Actual source code: plexpartition.c

petsc-3.6.4 2016-04-12
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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:   if (nroots > 0) {
 79:     DMPlexGetCellNumbering(dm, &cellNumbering);
 80:     ISGetIndices(cellNumbering, &cellNum);
 81:   }
 82:   for (*numVertices = 0, p = pStart; p < pEnd; p++) {
 83:     /* Skip non-owned cells in parallel (ParMetis expects no overlap) */
 84:     if (nroots > 0) {if (cellNum[p] < 0) continue;}
 85:     adjSize = PETSC_DETERMINE;
 86:     DMPlexGetAdjacency(dm, p, &adjSize, &adj);
 87:     for (a = 0; a < adjSize; ++a) {
 88:       const PetscInt point = adj[a];
 89:       if (point != p && pStart <= point && point < pEnd) {
 90:         PetscInt *PETSC_RESTRICT pBuf;
 91:         PetscSectionAddDof(section, p, 1);
 92:         PetscSegBufferGetInts(adjBuffer, 1, &pBuf);
 93:         *pBuf = point;
 94:       }
 95:     }
 96:     (*numVertices)++;
 97:   }
 98:   DMPlexSetAdjacencyUseCone(dm, useCone);
 99:   DMPlexSetAdjacencyUseClosure(dm, useClosure);
100:   /* Derive CSR graph from section/segbuffer */
101:   PetscSectionSetUp(section);
102:   PetscSectionGetStorageSize(section, &size);
103:   PetscMalloc1(*numVertices+1, &vOffsets);
104:   for (idx = 0, p = pStart; p < pEnd; p++) {
105:     if (nroots > 0) {if (cellNum[p] < 0) continue;}
106:     PetscSectionGetOffset(section, p, &(vOffsets[idx++]));
107:   }
108:   vOffsets[*numVertices] = size;
109:   if (offsets) *offsets = vOffsets;
110:   PetscSegBufferExtractAlloc(adjBuffer, &graph);
111:   if (nroots > 0) {
112:     ISLocalToGlobalMapping ltogCells;
113:     PetscInt n, size, *cells_arr;
114:     /* In parallel, apply a global cell numbering to the graph */
115:     ISRestoreIndices(cellNumbering, &cellNum);
116:     ISLocalToGlobalMappingCreateIS(cellNumbering, &ltogCells);
117:     ISLocalToGlobalMappingGetSize(ltogCells, &size);
118:     ISLocalToGlobalMappingGetIndices(ltogCells, (const PetscInt**)&cells_arr);
119:     /* Convert to positive global cell numbers */
120:     for (n=0; n<size; n++) {if (cells_arr[n] < 0) cells_arr[n] = -(cells_arr[n]+1);}
121:     ISLocalToGlobalMappingRestoreIndices(ltogCells, (const PetscInt**)&cells_arr);
122:     ISLocalToGlobalMappingApplyBlock(ltogCells, vOffsets[*numVertices], graph, graph);
123:     ISLocalToGlobalMappingDestroy(&ltogCells);
124:   }
125:   if (adjacency) *adjacency = graph;
126:   /* Clean up */
127:   PetscSegBufferDestroy(&adjBuffer);
128:   PetscSectionDestroy(&section);
129:   PetscFree(adj);
130:   return(0);
131: }

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

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

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

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

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

197:           DMPlexGetTreeChildren(dm,f,&numChildren,NULL);
198:           if (!numChildren) {
199:             adj[tmp[support[0]-cStart]++] = support[1];
200:             adj[tmp[support[1]-cStart]++] = support[0];
201:           }
202:         }
203:       }
204: #if defined(PETSC_USE_DEBUG)
205:       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);
206: #endif
207:       PetscFree(tmp);
208:     }
209:     if (numVertices) *numVertices = numCells;
210:     if (offsets)   *offsets   = off;
211:     if (adjacency) *adjacency = adj;
212:     return(0);
213:   }
214:   /* Setup face recognition */
215:   if (faceDepth == 1) {
216:     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 */

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

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

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

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

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

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

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

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

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

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

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

291:             for (f = 0; f < numFaceCases; ++f) {
292:               if (numFaceVertices[f] == meetSize) {
293:                 found = PETSC_TRUE;
294:                 break;
295:               }
296:             }
297:           }
298:           DMPlexRestoreMeet(dm, 2, cellPair, &meetSize, &meet);
299:         }
300:         if (found) {
301:           adj[off[cell-cStart]+cellOffset] = neighborCells[n];
302:           ++cellOffset;
303:         }
304:       }
305:     }
306:   }
307:   PetscFree(neighborCells);
308:   if (numVertices) *numVertices = numCells;
309:   if (offsets)   *offsets   = off;
310:   if (adjacency) *adjacency = adj;
311:   return(0);
312: }

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

319:   Not Collective

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

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

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

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

343:   Level: advanced

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

348: @*/
349: PetscErrorCode PetscPartitionerRegister(const char sname[], PetscErrorCode (*function)(PetscPartitioner))
350: {

354:   PetscFunctionListAdd(&PetscPartitionerList, sname, function);
355:   return(0);
356: }

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

363:   Collective on PetscPartitioner

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

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

372:   Level: intermediate

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

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

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

392:   if (part->ops->destroy) {
393:     (*part->ops->destroy)(part);
394:     part->ops->destroy = NULL;
395:   }
396:   (*r)(part);
397:   PetscObjectChangeTypeName((PetscObject) part, name);
398:   return(0);
399: }

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

406:   Not Collective

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

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

414:   Level: intermediate

416: .keywords: PetscPartitioner, get, type, name
417: .seealso: PetscPartitionerSetType(), PetscPartitionerCreate()
418: @*/
419: PetscErrorCode PetscPartitionerGetType(PetscPartitioner part, PetscPartitionerType *name)
420: {

426:   PetscPartitionerRegisterAll();
427:   *name = ((PetscObject) part)->type_name;
428:   return(0);
429: }

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

436:   Collective on PetscPartitioner

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

442:   Level: developer

444: .seealso: PetscPartitionerDestroy()
445: @*/
446: PetscErrorCode PetscPartitionerView(PetscPartitioner part, PetscViewer v)
447: {

452:   if (!v) {PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject) part), &v);}
453:   if (part->ops->view) {(*part->ops->view)(part, v);}
454:   return(0);
455: }

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

468:   if (!((PetscObject) part)->type_name) defaultType = PETSCPARTITIONERCHACO;
469:   else                                  defaultType = ((PetscObject) part)->type_name;
470:   PetscPartitionerRegisterAll();

472:   PetscObjectOptionsBegin((PetscObject) part);
473:   PetscOptionsFList("-petscpartitioner_type", "Graph partitioner", "PetscPartitionerSetType", PetscPartitionerList, defaultType, name, 256, &flg);
474:   if (flg) {
475:     PetscPartitionerSetType(part, name);
476:   } else if (!((PetscObject) part)->type_name) {
477:     PetscPartitionerSetType(part, defaultType);
478:   }
479:   PetscOptionsEnd();
480:   return(0);
481: }

485: /*@
486:   PetscPartitionerSetFromOptions - sets parameters in a PetscPartitioner from the options database

488:   Collective on PetscPartitioner

490:   Input Parameter:
491: . part - the PetscPartitioner object to set options for

493:   Level: developer

495: .seealso: PetscPartitionerView()
496: @*/
497: PetscErrorCode PetscPartitionerSetFromOptions(PetscPartitioner part)
498: {

503:   PetscPartitionerSetTypeFromOptions_Internal(part);

505:   PetscObjectOptionsBegin((PetscObject) part);
506:   if (part->ops->setfromoptions) {(*part->ops->setfromoptions)(part);}
507:   /* process any options handlers added with PetscObjectAddOptionsHandler() */
508:   PetscObjectProcessOptionsHandlers((PetscObject) part);
509:   PetscOptionsEnd();
510:   PetscPartitionerViewFromOptions(part, NULL, "-petscpartitioner_view");
511:   return(0);
512: }

516: /*@C
517:   PetscPartitionerSetUp - Construct data structures for the PetscPartitioner

519:   Collective on PetscPartitioner

521:   Input Parameter:
522: . part - the PetscPartitioner object to setup

524:   Level: developer

526: .seealso: PetscPartitionerView(), PetscPartitionerDestroy()
527: @*/
528: PetscErrorCode PetscPartitionerSetUp(PetscPartitioner part)
529: {

534:   if (part->ops->setup) {(*part->ops->setup)(part);}
535:   return(0);
536: }

540: /*@
541:   PetscPartitionerDestroy - Destroys a PetscPartitioner object

543:   Collective on PetscPartitioner

545:   Input Parameter:
546: . part - the PetscPartitioner object to destroy

548:   Level: developer

550: .seealso: PetscPartitionerView()
551: @*/
552: PetscErrorCode PetscPartitionerDestroy(PetscPartitioner *part)
553: {

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

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

563:   if ((*part)->ops->destroy) {(*(*part)->ops->destroy)(*part);}
564:   PetscHeaderDestroy(part);
565:   return(0);
566: }

570: /*@
571:   PetscPartitionerCreate - Creates an empty PetscPartitioner object. The type can then be set with PetscPartitionerSetType().

573:   Collective on MPI_Comm

575:   Input Parameter:
576: . comm - The communicator for the PetscPartitioner object

578:   Output Parameter:
579: . part - The PetscPartitioner object

581:   Level: beginner

583: .seealso: PetscPartitionerSetType(), PETSCPARTITIONERCHACO, PETSCPARTITIONERPARMETIS, PETSCPARTITIONERSHELL, PETSCPARTITIONERSIMPLE
584: @*/
585: PetscErrorCode PetscPartitionerCreate(MPI_Comm comm, PetscPartitioner *part)
586: {
587:   PetscPartitioner p;
588:   PetscErrorCode   ierr;

592:   *part = NULL;
593:   PetscFVInitializePackage();

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

597:   *part = p;
598:   return(0);
599: }

603: /*@
604:   PetscPartitionerPartition - Create a non-overlapping partition of the cells in the mesh

606:   Collective on DM

608:   Input Parameters:
609: + part    - The PetscPartitioner
610: - dm      - The mesh DM

612:   Output Parameters:
613: + partSection     - The PetscSection giving the division of points by partition
614: - partition       - The list of points by partition

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

618:   Level: developer

620: .seealso DMPlexDistribute(), PetscPartitionerSetPointHeight(), PetscPartitionerCreate()
621: @*/
622: PetscErrorCode PetscPartitionerPartition(PetscPartitioner part, DM dm, PetscSection partSection, IS *partition)
623: {
624:   PetscMPIInt    size;

632:   MPI_Comm_size(PetscObjectComm((PetscObject) part), &size);
633:   if (size == 1) {
634:     PetscInt *points;
635:     PetscInt  cStart, cEnd, c;

637:     DMPlexGetHeightStratum(dm, part->height, &cStart, &cEnd);
638:     PetscSectionSetChart(partSection, 0, size);
639:     PetscSectionSetDof(partSection, 0, cEnd-cStart);
640:     PetscSectionSetUp(partSection);
641:     PetscMalloc1(cEnd-cStart, &points);
642:     for (c = cStart; c < cEnd; ++c) points[c] = c;
643:     ISCreateGeneral(PetscObjectComm((PetscObject) part), cEnd-cStart, points, PETSC_OWN_POINTER, partition);
644:     return(0);
645:   }
646:   if (part->height == 0) {
647:     PetscInt  numVertices;
648:     PetscInt *start     = NULL;
649:     PetscInt *adjacency = NULL;

651:     DMPlexCreatePartitionerGraph(dm, 0, &numVertices, &start, &adjacency);
652:     if (!part->ops->partition) SETERRQ(PetscObjectComm((PetscObject) part), PETSC_ERR_ARG_WRONGSTATE, "PetscPartitioner has no type");
653:     (*part->ops->partition)(part, dm, size, numVertices, start, adjacency, partSection, partition);
654:     PetscFree(start);
655:     PetscFree(adjacency);
656:   } else SETERRQ1(PetscObjectComm((PetscObject) part), PETSC_ERR_ARG_OUTOFRANGE, "Invalid height %D for points to partition", part->height);
657:   return(0);
658: }

662: PetscErrorCode PetscPartitionerDestroy_Shell(PetscPartitioner part)
663: {
664:   PetscPartitioner_Shell *p = (PetscPartitioner_Shell *) part->data;
665:   PetscErrorCode          ierr;

668:   PetscSectionDestroy(&p->section);
669:   ISDestroy(&p->partition);
670:   PetscFree(p);
671:   return(0);
672: }

676: PetscErrorCode PetscPartitionerView_Shell_Ascii(PetscPartitioner part, PetscViewer viewer)
677: {
678:   PetscViewerFormat format;
679:   PetscErrorCode    ierr;

682:   PetscViewerGetFormat(viewer, &format);
683:   PetscViewerASCIIPrintf(viewer, "Shell Graph Partitioner:\n");
684:   return(0);
685: }

689: PetscErrorCode PetscPartitionerView_Shell(PetscPartitioner part, PetscViewer viewer)
690: {
691:   PetscBool      iascii;

697:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);
698:   if (iascii) {PetscPartitionerView_Shell_Ascii(part, viewer);}
699:   return(0);
700: }

704: PetscErrorCode PetscPartitionerPartition_Shell(PetscPartitioner part, DM dm, PetscInt nparts, PetscInt numVertices, PetscInt start[], PetscInt adjacency[], PetscSection partSection, IS *partition)
705: {
706:   PetscPartitioner_Shell *p = (PetscPartitioner_Shell *) part->data;
707:   PetscInt                np;
708:   PetscErrorCode          ierr;

711:   PetscSectionGetChart(p->section, NULL, &np);
712:   if (nparts != np) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of requested partitions %d != configured partitions %d", nparts, np);
713:   ISGetLocalSize(p->partition, &np);
714:   if (numVertices != np) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of input vertices %d != configured vertices %d", numVertices, np);
715:   PetscSectionCopy(p->section, partSection);
716:   *partition = p->partition;
717:   PetscObjectReference((PetscObject) p->partition);
718:   return(0);
719: }

723: PetscErrorCode PetscPartitionerInitialize_Shell(PetscPartitioner part)
724: {
726:   part->ops->view      = PetscPartitionerView_Shell;
727:   part->ops->destroy   = PetscPartitionerDestroy_Shell;
728:   part->ops->partition = PetscPartitionerPartition_Shell;
729:   return(0);
730: }

732: /*MC
733:   PETSCPARTITIONERSHELL = "shell" - A PetscPartitioner object

735:   Level: intermediate

737: .seealso: PetscPartitionerType, PetscPartitionerCreate(), PetscPartitionerSetType()
738: M*/

742: PETSC_EXTERN PetscErrorCode PetscPartitionerCreate_Shell(PetscPartitioner part)
743: {
744:   PetscPartitioner_Shell *p;
745:   PetscErrorCode          ierr;

749:   PetscNewLog(part, &p);
750:   part->data = p;

752:   PetscPartitionerInitialize_Shell(part);
753:   return(0);
754: }

758: /*@C
759:   PetscPartitionerShellSetPartition - Set an artifical partition for a mesh

761:   Collective on PART

763:   Input Parameters:
764: + part     - The PetscPartitioner
765: . numProcs - The number of partitions
766: . sizes    - array of size numProcs (or NULL) providing the number of points in each partition
767: - points   - array of size sum(sizes) (may be NULL iff sizes is NULL) providing the partition each point belongs to

769:   Level: developer

771:   Notes:

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

775: .seealso DMPlexDistribute(), PetscPartitionerCreate()
776: @*/
777: PetscErrorCode PetscPartitionerShellSetPartition(PetscPartitioner part, PetscInt numProcs, const PetscInt sizes[], const PetscInt points[])
778: {
779:   PetscPartitioner_Shell *p = (PetscPartitioner_Shell *) part->data;
780:   PetscInt                proc, numPoints;
781:   PetscErrorCode          ierr;

787:   PetscSectionDestroy(&p->section);
788:   ISDestroy(&p->partition);
789:   PetscSectionCreate(PetscObjectComm((PetscObject) part), &p->section);
790:   PetscSectionSetChart(p->section, 0, numProcs);
791:   if (sizes) {
792:     for (proc = 0; proc < numProcs; ++proc) {
793:       PetscSectionSetDof(p->section, proc, sizes[proc]);
794:     }
795:   }
796:   PetscSectionSetUp(p->section);
797:   PetscSectionGetStorageSize(p->section, &numPoints);
798:   ISCreateGeneral(PetscObjectComm((PetscObject) part), numPoints, points, PETSC_COPY_VALUES, &p->partition);
799:   return(0);
800: }

804: PetscErrorCode PetscPartitionerDestroy_Simple(PetscPartitioner part)
805: {
806:   PetscPartitioner_Simple *p = (PetscPartitioner_Simple *) part->data;
807:   PetscErrorCode          ierr;

810:   PetscFree(p);
811:   return(0);
812: }

816: PetscErrorCode PetscPartitionerView_Simple_Ascii(PetscPartitioner part, PetscViewer viewer)
817: {
818:   PetscViewerFormat format;
819:   PetscErrorCode    ierr;

822:   PetscViewerGetFormat(viewer, &format);
823:   PetscViewerASCIIPrintf(viewer, "Simple Graph Partitioner:\n");
824:   return(0);
825: }

829: PetscErrorCode PetscPartitionerView_Simple(PetscPartitioner part, PetscViewer viewer)
830: {
831:   PetscBool      iascii;

837:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);
838:   if (iascii) {PetscPartitionerView_Simple_Ascii(part, viewer);}
839:   return(0);
840: }

844: PetscErrorCode PetscPartitionerPartition_Simple(PetscPartitioner part, DM dm, PetscInt nparts, PetscInt numVertices, PetscInt start[], PetscInt adjacency[], PetscSection partSection, IS *partition)
845: {
846:   PetscInt       np;

850:   PetscSectionSetChart(partSection, 0, nparts);
851:   for (np = 0; np < nparts; ++np) {PetscSectionSetDof(partSection, np, numVertices/nparts + ((numVertices % nparts) > np));}
852:   PetscSectionSetUp(partSection);
853:   ISCreateStride(PETSC_COMM_SELF, numVertices, 0, 1, partition);
854:   return(0);
855: }

859: PetscErrorCode PetscPartitionerInitialize_Simple(PetscPartitioner part)
860: {
862:   part->ops->view      = PetscPartitionerView_Simple;
863:   part->ops->destroy   = PetscPartitionerDestroy_Simple;
864:   part->ops->partition = PetscPartitionerPartition_Simple;
865:   return(0);
866: }

868: /*MC
869:   PETSCPARTITIONERSIMPLE = "simple" - A PetscPartitioner object

871:   Level: intermediate

873: .seealso: PetscPartitionerType, PetscPartitionerCreate(), PetscPartitionerSetType()
874: M*/

878: PETSC_EXTERN PetscErrorCode PetscPartitionerCreate_Simple(PetscPartitioner part)
879: {
880:   PetscPartitioner_Simple *p;
881:   PetscErrorCode           ierr;

885:   PetscNewLog(part, &p);
886:   part->data = p;

888:   PetscPartitionerInitialize_Simple(part);
889:   return(0);
890: }

894: PetscErrorCode PetscPartitionerDestroy_Chaco(PetscPartitioner part)
895: {
896:   PetscPartitioner_Chaco *p = (PetscPartitioner_Chaco *) part->data;
897:   PetscErrorCode          ierr;

900:   PetscFree(p);
901:   return(0);
902: }

906: PetscErrorCode PetscPartitionerView_Chaco_Ascii(PetscPartitioner part, PetscViewer viewer)
907: {
908:   PetscViewerFormat format;
909:   PetscErrorCode    ierr;

912:   PetscViewerGetFormat(viewer, &format);
913:   PetscViewerASCIIPrintf(viewer, "Chaco Graph Partitioner:\n");
914:   return(0);
915: }

919: PetscErrorCode PetscPartitionerView_Chaco(PetscPartitioner part, PetscViewer viewer)
920: {
921:   PetscBool      iascii;

927:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);
928:   if (iascii) {PetscPartitionerView_Chaco_Ascii(part, viewer);}
929:   return(0);
930: }

932: #if defined(PETSC_HAVE_CHACO)
933: #if defined(PETSC_HAVE_UNISTD_H)
934: #include <unistd.h>
935: #endif
936: /* Chaco does not have an include file */
937: PETSC_EXTERN int interface(int nvtxs, int *start, int *adjacency, int *vwgts,
938:                        float *ewgts, float *x, float *y, float *z, char *outassignname,
939:                        char *outfilename, short *assignment, int architecture, int ndims_tot,
940:                        int mesh_dims[3], double *goal, int global_method, int local_method,
941:                        int rqi_flag, int vmax, int ndims, double eigtol, long seed);

943: extern int FREE_GRAPH;
944: #endif

948: PetscErrorCode PetscPartitionerPartition_Chaco(PetscPartitioner part, DM dm, PetscInt nparts, PetscInt numVertices, PetscInt start[], PetscInt adjacency[], PetscSection partSection, IS *partition)
949: {
950: #if defined(PETSC_HAVE_CHACO)
951:   enum {DEFAULT_METHOD = 1, INERTIAL_METHOD = 3};
952:   MPI_Comm       comm;
953:   int            nvtxs          = numVertices; /* number of vertices in full graph */
954:   int           *vwgts          = NULL;   /* weights for all vertices */
955:   float         *ewgts          = NULL;   /* weights for all edges */
956:   float         *x              = NULL, *y = NULL, *z = NULL; /* coordinates for inertial method */
957:   char          *outassignname  = NULL;   /*  name of assignment output file */
958:   char          *outfilename    = NULL;   /* output file name */
959:   int            architecture   = 1;      /* 0 => hypercube, d => d-dimensional mesh */
960:   int            ndims_tot      = 0;      /* total number of cube dimensions to divide */
961:   int            mesh_dims[3];            /* dimensions of mesh of processors */
962:   double        *goal          = NULL;    /* desired set sizes for each set */
963:   int            global_method = 1;       /* global partitioning algorithm */
964:   int            local_method  = 1;       /* local partitioning algorithm */
965:   int            rqi_flag      = 0;       /* should I use RQI/Symmlq eigensolver? */
966:   int            vmax          = 200;     /* how many vertices to coarsen down to? */
967:   int            ndims         = 1;       /* number of eigenvectors (2^d sets) */
968:   double         eigtol        = 0.001;   /* tolerance on eigenvectors */
969:   long           seed          = 123636512; /* for random graph mutations */
970:   short int     *assignment;              /* Output partition */
971:   int            fd_stdout, fd_pipe[2];
972:   PetscInt      *points;
973:   int            i, v, p;

977:   PetscObjectGetComm((PetscObject)dm,&comm);
978:   if (!numVertices) {
979:     PetscSectionSetChart(partSection, 0, nparts);
980:     PetscSectionSetUp(partSection);
981:     ISCreateGeneral(comm, 0, NULL, PETSC_OWN_POINTER, partition);
982:     return(0);
983:   }
984:   FREE_GRAPH = 0;                         /* Do not let Chaco free my memory */
985:   for (i = 0; i < start[numVertices]; ++i) ++adjacency[i];

987:   if (global_method == INERTIAL_METHOD) {
988:     /* manager.createCellCoordinates(nvtxs, &x, &y, &z); */
989:     SETERRQ(comm, PETSC_ERR_SUP, "Inertial partitioning not yet supported");
990:   }
991:   mesh_dims[0] = nparts;
992:   mesh_dims[1] = 1;
993:   mesh_dims[2] = 1;
994:   PetscMalloc1(nvtxs, &assignment);
995:   /* Chaco outputs to stdout. We redirect this to a buffer. */
996:   /* TODO: check error codes for UNIX calls */
997: #if defined(PETSC_HAVE_UNISTD_H)
998:   {
999:     int piperet;
1000:     piperet = pipe(fd_pipe);
1001:     if (piperet) SETERRQ(comm,PETSC_ERR_SYS,"Could not create pipe");
1002:     fd_stdout = dup(1);
1003:     close(1);
1004:     dup2(fd_pipe[1], 1);
1005:   }
1006: #endif
1007:   interface(nvtxs, (int*) start, (int*) adjacency, vwgts, ewgts, x, y, z, outassignname, outfilename,
1008:                    assignment, architecture, ndims_tot, mesh_dims, goal, global_method, local_method, rqi_flag,
1009:                    vmax, ndims, eigtol, seed);
1010: #if defined(PETSC_HAVE_UNISTD_H)
1011:   {
1012:     char msgLog[10000];
1013:     int  count;

1015:     fflush(stdout);
1016:     count = read(fd_pipe[0], msgLog, (10000-1)*sizeof(char));
1017:     if (count < 0) count = 0;
1018:     msgLog[count] = 0;
1019:     close(1);
1020:     dup2(fd_stdout, 1);
1021:     close(fd_stdout);
1022:     close(fd_pipe[0]);
1023:     close(fd_pipe[1]);
1024:     if (ierr) SETERRQ1(comm, PETSC_ERR_LIB, "Error in Chaco library: %s", msgLog);
1025:   }
1026: #endif
1027:   /* Convert to PetscSection+IS */
1028:   PetscSectionSetChart(partSection, 0, nparts);
1029:   for (v = 0; v < nvtxs; ++v) {
1030:     PetscSectionAddDof(partSection, assignment[v], 1);
1031:   }
1032:   PetscSectionSetUp(partSection);
1033:   PetscMalloc1(nvtxs, &points);
1034:   for (p = 0, i = 0; p < nparts; ++p) {
1035:     for (v = 0; v < nvtxs; ++v) {
1036:       if (assignment[v] == p) points[i++] = v;
1037:     }
1038:   }
1039:   if (i != nvtxs) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of points %D should be %D", i, nvtxs);
1040:   ISCreateGeneral(comm, nvtxs, points, PETSC_OWN_POINTER, partition);
1041:   if (global_method == INERTIAL_METHOD) {
1042:     /* manager.destroyCellCoordinates(nvtxs, &x, &y, &z); */
1043:   }
1044:   PetscFree(assignment);
1045:   for (i = 0; i < start[numVertices]; ++i) --adjacency[i];
1046:   return(0);
1047: #else
1048:   SETERRQ(PetscObjectComm((PetscObject) part), PETSC_ERR_SUP, "Mesh partitioning needs external package support.\nPlease reconfigure with --download-chaco.");
1049: #endif
1050: }

1054: PetscErrorCode PetscPartitionerInitialize_Chaco(PetscPartitioner part)
1055: {
1057:   part->ops->view      = PetscPartitionerView_Chaco;
1058:   part->ops->destroy   = PetscPartitionerDestroy_Chaco;
1059:   part->ops->partition = PetscPartitionerPartition_Chaco;
1060:   return(0);
1061: }

1063: /*MC
1064:   PETSCPARTITIONERCHACO = "chaco" - A PetscPartitioner object using the Chaco library

1066:   Level: intermediate

1068: .seealso: PetscPartitionerType, PetscPartitionerCreate(), PetscPartitionerSetType()
1069: M*/

1073: PETSC_EXTERN PetscErrorCode PetscPartitionerCreate_Chaco(PetscPartitioner part)
1074: {
1075:   PetscPartitioner_Chaco *p;
1076:   PetscErrorCode          ierr;

1080:   PetscNewLog(part, &p);
1081:   part->data = p;

1083:   PetscPartitionerInitialize_Chaco(part);
1084:   PetscCitationsRegister(ChacoPartitionerCitation, &ChacoPartitionercite);
1085:   return(0);
1086: }

1090: PetscErrorCode PetscPartitionerDestroy_ParMetis(PetscPartitioner part)
1091: {
1092:   PetscPartitioner_ParMetis *p = (PetscPartitioner_ParMetis *) part->data;
1093:   PetscErrorCode             ierr;

1096:   PetscFree(p);
1097:   return(0);
1098: }

1102: PetscErrorCode PetscPartitionerView_ParMetis_Ascii(PetscPartitioner part, PetscViewer viewer)
1103: {
1104:   PetscViewerFormat format;
1105:   PetscErrorCode    ierr;

1108:   PetscViewerGetFormat(viewer, &format);
1109:   PetscViewerASCIIPrintf(viewer, "ParMetis Graph Partitioner:\n");
1110:   return(0);
1111: }

1115: PetscErrorCode PetscPartitionerView_ParMetis(PetscPartitioner part, PetscViewer viewer)
1116: {
1117:   PetscBool      iascii;

1123:   PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &iascii);
1124:   if (iascii) {PetscPartitionerView_ParMetis_Ascii(part, viewer);}
1125:   return(0);
1126: }

1128: #if defined(PETSC_HAVE_PARMETIS)
1129: #include <parmetis.h>
1130: #endif

1134: PetscErrorCode PetscPartitionerPartition_ParMetis(PetscPartitioner part, DM dm, PetscInt nparts, PetscInt numVertices, PetscInt start[], PetscInt adjacency[], PetscSection partSection, IS *partition)
1135: {
1136: #if defined(PETSC_HAVE_PARMETIS)
1137:   MPI_Comm       comm;
1138:   PetscInt       nvtxs      = numVertices; /* The number of vertices in full graph */
1139:   PetscInt      *vtxdist;                  /* Distribution of vertices across processes */
1140:   PetscInt      *xadj       = start;       /* Start of edge list for each vertex */
1141:   PetscInt      *adjncy     = adjacency;   /* Edge lists for all vertices */
1142:   PetscInt      *vwgt       = NULL;        /* Vertex weights */
1143:   PetscInt      *adjwgt     = NULL;        /* Edge weights */
1144:   PetscInt       wgtflag    = 0;           /* Indicates which weights are present */
1145:   PetscInt       numflag    = 0;           /* Indicates initial offset (0 or 1) */
1146:   PetscInt       ncon       = 1;           /* The number of weights per vertex */
1147:   PetscReal     *tpwgts;                   /* The fraction of vertex weights assigned to each partition */
1148:   PetscReal     *ubvec;                    /* The balance intolerance for vertex weights */
1149:   PetscInt       options[5];               /* Options */
1150:   /* Outputs */
1151:   PetscInt       edgeCut;                  /* The number of edges cut by the partition */
1152:   PetscInt      *assignment, *points;
1153:   PetscMPIInt    rank, p, v, i;

1157:   PetscObjectGetComm((PetscObject) part, &comm);
1158:   MPI_Comm_rank(comm, &rank);
1159:   options[0] = 0; /* Use all defaults */
1160:   /* Calculate vertex distribution */
1161:   PetscMalloc4(nparts+1,&vtxdist,nparts*ncon,&tpwgts,ncon,&ubvec,nvtxs,&assignment);
1162:   vtxdist[0] = 0;
1163:   MPI_Allgather(&nvtxs, 1, MPIU_INT, &vtxdist[1], 1, MPIU_INT, comm);
1164:   for (p = 2; p <= nparts; ++p) {
1165:     vtxdist[p] += vtxdist[p-1];
1166:   }
1167:   /* Calculate weights */
1168:   for (p = 0; p < nparts; ++p) {
1169:     tpwgts[p] = 1.0/nparts;
1170:   }
1171:   ubvec[0] = 1.05;

1173:   if (nparts == 1) {
1174:     PetscMemzero(assignment, nvtxs * sizeof(PetscInt));
1175:   } else {
1176:     if (vtxdist[1] == vtxdist[nparts]) {
1177:       if (!rank) {
1178:         PetscStackPush("METIS_PartGraphKway");
1179:         METIS_PartGraphKway(&nvtxs, &ncon, xadj, adjncy, vwgt, NULL, adjwgt, &nparts, tpwgts, ubvec, NULL, &edgeCut, assignment);
1180:         PetscStackPop;
1181:         if (ierr != METIS_OK) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Error in METIS_PartGraphKway()");
1182:       }
1183:     } else {
1184:       PetscStackPush("ParMETIS_V3_PartKway");
1185:       ParMETIS_V3_PartKway(vtxdist, xadj, adjncy, vwgt, adjwgt, &wgtflag, &numflag, &ncon, &nparts, tpwgts, ubvec, options, &edgeCut, assignment, &comm);
1186:       PetscStackPop;
1187:       if (ierr != METIS_OK) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_LIB, "Error in ParMETIS_V3_PartKway()");
1188:     }
1189:   }
1190:   /* Convert to PetscSection+IS */
1191:   PetscSectionSetChart(partSection, 0, nparts);
1192:   for (v = 0; v < nvtxs; ++v) {PetscSectionAddDof(partSection, assignment[v], 1);}
1193:   PetscSectionSetUp(partSection);
1194:   PetscMalloc1(nvtxs, &points);
1195:   for (p = 0, i = 0; p < nparts; ++p) {
1196:     for (v = 0; v < nvtxs; ++v) {
1197:       if (assignment[v] == p) points[i++] = v;
1198:     }
1199:   }
1200:   if (i != nvtxs) SETERRQ2(comm, PETSC_ERR_PLIB, "Number of points %D should be %D", i, nvtxs);
1201:   ISCreateGeneral(comm, nvtxs, points, PETSC_OWN_POINTER, partition);
1202:   PetscFree4(vtxdist,tpwgts,ubvec,assignment);
1203:   return(0);
1204: #else
1205:   SETERRQ(PetscObjectComm((PetscObject) part), PETSC_ERR_SUP, "Mesh partitioning needs external package support.\nPlease reconfigure with --download-parmetis.");
1206: #endif
1207: }

1211: PetscErrorCode PetscPartitionerInitialize_ParMetis(PetscPartitioner part)
1212: {
1214:   part->ops->view      = PetscPartitionerView_ParMetis;
1215:   part->ops->destroy   = PetscPartitionerDestroy_ParMetis;
1216:   part->ops->partition = PetscPartitionerPartition_ParMetis;
1217:   return(0);
1218: }

1220: /*MC
1221:   PETSCPARTITIONERPARMETIS = "parmetis" - A PetscPartitioner object using the ParMetis library

1223:   Level: intermediate

1225: .seealso: PetscPartitionerType, PetscPartitionerCreate(), PetscPartitionerSetType()
1226: M*/

1230: PETSC_EXTERN PetscErrorCode PetscPartitionerCreate_ParMetis(PetscPartitioner part)
1231: {
1232:   PetscPartitioner_ParMetis *p;
1233:   PetscErrorCode          ierr;

1237:   PetscNewLog(part, &p);
1238:   part->data = p;

1240:   PetscPartitionerInitialize_ParMetis(part);
1241:   PetscCitationsRegister(ParMetisPartitionerCitation, &ParMetisPartitionercite);
1242:   return(0);
1243: }

1247: /*@
1248:   DMPlexGetPartitioner - Get the mesh partitioner

1250:   Not collective

1252:   Input Parameter:
1253: . dm - The DM

1255:   Output Parameter:
1256: . part - The PetscPartitioner

1258:   Level: developer

1260:   Note: This gets a borrowed reference, so the user should not destroy this PetscPartitioner.

1262: .seealso DMPlexDistribute(), DMPlexSetPartitioner(), PetscPartitionerCreate()
1263: @*/
1264: PetscErrorCode DMPlexGetPartitioner(DM dm, PetscPartitioner *part)
1265: {
1266:   DM_Plex *mesh = (DM_Plex *) dm->data;

1271:   *part = mesh->partitioner;
1272:   return(0);
1273: }

1277: /*@
1278:   DMPlexSetPartitioner - Set the mesh partitioner

1280:   logically collective on dm and part

1282:   Input Parameters:
1283: + dm - The DM
1284: - part - The partitioner

1286:   Level: developer

1288:   Note: Any existing PetscPartitioner will be destroyed.

1290: .seealso DMPlexDistribute(), DMPlexGetPartitioner(), PetscPartitionerCreate()
1291: @*/
1292: PetscErrorCode DMPlexSetPartitioner(DM dm, PetscPartitioner part)
1293: {
1294:   DM_Plex       *mesh = (DM_Plex *) dm->data;

1300:   PetscObjectReference((PetscObject)part);
1301:   PetscPartitionerDestroy(&mesh->partitioner);
1302:   mesh->partitioner = part;
1303:   return(0);
1304: }

1308: static PetscErrorCode DMPlexPartitionLabelClosure_Tree(DM dm, DMLabel label, PetscInt rank, PetscInt point)
1309: {
1310:   PetscInt       parent, closureSize, *closure = NULL, i, pStart, pEnd;

1314:   DMPlexGetTreeParent(dm,point,&parent,NULL);
1315:   if (parent == point) return(0);
1316:   DMPlexGetChart(dm,&pStart,&pEnd);
1317:   DMPlexGetTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);
1318:   for (i = 0; i < closureSize; i++) {
1319:     PetscInt cpoint = closure[2*i];

1321:     DMLabelSetValue(label,cpoint,rank);
1322:     DMPlexPartitionLabelClosure_Tree(dm,label,rank,cpoint);
1323:   }
1324:   DMPlexRestoreTransitiveClosure(dm,parent,PETSC_TRUE,&closureSize,&closure);
1325:   return(0);
1326: }

1330: /*@
1331:   DMPlexPartitionLabelClosure - Add the closure of all points to the partition label

1333:   Input Parameters:
1334: + dm     - The DM
1335: - label  - DMLabel assinging ranks to remote roots

1337:   Level: developer

1339: .seealso: DMPlexPartitionLabelCreateSF, DMPlexDistribute(), DMPlexCreateOverlap
1340: @*/
1341: PetscErrorCode DMPlexPartitionLabelClosure(DM dm, DMLabel label)
1342: {
1343:   IS              rankIS,   pointIS;
1344:   const PetscInt *ranks,   *points;
1345:   PetscInt        numRanks, numPoints, r, p, c, closureSize;
1346:   PetscInt       *closure = NULL;
1347:   PetscErrorCode  ierr;

1350:   DMLabelGetValueIS(label, &rankIS);
1351:   ISGetLocalSize(rankIS, &numRanks);
1352:   ISGetIndices(rankIS, &ranks);
1353:   for (r = 0; r < numRanks; ++r) {
1354:     const PetscInt rank = ranks[r];

1356:     DMLabelGetStratumIS(label, rank, &pointIS);
1357:     ISGetLocalSize(pointIS, &numPoints);
1358:     ISGetIndices(pointIS, &points);
1359:     for (p = 0; p < numPoints; ++p) {
1360:       DMPlexGetTransitiveClosure(dm, points[p], PETSC_TRUE, &closureSize, &closure);
1361:       for (c = 0; c < closureSize*2; c += 2) {
1362:         DMLabelSetValue(label, closure[c], rank);
1363:         DMPlexPartitionLabelClosure_Tree(dm,label,rank,closure[c]);
1364:       }
1365:     }
1366:     ISRestoreIndices(pointIS, &points);
1367:     ISDestroy(&pointIS);
1368:   }
1369:   if (closure) {DMPlexRestoreTransitiveClosure(dm, 0, PETSC_TRUE, &closureSize, &closure);}
1370:   ISRestoreIndices(rankIS, &ranks);
1371:   ISDestroy(&rankIS);
1372:   return(0);
1373: }

1377: /*@
1378:   DMPlexPartitionLabelAdjacency - Add one level of adjacent points to the partition label

1380:   Input Parameters:
1381: + dm     - The DM
1382: - label  - DMLabel assinging ranks to remote roots

1384:   Level: developer

1386: .seealso: DMPlexPartitionLabelCreateSF, DMPlexDistribute(), DMPlexCreateOverlap
1387: @*/
1388: PetscErrorCode DMPlexPartitionLabelAdjacency(DM dm, DMLabel label)
1389: {
1390:   IS              rankIS,   pointIS;
1391:   const PetscInt *ranks,   *points;
1392:   PetscInt        numRanks, numPoints, r, p, a, adjSize;
1393:   PetscInt       *adj = NULL;
1394:   PetscErrorCode  ierr;

1397:   DMLabelGetValueIS(label, &rankIS);
1398:   ISGetLocalSize(rankIS, &numRanks);
1399:   ISGetIndices(rankIS, &ranks);
1400:   for (r = 0; r < numRanks; ++r) {
1401:     const PetscInt rank = ranks[r];

1403:     DMLabelGetStratumIS(label, rank, &pointIS);
1404:     ISGetLocalSize(pointIS, &numPoints);
1405:     ISGetIndices(pointIS, &points);
1406:     for (p = 0; p < numPoints; ++p) {
1407:       adjSize = PETSC_DETERMINE;
1408:       DMPlexGetAdjacency(dm, points[p], &adjSize, &adj);
1409:       for (a = 0; a < adjSize; ++a) {DMLabelSetValue(label, adj[a], rank);}
1410:     }
1411:     ISRestoreIndices(pointIS, &points);
1412:     ISDestroy(&pointIS);
1413:   }
1414:   ISRestoreIndices(rankIS, &ranks);
1415:   ISDestroy(&rankIS);
1416:   PetscFree(adj);
1417:   return(0);
1418: }

1422: /*@
1423:   DMPlexPartitionLabelInvert - Create a partition label of remote roots from a local root label

1425:   Input Parameters:
1426: + dm        - The DM
1427: . rootLabel - DMLabel assinging ranks to local roots
1428: . processSF - A star forest mapping into the local index on each remote rank

1430:   Output Parameter:
1431: - leafLabel - DMLabel assinging ranks to remote roots

1433:   Note: The rootLabel defines a send pattern by mapping local points to remote target ranks. The
1434:   resulting leafLabel is a receiver mapping of remote roots to their parent rank.

1436:   Level: developer

1438: .seealso: DMPlexPartitionLabelCreateSF, DMPlexDistribute(), DMPlexCreateOverlap
1439: @*/
1440: PetscErrorCode DMPlexPartitionLabelInvert(DM dm, DMLabel rootLabel, PetscSF processSF, DMLabel leafLabel)
1441: {
1442:   MPI_Comm           comm;
1443:   PetscMPIInt        rank, numProcs;
1444:   PetscInt           p, n, numNeighbors, size, l, nleaves;
1445:   PetscSF            sfPoint;
1446:   PetscSFNode       *rootPoints, *leafPoints;
1447:   PetscSection       rootSection, leafSection;
1448:   const PetscSFNode *remote;
1449:   const PetscInt    *local, *neighbors;
1450:   IS                 valueIS;
1451:   PetscErrorCode     ierr;

1454:   PetscObjectGetComm((PetscObject) dm, &comm);
1455:   MPI_Comm_rank(comm, &rank);
1456:   MPI_Comm_size(comm, &numProcs);
1457:   DMGetPointSF(dm, &sfPoint);

1459:   /* Convert to (point, rank) and use actual owners */
1460:   PetscSectionCreate(comm, &rootSection);
1461:   PetscSectionSetChart(rootSection, 0, numProcs);
1462:   DMLabelGetValueIS(rootLabel, &valueIS);
1463:   ISGetLocalSize(valueIS, &numNeighbors);
1464:   ISGetIndices(valueIS, &neighbors);
1465:   for (n = 0; n < numNeighbors; ++n) {
1466:     PetscInt numPoints;

1468:     DMLabelGetStratumSize(rootLabel, neighbors[n], &numPoints);
1469:     PetscSectionAddDof(rootSection, neighbors[n], numPoints);
1470:   }
1471:   PetscSectionSetUp(rootSection);
1472:   PetscSectionGetStorageSize(rootSection, &size);
1473:   PetscMalloc1(size, &rootPoints);
1474:   PetscSFGetGraph(sfPoint, NULL, &nleaves, &local, &remote);
1475:   for (n = 0; n < numNeighbors; ++n) {
1476:     IS              pointIS;
1477:     const PetscInt *points;
1478:     PetscInt        off, numPoints, p;

1480:     PetscSectionGetOffset(rootSection, neighbors[n], &off);
1481:     DMLabelGetStratumIS(rootLabel, neighbors[n], &pointIS);
1482:     ISGetLocalSize(pointIS, &numPoints);
1483:     ISGetIndices(pointIS, &points);
1484:     for (p = 0; p < numPoints; ++p) {
1485:       if (local) {PetscFindInt(points[p], nleaves, local, &l);}
1486:       else       {l = -1;}
1487:       if (l >= 0) {rootPoints[off+p] = remote[l];}
1488:       else        {rootPoints[off+p].index = points[p]; rootPoints[off+p].rank = rank;}
1489:     }
1490:     ISRestoreIndices(pointIS, &points);
1491:     ISDestroy(&pointIS);
1492:   }
1493:   ISRestoreIndices(valueIS, &neighbors);
1494:   ISDestroy(&valueIS);
1495:   /* Communicate overlap */
1496:   PetscSectionCreate(comm, &leafSection);
1497:   DMPlexDistributeData(dm, processSF, rootSection, MPIU_2INT, rootPoints, leafSection, (void**) &leafPoints);
1498:   /* Filter remote contributions (ovLeafPoints) into the overlapSF */
1499:   PetscSectionGetStorageSize(leafSection, &size);
1500:   for (p = 0; p < size; p++) {
1501:     DMLabelSetValue(leafLabel, leafPoints[p].index, leafPoints[p].rank);
1502:   }
1503:   PetscFree(rootPoints);
1504:   PetscSectionDestroy(&rootSection);
1505:   PetscFree(leafPoints);
1506:   PetscSectionDestroy(&leafSection);
1507:   return(0);
1508: }

1512: /*@
1513:   DMPlexPartitionLabelCreateSF - Create a star forest from a label that assigns ranks to points

1515:   Input Parameters:
1516: + dm    - The DM
1517: . label - DMLabel assinging ranks to remote roots

1519:   Output Parameter:
1520: - sf    - The star forest communication context encapsulating the defined mapping

1522:   Note: The incoming label is a receiver mapping of remote points to their parent rank.

1524:   Level: developer

1526: .seealso: DMPlexDistribute(), DMPlexCreateOverlap
1527: @*/
1528: PetscErrorCode DMPlexPartitionLabelCreateSF(DM dm, DMLabel label, PetscSF *sf)
1529: {
1530:   PetscMPIInt     rank, numProcs;
1531:   PetscInt        n, numRemote, p, numPoints, pStart, pEnd, idx = 0;
1532:   PetscSFNode    *remotePoints;
1533:   IS              remoteRootIS;
1534:   const PetscInt *remoteRoots;

1538:   MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
1539:   MPI_Comm_size(PetscObjectComm((PetscObject) dm), &numProcs);

1541:   for (numRemote = 0, n = 0; n < numProcs; ++n) {
1542:     DMLabelGetStratumSize(label, n, &numPoints);
1543:     numRemote += numPoints;
1544:   }
1545:   PetscMalloc1(numRemote, &remotePoints);
1546:   /* Put owned points first */
1547:   DMLabelGetStratumSize(label, rank, &numPoints);
1548:   if (numPoints > 0) {
1549:     DMLabelGetStratumIS(label, rank, &remoteRootIS);
1550:     ISGetIndices(remoteRootIS, &remoteRoots);
1551:     for (p = 0; p < numPoints; p++) {
1552:       remotePoints[idx].index = remoteRoots[p];
1553:       remotePoints[idx].rank = rank;
1554:       idx++;
1555:     }
1556:     ISRestoreIndices(remoteRootIS, &remoteRoots);
1557:     ISDestroy(&remoteRootIS);
1558:   }
1559:   /* Now add remote points */
1560:   for (n = 0; n < numProcs; ++n) {
1561:     DMLabelGetStratumSize(label, n, &numPoints);
1562:     if (numPoints <= 0 || n == rank) continue;
1563:     DMLabelGetStratumIS(label, n, &remoteRootIS);
1564:     ISGetIndices(remoteRootIS, &remoteRoots);
1565:     for (p = 0; p < numPoints; p++) {
1566:       remotePoints[idx].index = remoteRoots[p];
1567:       remotePoints[idx].rank = n;
1568:       idx++;
1569:     }
1570:     ISRestoreIndices(remoteRootIS, &remoteRoots);
1571:     ISDestroy(&remoteRootIS);
1572:   }
1573:   PetscSFCreate(PetscObjectComm((PetscObject) dm), sf);
1574:   DMPlexGetChart(dm, &pStart, &pEnd);
1575:   PetscSFSetGraph(*sf, pEnd-pStart, numRemote, NULL, PETSC_OWN_POINTER, remotePoints, PETSC_OWN_POINTER);
1576:   return(0);
1577: }