Actual source code: plexpartition.c

petsc-3.7.3 2016-08-01
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  1: #include <petsc/private/dmpleximpl.h>   /*I      "petscdmplex.h"   I*/

  3: PetscClassId PETSCPARTITIONER_CLASSID = 0;

  5: PetscFunctionList PetscPartitionerList              = NULL;
  6: PetscBool         PetscPartitionerRegisterAllCalled = PETSC_FALSE;

  8: PetscBool ChacoPartitionercite = PETSC_FALSE;
  9: const char ChacoPartitionerCitation[] = "@inproceedings{Chaco95,\n"
 10:                                "  author    = {Bruce Hendrickson and Robert Leland},\n"
 11:                                "  title     = {A multilevel algorithm for partitioning graphs},\n"
 12:                                "  booktitle = {Supercomputing '95: Proceedings of the 1995 ACM/IEEE Conference on Supercomputing (CDROM)},"
 13:                                "  isbn      = {0-89791-816-9},\n"
 14:                                "  pages     = {28},\n"
 15:                                "  doi       = {http://doi.acm.org/10.1145/224170.224228},\n"
 16:                                "  publisher = {ACM Press},\n"
 17:                                "  address   = {New York},\n"
 18:                                "  year      = {1995}\n}\n";

 20: PetscBool ParMetisPartitionercite = PETSC_FALSE;
 21: const char ParMetisPartitionerCitation[] = "@article{KarypisKumar98,\n"
 22:                                "  author  = {George Karypis and Vipin Kumar},\n"
 23:                                "  title   = {A Parallel Algorithm for Multilevel Graph Partitioning and Sparse Matrix Ordering},\n"
 24:                                "  journal = {Journal of Parallel and Distributed Computing},\n"
 25:                                "  volume  = {48},\n"
 26:                                "  pages   = {71--85},\n"
 27:                                "  year    = {1998}\n}\n";

 31: /*@C
 32:   DMPlexCreatePartitionerGraph - Create a CSR graph of point connections for the partitioner

 34:   Input Parameters:
 35: + dm      - The mesh DM dm
 36: - height  - Height of the strata from which to construct the graph

 38:   Output Parameter:
 39: + numVertices - Number of vertices in the graph
 40: - offsets     - Point offsets in the graph
 41: - adjacency   - Point connectivity in the graph

 43:   The user can control the definition of adjacency for the mesh using DMPlexGetAdjacencyUseCone() and
 44:   DMPlexSetAdjacencyUseClosure(). They should choose the combination appropriate for the function
 45:   representation on the mesh.

 47:   Level: developer

 49: .seealso: PetscPartitionerGetType(), PetscPartitionerCreate(), DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure()
 50: @*/
 51: PetscErrorCode DMPlexCreatePartitionerGraph(DM dm, PetscInt height, PetscInt *numVertices, PetscInt **offsets, PetscInt **adjacency)
 52: {
 53:   PetscInt       p, pStart, pEnd, a, adjSize, idx, size, nroots;
 54:   PetscInt      *adj = NULL, *vOffsets = NULL, *graph = NULL;
 55:   IS             cellNumbering;
 56:   const PetscInt *cellNum;
 57:   PetscBool      useCone, useClosure;
 58:   PetscSection   section;
 59:   PetscSegBuffer adjBuffer;
 60:   PetscSF        sfPoint;
 61:   PetscMPIInt    rank;

 65:   MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
 66:   DMPlexGetHeightStratum(dm, height, &pStart, &pEnd);
 67:   DMGetPointSF(dm, &sfPoint);
 68:   PetscSFGetGraph(sfPoint, &nroots, NULL, NULL, NULL);
 69:   /* Build adjacency graph via a section/segbuffer */
 70:   PetscSectionCreate(PetscObjectComm((PetscObject) dm), &section);
 71:   PetscSectionSetChart(section, pStart, pEnd);
 72:   PetscSegBufferCreate(sizeof(PetscInt),1000,&adjBuffer);
 73:   /* Always use FVM adjacency to create partitioner graph */
 74:   DMPlexGetAdjacencyUseCone(dm, &useCone);
 75:   DMPlexGetAdjacencyUseClosure(dm, &useClosure);
 76:   DMPlexSetAdjacencyUseCone(dm, PETSC_TRUE);
 77:   DMPlexSetAdjacencyUseClosure(dm, PETSC_FALSE);
 78:   DMPlexCreateCellNumbering_Internal(dm, PETSC_TRUE, &cellNumbering);
 79:   ISGetIndices(cellNumbering, &cellNum);
 80:   for (*numVertices = 0, p = pStart; p < pEnd; p++) {
 81:     /* Skip non-owned cells in parallel (ParMetis expects no overlap) */
 82:     if (nroots > 0) {if (cellNum[p] < 0) continue;}
 83:     adjSize = PETSC_DETERMINE;
 84:     DMPlexGetAdjacency(dm, p, &adjSize, &adj);
 85:     for (a = 0; a < adjSize; ++a) {
 86:       const PetscInt point = adj[a];
 87:       if (point != p && pStart <= point && point < pEnd) {
 88:         PetscInt *PETSC_RESTRICT pBuf;
 89:         PetscSectionAddDof(section, p, 1);
 90:         PetscSegBufferGetInts(adjBuffer, 1, &pBuf);
 91:         *pBuf = point;
 92:       }
 93:     }
 94:     (*numVertices)++;
 95:   }
 96:   DMPlexSetAdjacencyUseCone(dm, useCone);
 97:   DMPlexSetAdjacencyUseClosure(dm, useClosure);
 98:   /* Derive CSR graph from section/segbuffer */
 99:   PetscSectionSetUp(section);
100:   PetscSectionGetStorageSize(section, &size);
101:   PetscMalloc1(*numVertices+1, &vOffsets);
102:   for (idx = 0, p = pStart; p < pEnd; p++) {
103:     if (nroots > 0) {if (cellNum[p] < 0) continue;}
104:     PetscSectionGetOffset(section, p, &(vOffsets[idx++]));
105:   }
106:   vOffsets[*numVertices] = size;
107:   if (offsets) *offsets = vOffsets;
108:   PetscSegBufferExtractAlloc(adjBuffer, &graph);
109:   {
110:     ISLocalToGlobalMapping ltogCells;
111:     PetscInt n, size, *cells_arr;
112:     /* In parallel, apply a global cell numbering to the graph */
113:     ISRestoreIndices(cellNumbering, &cellNum);
114:     ISLocalToGlobalMappingCreateIS(cellNumbering, &ltogCells);
115:     ISLocalToGlobalMappingGetSize(ltogCells, &size);
116:     ISLocalToGlobalMappingGetIndices(ltogCells, (const PetscInt**)&cells_arr);
117:     /* Convert to positive global cell numbers */
118:     for (n=0; n<size; n++) {if (cells_arr[n] < 0) cells_arr[n] = -(cells_arr[n]+1);}
119:     ISLocalToGlobalMappingRestoreIndices(ltogCells, (const PetscInt**)&cells_arr);
120:     ISLocalToGlobalMappingApplyBlock(ltogCells, vOffsets[*numVertices], graph, graph);
121:     ISLocalToGlobalMappingDestroy(&ltogCells);
122:     ISDestroy(&cellNumbering);
123:   }
124:   if (adjacency) *adjacency = graph;
125:   /* Clean up */
126:   PetscSegBufferDestroy(&adjBuffer);
127:   PetscSectionDestroy(&section);
128:   PetscFree(adj);
129:   return(0);
130: }

134: PetscErrorCode DMPlexCreateNeighborCSR(DM dm, PetscInt cellHeight, PetscInt *numVertices, PetscInt **offsets, PetscInt **adjacency)
135: {
136:   const PetscInt maxFaceCases = 30;
137:   PetscInt       numFaceCases = 0;
138:   PetscInt       numFaceVertices[30]; /* maxFaceCases, C89 sucks sucks sucks */
139:   PetscInt      *off, *adj;
140:   PetscInt      *neighborCells = NULL;
141:   PetscInt       dim, cellDim, depth = 0, faceDepth, cStart, cEnd, c, numCells, cell;

145:   /* For parallel partitioning, I think you have to communicate supports */
146:   DMGetDimension(dm, &dim);
147:   cellDim = dim - cellHeight;
148:   DMPlexGetDepth(dm, &depth);
149:   DMPlexGetHeightStratum(dm, cellHeight, &cStart, &cEnd);
150:   if (cEnd - cStart == 0) {
151:     if (numVertices) *numVertices = 0;
152:     if (offsets)   *offsets   = NULL;
153:     if (adjacency) *adjacency = NULL;
154:     return(0);
155:   }
156:   numCells  = cEnd - cStart;
157:   faceDepth = depth - cellHeight;
158:   if (dim == depth) {
159:     PetscInt f, fStart, fEnd;

161:     PetscCalloc1(numCells+1, &off);
162:     /* Count neighboring cells */
163:     DMPlexGetHeightStratum(dm, cellHeight+1, &fStart, &fEnd);
164:     for (f = fStart; f < fEnd; ++f) {
165:       const PetscInt *support;
166:       PetscInt        supportSize;
167:       DMPlexGetSupportSize(dm, f, &supportSize);
168:       DMPlexGetSupport(dm, f, &support);
169:       if (supportSize == 2) {
170:         PetscInt numChildren;

172:         DMPlexGetTreeChildren(dm,f,&numChildren,NULL);
173:         if (!numChildren) {
174:           ++off[support[0]-cStart+1];
175:           ++off[support[1]-cStart+1];
176:         }
177:       }
178:     }
179:     /* Prefix sum */
180:     for (c = 1; c <= numCells; ++c) off[c] += off[c-1];
181:     if (adjacency) {
182:       PetscInt *tmp;

184:       PetscMalloc1(off[numCells], &adj);
185:       PetscMalloc1(numCells+1, &tmp);
186:       PetscMemcpy(tmp, off, (numCells+1) * sizeof(PetscInt));
187:       /* Get neighboring cells */
188:       for (f = fStart; f < fEnd; ++f) {
189:         const PetscInt *support;
190:         PetscInt        supportSize;
191:         DMPlexGetSupportSize(dm, f, &supportSize);
192:         DMPlexGetSupport(dm, f, &support);
193:         if (supportSize == 2) {
194:           PetscInt numChildren;

196:           DMPlexGetTreeChildren(dm,f,&numChildren,NULL);
197:           if (!numChildren) {
198:             adj[tmp[support[0]-cStart]++] = support[1];
199:             adj[tmp[support[1]-cStart]++] = support[0];
200:           }
201:         }
202:       }
203: #if defined(PETSC_USE_DEBUG)
204:       for (c = 0; c < cEnd-cStart; ++c) if (tmp[c] != off[c+1]) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Offset %d != %d for cell %d", tmp[c], off[c], c+cStart);
205: #endif
206:       PetscFree(tmp);
207:     }
208:     if (numVertices) *numVertices = numCells;
209:     if (offsets)   *offsets   = off;
210:     if (adjacency) *adjacency = adj;
211:     return(0);
212:   }
213:   /* Setup face recognition */
214:   if (faceDepth == 1) {
215:     PetscInt cornersSeen[30] = {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0}; /* Could use PetscBT */

217:     for (c = cStart; c < cEnd; ++c) {
218:       PetscInt corners;

220:       DMPlexGetConeSize(dm, c, &corners);
221:       if (!cornersSeen[corners]) {
222:         PetscInt nFV;

224:         if (numFaceCases >= maxFaceCases) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_PLIB, "Exceeded maximum number of face recognition cases");
225:         cornersSeen[corners] = 1;

227:         DMPlexGetNumFaceVertices(dm, cellDim, corners, &nFV);

229:         numFaceVertices[numFaceCases++] = nFV;
230:       }
231:     }
232:   }
233:   PetscCalloc1(numCells+1, &off);
234:   /* Count neighboring cells */
235:   for (cell = cStart; cell < cEnd; ++cell) {
236:     PetscInt numNeighbors = PETSC_DETERMINE, n;

238:     DMPlexGetAdjacency_Internal(dm, cell, PETSC_TRUE, PETSC_FALSE, PETSC_FALSE, &numNeighbors, &neighborCells);
239:     /* Get meet with each cell, and check with recognizer (could optimize to check each pair only once) */
240:     for (n = 0; n < numNeighbors; ++n) {
241:       PetscInt        cellPair[2];
242:       PetscBool       found    = faceDepth > 1 ? PETSC_TRUE : PETSC_FALSE;
243:       PetscInt        meetSize = 0;
244:       const PetscInt *meet    = NULL;

246:       cellPair[0] = cell; cellPair[1] = neighborCells[n];
247:       if (cellPair[0] == cellPair[1]) continue;
248:       if (!found) {
249:         DMPlexGetMeet(dm, 2, cellPair, &meetSize, &meet);
250:         if (meetSize) {
251:           PetscInt f;

253:           for (f = 0; f < numFaceCases; ++f) {
254:             if (numFaceVertices[f] == meetSize) {
255:               found = PETSC_TRUE;
256:               break;
257:             }
258:           }
259:         }
260:         DMPlexRestoreMeet(dm, 2, cellPair, &meetSize, &meet);
261:       }
262:       if (found) ++off[cell-cStart+1];
263:     }
264:   }
265:   /* Prefix sum */
266:   for (cell = 1; cell <= numCells; ++cell) off[cell] += off[cell-1];

268:   if (adjacency) {
269:     PetscMalloc1(off[numCells], &adj);
270:     /* Get neighboring cells */
271:     for (cell = cStart; cell < cEnd; ++cell) {
272:       PetscInt numNeighbors = PETSC_DETERMINE, n;
273:       PetscInt cellOffset   = 0;

275:       DMPlexGetAdjacency_Internal(dm, cell, PETSC_TRUE, PETSC_FALSE, PETSC_FALSE, &numNeighbors, &neighborCells);
276:       /* Get meet with each cell, and check with recognizer (could optimize to check each pair only once) */
277:       for (n = 0; n < numNeighbors; ++n) {
278:         PetscInt        cellPair[2];
279:         PetscBool       found    = faceDepth > 1 ? PETSC_TRUE : PETSC_FALSE;
280:         PetscInt        meetSize = 0;
281:         const PetscInt *meet    = NULL;

283:         cellPair[0] = cell; cellPair[1] = neighborCells[n];
284:         if (cellPair[0] == cellPair[1]) continue;
285:         if (!found) {
286:           DMPlexGetMeet(dm, 2, cellPair, &meetSize, &meet);
287:           if (meetSize) {
288:             PetscInt f;

290:             for (f = 0; f < numFaceCases; ++f) {
291:               if (numFaceVertices[f] == meetSize) {
292:                 found = PETSC_TRUE;
293:                 break;
294:               }
295:             }
296:           }
297:           DMPlexRestoreMeet(dm, 2, cellPair, &meetSize, &meet);
298:         }
299:         if (found) {
300:           adj[off[cell-cStart]+cellOffset] = neighborCells[n];
301:           ++cellOffset;
302:         }
303:       }
304:     }
305:   }
306:   PetscFree(neighborCells);
307:   if (numVertices) *numVertices = numCells;
308:   if (offsets)   *offsets   = off;
309:   if (adjacency) *adjacency = adj;
310:   return(0);
311: }

315: /*@C
316:   PetscPartitionerRegister - Adds a new PetscPartitioner implementation

318:   Not Collective

320:   Input Parameters:
321: + name        - The name of a new user-defined creation routine
322: - create_func - The creation routine itself

324:   Notes:
325:   PetscPartitionerRegister() may be called multiple times to add several user-defined PetscPartitioners

327:   Sample usage:
328: .vb
329:     PetscPartitionerRegister("my_part", MyPetscPartitionerCreate);
330: .ve

332:   Then, your PetscPartitioner type can be chosen with the procedural interface via
333: .vb
334:     PetscPartitionerCreate(MPI_Comm, PetscPartitioner *);
335:     PetscPartitionerSetType(PetscPartitioner, "my_part");
336: .ve
337:    or at runtime via the option
338: .vb
339:     -petscpartitioner_type my_part
340: .ve

342:   Level: advanced

344: .keywords: PetscPartitioner, register
345: .seealso: PetscPartitionerRegisterAll(), PetscPartitionerRegisterDestroy()

347: @*/
348: PetscErrorCode PetscPartitionerRegister(const char sname[], PetscErrorCode (*function)(PetscPartitioner))
349: {

353:   PetscFunctionListAdd(&PetscPartitionerList, sname, function);
354:   return(0);
355: }

359: /*@C
360:   PetscPartitionerSetType - Builds a particular PetscPartitioner

362:   Collective on PetscPartitioner

364:   Input Parameters:
365: + part - The PetscPartitioner object
366: - name - The kind of partitioner

368:   Options Database Key:
369: . -petscpartitioner_type <type> - Sets the PetscPartitioner type; use -help for a list of available types

371:   Level: intermediate

373: .keywords: PetscPartitioner, set, type
374: .seealso: PetscPartitionerGetType(), PetscPartitionerCreate()
375: @*/
376: PetscErrorCode PetscPartitionerSetType(PetscPartitioner part, PetscPartitionerType name)
377: {
378:   PetscErrorCode (*r)(PetscPartitioner);
379:   PetscBool      match;

384:   PetscObjectTypeCompare((PetscObject) part, name, &match);
385:   if (match) return(0);

387:   PetscPartitionerRegisterAll();
388:   PetscFunctionListFind(PetscPartitionerList, name, &r);
389:   if (!r) SETERRQ1(PetscObjectComm((PetscObject) part), PETSC_ERR_ARG_UNKNOWN_TYPE, "Unknown PetscPartitioner type: %s", name);

391:   if (part->ops->destroy) {
392:     (*part->ops->destroy)(part);
393:     part->ops->destroy = NULL;
394:   }
395:   (*r)(part);
396:   PetscObjectChangeTypeName((PetscObject) part, name);
397:   return(0);
398: }

402: /*@C
403:   PetscPartitionerGetType - Gets the PetscPartitioner type name (as a string) from the object.

405:   Not Collective

407:   Input Parameter:
408: . part - The PetscPartitioner

410:   Output Parameter:
411: . name - The PetscPartitioner type name

413:   Level: intermediate

415: .keywords: PetscPartitioner, get, type, name
416: .seealso: PetscPartitionerSetType(), PetscPartitionerCreate()
417: @*/
418: PetscErrorCode PetscPartitionerGetType(PetscPartitioner part, PetscPartitionerType *name)
419: {

425:   PetscPartitionerRegisterAll();
426:   *name = ((PetscObject) part)->type_name;
427:   return(0);
428: }

432: /*@C
433:   PetscPartitionerView - Views a PetscPartitioner

435:   Collective on PetscPartitioner

437:   Input Parameter:
438: + part - the PetscPartitioner object to view
439: - v    - the viewer

441:   Level: developer

443: .seealso: PetscPartitionerDestroy()
444: @*/
445: PetscErrorCode PetscPartitionerView(PetscPartitioner part, PetscViewer v)
446: {

451:   if (!v) {PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject) part), &v);}
452:   if (part->ops->view) {(*part->ops->view)(part, v);}
453:   return(0);
454: }

458: PetscErrorCode PetscPartitionerSetTypeFromOptions_Internal(PetscPartitioner part)
459: {
460:   const char    *defaultType;
461:   char           name[256];
462:   PetscBool      flg;

467:   if (!((PetscObject) part)->type_name)
468: #if defined(PETSC_HAVE_CHACO)
469:     defaultType = PETSCPARTITIONERCHACO;
470: #elif defined(PETSC_HAVE_PARMETIS)
471:     defaultType = PETSCPARTITIONERPARMETIS;
472: #else
473:     defaultType = PETSCPARTITIONERSIMPLE;
474: #endif
475:   else
476:     defaultType = ((PetscObject) part)->type_name;
477:   PetscPartitionerRegisterAll();

479:   PetscObjectOptionsBegin((PetscObject) part);
480:   PetscOptionsFList("-petscpartitioner_type", "Graph partitioner", "PetscPartitionerSetType", PetscPartitionerList, defaultType, name, 256, &flg);
481:   if (flg) {
482:     PetscPartitionerSetType(part, name);
483:   } else if (!((PetscObject) part)->type_name) {
484:     PetscPartitionerSetType(part, defaultType);
485:   }
486:   PetscOptionsEnd();
487:   return(0);
488: }

492: /*@
493:   PetscPartitionerSetFromOptions - sets parameters in a PetscPartitioner from the options database

495:   Collective on PetscPartitioner

497:   Input Parameter:
498: . part - the PetscPartitioner object to set options for

500:   Level: developer

502: .seealso: PetscPartitionerView()
503: @*/
504: PetscErrorCode PetscPartitionerSetFromOptions(PetscPartitioner part)
505: {

510:   PetscPartitionerSetTypeFromOptions_Internal(part);

512:   PetscObjectOptionsBegin((PetscObject) part);
513:   if (part->ops->setfromoptions) {(*part->ops->setfromoptions)(part);}
514:   /* process any options handlers added with PetscObjectAddOptionsHandler() */
515:   PetscObjectProcessOptionsHandlers(PetscOptionsObject,(PetscObject) part);
516:   PetscOptionsEnd();
517:   PetscPartitionerViewFromOptions(part, NULL, "-petscpartitioner_view");
518:   return(0);
519: }

523: /*@C
524:   PetscPartitionerSetUp - Construct data structures for the PetscPartitioner

526:   Collective on PetscPartitioner

528:   Input Parameter:
529: . part - the PetscPartitioner object to setup

531:   Level: developer

533: .seealso: PetscPartitionerView(), PetscPartitionerDestroy()
534: @*/
535: PetscErrorCode PetscPartitionerSetUp(PetscPartitioner part)
536: {

541:   if (part->ops->setup) {(*part->ops->setup)(part);}
542:   return(0);
543: }

547: /*@
548:   PetscPartitionerDestroy - Destroys a PetscPartitioner object

550:   Collective on PetscPartitioner

552:   Input Parameter:
553: . part - the PetscPartitioner object to destroy

555:   Level: developer

557: .seealso: PetscPartitionerView()
558: @*/
559: PetscErrorCode PetscPartitionerDestroy(PetscPartitioner *part)
560: {

564:   if (!*part) return(0);

567:   if (--((PetscObject)(*part))->refct > 0) {*part = 0; return(0);}
568:   ((PetscObject) (*part))->refct = 0;

570:   if ((*part)->ops->destroy) {(*(*part)->ops->destroy)(*part);}
571:   PetscHeaderDestroy(part);
572:   return(0);
573: }

577: /*@
578:   PetscPartitionerCreate - Creates an empty PetscPartitioner object. The type can then be set with PetscPartitionerSetType().

580:   Collective on MPI_Comm

582:   Input Parameter:
583: . comm - The communicator for the PetscPartitioner object

585:   Output Parameter:
586: . part - The PetscPartitioner object

588:   Level: beginner

590: .seealso: PetscPartitionerSetType(), PETSCPARTITIONERCHACO, PETSCPARTITIONERPARMETIS, PETSCPARTITIONERSHELL, PETSCPARTITIONERSIMPLE, PETSCPARTITIONERGATHER
591: @*/
592: PetscErrorCode PetscPartitionerCreate(MPI_Comm comm, PetscPartitioner *part)
593: {
594:   PetscPartitioner p;
595:   PetscErrorCode   ierr;

599:   *part = NULL;
600:   PetscFVInitializePackage();

602:   PetscHeaderCreate(p, PETSCPARTITIONER_CLASSID, "PetscPartitioner", "Graph Partitioner", "PetscPartitioner", comm, PetscPartitionerDestroy, PetscPartitionerView);

604:   *part = p;
605:   return(0);
606: }

610: /*@
611:   PetscPartitionerPartition - Create a non-overlapping partition of the cells in the mesh

613:   Collective on DM

615:   Input Parameters:
616: + part    - The PetscPartitioner
617: - dm      - The mesh DM

619:   Output Parameters:
620: + partSection     - The PetscSection giving the division of points by partition
621: - partition       - The list of points by partition

623:   Note: Instead of cells, points at a given height can be partitioned by calling PetscPartitionerSetPointHeight()

625:   Level: developer

627: .seealso DMPlexDistribute(), PetscPartitionerSetPointHeight(), PetscPartitionerCreate()
628: @*/
629: PetscErrorCode PetscPartitionerPartition(PetscPartitioner part, DM dm, PetscSection partSection, IS *partition)
630: {
631:   PetscMPIInt    size;

639:   MPI_Comm_size(PetscObjectComm((PetscObject) part), &size);
640:   if (size == 1) {
641:     PetscInt *points;
642:     PetscInt  cStart, cEnd, c;

644:     DMPlexGetHeightStratum(dm, part->height, &cStart, &cEnd);
645:     PetscSectionSetChart(partSection, 0, size);
646:     PetscSectionSetDof(partSection, 0, cEnd-cStart);
647:     PetscSectionSetUp(partSection);
648:     PetscMalloc1(cEnd-cStart, &points);
649:     for (c = cStart; c < cEnd; ++c) points[c] = c;
650:     ISCreateGeneral(PetscObjectComm((PetscObject) part), cEnd-cStart, points, PETSC_OWN_POINTER, partition);
651:     return(0);
652:   }
653:   if (part->height == 0) {
654:     PetscInt  numVertices;
655:     PetscInt *start     = NULL;
656:     PetscInt *adjacency = NULL;

658:     DMPlexCreatePartitionerGraph(dm, 0, &numVertices, &start, &adjacency);
659:     if (!part->ops->partition) SETERRQ(PetscObjectComm((PetscObject) part), PETSC_ERR_ARG_WRONGSTATE, "PetscPartitioner has no type");
660:     (*part->ops->partition)(part, dm, size, numVertices, start, adjacency, partSection, partition);
661:     PetscFree(start);
662:     PetscFree(adjacency);
663:   } else SETERRQ1(PetscObjectComm((PetscObject) part), PETSC_ERR_ARG_OUTOFRANGE, "Invalid height %D for points to partition", part->height);
664:   return(0);
665: }

669: PetscErrorCode PetscPartitionerDestroy_Shell(PetscPartitioner part)
670: {
671:   PetscPartitioner_Shell *p = (PetscPartitioner_Shell *) part->data;
672:   PetscErrorCode          ierr;

675:   PetscSectionDestroy(&p->section);
676:   ISDestroy(&p->partition);
677:   PetscFree(p);
678:   return(0);
679: }

683: PetscErrorCode PetscPartitionerView_Shell_Ascii(PetscPartitioner part, PetscViewer viewer)
684: {
685:   PetscViewerFormat format;
686:   PetscErrorCode    ierr;

689:   PetscViewerGetFormat(viewer, &format);
690:   PetscViewerASCIIPrintf(viewer, "Shell Graph Partitioner:\n");
691:   return(0);
692: }

696: PetscErrorCode PetscPartitionerView_Shell(PetscPartitioner part, PetscViewer viewer)
697: {
698:   PetscBool      iascii;

704:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);
705:   if (iascii) {PetscPartitionerView_Shell_Ascii(part, viewer);}
706:   return(0);
707: }

711: PetscErrorCode PetscPartitionerPartition_Shell(PetscPartitioner part, DM dm, PetscInt nparts, PetscInt numVertices, PetscInt start[], PetscInt adjacency[], PetscSection partSection, IS *partition)
712: {
713:   PetscPartitioner_Shell *p = (PetscPartitioner_Shell *) part->data;
714:   PetscInt                np;
715:   PetscErrorCode          ierr;

718:   PetscSectionGetChart(p->section, NULL, &np);
719:   if (nparts != np) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of requested partitions %d != configured partitions %d", nparts, np);
720:   ISGetLocalSize(p->partition, &np);
721:   if (numVertices != np) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of input vertices %d != configured vertices %d", numVertices, np);
722:   PetscSectionCopy(p->section, partSection);
723:   *partition = p->partition;
724:   PetscObjectReference((PetscObject) p->partition);
725:   return(0);
726: }

730: PetscErrorCode PetscPartitionerInitialize_Shell(PetscPartitioner part)
731: {
733:   part->ops->view      = PetscPartitionerView_Shell;
734:   part->ops->destroy   = PetscPartitionerDestroy_Shell;
735:   part->ops->partition = PetscPartitionerPartition_Shell;
736:   return(0);
737: }

739: /*MC
740:   PETSCPARTITIONERSHELL = "shell" - A PetscPartitioner object

742:   Level: intermediate

744: .seealso: PetscPartitionerType, PetscPartitionerCreate(), PetscPartitionerSetType()
745: M*/

749: PETSC_EXTERN PetscErrorCode PetscPartitionerCreate_Shell(PetscPartitioner part)
750: {
751:   PetscPartitioner_Shell *p;
752:   PetscErrorCode          ierr;

756:   PetscNewLog(part, &p);
757:   part->data = p;

759:   PetscPartitionerInitialize_Shell(part);
760:   return(0);
761: }

765: /*@C
766:   PetscPartitionerShellSetPartition - Set an artifical partition for a mesh

768:   Collective on PART

770:   Input Parameters:
771: + part     - The PetscPartitioner
772: . numProcs - The number of partitions
773: . sizes    - array of size numProcs (or NULL) providing the number of points in each partition
774: - points   - array of size sum(sizes) (may be NULL iff sizes is NULL) providing the partition each point belongs to

776:   Level: developer

778:   Notes:

780:     It is safe to free the sizes and points arrays after use in this routine.

782: .seealso DMPlexDistribute(), PetscPartitionerCreate()
783: @*/
784: PetscErrorCode PetscPartitionerShellSetPartition(PetscPartitioner part, PetscInt numProcs, const PetscInt sizes[], const PetscInt points[])
785: {
786:   PetscPartitioner_Shell *p = (PetscPartitioner_Shell *) part->data;
787:   PetscInt                proc, numPoints;
788:   PetscErrorCode          ierr;

794:   PetscSectionDestroy(&p->section);
795:   ISDestroy(&p->partition);
796:   PetscSectionCreate(PetscObjectComm((PetscObject) part), &p->section);
797:   PetscSectionSetChart(p->section, 0, numProcs);
798:   if (sizes) {
799:     for (proc = 0; proc < numProcs; ++proc) {
800:       PetscSectionSetDof(p->section, proc, sizes[proc]);
801:     }
802:   }
803:   PetscSectionSetUp(p->section);
804:   PetscSectionGetStorageSize(p->section, &numPoints);
805:   ISCreateGeneral(PetscObjectComm((PetscObject) part), numPoints, points, PETSC_COPY_VALUES, &p->partition);
806:   return(0);
807: }

811: PetscErrorCode PetscPartitionerDestroy_Simple(PetscPartitioner part)
812: {
813:   PetscPartitioner_Simple *p = (PetscPartitioner_Simple *) part->data;
814:   PetscErrorCode          ierr;

817:   PetscFree(p);
818:   return(0);
819: }

823: PetscErrorCode PetscPartitionerView_Simple_Ascii(PetscPartitioner part, PetscViewer viewer)
824: {
825:   PetscViewerFormat format;
826:   PetscErrorCode    ierr;

829:   PetscViewerGetFormat(viewer, &format);
830:   PetscViewerASCIIPrintf(viewer, "Simple Graph Partitioner:\n");
831:   return(0);
832: }

836: PetscErrorCode PetscPartitionerView_Simple(PetscPartitioner part, PetscViewer viewer)
837: {
838:   PetscBool      iascii;

844:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);
845:   if (iascii) {PetscPartitionerView_Simple_Ascii(part, viewer);}
846:   return(0);
847: }

851: PetscErrorCode PetscPartitionerPartition_Simple(PetscPartitioner part, DM dm, PetscInt nparts, PetscInt numVertices, PetscInt start[], PetscInt adjacency[], PetscSection partSection, IS *partition)
852: {
853:   MPI_Comm       comm;
854:   PetscInt       np;
855:   PetscMPIInt    size;

859:   comm = PetscObjectComm((PetscObject)dm);
860:   MPI_Comm_size(comm,&size);
861:   PetscSectionSetChart(partSection, 0, nparts);
862:   ISCreateStride(PETSC_COMM_SELF, numVertices, 0, 1, partition);
863:   if (size == 1) {
864:     for (np = 0; np < nparts; ++np) {PetscSectionSetDof(partSection, np, numVertices/nparts + ((numVertices % nparts) > np));}
865:   }
866:   else {
867:     PetscMPIInt rank;
868:     PetscInt nvGlobal, *offsets, myFirst, myLast;

870:     PetscMalloc1(size+1,&offsets);
871:     offsets[0] = 0;
872:     MPI_Allgather(&numVertices,1,MPIU_INT,&offsets[1],1,MPIU_INT,comm);
873:     for (np = 2; np <= size; np++) {
874:       offsets[np] += offsets[np-1];
875:     }
876:     nvGlobal = offsets[size];
877:     MPI_Comm_rank(comm,&rank);
878:     myFirst = offsets[rank];
879:     myLast  = offsets[rank + 1] - 1;
880:     PetscFree(offsets);
881:     if (numVertices) {
882:       PetscInt firstPart = 0, firstLargePart = 0;
883:       PetscInt lastPart = 0, lastLargePart = 0;
884:       PetscInt rem = nvGlobal % nparts;
885:       PetscInt pSmall = nvGlobal/nparts;
886:       PetscInt pBig = nvGlobal/nparts + 1;


889:       if (rem) {
890:         firstLargePart = myFirst / pBig;
891:         lastLargePart  = myLast  / pBig;

893:         if (firstLargePart < rem) {
894:           firstPart = firstLargePart;
895:         }
896:         else {
897:           firstPart = rem + (myFirst - (rem * pBig)) / pSmall;
898:         }
899:         if (lastLargePart < rem) {
900:           lastPart = lastLargePart;
901:         }
902:         else {
903:           lastPart = rem + (myLast - (rem * pBig)) / pSmall;
904:         }
905:       }
906:       else {
907:         firstPart = myFirst / (nvGlobal/nparts);
908:         lastPart  = myLast  / (nvGlobal/nparts);
909:       }

911:       for (np = firstPart; np <= lastPart; np++) {
912:         PetscInt PartStart =  np    * (nvGlobal/nparts) + PetscMin(nvGlobal % nparts,np);
913:         PetscInt PartEnd   = (np+1) * (nvGlobal/nparts) + PetscMin(nvGlobal % nparts,np+1);

915:         PartStart = PetscMax(PartStart,myFirst);
916:         PartEnd   = PetscMin(PartEnd,myLast+1);
917:         PetscSectionSetDof(partSection,np,PartEnd-PartStart);
918:       }
919:     }
920:   }
921:   PetscSectionSetUp(partSection);
922:   return(0);
923: }

927: PetscErrorCode PetscPartitionerInitialize_Simple(PetscPartitioner part)
928: {
930:   part->ops->view      = PetscPartitionerView_Simple;
931:   part->ops->destroy   = PetscPartitionerDestroy_Simple;
932:   part->ops->partition = PetscPartitionerPartition_Simple;
933:   return(0);
934: }

936: /*MC
937:   PETSCPARTITIONERSIMPLE = "simple" - A PetscPartitioner object

939:   Level: intermediate

941: .seealso: PetscPartitionerType, PetscPartitionerCreate(), PetscPartitionerSetType()
942: M*/

946: PETSC_EXTERN PetscErrorCode PetscPartitionerCreate_Simple(PetscPartitioner part)
947: {
948:   PetscPartitioner_Simple *p;
949:   PetscErrorCode           ierr;

953:   PetscNewLog(part, &p);
954:   part->data = p;

956:   PetscPartitionerInitialize_Simple(part);
957:   return(0);
958: }

962: PetscErrorCode PetscPartitionerDestroy_Gather(PetscPartitioner part)
963: {
964:   PetscPartitioner_Gather *p = (PetscPartitioner_Gather *) part->data;
965:   PetscErrorCode          ierr;

968:   PetscFree(p);
969:   return(0);
970: }

974: PetscErrorCode PetscPartitionerView_Gather_Ascii(PetscPartitioner part, PetscViewer viewer)
975: {
976:   PetscViewerFormat format;
977:   PetscErrorCode    ierr;

980:   PetscViewerGetFormat(viewer, &format);
981:   PetscViewerASCIIPrintf(viewer, "Gather Graph Partitioner:\n");
982:   return(0);
983: }

987: PetscErrorCode PetscPartitionerView_Gather(PetscPartitioner part, PetscViewer viewer)
988: {
989:   PetscBool      iascii;

995:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);
996:   if (iascii) {PetscPartitionerView_Gather_Ascii(part, viewer);}
997:   return(0);
998: }

1002: PetscErrorCode PetscPartitionerPartition_Gather(PetscPartitioner part, DM dm, PetscInt nparts, PetscInt numVertices, PetscInt start[], PetscInt adjacency[], PetscSection partSection, IS *partition)
1003: {
1004:   PetscInt       np;

1008:   PetscSectionSetChart(partSection, 0, nparts);
1009:   ISCreateStride(PETSC_COMM_SELF, numVertices, 0, 1, partition);
1010:   PetscSectionSetDof(partSection,0,numVertices);
1011:   for (np = 1; np < nparts; ++np) {PetscSectionSetDof(partSection, np, 0);}
1012:   PetscSectionSetUp(partSection);
1013:   return(0);
1014: }

1018: PetscErrorCode PetscPartitionerInitialize_Gather(PetscPartitioner part)
1019: {
1021:   part->ops->view      = PetscPartitionerView_Gather;
1022:   part->ops->destroy   = PetscPartitionerDestroy_Gather;
1023:   part->ops->partition = PetscPartitionerPartition_Gather;
1024:   return(0);
1025: }

1027: /*MC
1028:   PETSCPARTITIONERGATHER = "gather" - A PetscPartitioner object

1030:   Level: intermediate

1032: .seealso: PetscPartitionerType, PetscPartitionerCreate(), PetscPartitionerSetType()
1033: M*/

1037: PETSC_EXTERN PetscErrorCode PetscPartitionerCreate_Gather(PetscPartitioner part)
1038: {
1039:   PetscPartitioner_Gather *p;
1040:   PetscErrorCode           ierr;

1044:   PetscNewLog(part, &p);
1045:   part->data = p;

1047:   PetscPartitionerInitialize_Gather(part);
1048:   return(0);
1049: }


1054: PetscErrorCode PetscPartitionerDestroy_Chaco(PetscPartitioner part)
1055: {
1056:   PetscPartitioner_Chaco *p = (PetscPartitioner_Chaco *) part->data;
1057:   PetscErrorCode          ierr;

1060:   PetscFree(p);
1061:   return(0);
1062: }

1066: PetscErrorCode PetscPartitionerView_Chaco_Ascii(PetscPartitioner part, PetscViewer viewer)
1067: {
1068:   PetscViewerFormat format;
1069:   PetscErrorCode    ierr;

1072:   PetscViewerGetFormat(viewer, &format);
1073:   PetscViewerASCIIPrintf(viewer, "Chaco Graph Partitioner:\n");
1074:   return(0);
1075: }

1079: PetscErrorCode PetscPartitionerView_Chaco(PetscPartitioner part, PetscViewer viewer)
1080: {
1081:   PetscBool      iascii;

1087:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);
1088:   if (iascii) {PetscPartitionerView_Chaco_Ascii(part, viewer);}
1089:   return(0);
1090: }

1092: #if defined(PETSC_HAVE_CHACO)
1093: #if defined(PETSC_HAVE_UNISTD_H)
1094: #include <unistd.h>
1095: #endif
1096: /* Chaco does not have an include file */
1097: PETSC_EXTERN int interface(int nvtxs, int *start, int *adjacency, int *vwgts,
1098:                        float *ewgts, float *x, float *y, float *z, char *outassignname,
1099:                        char *outfilename, short *assignment, int architecture, int ndims_tot,
1100:                        int mesh_dims[3], double *goal, int global_method, int local_method,
1101:                        int rqi_flag, int vmax, int ndims, double eigtol, long seed);

1103: extern int FREE_GRAPH;
1104: #endif

1108: PetscErrorCode PetscPartitionerPartition_Chaco(PetscPartitioner part, DM dm, PetscInt nparts, PetscInt numVertices, PetscInt start[], PetscInt adjacency[], PetscSection partSection, IS *partition)
1109: {
1110: #if defined(PETSC_HAVE_CHACO)
1111:   enum {DEFAULT_METHOD = 1, INERTIAL_METHOD = 3};
1112:   MPI_Comm       comm;
1113:   int            nvtxs          = numVertices; /* number of vertices in full graph */
1114:   int           *vwgts          = NULL;   /* weights for all vertices */
1115:   float         *ewgts          = NULL;   /* weights for all edges */
1116:   float         *x              = NULL, *y = NULL, *z = NULL; /* coordinates for inertial method */
1117:   char          *outassignname  = NULL;   /*  name of assignment output file */
1118:   char          *outfilename    = NULL;   /* output file name */
1119:   int            architecture   = 1;      /* 0 => hypercube, d => d-dimensional mesh */
1120:   int            ndims_tot      = 0;      /* total number of cube dimensions to divide */
1121:   int            mesh_dims[3];            /* dimensions of mesh of processors */
1122:   double        *goal          = NULL;    /* desired set sizes for each set */
1123:   int            global_method = 1;       /* global partitioning algorithm */
1124:   int            local_method  = 1;       /* local partitioning algorithm */
1125:   int            rqi_flag      = 0;       /* should I use RQI/Symmlq eigensolver? */
1126:   int            vmax          = 200;     /* how many vertices to coarsen down to? */
1127:   int            ndims         = 1;       /* number of eigenvectors (2^d sets) */
1128:   double         eigtol        = 0.001;   /* tolerance on eigenvectors */
1129:   long           seed          = 123636512; /* for random graph mutations */
1130:   short int     *assignment;              /* Output partition */
1131:   int            fd_stdout, fd_pipe[2];
1132:   PetscInt      *points;
1133:   int            i, v, p;

1137:   PetscObjectGetComm((PetscObject)dm,&comm);
1138:   if (!numVertices) {
1139:     PetscSectionSetChart(partSection, 0, nparts);
1140:     PetscSectionSetUp(partSection);
1141:     ISCreateGeneral(comm, 0, NULL, PETSC_OWN_POINTER, partition);
1142:     return(0);
1143:   }
1144:   FREE_GRAPH = 0;                         /* Do not let Chaco free my memory */
1145:   for (i = 0; i < start[numVertices]; ++i) ++adjacency[i];

1147:   if (global_method == INERTIAL_METHOD) {
1148:     /* manager.createCellCoordinates(nvtxs, &x, &y, &z); */
1149:     SETERRQ(comm, PETSC_ERR_SUP, "Inertial partitioning not yet supported");
1150:   }
1151:   mesh_dims[0] = nparts;
1152:   mesh_dims[1] = 1;
1153:   mesh_dims[2] = 1;
1154:   PetscMalloc1(nvtxs, &assignment);
1155:   /* Chaco outputs to stdout. We redirect this to a buffer. */
1156:   /* TODO: check error codes for UNIX calls */
1157: #if defined(PETSC_HAVE_UNISTD_H)
1158:   {
1159:     int piperet;
1160:     piperet = pipe(fd_pipe);
1161:     if (piperet) SETERRQ(comm,PETSC_ERR_SYS,"Could not create pipe");
1162:     fd_stdout = dup(1);
1163:     close(1);
1164:     dup2(fd_pipe[1], 1);
1165:   }
1166: #endif
1167:   interface(nvtxs, (int*) start, (int*) adjacency, vwgts, ewgts, x, y, z, outassignname, outfilename,
1168:                    assignment, architecture, ndims_tot, mesh_dims, goal, global_method, local_method, rqi_flag,
1169:                    vmax, ndims, eigtol, seed);
1170: #if defined(PETSC_HAVE_UNISTD_H)
1171:   {
1172:     char msgLog[10000];
1173:     int  count;

1175:     fflush(stdout);
1176:     count = read(fd_pipe[0], msgLog, (10000-1)*sizeof(char));
1177:     if (count < 0) count = 0;
1178:     msgLog[count] = 0;
1179:     close(1);
1180:     dup2(fd_stdout, 1);
1181:     close(fd_stdout);
1182:     close(fd_pipe[0]);
1183:     close(fd_pipe[1]);
1184:     if (ierr) SETERRQ1(comm, PETSC_ERR_LIB, "Error in Chaco library: %s", msgLog);
1185:   }
1186: #endif
1187:   /* Convert to PetscSection+IS */
1188:   PetscSectionSetChart(partSection, 0, nparts);
1189:   for (v = 0; v < nvtxs; ++v) {
1190:     PetscSectionAddDof(partSection, assignment[v], 1);
1191:   }
1192:   PetscSectionSetUp(partSection);
1193:   PetscMalloc1(nvtxs, &points);
1194:   for (p = 0, i = 0; p < nparts; ++p) {
1195:     for (v = 0; v < nvtxs; ++v) {
1196:       if (assignment[v] == p) points[i++] = v;
1197:     }
1198:   }
1199:   if (i != nvtxs) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of points %D should be %D", i, nvtxs);
1200:   ISCreateGeneral(comm, nvtxs, points, PETSC_OWN_POINTER, partition);
1201:   if (global_method == INERTIAL_METHOD) {
1202:     /* manager.destroyCellCoordinates(nvtxs, &x, &y, &z); */
1203:   }
1204:   PetscFree(assignment);
1205:   for (i = 0; i < start[numVertices]; ++i) --adjacency[i];
1206:   return(0);
1207: #else
1208:   SETERRQ(PetscObjectComm((PetscObject) part), PETSC_ERR_SUP, "Mesh partitioning needs external package support.\nPlease reconfigure with --download-chaco.");
1209: #endif
1210: }

1214: PetscErrorCode PetscPartitionerInitialize_Chaco(PetscPartitioner part)
1215: {
1217:   part->ops->view      = PetscPartitionerView_Chaco;
1218:   part->ops->destroy   = PetscPartitionerDestroy_Chaco;
1219:   part->ops->partition = PetscPartitionerPartition_Chaco;
1220:   return(0);
1221: }

1223: /*MC
1224:   PETSCPARTITIONERCHACO = "chaco" - A PetscPartitioner object using the Chaco library

1226:   Level: intermediate

1228: .seealso: PetscPartitionerType, PetscPartitionerCreate(), PetscPartitionerSetType()
1229: M*/

1233: PETSC_EXTERN PetscErrorCode PetscPartitionerCreate_Chaco(PetscPartitioner part)
1234: {
1235:   PetscPartitioner_Chaco *p;
1236:   PetscErrorCode          ierr;

1240:   PetscNewLog(part, &p);
1241:   part->data = p;

1243:   PetscPartitionerInitialize_Chaco(part);
1244:   PetscCitationsRegister(ChacoPartitionerCitation, &ChacoPartitionercite);
1245:   return(0);
1246: }

1250: PetscErrorCode PetscPartitionerDestroy_ParMetis(PetscPartitioner part)
1251: {
1252:   PetscPartitioner_ParMetis *p = (PetscPartitioner_ParMetis *) part->data;
1253:   PetscErrorCode             ierr;

1256:   PetscFree(p);
1257:   return(0);
1258: }

1262: PetscErrorCode PetscPartitionerView_ParMetis_Ascii(PetscPartitioner part, PetscViewer viewer)
1263: {
1264:   PetscViewerFormat format;
1265:   PetscErrorCode    ierr;

1268:   PetscViewerGetFormat(viewer, &format);
1269:   PetscViewerASCIIPrintf(viewer, "ParMetis Graph Partitioner:\n");
1270:   return(0);
1271: }

1275: PetscErrorCode PetscPartitionerView_ParMetis(PetscPartitioner part, PetscViewer viewer)
1276: {
1277:   PetscBool      iascii;

1283:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);
1284:   if (iascii) {PetscPartitionerView_ParMetis_Ascii(part, viewer);}
1285:   return(0);
1286: }

1288: #if defined(PETSC_HAVE_PARMETIS)
1289: #include <parmetis.h>
1290: #endif

1294: PetscErrorCode PetscPartitionerPartition_ParMetis(PetscPartitioner part, DM dm, PetscInt nparts, PetscInt numVertices, PetscInt start[], PetscInt adjacency[], PetscSection partSection, IS *partition)
1295: {
1296: #if defined(PETSC_HAVE_PARMETIS)
1297:   MPI_Comm       comm;
1298:   PetscInt       nvtxs      = numVertices; /* The number of vertices in full graph */
1299:   PetscInt      *vtxdist;                  /* Distribution of vertices across processes */
1300:   PetscInt      *xadj       = start;       /* Start of edge list for each vertex */
1301:   PetscInt      *adjncy     = adjacency;   /* Edge lists for all vertices */
1302:   PetscInt      *vwgt       = NULL;        /* Vertex weights */
1303:   PetscInt      *adjwgt     = NULL;        /* Edge weights */
1304:   PetscInt       wgtflag    = 0;           /* Indicates which weights are present */
1305:   PetscInt       numflag    = 0;           /* Indicates initial offset (0 or 1) */
1306:   PetscInt       ncon       = 1;           /* The number of weights per vertex */
1307:   PetscReal     *tpwgts;                   /* The fraction of vertex weights assigned to each partition */
1308:   PetscReal     *ubvec;                    /* The balance intolerance for vertex weights */
1309:   PetscInt       options[5];               /* Options */
1310:   /* Outputs */
1311:   PetscInt       edgeCut;                  /* The number of edges cut by the partition */
1312:   PetscInt      *assignment, *points;
1313:   PetscMPIInt    rank, p, v, i;

1317:   PetscObjectGetComm((PetscObject) part, &comm);
1318:   MPI_Comm_rank(comm, &rank);
1319:   options[0] = 0; /* Use all defaults */
1320:   /* Calculate vertex distribution */
1321:   PetscMalloc4(nparts+1,&vtxdist,nparts*ncon,&tpwgts,ncon,&ubvec,nvtxs,&assignment);
1322:   vtxdist[0] = 0;
1323:   MPI_Allgather(&nvtxs, 1, MPIU_INT, &vtxdist[1], 1, MPIU_INT, comm);
1324:   for (p = 2; p <= nparts; ++p) {
1325:     vtxdist[p] += vtxdist[p-1];
1326:   }
1327:   /* Calculate weights */
1328:   for (p = 0; p < nparts; ++p) {
1329:     tpwgts[p] = 1.0/nparts;
1330:   }
1331:   ubvec[0] = 1.05;

1333:   if (nparts == 1) {
1334:     PetscMemzero(assignment, nvtxs * sizeof(PetscInt));
1335:   } else {
1336:     if (vtxdist[1] == vtxdist[nparts]) {
1337:       if (!rank) {
1338:         PetscStackPush("METIS_PartGraphKway");
1339:         METIS_PartGraphKway(&nvtxs, &ncon, xadj, adjncy, vwgt, NULL, adjwgt, &nparts, tpwgts, ubvec, NULL, &edgeCut, assignment);
1340:         PetscStackPop;
1341:         if (ierr != METIS_OK) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Error in METIS_PartGraphKway()");
1342:       }
1343:     } else {
1344:       PetscStackPush("ParMETIS_V3_PartKway");
1345:       ParMETIS_V3_PartKway(vtxdist, xadj, adjncy, vwgt, adjwgt, &wgtflag, &numflag, &ncon, &nparts, tpwgts, ubvec, options, &edgeCut, assignment, &comm);
1346:       PetscStackPop;
1347:       if (ierr != METIS_OK) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Error in ParMETIS_V3_PartKway()");
1348:     }
1349:   }
1350:   /* Convert to PetscSection+IS */
1351:   PetscSectionSetChart(partSection, 0, nparts);
1352:   for (v = 0; v < nvtxs; ++v) {PetscSectionAddDof(partSection, assignment[v], 1);}
1353:   PetscSectionSetUp(partSection);
1354:   PetscMalloc1(nvtxs, &points);
1355:   for (p = 0, i = 0; p < nparts; ++p) {
1356:     for (v = 0; v < nvtxs; ++v) {
1357:       if (assignment[v] == p) points[i++] = v;
1358:     }
1359:   }
1360:   if (i != nvtxs) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of points %D should be %D", i, nvtxs);
1361:   ISCreateGeneral(comm, nvtxs, points, PETSC_OWN_POINTER, partition);
1362:   PetscFree4(vtxdist,tpwgts,ubvec,assignment);
1363:   return(0);
1364: #else
1365:   SETERRQ(PetscObjectComm((PetscObject) part), PETSC_ERR_SUP, "Mesh partitioning needs external package support.\nPlease reconfigure with --download-parmetis.");
1366: #endif
1367: }

1371: PetscErrorCode PetscPartitionerInitialize_ParMetis(PetscPartitioner part)
1372: {
1374:   part->ops->view      = PetscPartitionerView_ParMetis;
1375:   part->ops->destroy   = PetscPartitionerDestroy_ParMetis;
1376:   part->ops->partition = PetscPartitionerPartition_ParMetis;
1377:   return(0);
1378: }

1380: /*MC
1381:   PETSCPARTITIONERPARMETIS = "parmetis" - A PetscPartitioner object using the ParMetis library

1383:   Level: intermediate

1385: .seealso: PetscPartitionerType, PetscPartitionerCreate(), PetscPartitionerSetType()
1386: M*/

1390: PETSC_EXTERN PetscErrorCode PetscPartitionerCreate_ParMetis(PetscPartitioner part)
1391: {
1392:   PetscPartitioner_ParMetis *p;
1393:   PetscErrorCode          ierr;

1397:   PetscNewLog(part, &p);
1398:   part->data = p;

1400:   PetscPartitionerInitialize_ParMetis(part);
1401:   PetscCitationsRegister(ParMetisPartitionerCitation, &ParMetisPartitionercite);
1402:   return(0);
1403: }

1407: /*@
1408:   DMPlexGetPartitioner - Get the mesh partitioner

1410:   Not collective

1412:   Input Parameter:
1413: . dm - The DM

1415:   Output Parameter:
1416: . part - The PetscPartitioner

1418:   Level: developer

1420:   Note: This gets a borrowed reference, so the user should not destroy this PetscPartitioner.

1422: .seealso DMPlexDistribute(), DMPlexSetPartitioner(), PetscPartitionerCreate()
1423: @*/
1424: PetscErrorCode DMPlexGetPartitioner(DM dm, PetscPartitioner *part)
1425: {
1426:   DM_Plex *mesh = (DM_Plex *) dm->data;

1431:   *part = mesh->partitioner;
1432:   return(0);
1433: }

1437: /*@
1438:   DMPlexSetPartitioner - Set the mesh partitioner

1440:   logically collective on dm and part

1442:   Input Parameters:
1443: + dm - The DM
1444: - part - The partitioner

1446:   Level: developer

1448:   Note: Any existing PetscPartitioner will be destroyed.

1450: .seealso DMPlexDistribute(), DMPlexGetPartitioner(), PetscPartitionerCreate()
1451: @*/
1452: PetscErrorCode DMPlexSetPartitioner(DM dm, PetscPartitioner part)
1453: {
1454:   DM_Plex       *mesh = (DM_Plex *) dm->data;

1460:   PetscObjectReference((PetscObject)part);
1461:   PetscPartitionerDestroy(&mesh->partitioner);
1462:   mesh->partitioner = part;
1463:   return(0);
1464: }

1468: static PetscErrorCode DMPlexPartitionLabelClosure_Tree(DM dm, DMLabel label, PetscInt rank, PetscInt point, PetscBool up, PetscBool down)
1469: {

1473:   if (up) {
1474:     PetscInt parent;

1476:     DMPlexGetTreeParent(dm,point,&parent,NULL);
1477:     if (parent != point) {
1478:       PetscInt closureSize, *closure = NULL, i;

1480:       DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);
1481:       for (i = 0; i < closureSize; i++) {
1482:         PetscInt cpoint = closure[2*i];

1484:         DMLabelSetValue(label,cpoint,rank);
1485:         DMPlexPartitionLabelClosure_Tree(dm,label,rank,cpoint,PETSC_TRUE,PETSC_FALSE);
1486:       }
1487:       DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);
1488:     }
1489:   }
1490:   if (down) {
1491:     PetscInt numChildren;
1492:     const PetscInt *children;

1494:     DMPlexGetTreeChildren(dm,point,&numChildren,&children);
1495:     if (numChildren) {
1496:       PetscInt i;

1498:       for (i = 0; i < numChildren; i++) {
1499:         PetscInt cpoint = children[i];

1501:         DMLabelSetValue(label,cpoint,rank);
1502:         DMPlexPartitionLabelClosure_Tree(dm,label,rank,cpoint,PETSC_FALSE,PETSC_TRUE);
1503:       }
1504:     }
1505:   }
1506:   return(0);
1507: }

1511: /*@
1512:   DMPlexPartitionLabelClosure - Add the closure of all points to the partition label

1514:   Input Parameters:
1515: + dm     - The DM
1516: - label  - DMLabel assinging ranks to remote roots

1518:   Level: developer

1520: .seealso: DMPlexPartitionLabelCreateSF, DMPlexDistribute(), DMPlexCreateOverlap
1521: @*/
1522: PetscErrorCode DMPlexPartitionLabelClosure(DM dm, DMLabel label)
1523: {
1524:   IS              rankIS,   pointIS;
1525:   const PetscInt *ranks,   *points;
1526:   PetscInt        numRanks, numPoints, r, p, c, closureSize;
1527:   PetscInt       *closure = NULL;
1528:   PetscErrorCode  ierr;

1531:   DMLabelGetValueIS(label, &rankIS);
1532:   ISGetLocalSize(rankIS, &numRanks);
1533:   ISGetIndices(rankIS, &ranks);
1534:   for (r = 0; r < numRanks; ++r) {
1535:     const PetscInt rank = ranks[r];

1537:     DMLabelGetStratumIS(label, rank, &pointIS);
1538:     ISGetLocalSize(pointIS, &numPoints);
1539:     ISGetIndices(pointIS, &points);
1540:     for (p = 0; p < numPoints; ++p) {
1541:       DMPlexGetTransitiveClosure(dm, points[p], PETSC_TRUE, &closureSize, &closure);
1542:       for (c = 0; c < closureSize*2; c += 2) {
1543:         DMLabelSetValue(label, closure[c], rank);
1544:         DMPlexPartitionLabelClosure_Tree(dm,label,rank,closure[c],PETSC_TRUE,PETSC_TRUE);
1545:       }
1546:     }
1547:     ISRestoreIndices(pointIS, &points);
1548:     ISDestroy(&pointIS);
1549:   }
1550:   if (closure) {DMPlexRestoreTransitiveClosure(dm, 0, PETSC_TRUE, &closureSize, &closure);}
1551:   ISRestoreIndices(rankIS, &ranks);
1552:   ISDestroy(&rankIS);
1553:   return(0);
1554: }

1558: /*@
1559:   DMPlexPartitionLabelAdjacency - Add one level of adjacent points to the partition label

1561:   Input Parameters:
1562: + dm     - The DM
1563: - label  - DMLabel assinging ranks to remote roots

1565:   Level: developer

1567: .seealso: DMPlexPartitionLabelCreateSF, DMPlexDistribute(), DMPlexCreateOverlap
1568: @*/
1569: PetscErrorCode DMPlexPartitionLabelAdjacency(DM dm, DMLabel label)
1570: {
1571:   IS              rankIS,   pointIS;
1572:   const PetscInt *ranks,   *points;
1573:   PetscInt        numRanks, numPoints, r, p, a, adjSize;
1574:   PetscInt       *adj = NULL;
1575:   PetscErrorCode  ierr;

1578:   DMLabelGetValueIS(label, &rankIS);
1579:   ISGetLocalSize(rankIS, &numRanks);
1580:   ISGetIndices(rankIS, &ranks);
1581:   for (r = 0; r < numRanks; ++r) {
1582:     const PetscInt rank = ranks[r];

1584:     DMLabelGetStratumIS(label, rank, &pointIS);
1585:     ISGetLocalSize(pointIS, &numPoints);
1586:     ISGetIndices(pointIS, &points);
1587:     for (p = 0; p < numPoints; ++p) {
1588:       adjSize = PETSC_DETERMINE;
1589:       DMPlexGetAdjacency(dm, points[p], &adjSize, &adj);
1590:       for (a = 0; a < adjSize; ++a) {DMLabelSetValue(label, adj[a], rank);}
1591:     }
1592:     ISRestoreIndices(pointIS, &points);
1593:     ISDestroy(&pointIS);
1594:   }
1595:   ISRestoreIndices(rankIS, &ranks);
1596:   ISDestroy(&rankIS);
1597:   PetscFree(adj);
1598:   return(0);
1599: }

1603: /*@
1604:   DMPlexPartitionLabelPropagate - Propagate points in a partition label over the point SF

1606:   Input Parameters:
1607: + dm     - The DM
1608: - label  - DMLabel assinging ranks to remote roots

1610:   Level: developer

1612:   Note: This is required when generating multi-level overlaps to capture
1613:   overlap points from non-neighbouring partitions.

1615: .seealso: DMPlexPartitionLabelCreateSF, DMPlexDistribute(), DMPlexCreateOverlap
1616: @*/
1617: PetscErrorCode DMPlexPartitionLabelPropagate(DM dm, DMLabel label)
1618: {
1619:   MPI_Comm        comm;
1620:   PetscMPIInt     rank;
1621:   PetscSF         sfPoint;
1622:   DMLabel         lblRoots, lblLeaves;
1623:   IS              rankIS, pointIS;
1624:   const PetscInt *ranks;
1625:   PetscInt        numRanks, r;
1626:   PetscErrorCode  ierr;

1629:   PetscObjectGetComm((PetscObject) dm, &comm);
1630:   MPI_Comm_rank(comm, &rank);
1631:   DMGetPointSF(dm, &sfPoint);
1632:   /* Pull point contributions from remote leaves into local roots */
1633:   DMLabelGather(label, sfPoint, &lblLeaves);
1634:   DMLabelGetValueIS(lblLeaves, &rankIS);
1635:   ISGetLocalSize(rankIS, &numRanks);
1636:   ISGetIndices(rankIS, &ranks);
1637:   for (r = 0; r < numRanks; ++r) {
1638:     const PetscInt remoteRank = ranks[r];
1639:     if (remoteRank == rank) continue;
1640:     DMLabelGetStratumIS(lblLeaves, remoteRank, &pointIS);
1641:     DMLabelInsertIS(label, pointIS, remoteRank);
1642:     ISDestroy(&pointIS);
1643:   }
1644:   ISRestoreIndices(rankIS, &ranks);
1645:   ISDestroy(&rankIS);
1646:   DMLabelDestroy(&lblLeaves);
1647:   /* Push point contributions from roots into remote leaves */
1648:   DMLabelDistribute(label, sfPoint, &lblRoots);
1649:   DMLabelGetValueIS(lblRoots, &rankIS);
1650:   ISGetLocalSize(rankIS, &numRanks);
1651:   ISGetIndices(rankIS, &ranks);
1652:   for (r = 0; r < numRanks; ++r) {
1653:     const PetscInt remoteRank = ranks[r];
1654:     if (remoteRank == rank) continue;
1655:     DMLabelGetStratumIS(lblRoots, remoteRank, &pointIS);
1656:     DMLabelInsertIS(label, pointIS, remoteRank);
1657:     ISDestroy(&pointIS);
1658:   }
1659:   ISRestoreIndices(rankIS, &ranks);
1660:   ISDestroy(&rankIS);
1661:   DMLabelDestroy(&lblRoots);
1662:   return(0);
1663: }

1667: /*@
1668:   DMPlexPartitionLabelInvert - Create a partition label of remote roots from a local root label

1670:   Input Parameters:
1671: + dm        - The DM
1672: . rootLabel - DMLabel assinging ranks to local roots
1673: . processSF - A star forest mapping into the local index on each remote rank

1675:   Output Parameter:
1676: - leafLabel - DMLabel assinging ranks to remote roots

1678:   Note: The rootLabel defines a send pattern by mapping local points to remote target ranks. The
1679:   resulting leafLabel is a receiver mapping of remote roots to their parent rank.

1681:   Level: developer

1683: .seealso: DMPlexPartitionLabelCreateSF, DMPlexDistribute(), DMPlexCreateOverlap
1684: @*/
1685: PetscErrorCode DMPlexPartitionLabelInvert(DM dm, DMLabel rootLabel, PetscSF processSF, DMLabel leafLabel)
1686: {
1687:   MPI_Comm           comm;
1688:   PetscMPIInt        rank, numProcs;
1689:   PetscInt           p, n, numNeighbors, size, l, nleaves;
1690:   PetscSF            sfPoint;
1691:   PetscSFNode       *rootPoints, *leafPoints;
1692:   PetscSection       rootSection, leafSection;
1693:   const PetscSFNode *remote;
1694:   const PetscInt    *local, *neighbors;
1695:   IS                 valueIS;
1696:   PetscErrorCode     ierr;

1699:   PetscObjectGetComm((PetscObject) dm, &comm);
1700:   MPI_Comm_rank(comm, &rank);
1701:   MPI_Comm_size(comm, &numProcs);
1702:   DMGetPointSF(dm, &sfPoint);

1704:   /* Convert to (point, rank) and use actual owners */
1705:   PetscSectionCreate(comm, &rootSection);
1706:   PetscSectionSetChart(rootSection, 0, numProcs);
1707:   DMLabelGetValueIS(rootLabel, &valueIS);
1708:   ISGetLocalSize(valueIS, &numNeighbors);
1709:   ISGetIndices(valueIS, &neighbors);
1710:   for (n = 0; n < numNeighbors; ++n) {
1711:     PetscInt numPoints;

1713:     DMLabelGetStratumSize(rootLabel, neighbors[n], &numPoints);
1714:     PetscSectionAddDof(rootSection, neighbors[n], numPoints);
1715:   }
1716:   PetscSectionSetUp(rootSection);
1717:   PetscSectionGetStorageSize(rootSection, &size);
1718:   PetscMalloc1(size, &rootPoints);
1719:   PetscSFGetGraph(sfPoint, NULL, &nleaves, &local, &remote);
1720:   for (n = 0; n < numNeighbors; ++n) {
1721:     IS              pointIS;
1722:     const PetscInt *points;
1723:     PetscInt        off, numPoints, p;

1725:     PetscSectionGetOffset(rootSection, neighbors[n], &off);
1726:     DMLabelGetStratumIS(rootLabel, neighbors[n], &pointIS);
1727:     ISGetLocalSize(pointIS, &numPoints);
1728:     ISGetIndices(pointIS, &points);
1729:     for (p = 0; p < numPoints; ++p) {
1730:       if (local) {PetscFindInt(points[p], nleaves, local, &l);}
1731:       else       {l = -1;}
1732:       if (l >= 0) {rootPoints[off+p] = remote[l];}
1733:       else        {rootPoints[off+p].index = points[p]; rootPoints[off+p].rank = rank;}
1734:     }
1735:     ISRestoreIndices(pointIS, &points);
1736:     ISDestroy(&pointIS);
1737:   }
1738:   ISRestoreIndices(valueIS, &neighbors);
1739:   ISDestroy(&valueIS);
1740:   /* Communicate overlap */
1741:   PetscSectionCreate(comm, &leafSection);
1742:   DMPlexDistributeData(dm, processSF, rootSection, MPIU_2INT, rootPoints, leafSection, (void**) &leafPoints);
1743:   /* Filter remote contributions (ovLeafPoints) into the overlapSF */
1744:   PetscSectionGetStorageSize(leafSection, &size);
1745:   for (p = 0; p < size; p++) {
1746:     DMLabelSetValue(leafLabel, leafPoints[p].index, leafPoints[p].rank);
1747:   }
1748:   PetscFree(rootPoints);
1749:   PetscSectionDestroy(&rootSection);
1750:   PetscFree(leafPoints);
1751:   PetscSectionDestroy(&leafSection);
1752:   return(0);
1753: }

1757: /*@
1758:   DMPlexPartitionLabelCreateSF - Create a star forest from a label that assigns ranks to points

1760:   Input Parameters:
1761: + dm    - The DM
1762: . label - DMLabel assinging ranks to remote roots

1764:   Output Parameter:
1765: - sf    - The star forest communication context encapsulating the defined mapping

1767:   Note: The incoming label is a receiver mapping of remote points to their parent rank.

1769:   Level: developer

1771: .seealso: DMPlexDistribute(), DMPlexCreateOverlap
1772: @*/
1773: PetscErrorCode DMPlexPartitionLabelCreateSF(DM dm, DMLabel label, PetscSF *sf)
1774: {
1775:   PetscMPIInt     rank, numProcs;
1776:   PetscInt        n, numRemote, p, numPoints, pStart, pEnd, idx = 0;
1777:   PetscSFNode    *remotePoints;
1778:   IS              remoteRootIS;
1779:   const PetscInt *remoteRoots;

1783:   MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
1784:   MPI_Comm_size(PetscObjectComm((PetscObject) dm), &numProcs);

1786:   for (numRemote = 0, n = 0; n < numProcs; ++n) {
1787:     DMLabelGetStratumSize(label, n, &numPoints);
1788:     numRemote += numPoints;
1789:   }
1790:   PetscMalloc1(numRemote, &remotePoints);
1791:   /* Put owned points first */
1792:   DMLabelGetStratumSize(label, rank, &numPoints);
1793:   if (numPoints > 0) {
1794:     DMLabelGetStratumIS(label, rank, &remoteRootIS);
1795:     ISGetIndices(remoteRootIS, &remoteRoots);
1796:     for (p = 0; p < numPoints; p++) {
1797:       remotePoints[idx].index = remoteRoots[p];
1798:       remotePoints[idx].rank = rank;
1799:       idx++;
1800:     }
1801:     ISRestoreIndices(remoteRootIS, &remoteRoots);
1802:     ISDestroy(&remoteRootIS);
1803:   }
1804:   /* Now add remote points */
1805:   for (n = 0; n < numProcs; ++n) {
1806:     DMLabelGetStratumSize(label, n, &numPoints);
1807:     if (numPoints <= 0 || n == rank) continue;
1808:     DMLabelGetStratumIS(label, n, &remoteRootIS);
1809:     ISGetIndices(remoteRootIS, &remoteRoots);
1810:     for (p = 0; p < numPoints; p++) {
1811:       remotePoints[idx].index = remoteRoots[p];
1812:       remotePoints[idx].rank = n;
1813:       idx++;
1814:     }
1815:     ISRestoreIndices(remoteRootIS, &remoteRoots);
1816:     ISDestroy(&remoteRootIS);
1817:   }
1818:   PetscSFCreate(PetscObjectComm((PetscObject) dm), sf);
1819:   DMPlexGetChart(dm, &pStart, &pEnd);
1820:   PetscSFSetGraph(*sf, pEnd-pStart, numRemote, NULL, PETSC_OWN_POINTER, remotePoints, PETSC_OWN_POINTER);
1821:   return(0);
1822: }