparts]) {
    234:             if (partition->commRank() == 0) {
    235:               /* Parameters changes (Matt, check to make sure works):
    236:                * (removed) numflags
    237:                * (changed) options -> NULL implies all defaults (only for  METIS, not ParMETIS!)
    238:                */
    239:               METIS_PartGraphKway(&nvtxs, &ncon, xadj, adjncy, vwgt, NULL, adjwgt, &nparts, tpwgts, ubvec, NULL, &edgeCut, assignment);
    240:               if (partition->debug()) {std::cout << "Metis: edgecut is " << edgeCut << std::endl;}
    241:             }
    242:           } else {
    243:             MPI_Comm comm = partition->comm();

    245:             ParMETIS_V3_PartKway(vtxdist, xadj, adjncy, vwgt, adjwgt, &wgtflag, &numflag, &ncon, &nparts, tpwgts, ubvec, options, &edgeCut, assignment, &comm);
    246:             if (partition->debug()) {std::cout << "ParMetis: edgecut is " << edgeCut << std::endl;}
    247:           }
    248:         }
    249:         delete [] vtxdist;
    250:         delete [] tpwgts;
    251:         delete [] ubvec;

    253:         for(PetscInt v = 0; v < nvtxs; ++v) {partition->addFiberDimension(assignment[v], 1);}
    254:         partition->allocatePoint();
    255:         for(PetscInt p = 0; p < partition->commSize(); ++p) {
    256:           maxSize = std::max(maxSize, partition->getFiberDimension(p));
    257:         }
    258:         typename Section::value_type *values = new typename Section::value_type[maxSize];

    260:         for(PetscInt p = 0; p < partition->commSize(); ++p) {
    261:           int k = 0;

    263:           for(PetscInt v = 0; v < nvtxs; ++v) {
    264:             if (assignment[v] == p) values[k++] = manager.getCell(v);
    265:           }
    266:           if (k != partition->getFiberDimension(p)) throw ALE::Exception("Invalid partition");
    267:           partition->updatePoint(p, values);
    268:         }
    269:         delete [] values;

    271:         for(PetscInt i = 0; i < nvtxs; ++i) {this->_allocator.destroy(assignment+i);}
    272:         this->_allocator.deallocate(assignment, nvtxs);
    273:       };
    274:     };
    275:   };
    276: #endif
    277:   namespace Simple {
    278:     template<typename Alloc_ = malloc_allocator<short int> >
    279:     class Partitioner {
    280:     public:
    281:       typedef int    part_type;
    282:       typedef Alloc_ alloc_type;
    283:     protected:
    284:       alloc_type _allocator;
    285:     public:
    286:       Partitioner() {};
    287:       ~Partitioner() {};
    288:     public:
    289:       static bool zeroBase() {return true;}
    290:       template<typename Section, typename MeshManager>
    291:       void partition(const int numVertices, const int start[], const int adjacency[], const Obj<Section>& partition, const MeshManager& manager) {
    292:         const int numProcs = partition->commSize();
    293:         const int rank     = partition->commRank();
    294:         int       maxSize  = 0;

    296:         for(int p = 0; p < numProcs; ++p) {
    297:           partition->setFiberDimension(p, numVertices/numProcs + ((numVertices % numProcs) > rank));
    298:           maxSize = std::max(maxSize, partition->getFiberDimension(p));
    299:         }
    300:         partition->allocatePoint();
    301:         typename Section::value_type *values = new typename Section::value_type[maxSize];

    303:         for(int p = 0; p < partition->commSize(); ++p) {
    304:           const int start = p*(numVertices/numProcs)     + p*((numVertices % numProcs) > p+1);
    305:           const int end   = (p+1)*(numVertices/numProcs) + (p+1)*((numVertices % numProcs) > p+2);
    306:           int       k     = 0;

    308:           for(int v = start; v < end; ++v, ++k) {
    309:             values[k] = manager.getCell(v);
    310:           }
    311:           if (k != partition->getFiberDimension(p)) throw ALE::Exception("Invalid partition");
    312:           partition->updatePoint(p, values);
    313:         }
    314:         delete [] values;
    315:       }
    316:     };
    317:   }
    318: #ifdef PETSC_HAVE_CHACO
    319:   template<typename GraphPartitioner = ALE::Chaco::Partitioner<>, typename Alloc_ = malloc_allocator<int> >
    320: #elif defined(PETSC_HAVE_PARMETIS)
    321:   template<typename GraphPartitioner = ALE::ParMetis::Partitioner<>, typename Alloc_ = malloc_allocator<int> >
    322: #else
    323:   template<typename GraphPartitioner = ALE::Simple::Partitioner<>, typename Alloc_ = malloc_allocator<int> >
    324: #endif
    325:   class Partitioner {
    326:   public:
    327:     typedef Alloc_                               alloc_type;
    328:     typedef GraphPartitioner                     graph_partitioner_type;
    329:     typedef typename GraphPartitioner::part_type part_type;
    330:     template<typename Mesh>
    331:     class MeshManager {
    332:     public:
    333:       typedef typename Mesh::point_type point_type;
    334:     protected:
    335:       const Obj<Mesh>& mesh;
    336:       bool             simpleCellNumbering;
    337:       point_type      *cells;
    338:       std::map<point_type, point_type> numbers;
    339:     protected:
    340:       void createCells(const int height) {
    341:         const Obj<typename Mesh::label_sequence>&     mcells   = mesh->heightStratum(height);
    342:         const typename Mesh::label_sequence::iterator cEnd     = mcells->end();
    343:         const int                                     numCells = mcells->size();
    344:         int                                           c        = 0;

    346:         this->cells               = NULL;
    347:         this->simpleCellNumbering = true;
    348:         for(typename Mesh::label_sequence::iterator c_iter = mcells->begin(); c_iter != cEnd; ++c_iter, ++c) {
    349:           if (*c_iter != c) {
    350:             this->simpleCellNumbering = false;
    351:             break;
    352:           }
    353:         }
    354:         if (!this->simpleCellNumbering) {
    355:           this->cells = new point_type[numCells];
    356:           c           = 0;
    357:           for(typename Mesh::label_sequence::iterator c_iter = mcells->begin(); c_iter != cEnd; ++c_iter, ++c) {
    358:             // OPT: Could use map only for exceptional points
    359:             this->cells[c] = *c_iter;
    360:             this->numbers[*c_iter] = c;
    361:           }
    362:         }
    363:       };
    364:     public:
    365:       MeshManager(const Obj<Mesh>& mesh, const int height = 0): mesh(mesh) {
    366:         this->createCells(height);
    367:       };
    368:       ~MeshManager() {
    369:         if (this->cells) {delete [] this->cells;}
    370:       };
    371:     public:
    372:       template<typename Float>
    373:       void createCellCoordinates(const int numVertices, Float *X[], Float *Y[], Float *Z[]) const {
    374:         const Obj<typename Mesh::real_section_type>& coordinates = mesh->getRealSection("coordinates");
    375:         const int dim = mesh->getDimension();
    376:         typedef typename alloc_type::template rebind<Float>::other float_alloc_type;
    377:         Float *x = float_alloc_type().allocate(numVertices*3);
    378:         for(int i = 0; i < numVertices*3; ++i) {float_alloc_type().construct(x+i, 0.0);}
    379:         Float *y = x+numVertices;
    380:         Float *z = y+numVertices;
    381:         Float *vCoords[3];

    383:         vCoords[0] = x; vCoords[1] = y; vCoords[2] = z;
    384:         const Obj<typename Mesh::label_sequence>& cells = mesh->heightStratum(0);
    385:         const int corners = mesh->size(coordinates, *(cells->begin()))/dim;
    386:         int       c       = 0;

    388:         for(typename Mesh::label_sequence::iterator c_iter = cells->begin(); c_iter !=cells->end(); ++c_iter, ++c) {
    389:           const typename Mesh::real_section_type::value_type *coords = mesh->restrictClosure(coordinates, *c_iter);

    391:           for(int d = 0; d < dim; ++d) {
    392:             vCoords[d][c] = 0.0;
    393:           }
    394:           for(int v = 0; v < corners; ++v) {
    395:             for(int d = 0; d < dim; ++d) {
    396:               vCoords[d][c] += coords[v*dim+d];
    397:             }
    398:           }
    399:           for(int d = 0; d < dim; ++d) {
    400:             vCoords[d][c] /= corners;
    401:           }
    402:         }
    403:         *X = x;
    404:         *Y = y;
    405:         *Z = z;
    406:       }
    407:       template<typename Float>
    408:       void destroyCellCoordinates(const int numVertices, Float *X[], Float *Y[], Float *Z[]) const {
    409:         typedef typename alloc_type::template rebind<Float>::other float_alloc_type;
    410:         Float *x = *X;

    412:         for(int i = 0; i < numVertices*3; ++i) {float_alloc_type().destroy(x+i);}
    413:         float_alloc_type().deallocate(x, numVertices*3);
    414:       }
    415:       point_type getCell(const point_type cellNumber) const {
    416:         if (this->simpleCellNumbering) {
    417:           return cellNumber;
    418:         }
    419:         return this->cells[cellNumber];
    420:       }
    421:       point_type getNumber(const point_type cell) {
    422:         if (this->simpleCellNumbering) {
    423:           return cell;
    424:         }
    425:         return this->numbers[cell];
    426:       }
    427:     };
    428:     template<typename Sieve>
    429:     class OffsetVisitor {
    430:       const Sieve& sieve;
    431:       const Sieve& overlapSieve;
    432:       int         *offsets;
    433:     public:
    434:       OffsetVisitor(const Sieve& s, const Sieve& ovS, int off[]) : sieve(s), overlapSieve(ovS), offsets(off) {};
    435:       void visitPoint(const typename Sieve::point_type& point) {};
    436:       void visitArrow(const typename Sieve::arrow_type& arrow) {
    437:         const typename Sieve::point_type cell   = arrow.target;
    438:         const typename Sieve::point_type face   = arrow.source;
    439:         const int                        size   = this->sieve.getSupportSize(face);
    440:         const int                        ovSize = this->overlapSieve.getSupportSize(face);

    442:         if (size == 2) {
    443:           offsets[cell+1]++;
    444:         } else if ((size == 1) && (ovSize == 1)) {
    445:           offsets[cell+1]++;
    446:         }
    447:       };
    448:     };
    449:     template<typename Sieve>
    450:     class AdjVisitor {
    451:     protected:
    452:       typename Sieve::point_type cell;
    453:       int                       *adjacency;
    454:       const int                  cellOffset;
    455:       int                        offset;
    456:     public:
    457:       AdjVisitor(int adj[], const bool zeroBase) : adjacency(adj), cellOffset(zeroBase ? 0 : 1), offset(0) {};
    458:       void visitPoint(const typename Sieve::point_type& point) {};
    459:       void visitArrow(const typename Sieve::arrow_type& arrow) {
    460:         const int neighbor = arrow.target;

    462:         if (neighbor != this->cell) {
    463:           //std::cout << "Adding dual edge from " << cell << " to " << neighbor << std::endl;
    464:           this->adjacency[this->offset++] = neighbor + this->cellOffset;
    465:         }
    466:       };
    467:     public:
    468:       void setCell(const typename Sieve::point_type cell) {this->cell = cell;};
    469:       int  getOffset() {return this->offset;}
    470:     };
    471:     template<typename Mesh, int maxSize = 10>
    472:     class FaceRecognizer {
    473:     public:
    474:       typedef typename Mesh::point_type point_type;
    475:     protected:
    476:       int numCases;
    477:       int numFaceVertices[maxSize];
    478:     public:
    479:       FaceRecognizer(Mesh& mesh, const int debug = 0) : numCases(0) {
    480:         if (mesh.depth() != 1) {throw ALE::Exception("Only works for depth 1 meshes");}
    481:         const int                                 dim   = mesh.getDimension();
    482:         const Obj<typename Mesh::sieve_type>&     sieve = mesh.getSieve();
    483:         const Obj<typename Mesh::label_sequence>& cells = mesh.heightStratum(0);
    484:         std::set<int>                             cornersSeen;

    486:         if (debug) {std::cout << "Building Recognizer" << std::endl;}
    487:         for(typename Mesh::label_sequence::iterator c_iter = cells->begin(); c_iter != cells->end(); ++c_iter) {
    488:           const int corners = sieve->getConeSize(*c_iter);

    490:           if (cornersSeen.find(corners) == cornersSeen.end()) {
    491:             if (numCases >= maxSize) {throw ALE::Exception("Exceeded maximum number of cases");}
    492:             cornersSeen.insert(corners);

    494:             if (corners == dim+1) {
    495:               numFaceVertices[numCases] = dim;
    496:               if (debug) {std::cout << "  Recognizing simplices" << std::endl;}
    497:             } else if ((dim == 1) && (corners == 3)) {
    498:               numFaceVertices[numCases] = 3;
    499:               if (debug) {std::cout << "  Recognizing quadratic edges" << std::endl;}
    500:             } else if ((dim == 2) && (corners == 4)) {
    501:               numFaceVertices[numCases] = 2;
    502:               if (debug) {std::cout << "  Recognizing quads" << std::endl;}
    503:             } else if ((dim == 2) && (corners == 6)) {
    504:               numFaceVertices[numCases] = 3;
    505:               if (debug) {std::cout << "  Recognizing tri and quad cohesive Lagrange cells" << std::endl;}
    506:             } else if ((dim == 2) && (corners == 9)) {
    507:               numFaceVertices[numCases] = 3;
    508:               if (debug) {std::cout << "  Recognizing quadratic quads and quadratic quad cohesive Lagrange cells" << std::endl;}
    509:             } else if ((dim == 3) && (corners == 6)) {
    510:               numFaceVertices[numCases] = 4;
    511:               if (debug) {std::cout << "  Recognizing tet cohesive cells" << std::endl;}
    512:             } else if ((dim == 3) && (corners == 8)) {
    513:               numFaceVertices[numCases] = 4;
    514:               if (debug) {std::cout << "  Recognizing hexes" << std::endl;}
    515:             } else if ((dim == 3) && (corners == 9)) {
    516:               numFaceVertices[numCases] = 6;
    517:               if (debug) {std::cout << "  Recognizing tet cohesive Lagrange cells" << std::endl;}
    518:             } else if ((dim == 3) && (corners == 10)) {
    519:               numFaceVertices[numCases] = 6;
    520:               if (debug) {std::cout << "  Recognizing quadratic tets" << std::endl;}
    521:             } else if ((dim == 3) && (corners == 12)) {
    522:               numFaceVertices[numCases] = 6;
    523:               if (debug) {std::cout << "  Recognizing hex cohesive Lagrange cells" << std::endl;}
    524:             } else if ((dim == 3) && (corners == 18)) {
    525:               numFaceVertices[numCases] = 6;
    526:               if (debug) {std::cout << "  Recognizing quadratic tet cohesive Lagrange cells" << std::endl;}
    527:             } else if ((dim == 3) && (corners == 27)) {
    528:               numFaceVertices[numCases] = 9;
    529:               if (debug) {std::cout << "  Recognizing quadratic hexes and quadratic hex cohesive Lagrange cells" << std::endl;}
    530:             } else {
    531:               throw ALE::Exception("Could not determine number of face vertices");
    532:             }
    533:             ++numCases;
    534:           }
    535:         }
    536:       };
    537:       ~FaceRecognizer() {};
    538:     public:
    539:       bool operator()(point_type cellA, point_type cellB, int meetSize) {
    540:         // Could concievably make this depend on the cells, but it seems slow
    541:         for(int i = 0; i < numCases; ++i) {
    542:           if (meetSize == numFaceVertices[i]) {
    543:             //std::cout << "  Recognized case " << i <<"("<<numFaceVertices[i]<<") for <" << cellA <<","<< cellB << ">" << std::endl;
    544:             return true;
    545:           }
    546:         }
    547:         return false;
    548:       };
    549:     };
    550:     template<typename Mesh>
    551:     class SimpleFaceRecognizer {
    552:     public:
    553:       typedef typename Mesh::point_type point_type;
    554:     protected:
    555:       int dim;
    556:     public:
    557:       SimpleFaceRecognizer(Mesh& mesh, const int debug = 0) {
    558:         if (mesh.depth() != 1) {throw ALE::Exception("Only works for depth 1 meshes");}
    559:         this->dim = mesh.getDimension();
    560:       };
    561:       ~SimpleFaceRecognizer() {};
    562:     public:
    563:       bool operator()(point_type cellA, point_type cellB, int meetSize) {
    564:         if (meetSize >= dim) {
    565:           return true;
    566:         }
    567:         return false;
    568:       };
    569:     };
    570:     template<typename Sieve, typename Manager, typename Recognizer>
    571:     class MeetVisitor {
    572:     public:
    573:       typedef std::set<typename Sieve::point_type> neighbors_type;
    574:     protected:
    575:       const Sieve& sieve;
    576:       Manager& manager;
    577:       Recognizer& faceRecognizer;
    578:       const int numCells;
    579:       neighbors_type *neighborCells;
    580:       typename ISieveVisitor::PointRetriever<Sieve> *pR;
    581:       typename Sieve::point_type cell;
    582:     public:
    583:       MeetVisitor(const Sieve& s, Manager& manager, Recognizer& faceRecognizer, const int n) : sieve(s), manager(manager), faceRecognizer(faceRecognizer), numCells(n) {
    584:         this->neighborCells = new std::set<typename Sieve::point_type>[numCells];
    585:         this->pR            = new typename ISieveVisitor::PointRetriever<Sieve>(this->sieve.getMaxConeSize());
    586:       };
    587:       ~MeetVisitor() {delete [] this->neighborCells; delete this->pR;};
    588:       void visitArrow(const typename Sieve::arrow_type& arrow) {};
    589:       void visitPoint(const typename Sieve::point_type& point) {
    590:         const typename Sieve::point_type& neighbor = point;

    592:         if (this->cell == neighbor) return;
    593:         this->pR->clear();
    594:         this->sieve.meet(this->cell, neighbor, *this->pR);
    595:         if (faceRecognizer(this->cell, neighbor, this->pR->getSize())) {
    596:           this->neighborCells[this->manager.getNumber(this->cell)].insert(this->manager.getNumber(neighbor));
    597:         }
    598:       };
    599:     public:
    600:       void setCell(const typename Sieve::point_type& c) {this->cell = c;};
    601:       const neighbors_type *getNeighbors() {return this->neighborCells;};
    602:     };
    603:   public: // Creating overlaps
    604:     // Create a partition point overlap for distribution
    605:     //   This is the default overlap which comes from distributing a serial mesh on process 0
    606:     template<typename SendOverlap, typename RecvOverlap>
    607:     static void createDistributionPartOverlap(const Obj<SendOverlap>& sendOverlap, const Obj<RecvOverlap>& recvOverlap) {
    608:       const int rank = sendOverlap->commRank();
    609:       const int size = sendOverlap->commSize();

    611:       if (rank == 0) {
    612:         for(int p = 1; p < size; p++) {
    613:           // The arrow is from local partition point p (source) to remote partition point p (color) on rank p (target)
    614:           sendOverlap->addCone(p, p, p);
    615:         }
    616:       }
    617:       if (rank != 0) {
    618:         // The arrow is from remote partition point rank (color) on rank 0 (source) to local partition point rank (target)
    619:         recvOverlap->addCone(0, rank, rank);
    620:       }
    621:     }
    622:     // Create a mesh point overlap for distribution
    623:     //   A local numbering is created for the remote points
    624:     //   This is the default overlap which comes from distributing a serial mesh on process 0
    625:     template<typename Section, typename RecvPartOverlap, typename Renumbering, typename SendOverlap, typename RecvOverlap>
    626:     static void createDistributionMeshOverlap(const Obj<Section>& partition, const Obj<RecvPartOverlap>& recvPartOverlap, Renumbering& renumbering, const Obj<Section>& overlapPartition, const Obj<SendOverlap>& sendOverlap, const Obj<RecvOverlap>& recvOverlap) {
    627:       const typename Section::chart_type& chart = partition->getChart();
    628:       int numRanks = 0;

    630:       for(typename Section::chart_type::const_iterator p_iter = chart.begin(); p_iter != chart.end(); ++p_iter) {
    631:         if (*p_iter != sendOverlap->commRank() && partition->getFiberDimension(*p_iter)) numRanks++;
    632:       }
    633:       sendOverlap->setBaseSize(numRanks); // setNumRanks
    634:       for(typename Section::chart_type::const_iterator p_iter = chart.begin(); p_iter != chart.end(); ++p_iter) {
    635:         const int coneSize = partition->getFiberDimension(*p_iter);

    637:         if (*p_iter != sendOverlap->commRank() && coneSize) {
    638:           sendOverlap->setConeSize(*p_iter, coneSize); // setNumPoints
    639:         }
    640:       }
    641:       sendOverlap->assemble();
    642:       for(typename Section::chart_type::const_iterator p_iter = chart.begin(); p_iter != chart.end(); ++p_iter) {
    643:         if (*p_iter == sendOverlap->commRank()) continue;
    644:         const typename Section::value_type *points     = partition->restrictPoint(*p_iter);
    645:         const int                           numPoints  = partition->getFiberDimension(*p_iter);

    647:         for(int i = 0; i < numPoints; ++i) {
    648:           // Notice here that we do not know the local renumbering (but we do not use it)
    649:           sendOverlap->addArrow(points[i], *p_iter, points[i]);
    650:         }
    651:       }
    652:       sendOverlap->assemblePoints();
    653:       if (sendOverlap->debug()) {sendOverlap->view("Send mesh overlap");}
    654:       const typename RecvPartOverlap::capSequence::iterator rBegin = recvPartOverlap->capBegin();
    655:       const typename RecvPartOverlap::capSequence::iterator rEnd   = recvPartOverlap->capEnd();

    657:       recvOverlap->setCapSize(recvPartOverlap->getCapSize()); // setNumRanks
    658:       for(typename RecvPartOverlap::capSequence::iterator r_iter = rBegin; r_iter != rEnd; ++r_iter) {
    659:         const int                                                 rank   = *r_iter;
    660:         const typename RecvPartOverlap::supportSequence::iterator pBegin = recvPartOverlap->supportBegin(*r_iter);
    661:         const typename RecvPartOverlap::supportSequence::iterator pEnd   = recvPartOverlap->supportEnd(*r_iter);

    663:         for(typename RecvPartOverlap::supportSequence::iterator p_iter = pBegin; p_iter != pEnd; ++p_iter) {
    664:           const typename Section::point_type& remotePartPoint = p_iter.color();
    665:           const int                           numPoints       = overlapPartition->getFiberDimension(remotePartPoint);

    667:           recvOverlap->setSupportSize(rank, numPoints); // setNumPoints
    668:         }
    669:       }
    670:       recvOverlap->assemble();

    672:       for(typename RecvPartOverlap::capSequence::iterator r_iter = rBegin; r_iter != rEnd; ++r_iter) {
    673:         const int                                                 rank   = *r_iter;
    674:         const typename RecvPartOverlap::supportSequence::iterator pBegin = recvPartOverlap->supportBegin(*r_iter);
    675:         const typename RecvPartOverlap::supportSequence::iterator pEnd   = recvPartOverlap->supportEnd(*r_iter);

    677:         for(typename RecvPartOverlap::supportSequence::iterator p_iter = pBegin; p_iter != pEnd; ++p_iter) {
    678:           const typename Section::point_type& remotePartPoint = p_iter.color();
    679:           const typename Section::value_type *points          = overlapPartition->restrictPoint(remotePartPoint);
    680:           const int                           numPoints       = overlapPartition->getFiberDimension(remotePartPoint);

    682:           for(int i = 0; i < numPoints; ++i) {
    683:             recvOverlap->addArrow(rank, renumbering[points[i]], points[i]);
    684:           }
    685:         }
    686:       }
    687:       recvOverlap->assemblePoints();
    688:       if (recvOverlap->debug()) {recvOverlap->view("Receive mesh overlap");}
    689:     }
    690:     // Create a partition point overlap from a partition
    691:     //   The intention is to create an overlap which enables exchange of redistribution information
    692:     template<typename Section, typename SendOverlap, typename RecvOverlap>
    693:     static void createPartitionPartOverlap(const Obj<Section>& partition, const Obj<SendOverlap>& sendOverlap, const Obj<RecvOverlap>& recvOverlap) {
    694:       const typename Section::chart_type& chart      = partition->getChart();
    695:       const int                           rank       = partition->commRank();
    696:       const int                           size       = partition->commSize();
    697:       int                                *adj        = new int[size];
    698:       int                                *recvCounts = new int[size];
    699:       int                                 numNeighbors;

    701:       for(int p = 0; p < size; ++p) {
    702:         adj[p]        = 0;
    703:         recvCounts[p] = 1;
    704:       }
    705:       for(typename Section::chart_type::const_iterator p_iter = chart.begin(); p_iter != chart->end(); ++p_iter) {
    706:         const typename Section::value_type& p = partition->restrictPoint(*p_iter)[0];
    707:         // The arrow is from local partition point p (source) to remote partition point p (color) on rank p (target)
    708:         sendOverlap->addCone(p, p, p);
    709:         adj[p] = 1;
    710:       }
    711:       MPI_Reduce_Scatter(adj, &numNeighbors, recvCounts, size, MPI_INT, MPI_SUM, partition->comm());
    712:       MPI_Request *recvRequests = new MPI_Request[numNeighbors];
    713:       int          dummy        = 0;

    715:       // TODO: Get a unique tag
    716:       for(int n = 0; n < numNeighbors; ++n) {
    717:         MPI_Irecv(&dummy, 1, MPI_INT, MPI_ANY_SOURCE, 1, partition->comm(), &recvRequests[n]);
    718:       }
    719:       const Obj<typename SendOverlap::traits::baseSequence>      ranks        = sendOverlap->base();
    720:       const typename SendOverlap::traits::baseSequence::iterator rEnd         = ranks->end();
    721:       MPI_Request                                               *sendRequests = new MPI_Request[ranks->size()];
    722:       int                                                        s            = 0;

    724:       for(typename SendOverlap::traits::baseSequence::iterator r_iter = ranks->begin(); r_iter != rEnd; ++r_iter, ++s) {
    725:         MPI_Isend(&dummy, 1, MPI_INT, *r_iter, 1, partition->comm(), &sendRequests[s]);
    726:       }
    727:       for(int n = 0; n < numNeighbors; ++n) {
    728:         MPI_Status status;
    729:         int        idx;

    731:         MPI_Waitany(numNeighbors, recvRequests, &idx, &status);
    732:         // The arrow is from remote partition point rank (color) on rank p (source) to local partition point rank (target)
    733:         recvOverlap->addCone(status.MPI_SOURCE, rank, rank);
    734:       }
    735:       MPI_Waitall(ranks->size(), sendRequests, MPI_STATUSES_IGNORE);
    736:       delete [] sendRequests;
    737:       delete [] recvRequests;
    738:       delete [] adj;
    739:       delete [] recvCounts;
    740:     }
    741:   public: // Building CSR meshes
    742:     // This produces the dual graph (each cell is a vertex and each face is an edge)
    743:     //   numbering:   A contiguous numbering of the cells (not yet included)
    744:     //   numVertices: The number of vertices in the graph (cells in the mesh)
    745:     //   adjacency:   The vertices adjacent to each vertex (cells adjacent to each mesh cell)
    746:     // - We allow an exception to contiguous numbering.
    747:     //   If the cell id > numElements, we assign a new number starting at
    748:     //     the top and going downward. I know these might not match up with
    749:     //     the iterator order, but we can fix it later.
    750:     template<typename Mesh>
    751:     static void buildDualCSR(const Obj<Mesh>& mesh, int *numVertices, int **offsets, int **adjacency, const bool zeroBase = true) {
    752:       const Obj<typename Mesh::sieve_type>&         sieve        = mesh->getSieve();
    753:       const Obj<typename Mesh::label_sequence>&     cells        = mesh->heightStratum(0);
    754:       const typename Mesh::label_sequence::iterator cEnd         = cells->end();
    755:       const int                                     numCells     = cells->size();
    756:       int                                           newCell      = numCells;
    757:       Obj<typename Mesh::sieve_type>                overlapSieve = new typename Mesh::sieve_type(mesh->comm(), mesh->debug());
    758:       int                                           offset       = 0;
    759:       const int                                     cellOffset   = zeroBase ? 0 : 1;
    760:       const int                                     dim          = mesh->getDimension();
    761:       std::map<typename Mesh::point_type, typename Mesh::point_type> newCells;

    763:       // TODO: This is necessary for parallel partitioning
    764:       //completion::scatterSupports(sieve, overlapSieve, mesh->getSendOverlap(), mesh->getRecvOverlap(), mesh);
    765:       if (numCells == 0) {
    766:         *numVertices = 0;
    767:         *offsets     = NULL;
    768:         *adjacency   = NULL;
    769:         return;
    770:       }
    771:       int *off = alloc_type().allocate(numCells+1);
    772:       int *adj;
    773:       for(int i = 0; i < numCells+1; ++i) {alloc_type().construct(off+i, 0);}
    774:       if (mesh->depth() == dim) {
    775:         int c = 1;

    777:         for(typename Mesh::label_sequence::iterator c_iter = cells->begin(); c_iter != cEnd; ++c_iter, ++c) {
    778:           const Obj<typename Mesh::sieve_type::traits::coneSequence>&     faces = sieve->cone(*c_iter);
    779:           const typename Mesh::sieve_type::traits::coneSequence::iterator fEnd  = faces->end();

    781:           off[c] = off[c-1];
    782:           for(typename Mesh::sieve_type::traits::coneSequence::iterator f_iter = faces->begin(); f_iter != fEnd; ++f_iter) {
    783:             if (sieve->support(*f_iter)->size() == 2) {
    784:               off[c]++;
    785:             } else if ((sieve->support(*f_iter)->size() == 1) && (overlapSieve->support(*f_iter)->size() == 1)) {
    786:               off[c]++;
    787:             }
    788:           }
    789:         }
    790:         adj = alloc_type().allocate(off[numCells]);
    791:         for(int i = 0; i < off[numCells]; ++i) {alloc_type().construct(adj+i, 0);}
    792:         for(typename Mesh::label_sequence::iterator c_iter = cells->begin(); c_iter != cEnd; ++c_iter) {
    793:           const Obj<typename Mesh::sieve_type::traits::coneSequence>&     faces = sieve->cone(*c_iter);
    794:           const typename Mesh::sieve_type::traits::coneSequence::iterator fEnd  = faces->end();

    796:           for(typename Mesh::sieve_type::traits::coneSequence::iterator f_iter = faces->begin(); f_iter != fEnd; ++f_iter) {
    797:             const Obj<typename Mesh::sieve_type::traits::supportSequence>&     neighbors = sieve->support(*f_iter);
    798:             const typename Mesh::sieve_type::traits::supportSequence::iterator nEnd      = neighbors->end();

    800:             for(typename Mesh::sieve_type::traits::supportSequence::iterator n_iter = neighbors->begin(); n_iter != nEnd; ++n_iter) {
    801:               if (*n_iter != *c_iter) adj[offset++] = *n_iter + cellOffset;
    802:             }
    803:             const Obj<typename Mesh::sieve_type::traits::supportSequence>&     oNeighbors = overlapSieve->support(*f_iter);
    804:             const typename Mesh::sieve_type::traits::supportSequence::iterator onEnd      = oNeighbors->end();

    806:             for(typename Mesh::sieve_type::traits::supportSequence::iterator n_iter = oNeighbors->begin(); n_iter != onEnd; ++n_iter) {
    807:               adj[offset++] = *n_iter + cellOffset;
    808:             }
    809:           }
    810:         }
    811:       } else if (mesh->depth() == 1) {
    812:         std::set<typename Mesh::point_type> *neighborCells = new std::set<typename Mesh::point_type>[numCells];
    813:         const int                            corners       = sieve->cone(*cells->begin())->size();
    814:         int                                  faceVertices;

    816:         if (corners == dim+1) {
    817:           faceVertices = dim;
    818:         } else if ((dim == 2) && (corners == 4)) {
    819:           faceVertices = 2;
    820:         } else if ((dim == 3) && (corners == 8)) {
    821:           faceVertices = 4;
    822:         } else if ((dim == 2) && (corners == 6)) {
    823:           faceVertices = 3;
    824:         } else if ((dim == 2) && (corners == 9)) {
    825:           faceVertices = 3;
    826:         } else if ((dim == 3) && (corners == 10)) {
    827:           faceVertices = 6;
    828:         } else if ((dim == 3) && (corners == 27)) {
    829:           faceVertices = 9;
    830:         } else {
    831:           throw ALE::Exception("Could not determine number of face vertices");
    832:         }
    833:         for(typename Mesh::label_sequence::iterator c_iter = cells->begin(); c_iter != cells->end(); ++c_iter) {
    834:             const Obj<typename Mesh::sieve_type::traits::coneSequence>&     vertices = sieve->cone(*c_iter);
    835:             const typename Mesh::sieve_type::traits::coneSequence::iterator vEnd     = vertices->end();

    837:             for(typename Mesh::sieve_type::traits::coneSequence::iterator v_iter = vertices->begin(); v_iter != vEnd; ++v_iter) {
    838:               const Obj<typename Mesh::sieve_type::traits::supportSequence>&     neighbors = sieve->support(*v_iter);
    839:               const typename Mesh::sieve_type::traits::supportSequence::iterator nEnd      = neighbors->end();

    841:               for(typename Mesh::sieve_type::traits::supportSequence::iterator n_iter = neighbors->begin(); n_iter != nEnd; ++n_iter) {
    842:                 if (*c_iter == *n_iter) continue;
    843:                 if ((int) sieve->nMeet(*c_iter, *n_iter, 1)->size() == faceVertices) {
    844:                   if ((*c_iter < numCells) && (*n_iter < numCells)) {
    845:                     neighborCells[*c_iter].insert(*n_iter);
    846:                   } else {
    847:                     typename Mesh::point_type e = *c_iter, n = *n_iter;

    849:                     if (*c_iter >= numCells) {
    850:                       if (newCells.find(*c_iter) == newCells.end()) newCells[*c_iter] = --newCell;
    851:                       e = newCells[*c_iter];
    852:                     }
    853:                     if (*n_iter >= numCells) {
    854:                       if (newCells.find(*n_iter) == newCells.end()) newCells[*n_iter] = --newCell;
    855:                       n = newCells[*n_iter];
    856:                     }
    857:                     neighborCells[e].insert(n);
    858:                   }
    859:                 }
    860:               }
    861:             }
    862:           }
    863:           off[0] = 0;
    864:           for(int c = 1; c <= numCells; c++) {
    865:             off[c] = neighborCells[c-1].size() + off[c-1];
    866:           }
    867:           adj = alloc_type().allocate(off[numCells]);
    868:           for(int i = 0; i < off[numCells]; ++i) {alloc_type().construct(adj+i, 0);}
    869:           for(int c = 0; c < numCells; c++) {
    870:             for(typename std::set<typename Mesh::point_type>::iterator n_iter = neighborCells[c].begin(); n_iter != neighborCells[c].end(); ++n_iter) {
    871:               adj[offset++] = *n_iter + cellOffset;
    872:             }
    873:           }
    874:           delete [] neighborCells;
    875:       } else {
    876:         throw ALE::Exception("Dual creation not defined for partially interpolated meshes");
    877:       }
    878:       if (offset != off[numCells]) {
    879:         ostringstream msg;
    880:         msg << "ERROR: Total number of neighbors " << offset << " does not match the offset array " << off[numCells];
    881:         throw ALE::Exception(msg.str().c_str());
    882:       }
    883:       *numVertices = numCells;
    884:       *offsets     = off;
    885:       *adjacency   = adj;
    886:     }
    887:     template<typename Mesh>
    888:     static void buildDualCSRV(const Obj<Mesh>& mesh, MeshManager<Mesh>& manager, int *numVertices, int **offsets, int **adjacency, const bool zeroBase = true) {
    889:       const Obj<typename Mesh::sieve_type>&         sieve        = mesh->getSieve();
    890:       const Obj<typename Mesh::label_sequence>&     cells        = mesh->heightStratum(0);
    891:       const typename Mesh::label_sequence::iterator cEnd         = cells->end();
    892:       const int                                     numCells     = cells->size();
    893:       Obj<typename Mesh::sieve_type>                overlapSieve = new typename Mesh::sieve_type(mesh->comm(), mesh->debug());
    894:       int                                           offset       = 0;
    895:       const int                                     cellOffset   = zeroBase ? 0 : 1;
    896:       const int                                     dim          = mesh->getDimension();
    897:       std::map<typename Mesh::point_type, typename Mesh::point_type> newCells;

    899:       // TODO: This is necessary for parallel partitioning
    900:       //completion::scatterSupports(sieve, overlapSieve, mesh->getSendOverlap(), mesh->getRecvOverlap(), mesh);
    901:       overlapSieve->setChart(sieve->getChart());
    902:       overlapSieve->allocate();
    903:       if (numCells == 0) {
    904:         *numVertices = 0;
    905:         *offsets     = NULL;
    906:         *adjacency   = NULL;
    907:         return;
    908:       }
    909:       int *off = alloc_type().allocate(numCells+1);
    910:       int *adj;
    911:       for(int i = 0; i < numCells+1; ++i) {alloc_type().construct(off+i, 0);}
    912:       if (mesh->depth() == dim) {
    913:         OffsetVisitor<typename Mesh::sieve_type> oV(*sieve, *overlapSieve, off);

    915:         for(typename Mesh::label_sequence::iterator c_iter = cells->begin(); c_iter != cEnd; ++c_iter) {
    916:           sieve->cone(*c_iter, oV);
    917:         }
    918:         for(int p = 1; p <= numCells; ++p) {
    919:           off[p] = off[p] + off[p-1];
    920:         }
    921:         adj = alloc_type().allocate(off[numCells]);
    922:         for(int i = 0; i < off[numCells]; ++i) {alloc_type().construct(adj+i, 0);}
    923:         AdjVisitor<typename Mesh::sieve_type> aV(adj, zeroBase);
    924:         ISieveVisitor::SupportVisitor<typename Mesh::sieve_type, AdjVisitor<typename Mesh::sieve_type> > sV(*sieve, aV);
    925:         ISieveVisitor::SupportVisitor<typename Mesh::sieve_type, AdjVisitor<typename Mesh::sieve_type> > ovSV(*overlapSieve, aV);

    927:         for(typename Mesh::label_sequence::iterator c_iter = cells->begin(); c_iter != cEnd; ++c_iter) {
    928:           aV.setCell(*c_iter);
    929:           sieve->cone(*c_iter, sV);
    930:           sieve->cone(*c_iter, ovSV);
    931:         }
    932:         offset = aV.getOffset();
    933:       } else if (mesh->depth() == 1) {
    934:         typedef MeetVisitor<typename Mesh::sieve_type, MeshManager<Mesh>, SimpleFaceRecognizer<Mesh> > mv_type;
    935:         typedef typename ISieveVisitor::SupportVisitor<typename Mesh::sieve_type, mv_type>       sv_type;
    936:         SimpleFaceRecognizer<Mesh> faceRecognizer(*mesh);

    938:         mv_type mV(*sieve, manager, faceRecognizer, numCells);
    939:         sv_type sV(*sieve, mV);

    941:         for(typename Mesh::label_sequence::iterator c_iter = cells->begin(); c_iter != cells->end(); ++c_iter) {
    942:           mV.setCell(*c_iter);
    943:           sieve->cone(*c_iter, sV);
    944:         }
    945:         const typename mv_type::neighbors_type *neighborCells = mV.getNeighbors();

    947:         off[0] = 0;
    948:         for(int c = 1; c <= numCells; c++) {
    949:           off[c] = neighborCells[c-1].size() + off[c-1];
    950:         }
    951:         adj = alloc_type().allocate(off[numCells]);
    952:         for(int i = 0; i < off[numCells]; ++i) {alloc_type().construct(adj+i, 0);}
    953:         for(int c = 0; c < numCells; c++) {
    954:           for(typename mv_type::neighbors_type::const_iterator n_iter = neighborCells[c].begin(); n_iter != neighborCells[c].end(); ++n_iter) {
    955:             //std::cout << "Adding dual edge from " << c << " to " << *n_iter << std::endl;
    956:             adj[offset++] = *n_iter + cellOffset;
    957:           }
    958:         }
    959:       } else {
    960:         throw ALE::Exception("Dual creation not defined for partially interpolated meshes");
    961:       }
    962:       if (offset != off[numCells]) {
    963:         ostringstream msg;
    964:         msg << "ERROR: Total number of neighbors " << offset << " does not match the offset array " << off[numCells];
    965:         throw ALE::Exception(msg.str().c_str());
    966:       }
    967:       *numVertices = numCells;
    968:       *offsets     = off;
    969:       *adjacency   = adj;
    970:     }
    971:     // This produces a hypergraph (each face is a vertex and each cell is a hyperedge)
    972:     //   numbering: A contiguous numbering of the faces
    973:     //   numEdges:  The number of edges in the hypergraph
    974:     //   adjacency: The vertices in each edge
    975:     template<typename Mesh>
    976:     static void buildFaceDualCSR(const Obj<Mesh>& mesh, const Obj<typename Mesh::numbering_type>& numbering, int *numEdges, int **offsets, int **adjacency, const bool zeroBase = true) {
    977:       const Obj<typename Mesh::sieve_type>&         sieve = mesh->getSieve();
    978:       const Obj<typename Mesh::label_sequence>&     cells = mesh->heightStratum(0);
    979:       const typename Mesh::label_sequence::iterator cEnd  = cells->end();
    980:       const int faceOffset = zeroBase ? 0 : 1;
    981:       int       numCells = cells->size();
    982:       int       c        = 1;

    984:       if (mesh->depth() != mesh->getDimension()) {throw ALE::Exception("Not yet implemented for non-interpolated meshes");}
    985:       int *off = alloc_type().allocate(numCells+1);
    986:       for(int i = 0; i < numCells+1; ++i) {alloc_type().construct(off+i, 0);}
    987:       for(typename Mesh::label_sequence::iterator c_iter = cells->begin(); c_iter != cEnd; ++c_iter, ++c) {
    988:         off[c] = sieve->cone(*c_iter)->size() + off[c-1];
    989:       }
    990:       int *adj = alloc_type().allocate(off[numCells]);
    991:       for(int i = 0; i < off[numCells]; ++i) {alloc_type().construct(adj+i, 0);}
    992:       int  offset = 0;
    993:       for(typename Mesh::label_sequence::iterator c_iter = cells->begin(); c_iter != cEnd; ++c_iter) {
    994:         const Obj<typename Mesh::sieve_type::traits::coneSequence>&     faces = sieve->cone(*c_iter);
    995:         const typename Mesh::sieve_type::traits::coneSequence::iterator fEnd  = faces->end();

    997:         for(typename Mesh::sieve_type::traits::coneSequence::iterator f_iter = faces->begin(); f_iter != fEnd; ++f_iter, ++offset) {
    998:           adj[offset] = numbering->getIndex(*f_iter) + faceOffset;
    999:         }
    1000:       }
    1001:       if (offset != off[numCells]) {
    1002:         ostringstream msg;
    1003:         msg << "ERROR: Total number of neighbors " << offset << " does not match the offset array " << off[numCells];
    1004:         throw ALE::Exception(msg.str().c_str());
    1005:       }
    1006:       *numEdges  = numCells;
    1007:       *offsets   = off;
    1008:       *adjacency = adj;
    1009:     }
    1010:     template<typename Mesh>
    1011:     static void buildFaceDualCSRV(const Obj<Mesh>& mesh, const Obj<typename Mesh::numbering_type>& numbering, int *numEdges, int **offsets, int **adjacency, const bool zeroBase = true) {
    1012:       throw ALE::Exception("Not implemented");
    1013:     }
    1014:     static void destroyCSR(int numPoints, int *offsets, int *adjacency) {
    1015:       if (adjacency) {
    1016:         for(int i = 0; i < offsets[numPoints]; ++i) {alloc_type().destroy(adjacency+i);}
    1017:         alloc_type().deallocate(adjacency, offsets[numPoints]);
    1018:       }
    1019:       if (offsets) {
    1020:         for(int i = 0; i < numPoints+1; ++i) {alloc_type().destroy(offsets+i);}
    1021:         alloc_type().deallocate(offsets, numPoints+1);
    1022:       }
    1023:     }
    1024:     template<typename OldSection, typename Partition, typename Renumbering, typename NewSection>
    1025:     static void createLocalSection(const Obj<OldSection>& oldSection, const Obj<Partition>& partition, Renumbering& renumbering, const Obj<NewSection>& newSection) {
    1026:       const typename Partition::value_type *points    = partition->restrictPoint(oldSection->commRank());
    1027:       const int                             numPoints = partition->getFiberDimension(oldSection->commRank());

    1029:       for(int p = 0; p < numPoints; ++p) {
    1030:         if (oldSection->hasPoint(points[p])) {
    1031:           newSection->setFiberDimension(renumbering[points[p]], oldSection->getFiberDimension(points[p]));
    1032:         }
    1033:       }
    1034:       if (numPoints) {newSection->allocatePoint();}
    1035:       for(int p = 0; p < numPoints; ++p) {
    1036:         if (oldSection->hasPoint(points[p])) {
    1037:           newSection->updatePointAll(renumbering[points[p]], oldSection->restrictPoint(points[p]));
    1038:         }
    1039:       }
    1040:     }
    1041:     // Specialize to ArrowSection
    1042:     template<typename OldSection, typename Partition, typename Renumbering>
    1043:     static void createLocalSection(const Obj<OldSection>& oldSection, const Obj<Partition>& partition, Renumbering& renumbering, const Obj<UniformSection<MinimalArrow<int,int>,int> >& newSection) {
    1044:       typedef UniformSection<MinimalArrow<int,int>,int> NewSection;
    1045:       const typename Partition::value_type    *points    = partition->restrictPoint(oldSection->commRank());
    1046:       const int                                numPoints = partition->getFiberDimension(oldSection->commRank());
    1047:       const typename OldSection::chart_type&   oldChart  = oldSection->getChart();
    1048:       std::set<typename Partition::value_type> myPoints;

    1050:       for(int p = 0; p < numPoints; ++p) {
    1051:         myPoints.insert(points[p]);
    1052:       }
    1053:       for(typename OldSection::chart_type::const_iterator c_iter = oldChart.begin(); c_iter != oldChart.end(); ++c_iter) {
    1054:         if (myPoints.count(c_iter->source) && myPoints.count(c_iter->target)) {
    1055:           newSection->setFiberDimension(typename OldSection::point_type(renumbering[c_iter->source], renumbering[c_iter->target]), oldSection->getFiberDimension(*c_iter));
    1056:         }
    1057:       }
    1058:       if (oldChart.size()) {newSection->allocatePoint();}
    1059:       for(typename OldSection::chart_type::const_iterator c_iter = oldChart.begin(); c_iter != oldChart.end(); ++c_iter) {
    1060:         if (myPoints.count(c_iter->source) && myPoints.count(c_iter->target)) {
    1061:           const typename OldSection::value_type *values = oldSection->restrictPoint(*c_iter);

    1063:           newSection->updatePointAll(typename OldSection::point_type(renumbering[c_iter->source], renumbering[c_iter->target]), values);
    1064:         }
    1065:       }
    1066:     }
    1067:     template<typename Sifter, typename Section, typename Renumbering>
    1068:     static void createLocalSifter(const Obj<Sifter>& sifter, const Obj<Section>& partition, Renumbering& renumbering, const Obj<Sifter>& localSifter) {
    1069:       const typename Section::value_type *points    = partition->restrictPoint(sifter->commRank());
    1070:       const int                           numPoints = partition->getFiberDimension(sifter->commRank());

    1072:       for(int p = 0; p < numPoints; ++p) {
    1073:         const Obj<typename Sifter::traits::coneSequence>&     cone = sifter->cone(points[p]);
    1074:         const typename Sifter::traits::coneSequence::iterator cEnd = cone->end();

    1076:         for(typename Sifter::traits::coneSequence::iterator c_iter = cone->begin(); c_iter != cEnd; ++c_iter) {
    1077:           localSifter->addArrow(*c_iter, renumbering[points[p]]);
    1078:         }
    1079:       }
    1080:     }
    1081:     template<typename Sieve, typename Section, typename Renumbering>
    1082:     static void createLocalSieve(const Obj<Sieve>& sieve, const Obj<Section>& partition, Renumbering& renumbering, const Obj<Sieve>& localSieve, const int height = 0) {
    1083:       const typename Section::value_type *points    = partition->restrictPoint(sieve->commRank());
    1084:       const int                           numPoints = partition->getFiberDimension(sieve->commRank());

    1086:       for(int p = 0; p < numPoints; ++p) {
    1087:         Obj<typename Sieve::coneSet> current = new typename Sieve::coneSet();
    1088:         Obj<typename Sieve::coneSet> next    = new typename Sieve::coneSet();
    1089:         Obj<typename Sieve::coneSet> tmp;

    1091:         current->insert(points[p]);
    1092:         while(current->size()) {
    1093:           for(typename Sieve::coneSet::const_iterator p_iter = current->begin(); p_iter != current->end(); ++p_iter) {
    1094:             const Obj<typename Sieve::traits::coneSequence>& cone = sieve->cone(*p_iter);

    1096:             for(typename Sieve::traits::coneSequence::iterator c_iter = cone->begin(); c_iter != cone->end(); ++c_iter) {
    1097:               localSieve->addArrow(renumbering[*c_iter], renumbering[*p_iter], c_iter.color());
    1098:               next->insert(*c_iter);
    1099:             }
    1100:           }
    1101:           tmp = current; current = next; next = tmp;
    1102:           next->clear();
    1103:         }
    1104:         if (height) {
    1105:           current->insert(points[p]);
    1106:           while(current->size()) {
    1107:             for(typename Sieve::coneSet::const_iterator p_iter = current->begin(); p_iter != current->end(); ++p_iter) {
    1108:               const Obj<typename Sieve::traits::supportSequence>& support = sieve->support(*p_iter);

    1110:               for(typename Sieve::traits::supportSequence::iterator s_iter = support->begin(); s_iter != support->end(); ++s_iter) {
    1111:                 localSieve->addArrow(renumbering[*p_iter], renumbering[*s_iter], s_iter.color());
    1112:                 next->insert(*s_iter);
    1113:               }
    1114:             }
    1115:             tmp = current; current = next; next = tmp;
    1116:             next->clear();
    1117:           }
    1118:         }
    1119:       }
    1120:     }
    1121:     template<typename Mesh, typename Section, typename Renumbering>
    1122:     static void createLocalMesh(const Obj<Mesh>& mesh, const Obj<Section>& partition, Renumbering& renumbering, const Obj<Mesh>& localMesh, const int height = 0) {
    1123:       const Obj<typename Mesh::sieve_type>& sieve      = mesh->getSieve();
    1124:       const Obj<typename Mesh::sieve_type>& localSieve = localMesh->getSieve();

    1126:       createLocalSieve(sieve, partition, renumbering, localSieve, height);
    1127:     }
    1128:     template<typename Sieve, typename Section, typename Renumbering>
    1129:     static void sizeLocalSieveV(const Obj<Sieve>& sieve, const Obj<Section>& partition, Renumbering& renumbering, const Obj<Sieve>& localSieve, const int height = 0) {
    1130:       typedef std::set<typename Sieve::point_type> pointSet;
    1131:       const typename Section::value_type *points    = partition->restrictPoint(sieve->commRank());
    1132:       const int                           numPoints = partition->getFiberDimension(sieve->commRank());
    1133:       int                                 maxSize   = std::max(0, std::max(sieve->getMaxConeSize(), sieve->getMaxSupportSize()));
    1134:       const pointSet                      pSet(points, &points[numPoints]);
    1135:       ISieveVisitor::FilteredPointRetriever<Sieve,pointSet,Renumbering> fV(pSet, renumbering, maxSize);

    1137:       for(int p = 0; p < numPoints; ++p) {
    1138:         sieve->cone(points[p], fV);
    1139:         localSieve->setConeSize(renumbering[points[p]], fV.getSize());
    1140:         fV.clear();
    1141:         sieve->support(points[p], fV);
    1142:         localSieve->setSupportSize(renumbering[points[p]], fV.getSize());
    1143:         fV.clear();
    1144:       }
    1145:     }
    1146:     template<typename Mesh, typename Section, typename Renumbering>
    1147:     static void sizeLocalMeshV(const Obj<Mesh>& mesh, const Obj<Section>& partition, Renumbering& renumbering, const Obj<Mesh>& localMesh, const int height = 0) {
    1148:       const Obj<typename Mesh::sieve_type>& sieve      = mesh->getSieve();
    1149:       const Obj<typename Mesh::sieve_type>& localSieve = localMesh->getSieve();

    1151:       sizeLocalSieveV(sieve, partition, renumbering, localSieve, height);
    1152:     }
    1153:     template<typename Sieve, typename Section, typename Renumbering>
    1154:     static void createLocalLabelV(const Obj<Sieve>& sieve, const Obj<Section>& partition, Renumbering& renumbering, const Obj<Sieve>& localSieve, const int height = 0) {
    1155:       typedef std::set<typename Sieve::point_type> pointSet;
    1156:       typedef ISieveVisitor::FilteredPointRetriever<Sieve,pointSet,Renumbering> visitor_type;
    1157:       const typename Section::value_type *points    = partition->restrictPoint(sieve->commRank());
    1158:       const int                           numPoints = partition->getFiberDimension(sieve->commRank());
    1159:       int                                 maxSize   = std::max(0, std::max(sieve->getMaxConeSize(), sieve->getMaxSupportSize()));
    1160:       typename Sieve::point_type         *oPoints   = new typename Sieve::point_type[std::max(1, sieve->getMaxConeSize())];
    1161:       int                                *oOrients  = new int[std::max(1, sieve->getMaxConeSize())];
    1162:       const pointSet                      pSet(points, &points[numPoints]);
    1163:       visitor_type fV(pSet, renumbering, maxSize);

    1165:       for(int p = 0; p < numPoints; ++p) {
    1166:         fV.useRenumbering(false);
    1167:         sieve->orientedCone(points[p], fV);
    1168:         const typename visitor_type::oriented_point_type *q = fV.getOrientedPoints();
    1169:         const int                                         n = fV.getOrientedSize();
    1170:         for(int i = 0; i < n; ++i) {
    1171:           oPoints[i]  = q[i].first;
    1172:           oOrients[i] = q[i].second;
    1173:         }
    1174:         localSieve->setCone(oPoints, renumbering[points[p]]);
    1175:         localSieve->setConeOrientation(oOrients, renumbering[points[p]]);
    1176:         fV.clear();
    1177:         fV.useRenumbering(true);
    1178:         sieve->support(points[p], fV);
    1179:         if (fV.getSize()) {localSieve->setSupport(points[p], fV.getPoints());}
    1180:         fV.clear();
    1181:       }
    1182:       delete [] oPoints;
    1183:       delete [] oOrients;
    1184:     }
    1185:     template<typename Sieve, typename Section, typename Renumbering>
    1186:     static void createLocalSieveV(const Obj<Sieve>& sieve, const Obj<Section>& partition, Renumbering& renumbering, const Obj<Sieve>& localSieve, const int height = 0) {
    1187:       typedef std::set<typename Sieve::point_type> pointSet;
    1188:       typedef ISieveVisitor::FilteredPointRetriever<Sieve,pointSet,Renumbering> visitor_type;
    1189:       const typename Section::value_type *points    = partition->restrictPoint(sieve->commRank());
    1190:       const int                           numPoints = partition->getFiberDimension(sieve->commRank());
    1191:       int                                 maxSize   = std::max(0, std::max(sieve->getMaxConeSize(), sieve->getMaxSupportSize()));
    1192:       typename Sieve::point_type         *oPoints   = new typename Sieve::point_type[std::max(1, sieve->getMaxConeSize())];
    1193:       int                                *oOrients  = new int[std::max(1, sieve->getMaxConeSize())];
    1194:       const pointSet                      pSet(points, &points[numPoints]);
    1195:       visitor_type fV(pSet, renumbering, maxSize);

    1197:       for(int p = 0; p < numPoints; ++p) {
    1198:         ///sieve->cone(points[p], fV);
    1199:         ///localSiaeve->setCone(fV.getPoints(), renumbering[points[p]]);
    1200:         sieve->orientedCone(points[p], fV);
    1201:         const typename visitor_type::oriented_point_type *q = fV.getOrientedPoints();
    1202:         const int                                         n = fV.getOrientedSize();
    1203:         for(int i = 0; i < n; ++i) {
    1204:           oPoints[i]  = q[i].first;
    1205:           oOrients[i] = q[i].second;
    1206:         }
    1207:         localSieve->setCone(oPoints, renumbering[points[p]]);
    1208:         localSieve->setConeOrientation(oOrients, renumbering[points[p]]);
    1209:         fV.clear();
    1210:         sieve->support(points[p], fV);
    1211:         localSieve->setSupport(renumbering[points[p]], fV.getPoints());
    1212:         fV.clear();
    1213:       }
    1214:       delete [] oPoints;
    1215:       delete [] oOrients;
    1216:     }
    1217:     template<typename Mesh, typename Section, typename Renumbering>
    1218:     static void createLocalMeshV(const Obj<Mesh>& mesh, const Obj<Section>& partition, Renumbering& renumbering, const Obj<Mesh>& localMesh, const int height = 0) {
    1219:       const Obj<typename Mesh::sieve_type>& sieve      = mesh->getSieve();
    1220:       const Obj<typename Mesh::sieve_type>& localSieve = localMesh->getSieve();

    1222:       createLocalSieveV(sieve, partition, renumbering, localSieve, height);
    1223:     }
    1224:   public: // Partitioning
    1225:     //   partition:    Should be properly allocated on input
    1226:     //   height:       Height of the point set to uniquely partition
    1227:     // TODO: Could rebind assignment section to the type of the output
    1228:     template<typename Mesh, typename Section>
    1229:     static void createPartition(const Obj<Mesh>& mesh, const Obj<Section>& partition, const int height = 0) {
    1230:       MeshManager<Mesh> manager(mesh, height);
    1231:       int              *start     = NULL;
    1232:       int              *adjacency = NULL;

    1234:       if (height == 0) {
    1235:         int numVertices;

    1237:         buildDualCSR(mesh, &numVertices, &start, &adjacency, GraphPartitioner::zeroBase());
    1238:         GraphPartitioner().partition(numVertices, start, adjacency, partition, manager);
    1239:         destroyCSR(numVertices, start, adjacency);
    1240:       } else if (height == 1) {
    1241:         int numEdges;

    1243:         buildFaceDualCSR(mesh, mesh->getFactory()->getNumbering(mesh, mesh->depth()-1), &numEdges, &start, &adjacency, GraphPartitioner::zeroBase());
    1244:         GraphPartitioner().partition(numEdges, start, adjacency, partition, manager);
    1245:         destroyCSR(numEdges, start, adjacency);
    1246:       } else {
    1247:         throw ALE::Exception("Invalid partition height");
    1248:       }
    1249:     }
    1250:     template<typename Mesh, typename Section>
    1251:     static void createPartitionV(const Obj<Mesh>& mesh, const Obj<Section>& partition, const int height = 0) {
    1252:       MeshManager<Mesh> manager(mesh, height);
    1253:       int              *start     = NULL;
    1254:       int              *adjacency = NULL;

    1256:       PETSc::Log::Event("PartitionCreate").begin();
    1257:       if (height == 0) {
    1258:         int numVertices;

    1260:         buildDualCSRV(mesh, manager, &numVertices, &start, &adjacency, GraphPartitioner::zeroBase());
    1261:         GraphPartitioner().partition(numVertices, start, adjacency, partition, manager);
    1262:         destroyCSR(numVertices, start, adjacency);
    1263:       } else if (height == 1) {
    1264:         int numEdges;

    1266:         throw ALE::Exception("Not yet implemented");
    1267: #if 0
    1268:         buildFaceDualCSRV(mesh, mesh->getFactory()->getNumbering(mesh, mesh->depth()-1), &numEdges, &start, &adjacency, GraphPartitioner::zeroBase());
    1269: #endif
    1270:         GraphPartitioner().partition(numEdges, start, adjacency, partition, manager);
    1271:         destroyCSR(numEdges, start, adjacency);
    1272:       } else {
    1273:         throw ALE::Exception("Invalid partition height");
    1274:       }
    1275:       PETSc::Log::Event("PartitionCreate").end();
    1276:     }
    1277:     // Add in the points in the closure (and star) of the partitioned points
    1278:     template<typename Mesh, typename Section>
    1279:     static void createPartitionClosure(const Obj<Mesh>& mesh, const Obj<Section>& pointPartition, const Obj<Section>& partition, const int height = 0) {
    1280:       const Obj<typename Mesh::sieve_type>& sieve = mesh->getSieve();
    1281:       const typename Section::chart_type&   chart = pointPartition->getChart();
    1282:       size_t                                size  = 0;

    1284:       for(typename Section::chart_type::const_iterator r_iter = chart.begin(); r_iter != chart.end(); ++r_iter) {
    1285:         const typename Section::value_type    *points    = pointPartition->restrictPoint(*r_iter);
    1286:         const int                              numPoints = pointPartition->getFiberDimension(*r_iter);
    1287:         std::set<typename Section::value_type> closure;

    1289:         // TODO: Use Quiver's closure() here instead
    1290:         for(int p = 0; p < numPoints; ++p) {
    1291:           Obj<typename Mesh::sieve_type::coneSet> current = new typename Mesh::sieve_type::coneSet();
    1292:           Obj<typename Mesh::sieve_type::coneSet> next    = new typename Mesh::sieve_type::coneSet();
    1293:           Obj<typename Mesh::sieve_type::coneSet> tmp;

    1295:           current->insert(points[p]);
    1296:           closure.insert(points[p]);
    1297:           while(current->size()) {
    1298:             for(typename Mesh::sieve_type::coneSet::const_iterator p_iter = current->begin(); p_iter != current->end(); ++p_iter) {
    1299:               const Obj<typename Mesh::sieve_type::traits::coneSequence>& cone = sieve->cone(*p_iter);

    1301:               for(typename Mesh::sieve_type::traits::coneSequence::iterator c_iter = cone->begin(); c_iter != cone->end(); ++c_iter) {
    1302:                 closure.insert(*c_iter);
    1303:                 next->insert(*c_iter);
    1304:               }
    1305:             }
    1306:             tmp = current; current = next; next = tmp;
    1307:             next->clear();
    1308:           }
    1309:           if (height) {
    1310:             current->insert(points[p]);
    1311:             while(current->size()) {
    1312:               for(typename Mesh::sieve_type::coneSet::const_iterator p_iter = current->begin(); p_iter != current->end(); ++p_iter) {
    1313:                 const Obj<typename Mesh::sieve_type::traits::supportSequence>& support = sieve->support(*p_iter);

    1315:                 for(typename Mesh::sieve_type::traits::supportSequence::iterator s_iter = support->begin(); s_iter != support->end(); ++s_iter) {
    1316:                   closure.insert(*s_iter);
    1317:                   next->insert(*s_iter);
    1318:                 }
    1319:               }
    1320:               tmp = current; current = next; next = tmp;
    1321:               next->clear();
    1322:             }
    1323:           }
    1324:         }
    1325:         partition->setFiberDimension(*r_iter, closure.size());
    1326:         size = std::max(size, closure.size());
    1327:       }
    1328:       partition->allocatePoint();
    1329:       typename Section::value_type *values = new typename Section::value_type[size];

    1331:       for(typename Section::chart_type::const_iterator r_iter = chart.begin(); r_iter != chart.end(); ++r_iter) {
    1332:         const typename Section::value_type    *points    = pointPartition->restrictPoint(*r_iter);
    1333:         const int                              numPoints = pointPartition->getFiberDimension(*r_iter);
    1334:         std::set<typename Section::value_type> closure;

    1336:         // TODO: Use Quiver's closure() here instead
    1337:         for(int p = 0; p < numPoints; ++p) {
    1338:           Obj<typename Mesh::sieve_type::coneSet> current = new typename Mesh::sieve_type::coneSet();
    1339:           Obj<typename Mesh::sieve_type::coneSet> next    = new typename Mesh::sieve_type::coneSet();
    1340:           Obj<typename Mesh::sieve_type::coneSet> tmp;

    1342:           current->insert(points[p]);
    1343:           closure.insert(points[p]);
    1344:           while(current->size()) {
    1345:             for(typename Mesh::sieve_type::coneSet::const_iterator p_iter = current->begin(); p_iter != current->end(); ++p_iter) {
    1346:               const Obj<typename Mesh::sieve_type::traits::coneSequence>& cone = sieve->cone(*p_iter);

    1348:               for(typename Mesh::sieve_type::traits::coneSequence::iterator c_iter = cone->begin(); c_iter != cone->end(); ++c_iter) {
    1349:                 closure.insert(*c_iter);
    1350:                 next->insert(*c_iter);
    1351:               }
    1352:             }
    1353:             tmp = current; current = next; next = tmp;
    1354:             next->clear();
    1355:           }
    1356:           if (height) {
    1357:             current->insert(points[p]);
    1358:             while(current->size()) {
    1359:               for(typename Mesh::sieve_type::coneSet::const_iterator p_iter = current->begin(); p_iter != current->end(); ++p_iter) {
    1360:                 const Obj<typename Mesh::sieve_type::traits::supportSequence>& support = sieve->support(*p_iter);

    1362:                 for(typename Mesh::sieve_type::traits::supportSequence::iterator s_iter = support->begin(); s_iter != support->end(); ++s_iter) {
    1363:                   closure.insert(*s_iter);
    1364:                   next->insert(*s_iter);
    1365:                 }
    1366:               }
    1367:               tmp = current; current = next; next = tmp;
    1368:               next->clear();
    1369:             }
    1370:           }
    1371:         }
    1372:         int i = 0;

    1374:         for(typename std::set<typename Section::value_type>::const_iterator p_iter = closure.begin(); p_iter != closure.end(); ++p_iter, ++i) {
    1375:           values[i] = *p_iter;
    1376:         }
    1377:         partition->updatePoint(*r_iter, values);
    1378:       }
    1379:       delete [] values;
    1380:     }
    1381:     template<typename Mesh, typename Section>
    1382:     static void createPartitionClosureV(const Obj<Mesh>& mesh, const Obj<Section>& pointPartition, const Obj<Section>& partition, const int height = 0) {
    1383:       typedef ISieveVisitor::TransitiveClosureVisitor<typename Mesh::sieve_type> visitor_type;
    1384:       const Obj<typename Mesh::sieve_type>& sieve = mesh->getSieve();
    1385:       const typename Section::chart_type&   chart = pointPartition->getChart();
    1386:       size_t                                size  = 0;

    1388:       PETSc::Log::Event("PartitionClosure").begin();
    1389:       for(typename Section::chart_type::const_iterator r_iter = chart.begin(); r_iter != chart.end(); ++r_iter) {
    1390:         const typename Section::value_type *points    = pointPartition->restrictPoint(*r_iter);
    1391:         const int                           numPoints = pointPartition->getFiberDimension(*r_iter);
    1392:         typename visitor_type::visitor_type nV;
    1393:         visitor_type                        cV(*sieve, nV);

    1395:         for(int p = 0; p < numPoints; ++p) {
    1396:           sieve->cone(points[p], cV);
    1397:           if (height) {
    1398:             cV.setIsCone(false);
    1399:             sieve->support(points[p], cV);
    1400:           }
    1401:         }
    1402:         partition->setFiberDimension(*r_iter, cV.getPoints().size());
    1403:         size = std::max(size, cV.getPoints().size());
    1404:       }
    1405:       partition->allocatePoint();
    1406:       typename Section::value_type *values = new typename Section::value_type[size];

    1408:       for(typename Section::chart_type::const_iterator r_iter = chart.begin(); r_iter != chart.end(); ++r_iter) {
    1409:         const typename Section::value_type *points    = pointPartition->restrictPoint(*r_iter);
    1410:         const int                           numPoints = pointPartition->getFiberDimension(*r_iter);
    1411:         typename visitor_type::visitor_type nV;
    1412:         visitor_type                        cV(*sieve, nV);

    1414:         for(int p = 0; p < numPoints; ++p) {
    1415:           sieve->cone(points[p], cV);
    1416:           if (height) {
    1417:             cV.setIsCone(false);
    1418:             sieve->support(points[p], cV);
    1419:           }
    1420:         }
    1421:         int i = 0;

    1423:         for(typename std::set<typename Mesh::point_type>::const_iterator p_iter = cV.getPoints().begin(); p_iter != cV.getPoints().end(); ++p_iter, ++i) {
    1424:           values[i] = *p_iter;
    1425:         }
    1426:         partition->updatePoint(*r_iter, values);
    1427:       }
    1428:       delete [] values;
    1429:       PETSc::Log::Event("PartitionClosure").end();
    1430:     }
    1433:     template<typename Mesh>
    1434:     static PetscErrorCode createPartitionClosureV(const Obj<Mesh>& mesh, PetscSection pointSection, IS pointPartition, PetscSection *section, IS *partition, const int height = 0) {
    1435:       typedef ISieveVisitor::TransitiveClosureVisitor<typename Mesh::sieve_type> visitor_type;
    1436:       const Obj<typename Mesh::sieve_type>& sieve = mesh->getSieve();
    1437:       const PetscInt                       *partArray;
    1438:       PetscInt                             *allPoints;
    1439:       PetscInt                              rStart, rEnd, size;
    1440:       PetscErrorCode                        ierr;

    1443:       PETSc::Log::Event("PartitionClosure").begin();
    1444:       PetscSectionGetChart(pointSection, &rStart, &rEnd);
    1445:       ISGetIndices(pointPartition, &partArray);
    1446:       PetscSectionCreate(mesh->comm(), section);
    1447:       PetscSectionSetChart(*section, rStart, rEnd);
    1448:       for(PetscInt rank = rStart; rank < rEnd; ++rank) {
    1449:         PetscInt numPoints, offset;

    1451:         PetscSectionGetDof(pointSection, rank, &numPoints);
    1452:         PetscSectionGetOffset(pointSection, rank, &offset);
    1453:         {
    1454:           const PetscInt                     *points = &partArray[offset];
    1455:           typename visitor_type::visitor_type nV;
    1456:           visitor_type                        cV(*sieve, nV);

    1458:           for(PetscInt p = 0; p < numPoints; ++p) {
    1459:             sieve->cone(points[p], cV);
    1460:             if (height) {
    1461:               cV.setIsCone(false);
    1462:               sieve->support(points[p], cV);
    1463:             }
    1464:           }
    1465:           PetscSectionSetDof(*section, rank, cV.getPoints().size());
    1466:         }
    1467:       }
    1468:       PetscSectionSetUp(*section);
    1469:       PetscSectionGetStorageSize(*section, &size);
    1470:       PetscMalloc(size * sizeof(PetscInt), &allPoints);

    1472:       for(PetscInt rank = rStart; rank < rEnd; ++rank) {
    1473:         PetscInt numPoints, offset, newOffset;

    1475:         PetscSectionGetDof(pointSection, rank, &numPoints);
    1476:         PetscSectionGetOffset(pointSection, rank, &offset);
    1477:         {
    1478:           const PetscInt                     *points = &partArray[offset];
    1479:           typename visitor_type::visitor_type nV;
    1480:           visitor_type                        cV(*sieve, nV);

    1482:           for(int p = 0; p < numPoints; ++p) {
    1483:             sieve->cone(points[p], cV);
    1484:             if (height) {
    1485:               cV.setIsCone(false);
    1486:               sieve->support(points[p], cV);
    1487:             }
    1488:           }
    1489:           PetscSectionGetOffset(*section, rank, &newOffset);

    1491:           for(typename std::set<typename Mesh::point_type>::const_iterator p_iter = cV.getPoints().begin(); p_iter != cV.getPoints().end(); ++p_iter, ++newOffset) {
    1492:             allPoints[newOffset] = *p_iter;
    1493:           }
    1494:         }
    1495:       }
    1496:       ISRestoreIndices(pointPartition, &partArray);
    1497:       ISCreateGeneral(mesh->comm(), size, allPoints, PETSC_OWN_POINTER, partition);
    1498:       PETSc::Log::Event("PartitionClosure").end();
    1499:       return(0);
    1500:     }
    1501:     // Create a section mapping points to partitions
    1502:     template<typename Section, typename MapSection>
    1503:     static void createPartitionMap(const Obj<Section>& partition, const Obj<MapSection>& partitionMap) {
    1504:       const typename Section::chart_type& chart = partition->getChart();

    1506:       for(typename Section::chart_type::const_iterator p_iter = chart.begin(); p_iter != chart.end(); ++p_iter) {
    1507:         partitionMap->setFiberDimension(*p_iter, 1);
    1508:       }
    1509:       partitionMap->allocatePoint();
    1510:       for(typename Section::chart_type::const_iterator p_iter = chart.begin(); p_iter != chart.end(); ++p_iter) {
    1511:         const typename Section::value_type *points = partition->restrictPoint(*p_iter);
    1512:         const int                           size   = partition->getFiberDimension(*p_iter);
    1513:         const typename Section::point_type  part   = *p_iter;

    1515:         for(int i = 0; i < size; ++i) {
    1516:           partitionMap->updatePoint(points[i], &part);
    1517:         }
    1518:       }
    1519:     }
    1520:   };
    1521: #endif

    1523:   namespace New {
    1524:     template<typename Bundle_, typename Alloc_ = typename Bundle_::alloc_type>
    1525:     class Partitioner {
    1526:     public:
    1527:       typedef Bundle_                          bundle_type;
    1528:       typedef Alloc_                           alloc_type;
    1529:       typedef typename bundle_type::sieve_type sieve_type;
    1530:       typedef typename bundle_type::point_type point_type;
    1531:     public:
    1534:       // This creates a CSR representation of the adjacency matrix for cells
    1535:       // - We allow an exception to contiguous numbering.
    1536:       //   If the cell id > numElements, we assign a new number starting at
    1537:       //     the top and going downward. I know these might not match up with
    1538:       //     the iterator order, but we can fix it later.
    1539:       static void buildDualCSR(const Obj<bundle_type>& bundle, const int dim, int **offsets, int **adjacency) {
    1540:         ALE_LOG_EVENT_BEGIN;
    1541:         typedef typename ALE::New::Completion<bundle_type, point_type, alloc_type> completion;
    1542:         const Obj<sieve_type>&                           sieve        = bundle->getSieve();
    1543:         const Obj<typename bundle_type::label_sequence>& elements     = bundle->heightStratum(0);
    1544:         Obj<sieve_type>                                  overlapSieve = new sieve_type(bundle->comm(), bundle->debug());
    1545:         std::map<point_type, point_type>                 newCells;
    1546:         int  numElements = elements->size();
    1547:         int  newCell     = numElements;
    1548:         int *off         = new int[numElements+1];
    1549:         int  offset      = 0;
    1550:         int *adj;

    1552:         completion::scatterSupports(sieve, overlapSieve, bundle->getSendOverlap(), bundle->getRecvOverlap(), bundle);
    1553:         if (numElements == 0) {
    1554:           *offsets   = NULL;
    1555:           *adjacency = NULL;
    1556:           ALE_LOG_EVENT_END;
    1557:           return;
    1558:         }
    1559:         if (bundle->depth() == dim) {
    1560:           int e = 1;

    1562:           off[0] = 0;
    1563:           for(typename bundle_type::label_sequence::iterator e_iter = elements->begin(); e_iter != elements->end(); ++e_iter) {
    1564:             const Obj<typename sieve_type::traits::coneSequence>& faces  = sieve->cone(*e_iter);
    1565:             typename sieve_type::traits::coneSequence::iterator   fBegin = faces->begin();
    1566:             typename sieve_type::traits::coneSequence::iterator   fEnd   = faces->end();

    1568:             off[e] = off[e-1];
    1569:             for(typename sieve_type::traits::coneSequence::iterator f_iter = fBegin; f_iter != fEnd; ++f_iter) {
    1570:               if (sieve->support(*f_iter)->size() == 2) {
    1571:                 off[e]++;
    1572:               } else if ((sieve->support(*f_iter)->size() == 1) && (overlapSieve->support(*f_iter)->size() == 1)) {
    1573:                 off[e]++;
    1574:               }
    1575:             }
    1576:             e++;
    1577:           }
    1578:           adj = new int[off[numElements]];
    1579:           for(typename bundle_type::label_sequence::iterator e_iter = elements->begin(); e_iter != elements->end(); ++e_iter) {
    1580:             const Obj<typename sieve_type::traits::coneSequence>& faces  = sieve->cone(*e_iter);
    1581:             typename sieve_type::traits::coneSequence::iterator   fBegin = faces->begin();
    1582:             typename sieve_type::traits::coneSequence::iterator   fEnd   = faces->end();

    1584:             for(typename sieve_type::traits::coneSequence::iterator f_iter = fBegin; f_iter != fEnd; ++f_iter) {
    1585:               const Obj<typename sieve_type::traits::supportSequence>& neighbors = sieve->support(*f_iter);
    1586:               typename sieve_type::traits::supportSequence::iterator   nBegin    = neighbors->begin();
    1587:               typename sieve_type::traits::supportSequence::iterator   nEnd      = neighbors->end();

    1589:               for(typename sieve_type::traits::supportSequence::iterator n_iter = nBegin; n_iter != nEnd; ++n_iter) {
    1590:                 if (*n_iter != *e_iter) adj[offset++] = *n_iter;
    1591:               }
    1592:               const Obj<typename sieve_type::traits::supportSequence>& oNeighbors = overlapSieve->support(*f_iter);
    1593:               typename sieve_type::traits::supportSequence::iterator   onBegin    = oNeighbors->begin();
    1594:               typename sieve_type::traits::supportSequence::iterator   onEnd      = oNeighbors->end();

    1596:               for(typename sieve_type::traits::supportSequence::iterator n_iter = onBegin; n_iter != onEnd; ++n_iter) {
    1597:                 adj[offset++] = *n_iter;
    1598:               }
    1599:             }
    1600:           }
    1601:         } else if (bundle->depth() == 1) {
    1602:           std::set<point_type> *neighborCells = new std::set<point_type>[numElements];
    1603:           int corners      = sieve->cone(*elements->begin())->size();
    1604:           int faceVertices = -1;

    1606:           if (corners == dim+1) {
    1607:             faceVertices = dim;
    1608:           } else if ((dim == 2) && (corners == 4)) {
    1609:             faceVertices = 2;
    1610:           } else if ((dim == 3) && (corners == 8)) {
    1611:             faceVertices = 4;
    1612:           } else if ((dim == 2) && (corners == 6)) {
    1613:             faceVertices = 3;
    1614:           } else if ((dim == 2) && (corners == 9)) {
    1615:             faceVertices = 3;
    1616:           } else if ((dim == 3) && (corners == 10)) {
    1617:             faceVertices = 6;
    1618:           } else if ((dim == 3) && (corners == 27)) {
    1619:             faceVertices = 9;
    1620:           } else {
    1621:             throw ALE::Exception("Could not determine number of face vertices");
    1622:           }
    1623:           for(typename bundle_type::label_sequence::iterator e_iter = elements->begin(); e_iter != elements->end(); ++e_iter) {
    1624:             const Obj<typename sieve_type::traits::coneSequence>& vertices  = sieve->cone(*e_iter);
    1625:             typename sieve_type::traits::coneSequence::iterator vEnd = vertices->end();

    1627:             for(typename sieve_type::traits::coneSequence::iterator v_iter = vertices->begin(); v_iter != vEnd; ++v_iter) {
    1628:               const Obj<typename sieve_type::traits::supportSequence>& neighbors = sieve->support(*v_iter);
    1629:               typename sieve_type::traits::supportSequence::iterator nEnd = neighbors->end();

    1631:               for(typename sieve_type::traits::supportSequence::iterator n_iter = neighbors->begin(); n_iter != nEnd; ++n_iter) {
    1632:                 if (*e_iter == *n_iter) continue;
    1633:                 if ((int) sieve->nMeet(*e_iter, *n_iter, 1)->size() == faceVertices) {
    1634:                   if ((*e_iter < numElements) && (*n_iter < numElements)) {
    1635:                     neighborCells[*e_iter].insert(*n_iter);
    1636:                   } else {
    1637:                     point_type e = *e_iter, n = *n_iter;

    1639:                     if (*e_iter >= numElements) {
    1640:                       if (newCells.find(*e_iter) == newCells.end()) newCells[*e_iter] = --newCell;
    1641:                       e = newCells[*e_iter];
    1642:                     }
    1643:                     if (*n_iter >= numElements) {
    1644:                       if (newCells.find(*n_iter) == newCells.end()) newCells[*n_iter] = --newCell;
    1645:                       n = newCells[*n_iter];
    1646:                     }
    1647:                     neighborCells[e].insert(n);
    1648:                   }
    1649:                 }
    1650:               }
    1651:             }
    1652:           }
    1653:           off[0] = 0;
    1654:           for(int e = 1; e <= numElements; e++) {
    1655:             off[e] = neighborCells[e-1].size() + off[e-1];
    1656:           }
    1657:           adj = new int[off[numElements]];
    1658:           for(int e = 0; e < numElements; e++) {
    1659:             for(typename std::set<point_type>::iterator n_iter = neighborCells[e].begin(); n_iter != neighborCells[e].end(); ++n_iter) {
    1660:               adj[offset++] = *n_iter;
    1661:             }
    1662:           }
    1663:           delete [] neighborCells;
    1664:         } else {
    1665:           throw ALE::Exception("Dual creation not defined for partially interpolated meshes");
    1666:         }
    1667:         if (offset != off[numElements]) {
    1668:           ostringstream msg;
    1669:           msg << "ERROR: Total number of neighbors " << offset << " does not match the offset array " << off[numElements];
    1670:           throw ALE::Exception(msg.str().c_str());
    1671:         }
    1672:         //std::cout << "numElements: " << numElements << " newCell: " << newCell << std::endl;
    1673:         *offsets   = off;
    1674:         *adjacency = adj;
    1675:         ALE_LOG_EVENT_END;
    1676:       };
    1679:       // This creates a CSR representation of the adjacency hypergraph for faces
    1680:       static void buildFaceCSR(const Obj<bundle_type>& bundle, const int dim, const Obj<typename bundle_type::numbering_type>& fNumbering, int *numEdges, int **offsets, int **adjacency) {
    1681:         ALE_LOG_EVENT_BEGIN;
    1682:         const Obj<sieve_type>&                           sieve    = bundle->getSieve();
    1683:         const Obj<typename bundle_type::label_sequence>& elements = bundle->heightStratum(0);
    1684:         int  numElements = elements->size();
    1685:         int *off         = new int[numElements+1];
    1686:         int  e;

    1688:         if (bundle->depth() != dim) {
    1689:           throw ALE::Exception("Not yet implemented for non-interpolated meshes");
    1690:         }
    1691:         off[0] = 0;
    1692:         e      = 1;
    1693:         for(typename bundle_type::label_sequence::iterator e_iter = elements->begin(); e_iter != elements->end(); ++e_iter) {
    1694:           off[e] = sieve->cone(*e_iter)->size() + off[e-1];
    1695:           e++;
    1696:         }
    1697:         int *adj    = new int[off[numElements]];
    1698:         int  offset = 0;
    1699:         for(typename bundle_type::label_sequence::iterator e_iter = elements->begin(); e_iter != elements->end(); ++e_iter) {
    1700:           const Obj<typename sieve_type::traits::coneSequence>& faces = sieve->cone(*e_iter);
    1701:           typename sieve_type::traits::coneSequence::iterator   fEnd  = faces->end();

    1703:           for(typename sieve_type::traits::coneSequence::iterator f_iter = faces->begin(); f_iter != fEnd; ++f_iter) {
    1704:             adj[offset++] = fNumbering->getIndex(*f_iter);
    1705:           }
    1706:         }
    1707:         if (offset != off[numElements]) {
    1708:           ostringstream msg;
    1709:           msg << "ERROR: Total number of neighbors " << offset << " does not match the offset array " << off[numElements];
    1710:           throw ALE::Exception(msg.str().c_str());
    1711:         }
    1712:         *numEdges  = numElements;
    1713:         *offsets   = off;
    1714:         *adjacency = adj;
    1715:         ALE_LOG_EVENT_END;
    1716:       };
    1717:       template<typename PartitionType>
    1718:       static PartitionType *subordinatePartition(const Obj<bundle_type>& bundle, int levels, const Obj<bundle_type>& subBundle, PartitionType assignment[]) {
    1719:         const Obj<typename bundle_type::numbering_type>& cNumbering = bundle->getFactory()->getLocalNumbering(bundle, bundle->depth());
    1720:         const Obj<typename bundle_type::label_sequence>& cells      = subBundle->heightStratum(0);
    1721:         const Obj<typename bundle_type::numbering_type>& sNumbering = bundle->getFactory()->getLocalNumbering(subBundle, subBundle->depth());
    1722:         const int        numCells      = cells->size();
    1723:         PartitionType   *subAssignment = new PartitionType[numCells];

    1725:         if (levels != 1) {
    1726:           throw ALE::Exception("Cannot calculate subordinate partition for any level separation other than 1");
    1727:         } else {
    1728:           const Obj<typename bundle_type::sieve_type>&   sieve    = bundle->getSieve();
    1729:           const Obj<typename bundle_type::sieve_type>&   subSieve = subBundle->getSieve();
    1730:           Obj<typename bundle_type::sieve_type::coneSet> tmpSet   = new typename bundle_type::sieve_type::coneSet();
    1731:           Obj<typename bundle_type::sieve_type::coneSet> tmpSet2  = new typename bundle_type::sieve_type::coneSet();

    1733:           for(typename bundle_type::label_sequence::iterator c_iter = cells->begin(); c_iter != cells->end(); ++c_iter) {
    1734:             const Obj<typename bundle_type::sieve_type::coneSequence>& cone = subSieve->cone(*c_iter);

    1736:             Obj<typename bundle_type::sieve_type::supportSet> cell = sieve->nJoin1(cone);
    1737:             if (cell->size() != 1) {
    1738:               std::cout << "Indeterminate subordinate partition for face " << *c_iter << std::endl;
    1739:               for(typename bundle_type::sieve_type::supportSet::iterator s_iter = cell->begin(); s_iter != cell->end(); ++s_iter) {
    1740:                 std::cout << "  cell " << *s_iter << std::endl;
    1741:               }
    1742:               // Could relax this to choosing the first one
    1743:               throw ALE::Exception("Indeterminate subordinate partition");
    1744:             }
    1745:             subAssignment[sNumbering->getIndex(*c_iter)] = assignment[cNumbering->getIndex(*cell->begin())];
    1746:             tmpSet->clear();
    1747:             tmpSet2->clear();
    1748:           }
    1749:         }
    1750:         return subAssignment;
    1751:       }
    1752:     };
    1753: #ifdef PETSC_HAVE_CHACO
    1754:     namespace Chaco {
    1755:       template<typename Bundle_>
    1756:       class Partitioner {
    1757:       public:
    1758:         typedef Bundle_                          bundle_type;
    1759:         typedef typename bundle_type::sieve_type sieve_type;
    1760:         typedef typename bundle_type::point_type point_type;
    1761:         typedef short int                        part_type;
    1762:       public:
    1765:         static part_type *partitionSieve(const Obj<bundle_type>& bundle, const int dim) {
    1766:           part_type *assignment = NULL; /* set number of each vtx (length n) */
    1767:           int       *start;             /* start of edge list for each vertex */
    1768:           int       *adjacency;         /* = adj -> j; edge list data  */

    1770:           ALE_LOG_EVENT_BEGIN;
    1771:           ALE::New::Partitioner<bundle_type>::buildDualCSR(bundle, dim, &start, &adjacency);
    1772:           if (bundle->commRank() == 0) {
    1773:             /* arguments for Chaco library */
    1774:             FREE_GRAPH = 0;                         /* Do not let Chaco free my memory */
    1775:             int nvtxs;                              /* number of vertices in full graph */
    1776:             int *vwgts = NULL;                      /* weights for all vertices */
    1777:             float *ewgts = NULL;                    /* weights for all edges */
    1778:             float *x = NULL, *y = NULL, *z = NULL;  /* coordinates for inertial method */
    1779:             char *outassignname = NULL;             /*  name of assignment output file */
    1780:             char *outfilename = NULL;               /* output file name */
    1781:             int architecture = dim;                 /* 0 => hypercube, d => d-dimensional mesh */
    1782:             int ndims_tot = 0;                      /* total number of cube dimensions to divide */
    1783:             int mesh_dims[3];                       /* dimensions of mesh of processors */
    1784:             double *goal = NULL;                    /* desired set sizes for each set */
    1785:             int global_method = 1;                  /* global partitioning algorithm */
    1786:             int local_method = 1;                   /* local partitioning algorithm */
    1787:             int rqi_flag = 0;                       /* should I use RQI/Symmlq eigensolver? */
    1788:             int vmax = 200;                         /* how many vertices to coarsen down to? */
    1789:             int ndims = 1;                          /* number of eigenvectors (2^d sets) */
    1790:             double eigtol = 0.001;                  /* tolerance on eigenvectors */
    1791:             long seed = 123636512;                  /* for random graph mutations */
    1792:             float *vCoords[3];

    1795:             PetscOptionsGetInt(NULL, "-partitioner_chaco_global_method", &global_method, NULL);CHKERROR(ierr, "Error in PetscOptionsGetInt");
    1796:             PetscOptionsGetInt(NULL, "-partitioner_chaco_local_method",  &local_method,  NULL);CHKERROR(ierr, "Error in PetscOptionsGetInt");
    1797:             if (global_method == 3) {
    1798:               // Inertial Partitioning
    1799:               PetscMalloc3(nvtxs,float,&x,nvtxs,float,&y,nvtxs,float,&z);CHKERROR(ierr, "Error in PetscMalloc");
    1800:               vCoords[0] = x; vCoords[1] = y; vCoords[2] = z;
    1801:               const Obj<typename bundle_type::label_sequence>&    cells       = bundle->heightStratum(0);
    1802:               const Obj<typename bundle_type::real_section_type>& coordinates = bundle->getRealSection("coordinates");
    1803:               const int corners = bundle->size(coordinates, *(cells->begin()))/dim;
    1804:               int       c       = 0;

    1806:               for(typename bundle_type::label_sequence::iterator c_iter = cells->begin(); c_iter !=cells->end(); ++c_iter, ++c) {
    1807:                 const double *coords = bundle->restrictClosure(coordinates, *c_iter);

    1809:                 for(int d = 0; d < dim; ++d) {
    1810:                   vCoords[d][c] = 0.0;
    1811:                 }
    1812:                 for(int v = 0; v < corners; ++v) {
    1813:                   for(int d = 0; d < dim; ++d) {
    1814:                     vCoords[d][c] += coords[v*dim+d];
    1815:                   }
    1816:                 }
    1817:                 for(int d = 0; d < dim; ++d) {
    1818:                   vCoords[d][c] /= corners;
    1819:                 }
    1820:               }
    1821:             }

    1823:             nvtxs = bundle->heightStratum(0)->size();
    1824:             mesh_dims[0] = bundle->commSize(); mesh_dims[1] = 1; mesh_dims[2] = 1;
    1825:             for(int e = 0; e < start[nvtxs]; e++) {
    1826:               adjacency[e]++;
    1827:             }
    1828:             assignment = new part_type[nvtxs];
    1829:             PetscMemzero(assignment, nvtxs * sizeof(part_type));CHKERROR(ierr, "Error in PetscMemzero");

    1831:             /* redirect output to buffer: chaco -> msgLog */
    1832: #ifdef PETSC_HAVE_UNISTD_H
    1833:             char *msgLog;
    1834:             int fd_stdout, fd_pipe[2], count;

    1836:             fd_stdout = dup(1);
    1837:             pipe(fd_pipe);
    1838:             close(1);
    1839:             dup2(fd_pipe[1], 1);
    1840:             msgLog = new char[16284];
    1841: #endif

    1843:             interface(nvtxs, start, adjacency, vwgts, ewgts, x, y, z,
    1844:                              outassignname, outfilename, assignment, architecture, ndims_tot,
    1845:                              mesh_dims, goal, global_method, local_method, rqi_flag, vmax, ndims,
    1846:                              eigtol, seed);

    1848: #ifdef PETSC_HAVE_UNISTD_H
    1849:             int SIZE_LOG  = 10000;

    1851:             fflush(stdout);
    1852:             count = read(fd_pipe[0], msgLog, (SIZE_LOG - 1) * sizeof(char));
    1853:             if (count < 0) count = 0;
    1854:             msgLog[count] = 0;
    1855:             close(1);
    1856:             dup2(fd_stdout, 1);
    1857:             close(fd_stdout);
    1858:             close(fd_pipe[0]);
    1859:             close(fd_pipe[1]);
    1860:             if (bundle->debug()) {
    1861:               std::cout << msgLog << std::endl;
    1862:             }
    1863:             delete [] msgLog;
    1864: #endif
    1865:             if (global_method == 3) {
    1866:               // Inertial Partitioning
    1867:               PetscFree3(x, y, z);CHKERROR(ierr, "Error in PetscFree");
    1868:             }
    1869:           }
    1870:           if (adjacency) delete [] adjacency;
    1871:           if (start)     delete [] start;
    1872:           ALE_LOG_EVENT_END;
    1873:           return assignment;
    1874:         };
    1875:         static part_type *partitionSieveByFace(const Obj<bundle_type>& bundle, const int dim) {
    1876:           throw ALE::Exception("Chaco cannot partition a mesh by faces");
    1877:         };
    1878:       };
    1879:     };
    1880: #endif
    1881: #ifdef PETSC_HAVE_PARMETIS
    1882:     namespace ParMetis {
    1883:       template<typename Bundle_>
    1884:       class Partitioner {
    1885:       public:
    1886:         typedef Bundle_                          bundle_type;
    1887:         typedef typename bundle_type::sieve_type sieve_type;
    1888:         typedef typename bundle_type::point_type point_type;
    1889:         typedef int                              part_type;
    1890:       public:
    1893:         static part_type *partitionSieve(const Obj<bundle_type>& bundle, const int dim) {
    1894:           PetscInt    nvtxs      = 0;    // The number of vertices in full graph
    1895:           PetscInt   *vtxdist;           // Distribution of vertices across processes
    1896:           PetscInt   *xadj;              // Start of edge list for each vertex
    1897:           PetscInt   *adjncy;            // Edge lists for all vertices
    1898:           PetscInt   *vwgt       = NULL; // Vertex weights
    1899:           PetscInt   *adjwgt     = NULL; // Edge weights
    1900:           PetscInt    wgtflag    = 0;    // Indicates which weights are present
    1901:           PetscInt    numflag    = 0;    // Indicates initial offset (0 or 1)
    1902:           PetscInt    ncon       = 1;    // The number of weights per vertex
    1903:           PetscInt    nparts     = bundle->commSize(); // The number of partitions
    1904:           PetscReal  *tpwgts;            // The fraction of vertex weights assigned to each partition
    1905:           PetscReal  *ubvec;             // The balance intolerance for vertex weights
    1906:           int         options[5];        // Options
    1907:           // Outputs
    1908:           PetscInt    edgeCut;           // The number of edges cut by the partition
    1909:           PetscInt   *assignment = NULL; // The vertex partition

    1911:           options[0] = 0; // Use all defaults
    1912:           vtxdist    = new PetscInt[nparts+1];
    1913:           vtxdist[0] = 0;
    1914:           tpwgts     = new PetscReal[ncon*nparts];
    1915:           for(PetscInt p = 0; p < nparts; ++p) {
    1916:             tpwgts[p] = 1.0/nparts;
    1917:           }
    1918:           ubvec      = new PetscReal[ncon];
    1919:           ubvec[0]   = 1.05;
    1920:           nvtxs      = bundle->heightStratum(0)->size();
    1921:           assignment = new part_type[nvtxs];
    1922:           MPI_Allgather(&nvtxs, 1, MPIU_INT, &vtxdist[1], 1, MPIU_INT, bundle->comm());
    1923:           for(PetscInt p = 2; p <= nparts; ++p) {
    1924:             vtxdist[p] += vtxdist[p-1];
    1925:           }
    1926:           if (bundle->commSize() == 1) {
    1927:             PetscMemzero(assignment, nvtxs * sizeof(part_type));
    1928:           } else {
    1929:             ALE::New::Partitioner<bundle_type>::buildDualCSR(bundle, dim, &xadj, &adjncy);

    1931:             if (bundle->debug() && nvtxs) {
    1932:               for(PetscInt p = 0; p <= nvtxs; ++p) {
    1933:                 std::cout << "["<<bundle->commRank()<<"]xadj["<<p<<"] = " << xadj[p] << std::endl;
    1934:               }
    1935:               for(PetscInt i = 0; i < xadj[nvtxs]; ++i) {
    1936:                 std::cout << "["<<bundle->commRank()<<"]adjncy["<<i<<"] = " << adjncy[i] << std::endl;
    1937:               }
    1938:             }
    1939:             if (vtxdist[1] == vtxdist[nparts]) {
    1940:               if (bundle->commRank() == 0) {
    1941:                 /* Parameters changes (Matt, check to make sure it's right):
    1942:                  * (removed) numflags
    1943:                  */
    1944:                 METIS_PartGraphKway(&nvtxs, &ncon, xadj, adjncy, vwgt, NULL, adjwgt, &nparts, tpwgts, ubvec, NULL, &edgeCut, assignment);
    1945:                 if (bundle->debug()) {std::cout << "Metis: edgecut is " << edgeCut << std::endl;}
    1946:               }
    1947:             } else {
    1948:               MPI_Comm comm = bundle->comm();

    1950:               ParMETIS_V3_PartKway(vtxdist, xadj, adjncy, vwgt, adjwgt, &wgtflag, &numflag, &ncon, &nparts, tpwgts, ubvec, options, &edgeCut, assignment, &comm);
    1951:               if (bundle->debug()) {std::cout << "ParMetis: edgecut is " << edgeCut << std::endl;}
    1952:             }
    1953:             if (xadj   != NULL) delete [] xadj;
    1954:             if (adjncy != NULL) delete [] adjncy;
    1955:           }
    1956:           delete [] vtxdist;
    1957:           delete [] tpwgts;
    1958:           delete [] ubvec;
    1959:           return assignment;
    1960:         };
    1963:         static part_type *partitionSieveByFace(const Obj<bundle_type>& bundle, const int dim) {
    1964: #ifdef PETSC_HAVE_HMETIS
    1965:           int   *assignment = NULL; // The vertex partition
    1966:           int    nvtxs;      // The number of vertices
    1967:           int    nhedges;    // The number of hyperedges
    1968:           int   *vwgts;      // The vertex weights
    1969:           int   *eptr;       // The offsets of each hyperedge
    1970:           int   *eind;       // The vertices in each hyperedge, indexed by eptr
    1971:           int   *hewgts;     // The hyperedge weights
    1972:           int    nparts;     // The number of partitions
    1973:           int    ubfactor;   // The allowed load imbalance (1-50)
    1974:           int    options[9]; // Options
    1975:           // Outputs
    1976:           int    edgeCut;    // The number of edges cut by the partition
    1977:           const Obj<ALE::Mesh::numbering_type>& fNumbering = bundle->getFactory()->getNumbering(bundle, bundle->depth()-1);

    1979:           if (topology->commRank() == 0) {
    1980:             nvtxs      = bundle->heightStratum(1)->size();
    1981:             vwgts      = NULL;
    1982:             hewgts     = NULL;
    1983:             nparts     = bundle->commSize();
    1984:             ubfactor   = 5;
    1985:             options[0] = 1;  // Use all defaults
    1986:             options[1] = 10; // Number of bisections tested
    1987:             options[2] = 1;  // Vertex grouping scheme
    1988:             options[3] = 1;  // Objective function
    1989:             options[4] = 1;  // V-cycle refinement
    1990:             options[5] = 0;
    1991:             options[6] = 0;
    1992:             options[7] = 1; // Random seed
    1993:             options[8] = 24; // Debugging level
    1994:             assignment = new part_type[nvtxs];

    1996:             if (bundle->commSize() == 1) {
    1997:               PetscMemzero(assignment, nvtxs * sizeof(part_type));
    1998:             } else {
    1999:               ALE::New::Partitioner<bundle_type>::buildFaceCSR(bundle, dim, fNumbering, &nhedges, &eptr, &eind);
    2000:               HMETIS_PartKway(nvtxs, nhedges, vwgts, eptr, eind, hewgts, nparts, ubfactor, options, assignment, &edgeCut);

    2002:               delete [] eptr;
    2003:               delete [] eind;
    2004:             }
    2005:             if (bundle->debug()) {for (int i = 0; i<nvtxs; i++) printf("[%d] %d\n", PetscGlobalRank, assignment[i]);}
    2006:           } else {
    2007:             assignment = NULL;
    2008:           }
    2009:           return assignment;
    2010: #else
    2011:           throw ALE::Exception("hmetis partitioner is not available.");
    2012: #endif
    2013:         };
    2014:       };
    2015:     };
    2016: #endif
    2017: #ifdef PETSC_HAVE_ZOLTAN
    2018:     namespace Zoltan {
    2019:       template<typename Bundle_>
    2020:       class Partitioner {
    2021:       public:
    2022:         typedef Bundle_                          bundle_type;
    2023:         typedef typename bundle_type::sieve_type sieve_type;
    2024:         typedef typename bundle_type::point_type point_type;
    2025:         typedef int                              part_type;
    2026:       public:
    2027:         static part_type *partitionSieve(const Obj<bundle_type>& bundle, const int dim) {
    2028:           throw ALE::Exception("Zoltan partition by cells not implemented");
    2029:         };
    2032:         static part_type *partitionSieveByFace(const Obj<bundle_type>& bundle, const int dim) {
    2033:           // Outputs
    2034:           float         version;           // The library version
    2035:           int           changed;           // Did the partition change?
    2036:           int           numGidEntries;     // Number of array entries for a single global ID (1)
    2037:           int           numLidEntries;     // Number of array entries for a single local ID (1)
    2038:           int           numImport;         // The number of imported points
    2039:           ZOLTAN_ID_PTR import_global_ids; // The imported points
    2040:           ZOLTAN_ID_PTR import_local_ids;  // The imported points
    2041:           int          *import_procs;      // The proc each point was imported from
    2042:           int          *import_to_part;    // The partition of each imported point
    2043:           int           numExport;         // The number of exported points
    2044:           ZOLTAN_ID_PTR export_global_ids; // The exported points
    2045:           ZOLTAN_ID_PTR export_local_ids;  // The exported points
    2046:           int          *export_procs;      // The proc each point was exported to
    2047:           int          *export_to_part;    // The partition assignment of all local points
    2048:           int          *assignment;        // The partition assignment of all local points
    2049:           const Obj<typename bundle_type::numbering_type>& fNumbering = bundle->getFactory()->getNumbering(bundle, bundle->depth()-1);

    2051:           if (bundle->commSize() == 1) {
    2052:             PetscMemzero(assignment, bundle->heightStratum(1)->size() * sizeof(part_type));
    2053:           } else {
    2054:             if (bundle->commRank() == 0) {
    2055:               nvtxs_Zoltan = bundle->heightStratum(1)->size();
    2056:               ALE::New::Partitioner<bundle_type>::buildFaceCSR(bundle, dim, fNumbering, &nhedges_Zoltan, &eptr_Zoltan, &eind_Zoltan);
    2057:               assignment = new int[nvtxs_Zoltan];
    2058:             } else {
    2059:               nvtxs_Zoltan   = bundle->heightStratum(1)->size();
    2060:               nhedges_Zoltan = 0;
    2061:               eptr_Zoltan    = new int[1];
    2062:               eind_Zoltan    = new int[1];
    2063:               eptr_Zoltan[0] = 0;
    2064:               assignment     = NULL;
    2065:             }

    2067:             int Zoltan_Initialize(0, NULL, &version);
    2068:             struct Zoltan_Struct *zz = Zoltan_Create(bundle->comm());
    2069:             // General parameters
    2070:             Zoltan_Set_Param(zz, "DEBUG_LEVEL", "2");
    2071:             Zoltan_Set_Param(zz, "LB_METHOD", "PHG");
    2072:             Zoltan_Set_Param(zz, "RETURN_LISTS", "PARTITION");
    2073:             // PHG parameters
    2074:             Zoltan_Set_Param(zz, "PHG_OUTPUT_LEVEL", "2");
    2075:             Zoltan_Set_Param(zz, "PHG_EDGE_SIZE_THRESHOLD", "1.0"); // Do not throw out dense edges
    2076:             // Call backs
    2077:             Zoltan_Set_Num_Obj_Fn(zz, getNumVertices_Zoltan, NULL);
    2078:             Zoltan_Set_Obj_List_Fn(zz, getLocalElements_Zoltan, NULL);
    2079:             Zoltan_Set_HG_Size_CS_Fn(zz, getHgSizes_Zoltan, NULL);
    2080:             Zoltan_Set_HG_CS_Fn(zz, getHg_Zoltan, NULL);
    2081:             // Debugging
    2082:             //Zoltan_Generate_Files(zz, "zoltan.debug", 1, 0, 0, 1); // if using hypergraph callbacks

    2084:             Zoltan_LB_Partition(zz, &changed, &numGidEntries, &numLidEntries,
    2085:                                        &numImport, &import_global_ids, &import_local_ids, &import_procs, &import_to_part,
    2086:                                        &numExport, &export_global_ids, &export_local_ids, &export_procs, &export_to_part);
    2087:             for(int v = 0; v < nvtxs_Zoltan; ++v) {
    2088:               assignment[v] = export_to_part[v];
    2089:             }
    2090:             Zoltan_LB_Free_Part(&import_global_ids, &import_local_ids, &import_procs, &import_to_part);
    2091:             Zoltan_LB_Free_Part(&export_global_ids, &export_local_ids, &export_procs, &export_to_part);
    2092:             Zoltan_Destroy(&zz);

    2094:             delete [] eptr_Zoltan;
    2095:             delete [] eind_Zoltan;
    2096:           }
    2097:           if (assignment) {for (int i=0; i<nvtxs_Zoltan; i++) printf("[%d] %d\n",PetscGlobalRank,assignment[i]);}
    2098:           return assignment;
    2099:         };
    2100:       };
    2101:     };
    2102: #endif
    2103:   }
    2104: }
    2105: #endif