Actual source code: plexdistribute.c

petsc-master 2015-06-02
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  1: #include <petsc/private/dmpleximpl.h>   /*I      "petscdmplex.h"   I*/

  5: /*@
  6:   DMPlexSetAdjacencyUseCone - Define adjacency in the mesh using either the cone or the support first

  8:   Input Parameters:
  9: + dm      - The DM object
 10: - useCone - Flag to use the cone first

 12:   Level: intermediate

 14:   Notes:
 15: $     FEM:   Two points p and q are adjacent if q \in closure(star(p)),   useCone = PETSC_FALSE, useClosure = PETSC_TRUE
 16: $     FVM:   Two points p and q are adjacent if q \in support(p+cone(p)), useCone = PETSC_TRUE,  useClosure = PETSC_FALSE
 17: $     FVM++: Two points p and q are adjacent if q \in star(closure(p)),   useCone = PETSC_TRUE,  useClosure = PETSC_TRUE

 19: .seealso: DMPlexGetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure(), DMPlexGetAdjacencyUseClosure(), DMPlexDistribute(), DMPlexPreallocateOperator()
 20: @*/
 21: PetscErrorCode DMPlexSetAdjacencyUseCone(DM dm, PetscBool useCone)
 22: {
 23:   DM_Plex *mesh = (DM_Plex *) dm->data;

 27:   mesh->useCone = useCone;
 28:   return(0);
 29: }

 33: /*@
 34:   DMPlexGetAdjacencyUseCone - Query whether adjacency in the mesh uses the cone or the support first

 36:   Input Parameter:
 37: . dm      - The DM object

 39:   Output Parameter:
 40: . useCone - Flag to use the cone first

 42:   Level: intermediate

 44:   Notes:
 45: $     FEM:   Two points p and q are adjacent if q \in closure(star(p)),   useCone = PETSC_FALSE, useClosure = PETSC_TRUE
 46: $     FVM:   Two points p and q are adjacent if q \in support(p+cone(p)), useCone = PETSC_TRUE,  useClosure = PETSC_FALSE
 47: $     FVM++: Two points p and q are adjacent if q \in star(closure(p)),   useCone = PETSC_TRUE,  useClosure = PETSC_TRUE

 49: .seealso: DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure(), DMPlexGetAdjacencyUseClosure(), DMPlexDistribute(), DMPlexPreallocateOperator()
 50: @*/
 51: PetscErrorCode DMPlexGetAdjacencyUseCone(DM dm, PetscBool *useCone)
 52: {
 53:   DM_Plex *mesh = (DM_Plex *) dm->data;

 58:   *useCone = mesh->useCone;
 59:   return(0);
 60: }

 64: /*@
 65:   DMPlexSetAdjacencyUseClosure - Define adjacency in the mesh using the transitive closure

 67:   Input Parameters:
 68: + dm      - The DM object
 69: - useClosure - Flag to use the closure

 71:   Level: intermediate

 73:   Notes:
 74: $     FEM:   Two points p and q are adjacent if q \in closure(star(p)),   useCone = PETSC_FALSE, useClosure = PETSC_TRUE
 75: $     FVM:   Two points p and q are adjacent if q \in support(p+cone(p)), useCone = PETSC_TRUE,  useClosure = PETSC_FALSE
 76: $     FVM++: Two points p and q are adjacent if q \in star(closure(p)),   useCone = PETSC_TRUE,  useClosure = PETSC_TRUE

 78: .seealso: DMPlexGetAdjacencyUseClosure(), DMPlexSetAdjacencyUseCone(), DMPlexGetAdjacencyUseCone(), DMPlexDistribute(), DMPlexPreallocateOperator()
 79: @*/
 80: PetscErrorCode DMPlexSetAdjacencyUseClosure(DM dm, PetscBool useClosure)
 81: {
 82:   DM_Plex *mesh = (DM_Plex *) dm->data;

 86:   mesh->useClosure = useClosure;
 87:   return(0);
 88: }

 92: /*@
 93:   DMPlexGetAdjacencyUseClosure - Query whether adjacency in the mesh uses the transitive closure

 95:   Input Parameter:
 96: . dm      - The DM object

 98:   Output Parameter:
 99: . useClosure - Flag to use the closure

101:   Level: intermediate

103:   Notes:
104: $     FEM:   Two points p and q are adjacent if q \in closure(star(p)),   useCone = PETSC_FALSE, useClosure = PETSC_TRUE
105: $     FVM:   Two points p and q are adjacent if q \in support(p+cone(p)), useCone = PETSC_TRUE,  useClosure = PETSC_FALSE
106: $     FVM++: Two points p and q are adjacent if q \in star(closure(p)),   useCone = PETSC_TRUE,  useClosure = PETSC_TRUE

108: .seealso: DMPlexSetAdjacencyUseClosure(), DMPlexSetAdjacencyUseCone(), DMPlexGetAdjacencyUseCone(), DMPlexDistribute(), DMPlexPreallocateOperator()
109: @*/
110: PetscErrorCode DMPlexGetAdjacencyUseClosure(DM dm, PetscBool *useClosure)
111: {
112:   DM_Plex *mesh = (DM_Plex *) dm->data;

117:   *useClosure = mesh->useClosure;
118:   return(0);
119: }

123: /*@
124:   DMPlexSetAdjacencyUseAnchors - Define adjacency in the mesh using the point-to-point constraints.

126:   Input Parameters:
127: + dm      - The DM object
128: - useAnchors - Flag to use the constraints.  If PETSC_TRUE, then constrained points are omitted from DMPlexGetAdjacency(), and their anchor points appear in their place.

130:   Level: intermediate

132: .seealso: DMPlexGetAdjacencyUseClosure(), DMPlexSetAdjacencyUseCone(), DMPlexGetAdjacencyUseCone(), DMPlexDistribute(), DMPlexPreallocateOperator(), DMPlexSetAnchors()
133: @*/
134: PetscErrorCode DMPlexSetAdjacencyUseAnchors(DM dm, PetscBool useAnchors)
135: {
136:   DM_Plex *mesh = (DM_Plex *) dm->data;

140:   mesh->useAnchors = useAnchors;
141:   return(0);
142: }

146: /*@
147:   DMPlexGetAdjacencyUseAnchors - Query whether adjacency in the mesh uses the point-to-point constraints.

149:   Input Parameter:
150: . dm      - The DM object

152:   Output Parameter:
153: . useAnchors - Flag to use the closure.  If PETSC_TRUE, then constrained points are omitted from DMPlexGetAdjacency(), and their anchor points appear in their place.

155:   Level: intermediate

157: .seealso: DMPlexSetAdjacencyUseAnchors(), DMPlexSetAdjacencyUseCone(), DMPlexGetAdjacencyUseCone(), DMPlexDistribute(), DMPlexPreallocateOperator(), DMPlexSetAnchors()
158: @*/
159: PetscErrorCode DMPlexGetAdjacencyUseAnchors(DM dm, PetscBool *useAnchors)
160: {
161:   DM_Plex *mesh = (DM_Plex *) dm->data;

166:   *useAnchors = mesh->useAnchors;
167:   return(0);
168: }

172: static PetscErrorCode DMPlexGetAdjacency_Cone_Internal(DM dm, PetscInt p, PetscInt *adjSize, PetscInt adj[])
173: {
174:   const PetscInt *cone = NULL;
175:   PetscInt        numAdj = 0, maxAdjSize = *adjSize, coneSize, c;
176:   PetscErrorCode  ierr;

179:   DMPlexGetConeSize(dm, p, &coneSize);
180:   DMPlexGetCone(dm, p, &cone);
181:   for (c = 0; c <= coneSize; ++c) {
182:     const PetscInt  point   = !c ? p : cone[c-1];
183:     const PetscInt *support = NULL;
184:     PetscInt        supportSize, s, q;

186:     DMPlexGetSupportSize(dm, point, &supportSize);
187:     DMPlexGetSupport(dm, point, &support);
188:     for (s = 0; s < supportSize; ++s) {
189:       for (q = 0; q < numAdj || (adj[numAdj++] = support[s],0); ++q) {
190:         if (support[s] == adj[q]) break;
191:       }
192:       if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize);
193:     }
194:   }
195:   *adjSize = numAdj;
196:   return(0);
197: }

201: static PetscErrorCode DMPlexGetAdjacency_Support_Internal(DM dm, PetscInt p, PetscInt *adjSize, PetscInt adj[])
202: {
203:   const PetscInt *support = NULL;
204:   PetscInt        numAdj   = 0, maxAdjSize = *adjSize, supportSize, s;
205:   PetscErrorCode  ierr;

208:   DMPlexGetSupportSize(dm, p, &supportSize);
209:   DMPlexGetSupport(dm, p, &support);
210:   for (s = 0; s <= supportSize; ++s) {
211:     const PetscInt  point = !s ? p : support[s-1];
212:     const PetscInt *cone  = NULL;
213:     PetscInt        coneSize, c, q;

215:     DMPlexGetConeSize(dm, point, &coneSize);
216:     DMPlexGetCone(dm, point, &cone);
217:     for (c = 0; c < coneSize; ++c) {
218:       for (q = 0; q < numAdj || (adj[numAdj++] = cone[c],0); ++q) {
219:         if (cone[c] == adj[q]) break;
220:       }
221:       if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize);
222:     }
223:   }
224:   *adjSize = numAdj;
225:   return(0);
226: }

230: static PetscErrorCode DMPlexGetAdjacency_Transitive_Internal(DM dm, PetscInt p, PetscBool useClosure, PetscInt *adjSize, PetscInt adj[])
231: {
232:   PetscInt      *star = NULL;
233:   PetscInt       numAdj = 0, maxAdjSize = *adjSize, starSize, s;

237:   DMPlexGetTransitiveClosure(dm, p, useClosure, &starSize, &star);
238:   for (s = 0; s < starSize*2; s += 2) {
239:     const PetscInt *closure = NULL;
240:     PetscInt        closureSize, c, q;

242:     DMPlexGetTransitiveClosure(dm, star[s], (PetscBool)!useClosure, &closureSize, (PetscInt**) &closure);
243:     for (c = 0; c < closureSize*2; c += 2) {
244:       for (q = 0; q < numAdj || (adj[numAdj++] = closure[c],0); ++q) {
245:         if (closure[c] == adj[q]) break;
246:       }
247:       if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize);
248:     }
249:     DMPlexRestoreTransitiveClosure(dm, star[s], (PetscBool)!useClosure, &closureSize, (PetscInt**) &closure);
250:   }
251:   DMPlexRestoreTransitiveClosure(dm, p, useClosure, &starSize, &star);
252:   *adjSize = numAdj;
253:   return(0);
254: }

258: PetscErrorCode DMPlexGetAdjacency_Internal(DM dm, PetscInt p, PetscBool useCone, PetscBool useTransitiveClosure, PetscBool useAnchors, PetscInt *adjSize, PetscInt *adj[])
259: {
260:   static PetscInt asiz = 0;
261:   PetscInt maxAnchors = 1;
262:   PetscInt aStart = -1, aEnd = -1;
263:   PetscInt maxAdjSize;
264:   PetscSection aSec = NULL;
265:   IS aIS = NULL;
266:   const PetscInt *anchors;
267:   PetscErrorCode  ierr;

270:   if (useAnchors) {
271:     DMPlexGetAnchors(dm,&aSec,&aIS);
272:     if (aSec) {
273:       PetscSectionGetMaxDof(aSec,&maxAnchors);
274:       maxAnchors = PetscMax(1,maxAnchors);
275:       PetscSectionGetChart(aSec,&aStart,&aEnd);
276:       ISGetIndices(aIS,&anchors);
277:     }
278:   }
279:   if (!*adj) {
280:     PetscInt depth, coneSeries, supportSeries, maxC, maxS, pStart, pEnd;

282:     DMPlexGetChart(dm, &pStart,&pEnd);
283:     DMPlexGetDepth(dm, &depth);
284:     DMPlexGetMaxSizes(dm, &maxC, &maxS);
285:     coneSeries    = (maxC > 1) ? ((PetscPowInt(maxC,depth+1)-1)/(maxC-1)) : depth+1;
286:     supportSeries = (maxS > 1) ? ((PetscPowInt(maxS,depth+1)-1)/(maxS-1)) : depth+1;
287:     asiz  = PetscMax(PetscPowInt(maxS,depth)*coneSeries,PetscPowInt(maxC,depth)*supportSeries);
288:     asiz *= maxAnchors;
289:     asiz  = PetscMin(asiz,pEnd-pStart);
290:     PetscMalloc1(asiz,adj);
291:   }
292:   if (*adjSize < 0) *adjSize = asiz;
293:   maxAdjSize = *adjSize;
294:   if (useTransitiveClosure) {
295:     DMPlexGetAdjacency_Transitive_Internal(dm, p, useCone, adjSize, *adj);
296:   } else if (useCone) {
297:     DMPlexGetAdjacency_Cone_Internal(dm, p, adjSize, *adj);
298:   } else {
299:     DMPlexGetAdjacency_Support_Internal(dm, p, adjSize, *adj);
300:   }
301:   if (useAnchors && aSec) {
302:     PetscInt origSize = *adjSize;
303:     PetscInt numAdj = origSize;
304:     PetscInt i = 0, j;
305:     PetscInt *orig = *adj;

307:     while (i < origSize) {
308:       PetscInt p = orig[i];
309:       PetscInt aDof = 0;

311:       if (p >= aStart && p < aEnd) {
312:         PetscSectionGetDof(aSec,p,&aDof);
313:       }
314:       if (aDof) {
315:         PetscInt aOff;
316:         PetscInt s, q;

318:         for (j = i + 1; j < numAdj; j++) {
319:           orig[j - 1] = orig[j];
320:         }
321:         origSize--;
322:         numAdj--;
323:         PetscSectionGetOffset(aSec,p,&aOff);
324:         for (s = 0; s < aDof; ++s) {
325:           for (q = 0; q < numAdj || (orig[numAdj++] = anchors[aOff+s],0); ++q) {
326:             if (anchors[aOff+s] == orig[q]) break;
327:           }
328:           if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize);
329:         }
330:       }
331:       else {
332:         i++;
333:       }
334:     }
335:     *adjSize = numAdj;
336:     ISRestoreIndices(aIS,&anchors);
337:   }
338:   return(0);
339: }

343: /*@
344:   DMPlexGetAdjacency - Return all points adjacent to the given point

346:   Input Parameters:
347: + dm - The DM object
348: . p  - The point
349: . adjSize - The maximum size of adj if it is non-NULL, or PETSC_DETERMINE
350: - adj - Either NULL so that the array is allocated, or an existing array with size adjSize

352:   Output Parameters:
353: + adjSize - The number of adjacent points
354: - adj - The adjacent points

356:   Level: advanced

358:   Notes: The user must PetscFree the adj array if it was not passed in.

360: .seealso: DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure(), DMPlexDistribute(), DMCreateMatrix(), DMPlexPreallocateOperator()
361: @*/
362: PetscErrorCode DMPlexGetAdjacency(DM dm, PetscInt p, PetscInt *adjSize, PetscInt *adj[])
363: {
364:   DM_Plex       *mesh = (DM_Plex *) dm->data;

371:   DMPlexGetAdjacency_Internal(dm, p, mesh->useCone, mesh->useClosure, mesh->useAnchors, adjSize, adj);
372:   return(0);
373: }
376: /*@
377:   DMPlexCreateTwoSidedProcessSF - Create an SF which just has process connectivity

379:   Collective on DM

381:   Input Parameters:
382: + dm      - The DM
383: - sfPoint - The PetscSF which encodes point connectivity

385:   Output Parameters:
386: + processRanks - A list of process neighbors, or NULL
387: - sfProcess    - An SF encoding the two-sided process connectivity, or NULL

389:   Level: developer

391: .seealso: PetscSFCreate(), DMPlexCreateProcessSF()
392: @*/
393: PetscErrorCode DMPlexCreateTwoSidedProcessSF(DM dm, PetscSF sfPoint, PetscSection rootRankSection, IS rootRanks, PetscSection leafRankSection, IS leafRanks, IS *processRanks, PetscSF *sfProcess)
394: {
395:   const PetscSFNode *remotePoints;
396:   PetscInt          *localPointsNew;
397:   PetscSFNode       *remotePointsNew;
398:   const PetscInt    *nranks;
399:   PetscInt          *ranksNew;
400:   PetscBT            neighbors;
401:   PetscInt           pStart, pEnd, p, numLeaves, l, numNeighbors, n;
402:   PetscMPIInt        numProcs, proc, rank;
403:   PetscErrorCode     ierr;

410:   MPI_Comm_size(PetscObjectComm((PetscObject) dm), &numProcs);
411:   MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);
412:   PetscSFGetGraph(sfPoint, NULL, &numLeaves, NULL, &remotePoints);
413:   PetscBTCreate(numProcs, &neighbors);
414:   PetscBTMemzero(numProcs, neighbors);
415:   /* Compute root-to-leaf process connectivity */
416:   PetscSectionGetChart(rootRankSection, &pStart, &pEnd);
417:   ISGetIndices(rootRanks, &nranks);
418:   for (p = pStart; p < pEnd; ++p) {
419:     PetscInt ndof, noff, n;

421:     PetscSectionGetDof(rootRankSection, p, &ndof);
422:     PetscSectionGetOffset(rootRankSection, p, &noff);
423:     for (n = 0; n < ndof; ++n) {PetscBTSet(neighbors, nranks[noff+n]);}
424:   }
425:   ISRestoreIndices(rootRanks, &nranks);
426:   /* Compute leaf-to-neighbor process connectivity */
427:   PetscSectionGetChart(leafRankSection, &pStart, &pEnd);
428:   ISGetIndices(leafRanks, &nranks);
429:   for (p = pStart; p < pEnd; ++p) {
430:     PetscInt ndof, noff, n;

432:     PetscSectionGetDof(leafRankSection, p, &ndof);
433:     PetscSectionGetOffset(leafRankSection, p, &noff);
434:     for (n = 0; n < ndof; ++n) {PetscBTSet(neighbors, nranks[noff+n]);}
435:   }
436:   ISRestoreIndices(leafRanks, &nranks);
437:   /* Compute leaf-to-root process connectivity */
438:   for (l = 0; l < numLeaves; ++l) {PetscBTSet(neighbors, remotePoints[l].rank);}
439:   /* Calculate edges */
440:   PetscBTClear(neighbors, rank);
441:   for(proc = 0, numNeighbors = 0; proc < numProcs; ++proc) {if (PetscBTLookup(neighbors, proc)) ++numNeighbors;}
442:   PetscMalloc1(numNeighbors, &ranksNew);
443:   PetscMalloc1(numNeighbors, &localPointsNew);
444:   PetscMalloc1(numNeighbors, &remotePointsNew);
445:   for(proc = 0, n = 0; proc < numProcs; ++proc) {
446:     if (PetscBTLookup(neighbors, proc)) {
447:       ranksNew[n]              = proc;
448:       localPointsNew[n]        = proc;
449:       remotePointsNew[n].index = rank;
450:       remotePointsNew[n].rank  = proc;
451:       ++n;
452:     }
453:   }
454:   PetscBTDestroy(&neighbors);
455:   if (processRanks) {ISCreateGeneral(PetscObjectComm((PetscObject)dm), numNeighbors, ranksNew, PETSC_OWN_POINTER, processRanks);}
456:   else              {PetscFree(ranksNew);}
457:   if (sfProcess) {
458:     PetscSFCreate(PetscObjectComm((PetscObject)dm), sfProcess);
459:     PetscObjectSetName((PetscObject) *sfProcess, "Two-Sided Process SF");
460:     PetscSFSetFromOptions(*sfProcess);
461:     PetscSFSetGraph(*sfProcess, numProcs, numNeighbors, localPointsNew, PETSC_OWN_POINTER, remotePointsNew, PETSC_OWN_POINTER);
462:   }
463:   return(0);
464: }

468: /*@
469:   DMPlexDistributeOwnership - Compute owner information for shared points. This basically gets two-sided for an SF.

471:   Collective on DM

473:   Input Parameter:
474: . dm - The DM

476:   Output Parameters:
477: + rootSection - The number of leaves for a given root point
478: . rootrank    - The rank of each edge into the root point
479: . leafSection - The number of processes sharing a given leaf point
480: - leafrank    - The rank of each process sharing a leaf point

482:   Level: developer

484: .seealso: DMPlexCreateOverlap()
485: @*/
486: PetscErrorCode DMPlexDistributeOwnership(DM dm, PetscSection rootSection, IS *rootrank, PetscSection leafSection, IS *leafrank)
487: {
488:   MPI_Comm        comm;
489:   PetscSF         sfPoint;
490:   const PetscInt *rootdegree;
491:   PetscInt       *myrank, *remoterank;
492:   PetscInt        pStart, pEnd, p, nedges;
493:   PetscMPIInt     rank;
494:   PetscErrorCode  ierr;

497:   PetscObjectGetComm((PetscObject) dm, &comm);
498:   MPI_Comm_rank(comm, &rank);
499:   DMPlexGetChart(dm, &pStart, &pEnd);
500:   DMGetPointSF(dm, &sfPoint);
501:   /* Compute number of leaves for each root */
502:   PetscObjectSetName((PetscObject) rootSection, "Root Section");
503:   PetscSectionSetChart(rootSection, pStart, pEnd);
504:   PetscSFComputeDegreeBegin(sfPoint, &rootdegree);
505:   PetscSFComputeDegreeEnd(sfPoint, &rootdegree);
506:   for (p = pStart; p < pEnd; ++p) {PetscSectionSetDof(rootSection, p, rootdegree[p-pStart]);}
507:   PetscSectionSetUp(rootSection);
508:   /* Gather rank of each leaf to root */
509:   PetscSectionGetStorageSize(rootSection, &nedges);
510:   PetscMalloc1(pEnd-pStart, &myrank);
511:   PetscMalloc1(nedges,  &remoterank);
512:   for (p = 0; p < pEnd-pStart; ++p) myrank[p] = rank;
513:   PetscSFGatherBegin(sfPoint, MPIU_INT, myrank, remoterank);
514:   PetscSFGatherEnd(sfPoint, MPIU_INT, myrank, remoterank);
515:   PetscFree(myrank);
516:   ISCreateGeneral(comm, nedges, remoterank, PETSC_OWN_POINTER, rootrank);
517:   /* Distribute remote ranks to leaves */
518:   PetscObjectSetName((PetscObject) leafSection, "Leaf Section");
519:   DMPlexDistributeFieldIS(dm, sfPoint, rootSection, *rootrank, leafSection, leafrank);
520:   return(0);
521: }

525: /*@C
526:   DMPlexCreateOverlap - Compute owner information for shared points. This basically gets two-sided for an SF.

528:   Collective on DM

530:   Input Parameters:
531: + dm          - The DM
532: . levels      - Number of overlap levels
533: . rootSection - The number of leaves for a given root point
534: . rootrank    - The rank of each edge into the root point
535: . leafSection - The number of processes sharing a given leaf point
536: - leafrank    - The rank of each process sharing a leaf point

538:   Output Parameters:
539: + ovLabel     - DMLabel containing remote overlap contributions as point/rank pairings

541:   Level: developer

543: .seealso: DMPlexDistributeOwnership(), DMPlexDistribute()
544: @*/
545: PetscErrorCode DMPlexCreateOverlap(DM dm, PetscInt levels, PetscSection rootSection, IS rootrank, PetscSection leafSection, IS leafrank, DMLabel *ovLabel)
546: {
547:   MPI_Comm           comm;
548:   DMLabel            ovAdjByRank; /* A DMLabel containing all points adjacent to shared points, separated by rank (value in label) */
549:   PetscSF            sfPoint, sfProc;
550:   const PetscSFNode *remote;
551:   const PetscInt    *local;
552:   const PetscInt    *nrank, *rrank;
553:   PetscInt          *adj = NULL;
554:   PetscInt           pStart, pEnd, p, sStart, sEnd, nleaves, l;
555:   PetscMPIInt        rank, numProcs;
556:   PetscBool          useCone, useClosure, flg;
557:   PetscErrorCode     ierr;

560:   PetscObjectGetComm((PetscObject) dm, &comm);
561:   MPI_Comm_size(comm, &numProcs);
562:   MPI_Comm_rank(comm, &rank);
563:   DMGetPointSF(dm, &sfPoint);
564:   DMPlexGetChart(dm, &pStart, &pEnd);
565:   PetscSectionGetChart(leafSection, &sStart, &sEnd);
566:   PetscSFGetGraph(sfPoint, NULL, &nleaves, &local, &remote);
567:   DMLabelCreate("Overlap adjacency", &ovAdjByRank);
568:   /* Handle leaves: shared with the root point */
569:   for (l = 0; l < nleaves; ++l) {
570:     PetscInt adjSize = PETSC_DETERMINE, a;

572:     DMPlexGetAdjacency(dm, local[l], &adjSize, &adj);
573:     for (a = 0; a < adjSize; ++a) {DMLabelSetValue(ovAdjByRank, adj[a], remote[l].rank);}
574:   }
575:   ISGetIndices(rootrank, &rrank);
576:   ISGetIndices(leafrank, &nrank);
577:   /* Handle roots */
578:   for (p = pStart; p < pEnd; ++p) {
579:     PetscInt adjSize = PETSC_DETERMINE, neighbors = 0, noff, n, a;

581:     if ((p >= sStart) && (p < sEnd)) {
582:       /* Some leaves share a root with other leaves on different processes */
583:       PetscSectionGetDof(leafSection, p, &neighbors);
584:       if (neighbors) {
585:         PetscSectionGetOffset(leafSection, p, &noff);
586:         DMPlexGetAdjacency(dm, p, &adjSize, &adj);
587:         for (n = 0; n < neighbors; ++n) {
588:           const PetscInt remoteRank = nrank[noff+n];

590:           if (remoteRank == rank) continue;
591:           for (a = 0; a < adjSize; ++a) {DMLabelSetValue(ovAdjByRank, adj[a], remoteRank);}
592:         }
593:       }
594:     }
595:     /* Roots are shared with leaves */
596:     PetscSectionGetDof(rootSection, p, &neighbors);
597:     if (!neighbors) continue;
598:     PetscSectionGetOffset(rootSection, p, &noff);
599:     DMPlexGetAdjacency(dm, p, &adjSize, &adj);
600:     for (n = 0; n < neighbors; ++n) {
601:       const PetscInt remoteRank = rrank[noff+n];

603:       if (remoteRank == rank) continue;
604:       for (a = 0; a < adjSize; ++a) {DMLabelSetValue(ovAdjByRank, adj[a], remoteRank);}
605:     }
606:   }
607:   PetscFree(adj);
608:   ISRestoreIndices(rootrank, &rrank);
609:   ISRestoreIndices(leafrank, &nrank);
610:   /* Add additional overlap levels */
611:   for (l = 1; l < levels; l++) {DMPlexPartitionLabelAdjacency(dm, ovAdjByRank);}
612:   /* We require the closure in the overlap */
613:   DMPlexGetAdjacencyUseCone(dm, &useCone);
614:   DMPlexGetAdjacencyUseClosure(dm, &useClosure);
615:   if (useCone || !useClosure) {
616:     DMPlexPartitionLabelClosure(dm, ovAdjByRank);
617:   }
618:   PetscOptionsHasName(((PetscObject) dm)->prefix, "-overlap_view", &flg);
619:   if (flg) {
620:     PetscViewerASCIISynchronizedAllow(PETSC_VIEWER_STDOUT_WORLD, PETSC_TRUE);
621:     DMLabelView(ovAdjByRank, PETSC_VIEWER_STDOUT_WORLD);
622:   }
623:   /* Make process SF and invert sender to receiver label */
624:   DMPlexCreateTwoSidedProcessSF(dm, sfPoint, rootSection, rootrank, leafSection, leafrank, NULL, &sfProc);
625:   DMLabelCreate("Overlap label", ovLabel);
626:   DMPlexPartitionLabelInvert(dm, ovAdjByRank, sfProc, *ovLabel);
627:   /* Add owned points, except for shared local points */
628:   for (p = pStart; p < pEnd; ++p) {DMLabelSetValue(*ovLabel, p, rank);}
629:   for (l = 0; l < nleaves; ++l) {
630:     DMLabelClearValue(*ovLabel, local[l], rank);
631:     DMLabelSetValue(*ovLabel, remote[l].index, remote[l].rank);
632:   }
633:   /* Clean up */
634:   DMLabelDestroy(&ovAdjByRank);
635:   PetscSFDestroy(&sfProc);
636:   return(0);
637: }

641: PetscErrorCode DMPlexCreateOverlapMigrationSF(DM dm, PetscSF overlapSF, PetscSF *migrationSF)
642: {
643:   MPI_Comm           comm;
644:   PetscMPIInt        rank, numProcs;
645:   PetscInt           d, dim, p, pStart, pEnd, nroots, nleaves, newLeaves, point, numSharedPoints;
646:   PetscInt          *pointDepths, *remoteDepths, *ilocal;
647:   PetscInt          *depthRecv, *depthShift, *depthIdx;
648:   PetscSFNode       *iremote;
649:   PetscSF            pointSF;
650:   const PetscInt    *sharedLocal;
651:   const PetscSFNode *overlapRemote, *sharedRemote;
652:   PetscErrorCode     ierr;

656:   PetscObjectGetComm((PetscObject)dm, &comm);
657:   MPI_Comm_rank(comm, &rank);
658:   MPI_Comm_size(comm, &numProcs);
659:   DMGetDimension(dm, &dim);

661:   /* Before building the migration SF we need to know the new stratum offsets */
662:   PetscSFGetGraph(overlapSF, &nroots, &nleaves, NULL, &overlapRemote);
663:   PetscMalloc2(nroots, &pointDepths, nleaves, &remoteDepths);
664:   for (d=0; d<dim+1; d++) {
665:     DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
666:     for (p=pStart; p<pEnd; p++) pointDepths[p] = d;
667:   }
668:   for (p=0; p<nleaves; p++) remoteDepths[p] = -1;
669:   PetscSFBcastBegin(overlapSF, MPIU_INT, pointDepths, remoteDepths);
670:   PetscSFBcastEnd(overlapSF, MPIU_INT, pointDepths, remoteDepths);

672:   /* Count recevied points in each stratum and compute the internal strata shift */
673:   PetscMalloc3(dim+1, &depthRecv, dim+1, &depthShift, dim+1, &depthIdx);
674:   for (d=0; d<dim+1; d++) depthRecv[d]=0;
675:   for (p=0; p<nleaves; p++) depthRecv[remoteDepths[p]]++;
676:   depthShift[dim] = 0;
677:   for (d=0; d<dim; d++) depthShift[d] = depthRecv[dim];
678:   for (d=1; d<dim; d++) depthShift[d] += depthRecv[0];
679:   for (d=dim-2; d>0; d--) depthShift[d] += depthRecv[d+1];
680:   for (d=0; d<dim+1; d++) {
681:     DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
682:     depthIdx[d] = pStart + depthShift[d];
683:   }

685:   /* Form the overlap SF build an SF that describes the full overlap migration SF */
686:   DMPlexGetChart(dm, &pStart, &pEnd);
687:   newLeaves = pEnd - pStart + nleaves;
688:   PetscMalloc1(newLeaves, &ilocal);
689:   PetscMalloc1(newLeaves, &iremote);
690:   /* First map local points to themselves */
691:   for (d=0; d<dim+1; d++) {
692:     DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
693:     for (p=pStart; p<pEnd; p++) {
694:       point = p + depthShift[d];
695:       ilocal[point] = point;
696:       iremote[point].index = p;
697:       iremote[point].rank = rank;
698:       depthIdx[d]++;
699:     }
700:   }

702:   /* Add in the remote roots for currently shared points */
703:   DMGetPointSF(dm, &pointSF);
704:   PetscSFGetGraph(pointSF, NULL, &numSharedPoints, &sharedLocal, &sharedRemote);
705:   for (d=0; d<dim+1; d++) {
706:     DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
707:     for (p=0; p<numSharedPoints; p++) {
708:       if (pStart <= sharedLocal[p] && sharedLocal[p] < pEnd) {
709:         point = sharedLocal[p] + depthShift[d];
710:         iremote[point].index = sharedRemote[p].index;
711:         iremote[point].rank = sharedRemote[p].rank;
712:       }
713:     }
714:   }

716:   /* Now add the incoming overlap points */
717:   for (p=0; p<nleaves; p++) {
718:     point = depthIdx[remoteDepths[p]];
719:     ilocal[point] = point;
720:     iremote[point].index = overlapRemote[p].index;
721:     iremote[point].rank = overlapRemote[p].rank;
722:     depthIdx[remoteDepths[p]]++;
723:   }
724:   PetscFree2(pointDepths,remoteDepths);

726:   PetscSFCreate(comm, migrationSF);
727:   PetscObjectSetName((PetscObject) *migrationSF, "Overlap Migration SF");
728:   PetscSFSetFromOptions(*migrationSF);
729:   DMPlexGetChart(dm, &pStart, &pEnd);
730:   PetscSFSetGraph(*migrationSF, pEnd-pStart, newLeaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER);

732:   PetscFree3(depthRecv, depthShift, depthIdx);
733:   return(0);
734: }

738: /*@
739:   DMPlexStratifyMigrationSF - Add partition overlap to a distributed non-overlapping DM.

741:   Input Parameter:
742: + dm          - The DM
743: - sf          - A star forest with non-ordered leaves, usually defining a DM point migration

745:   Output Parameter:
746: . migrationSF - A star forest with added leaf indirection that ensures the resulting DM is stratified

748:   Level: developer

750: .seealso: DMPlexPartitionLabelCreateSF(), DMPlexDistribute(), DMPlexDistributeOverlap()
751: @*/
752: PetscErrorCode DMPlexStratifyMigrationSF(DM dm, PetscSF sf, PetscSF *migrationSF)
753: {
754:   MPI_Comm           comm;
755:   PetscMPIInt        rank, numProcs;
756:   PetscInt           d, ldepth, depth, p, pStart, pEnd, nroots, nleaves;
757:   PetscInt          *pointDepths, *remoteDepths, *ilocal;
758:   PetscInt          *depthRecv, *depthShift, *depthIdx;
759:   const PetscSFNode *iremote;
760:   PetscErrorCode     ierr;

764:   PetscObjectGetComm((PetscObject) dm, &comm);
765:   MPI_Comm_rank(comm, &rank);
766:   MPI_Comm_size(comm, &numProcs);
767:   DMPlexGetDepth(dm, &ldepth);
768:   MPI_Allreduce(&ldepth, &depth, 1, MPIU_INT, MPI_MAX, comm);
769:   if ((ldepth >= 0) && (depth != ldepth)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Inconsistent Plex depth %d != %d", ldepth, depth);

771:   /* Before building the migration SF we need to know the new stratum offsets */
772:   PetscSFGetGraph(sf, &nroots, &nleaves, NULL, &iremote);
773:   PetscMalloc2(nroots, &pointDepths, nleaves, &remoteDepths);
774:   for (d = 0; d < depth+1; ++d) {
775:     DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
776:     for (p = pStart; p < pEnd; ++p) pointDepths[p] = d;
777:   }
778:   for (p = 0; p < nleaves; ++p) remoteDepths[p] = -1;
779:   PetscSFBcastBegin(sf, MPIU_INT, pointDepths, remoteDepths);
780:   PetscSFBcastEnd(sf, MPIU_INT, pointDepths, remoteDepths);
781:   /* Count recevied points in each stratum and compute the internal strata shift */
782:   PetscMalloc3(depth+1, &depthRecv, depth+1, &depthShift, depth+1, &depthIdx);
783:   for (d = 0; d < depth+1; ++d) depthRecv[d] = 0;
784:   for (p = 0; p < nleaves; ++p) depthRecv[remoteDepths[p]]++;
785:   depthShift[depth] = 0;
786:   for (d = 0; d < depth; ++d) depthShift[d] = depthRecv[depth];
787:   for (d = 1; d < depth; ++d) depthShift[d] += depthRecv[0];
788:   for (d = depth-2; d > 0; --d) depthShift[d] += depthRecv[d+1];
789:   for (d = 0; d < depth+1; ++d) {depthIdx[d] = 0;}
790:   /* Derive a new local permutation based on stratified indices */
791:   PetscMalloc1(nleaves, &ilocal);
792:   for (p = 0; p < nleaves; ++p) {
793:     const PetscInt dep = remoteDepths[p];

795:     ilocal[p] = depthShift[dep] + depthIdx[dep];
796:     depthIdx[dep]++;
797:   }
798:   PetscSFCreate(comm, migrationSF);
799:   PetscObjectSetName((PetscObject) *migrationSF, "Migration SF");
800:   PetscSFSetGraph(*migrationSF, nroots, nleaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_COPY_VALUES);
801:   PetscFree2(pointDepths,remoteDepths);
802:   PetscFree3(depthRecv, depthShift, depthIdx);
803:   return(0);
804: }

808: /*@
809:   DMPlexDistributeField - Distribute field data to match a given PetscSF, usually the SF from mesh distribution

811:   Collective on DM

813:   Input Parameters:
814: + dm - The DMPlex object
815: . pointSF - The PetscSF describing the communication pattern
816: . originalSection - The PetscSection for existing data layout
817: - originalVec - The existing data

819:   Output Parameters:
820: + newSection - The PetscSF describing the new data layout
821: - newVec - The new data

823:   Level: developer

825: .seealso: DMPlexDistribute(), DMPlexDistributeFieldIS(), DMPlexDistributeData()
826: @*/
827: PetscErrorCode DMPlexDistributeField(DM dm, PetscSF pointSF, PetscSection originalSection, Vec originalVec, PetscSection newSection, Vec newVec)
828: {
829:   PetscSF        fieldSF;
830:   PetscInt      *remoteOffsets, fieldSize;
831:   PetscScalar   *originalValues, *newValues;

835:   PetscLogEventBegin(DMPLEX_DistributeField,dm,0,0,0);
836:   PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);

838:   PetscSectionGetStorageSize(newSection, &fieldSize);
839:   VecSetSizes(newVec, fieldSize, PETSC_DETERMINE);
840:   VecSetType(newVec,dm->vectype);

842:   VecGetArray(originalVec, &originalValues);
843:   VecGetArray(newVec, &newValues);
844:   PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);
845:   PetscSFBcastBegin(fieldSF, MPIU_SCALAR, originalValues, newValues);
846:   PetscSFBcastEnd(fieldSF, MPIU_SCALAR, originalValues, newValues);
847:   PetscSFDestroy(&fieldSF);
848:   VecRestoreArray(newVec, &newValues);
849:   VecRestoreArray(originalVec, &originalValues);
850:   PetscLogEventEnd(DMPLEX_DistributeField,dm,0,0,0);
851:   return(0);
852: }

856: /*@
857:   DMPlexDistributeFieldIS - Distribute field data to match a given PetscSF, usually the SF from mesh distribution

859:   Collective on DM

861:   Input Parameters:
862: + dm - The DMPlex object
863: . pointSF - The PetscSF describing the communication pattern
864: . originalSection - The PetscSection for existing data layout
865: - originalIS - The existing data

867:   Output Parameters:
868: + newSection - The PetscSF describing the new data layout
869: - newIS - The new data

871:   Level: developer

873: .seealso: DMPlexDistribute(), DMPlexDistributeField(), DMPlexDistributeData()
874: @*/
875: PetscErrorCode DMPlexDistributeFieldIS(DM dm, PetscSF pointSF, PetscSection originalSection, IS originalIS, PetscSection newSection, IS *newIS)
876: {
877:   PetscSF         fieldSF;
878:   PetscInt       *newValues, *remoteOffsets, fieldSize;
879:   const PetscInt *originalValues;
880:   PetscErrorCode  ierr;

883:   PetscLogEventBegin(DMPLEX_DistributeField,dm,0,0,0);
884:   PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);

886:   PetscSectionGetStorageSize(newSection, &fieldSize);
887:   PetscMalloc1(fieldSize, &newValues);

889:   ISGetIndices(originalIS, &originalValues);
890:   PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);
891:   PetscSFBcastBegin(fieldSF, MPIU_INT, (PetscInt *) originalValues, newValues);
892:   PetscSFBcastEnd(fieldSF, MPIU_INT, (PetscInt *) originalValues, newValues);
893:   PetscSFDestroy(&fieldSF);
894:   ISRestoreIndices(originalIS, &originalValues);
895:   ISCreateGeneral(PetscObjectComm((PetscObject) pointSF), fieldSize, newValues, PETSC_OWN_POINTER, newIS);
896:   PetscLogEventEnd(DMPLEX_DistributeField,dm,0,0,0);
897:   return(0);
898: }

902: /*@
903:   DMPlexDistributeData - Distribute field data to match a given PetscSF, usually the SF from mesh distribution

905:   Collective on DM

907:   Input Parameters:
908: + dm - The DMPlex object
909: . pointSF - The PetscSF describing the communication pattern
910: . originalSection - The PetscSection for existing data layout
911: . datatype - The type of data
912: - originalData - The existing data

914:   Output Parameters:
915: + newSection - The PetscSection describing the new data layout
916: - newData - The new data

918:   Level: developer

920: .seealso: DMPlexDistribute(), DMPlexDistributeField()
921: @*/
922: PetscErrorCode DMPlexDistributeData(DM dm, PetscSF pointSF, PetscSection originalSection, MPI_Datatype datatype, void *originalData, PetscSection newSection, void **newData)
923: {
924:   PetscSF        fieldSF;
925:   PetscInt      *remoteOffsets, fieldSize;
926:   PetscMPIInt    dataSize;

930:   PetscLogEventBegin(DMPLEX_DistributeData,dm,0,0,0);
931:   PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);

933:   PetscSectionGetStorageSize(newSection, &fieldSize);
934:   MPI_Type_size(datatype, &dataSize);
935:   PetscMalloc(fieldSize * dataSize, newData);

937:   PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);
938:   PetscSFBcastBegin(fieldSF, datatype, originalData, *newData);
939:   PetscSFBcastEnd(fieldSF, datatype, originalData, *newData);
940:   PetscSFDestroy(&fieldSF);
941:   PetscLogEventEnd(DMPLEX_DistributeData,dm,0,0,0);
942:   return(0);
943: }

947: PetscErrorCode DMPlexDistributeCones(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping renumbering, DM dmParallel)
948: {
949:   DM_Plex               *mesh  = (DM_Plex*) dm->data;
950:   DM_Plex               *pmesh = (DM_Plex*) (dmParallel)->data;
951:   MPI_Comm               comm;
952:   PetscSF                coneSF;
953:   PetscSection           originalConeSection, newConeSection;
954:   PetscInt              *remoteOffsets, *cones, *newCones, newConesSize;
955:   PetscBool              flg;
956:   PetscErrorCode         ierr;

961:   PetscLogEventBegin(DMPLEX_DistributeCones,dm,0,0,0);

963:   /* Distribute cone section */
964:   PetscObjectGetComm((PetscObject)dm, &comm);
965:   DMPlexGetConeSection(dm, &originalConeSection);
966:   DMPlexGetConeSection(dmParallel, &newConeSection);
967:   PetscSFDistributeSection(migrationSF, originalConeSection, &remoteOffsets, newConeSection);
968:   DMSetUp(dmParallel);
969:   {
970:     PetscInt pStart, pEnd, p;

972:     PetscSectionGetChart(newConeSection, &pStart, &pEnd);
973:     for (p = pStart; p < pEnd; ++p) {
974:       PetscInt coneSize;
975:       PetscSectionGetDof(newConeSection, p, &coneSize);
976:       pmesh->maxConeSize = PetscMax(pmesh->maxConeSize, coneSize);
977:     }
978:   }
979:   /* Communicate and renumber cones */
980:   PetscSFCreateSectionSF(migrationSF, originalConeSection, remoteOffsets, newConeSection, &coneSF);
981:   DMPlexGetCones(dm, &cones);
982:   DMPlexGetCones(dmParallel, &newCones);
983:   PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones);
984:   PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones);
985:   PetscSectionGetStorageSize(newConeSection, &newConesSize);
986:   ISGlobalToLocalMappingApplyBlock(renumbering, IS_GTOLM_MASK, newConesSize, newCones, NULL, newCones);
987: #if PETSC_USE_DEBUG
988:   {
989:     PetscInt  p;
990:     PetscBool valid = PETSC_TRUE;
991:     for (p = 0; p < newConesSize; ++p) {
992:       if (newCones[p] < 0) {valid = PETSC_FALSE; PetscPrintf(PETSC_COMM_SELF, "Point %d not in overlap SF\n", p);}
993:     }
994:     if (!valid) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid global to local map");
995:   }
996: #endif
997:   PetscOptionsHasName(((PetscObject) dm)->prefix, "-cones_view", &flg);
998:   if (flg) {
999:     PetscPrintf(comm, "Serial Cone Section:\n");
1000:     PetscSectionView(originalConeSection, PETSC_VIEWER_STDOUT_WORLD);
1001:     PetscPrintf(comm, "Parallel Cone Section:\n");
1002:     PetscSectionView(newConeSection, PETSC_VIEWER_STDOUT_WORLD);
1003:     PetscSFView(coneSF, NULL);
1004:   }
1005:   DMPlexGetConeOrientations(dm, &cones);
1006:   DMPlexGetConeOrientations(dmParallel, &newCones);
1007:   PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones);
1008:   PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones);
1009:   PetscSFDestroy(&coneSF);
1010:   PetscLogEventEnd(DMPLEX_DistributeCones,dm,0,0,0);
1011:   /* Create supports and stratify sieve */
1012:   {
1013:     PetscInt pStart, pEnd;

1015:     PetscSectionGetChart(pmesh->coneSection, &pStart, &pEnd);
1016:     PetscSectionSetChart(pmesh->supportSection, pStart, pEnd);
1017:   }
1018:   DMPlexSymmetrize(dmParallel);
1019:   DMPlexStratify(dmParallel);
1020:   pmesh->useCone    = mesh->useCone;
1021:   pmesh->useClosure = mesh->useClosure;
1022:   return(0);
1023: }

1027: PetscErrorCode DMPlexDistributeCoordinates(DM dm, PetscSF migrationSF, DM dmParallel)
1028: {
1029:   MPI_Comm         comm;
1030:   PetscSection     originalCoordSection, newCoordSection;
1031:   Vec              originalCoordinates, newCoordinates;
1032:   PetscInt         bs;
1033:   const char      *name;
1034:   const PetscReal *maxCell, *L;
1035:   const DMBoundaryType *bd;
1036:   PetscErrorCode   ierr;


1042:   PetscObjectGetComm((PetscObject)dm, &comm);
1043:   DMGetCoordinateSection(dm, &originalCoordSection);
1044:   DMGetCoordinateSection(dmParallel, &newCoordSection);
1045:   DMGetCoordinatesLocal(dm, &originalCoordinates);
1046:   if (originalCoordinates) {
1047:     VecCreate(comm, &newCoordinates);
1048:     PetscObjectGetName((PetscObject) originalCoordinates, &name);
1049:     PetscObjectSetName((PetscObject) newCoordinates, name);

1051:     DMPlexDistributeField(dm, migrationSF, originalCoordSection, originalCoordinates, newCoordSection, newCoordinates);
1052:     DMSetCoordinatesLocal(dmParallel, newCoordinates);
1053:     VecGetBlockSize(originalCoordinates, &bs);
1054:     VecSetBlockSize(newCoordinates, bs);
1055:     VecDestroy(&newCoordinates);
1056:   }
1057:   DMGetPeriodicity(dm, &maxCell, &L, &bd);
1058:   if (L) {DMSetPeriodicity(dmParallel, maxCell, L, bd);}
1059:   return(0);
1060: }

1064: /* Here we are assuming that process 0 always has everything */
1065: PetscErrorCode DMPlexDistributeLabels(DM dm, PetscSF migrationSF, DM dmParallel)
1066: {
1067:   MPI_Comm       comm;
1068:   PetscMPIInt    rank;
1069:   PetscInt       numLabels, numLocalLabels, l;
1070:   PetscBool      hasLabels = PETSC_FALSE;

1076:   PetscLogEventBegin(DMPLEX_DistributeLabels,dm,0,0,0);
1077:   PetscObjectGetComm((PetscObject)dm, &comm);
1078:   MPI_Comm_rank(comm, &rank);

1080:   /* Everyone must have either the same number of labels, or none */
1081:   DMPlexGetNumLabels(dm, &numLocalLabels);
1082:   numLabels = numLocalLabels;
1083:   MPI_Bcast(&numLabels, 1, MPIU_INT, 0, comm);
1084:   if (numLabels == numLocalLabels) hasLabels = PETSC_TRUE;
1085:   for (l = numLabels-1; l >= 0; --l) {
1086:     DMLabel     label = NULL, labelNew = NULL;
1087:     PetscBool   isdepth;

1089:     if (hasLabels) {
1090:       DMPlexGetLabelByNum(dm, l, &label);
1091:       /* Skip "depth" because it is recreated */
1092:       PetscStrcmp(label->name, "depth", &isdepth);
1093:     }
1094:     MPI_Bcast(&isdepth, 1, MPIU_BOOL, 0, comm);
1095:     if (isdepth) continue;
1096:     DMLabelDistribute(label, migrationSF, &labelNew);
1097:     DMPlexAddLabel(dmParallel, labelNew);
1098:   }
1099:   PetscLogEventEnd(DMPLEX_DistributeLabels,dm,0,0,0);
1100:   return(0);
1101: }

1105: PetscErrorCode DMPlexDistributeSetupHybrid(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping renumbering, DM dmParallel)
1106: {
1107:   DM_Plex        *mesh  = (DM_Plex*) dm->data;
1108:   DM_Plex        *pmesh = (DM_Plex*) (dmParallel)->data;
1109:   MPI_Comm        comm;
1110:   const PetscInt *gpoints;
1111:   PetscInt        dim, depth, n, d;
1112:   PetscErrorCode  ierr;


1118:   PetscObjectGetComm((PetscObject)dm, &comm);
1119:   DMGetDimension(dm, &dim);

1121:   /* Setup hybrid structure */
1122:   for (d = 0; d <= dim; ++d) {pmesh->hybridPointMax[d] = mesh->hybridPointMax[d];}
1123:   MPI_Bcast(pmesh->hybridPointMax, dim+1, MPIU_INT, 0, comm);
1124:   ISLocalToGlobalMappingGetSize(renumbering, &n);
1125:   ISLocalToGlobalMappingGetIndices(renumbering, &gpoints);
1126:   DMPlexGetDepth(dm, &depth);
1127:   for (d = 0; d <= dim; ++d) {
1128:     PetscInt pmax = pmesh->hybridPointMax[d], newmax = 0, pEnd, stratum[2], p;

1130:     if (pmax < 0) continue;
1131:     DMPlexGetDepthStratum(dm, d > depth ? depth : d, &stratum[0], &stratum[1]);
1132:     DMPlexGetDepthStratum(dmParallel, d, NULL, &pEnd);
1133:     MPI_Bcast(stratum, 2, MPIU_INT, 0, comm);
1134:     for (p = 0; p < n; ++p) {
1135:       const PetscInt point = gpoints[p];

1137:       if ((point >= stratum[0]) && (point < stratum[1]) && (point >= pmax)) ++newmax;
1138:     }
1139:     if (newmax > 0) pmesh->hybridPointMax[d] = pEnd - newmax;
1140:     else            pmesh->hybridPointMax[d] = -1;
1141:   }
1142:   ISLocalToGlobalMappingRestoreIndices(renumbering, &gpoints);
1143:   return(0);
1144: }

1148: PetscErrorCode DMPlexDistributeSetupTree(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping renumbering, DM dmParallel)
1149: {
1150:   DM_Plex        *mesh  = (DM_Plex*) dm->data;
1151:   DM_Plex        *pmesh = (DM_Plex*) (dmParallel)->data;
1152:   MPI_Comm        comm;
1153:   DM              refTree;
1154:   PetscSection    origParentSection, newParentSection;
1155:   PetscInt        *origParents, *origChildIDs;
1156:   PetscBool       flg;
1157:   PetscErrorCode  ierr;

1162:   PetscObjectGetComm((PetscObject)dm, &comm);

1164:   /* Set up tree */
1165:   DMPlexGetReferenceTree(dm,&refTree);
1166:   DMPlexSetReferenceTree(dmParallel,refTree);
1167:   DMPlexGetTree(dm,&origParentSection,&origParents,&origChildIDs,NULL,NULL);
1168:   if (origParentSection) {
1169:     PetscInt        pStart, pEnd;
1170:     PetscInt        *newParents, *newChildIDs;
1171:     PetscInt        *remoteOffsetsParents, newParentSize;
1172:     PetscSF         parentSF;

1174:     DMPlexGetChart(dmParallel, &pStart, &pEnd);
1175:     PetscSectionCreate(PetscObjectComm((PetscObject)dmParallel),&newParentSection);
1176:     PetscSectionSetChart(newParentSection,pStart,pEnd);
1177:     PetscSFDistributeSection(migrationSF, origParentSection, &remoteOffsetsParents, newParentSection);
1178:     PetscSFCreateSectionSF(migrationSF, origParentSection, remoteOffsetsParents, newParentSection, &parentSF);
1179:     PetscSectionGetStorageSize(newParentSection,&newParentSize);
1180:     PetscMalloc2(newParentSize,&newParents,newParentSize,&newChildIDs);
1181:     PetscSFBcastBegin(parentSF, MPIU_INT, origParents, newParents);
1182:     PetscSFBcastEnd(parentSF, MPIU_INT, origParents, newParents);
1183:     PetscSFBcastBegin(parentSF, MPIU_INT, origChildIDs, newChildIDs);
1184:     PetscSFBcastEnd(parentSF, MPIU_INT, origChildIDs, newChildIDs);
1185:     ISGlobalToLocalMappingApplyBlock(renumbering,IS_GTOLM_MASK, newParentSize, newParents, NULL, newParents);
1186: #if PETSC_USE_DEBUG
1187:     {
1188:       PetscInt  p;
1189:       PetscBool valid = PETSC_TRUE;
1190:       for (p = 0; p < newParentSize; ++p) {
1191:         if (newParents[p] < 0) {valid = PETSC_FALSE; PetscPrintf(PETSC_COMM_SELF, "Point %d not in overlap SF\n", p);}
1192:       }
1193:       if (!valid) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid global to local map");
1194:     }
1195: #endif
1196:     PetscOptionsHasName(((PetscObject) dm)->prefix, "-parents_view", &flg);
1197:     if (flg) {
1198:       PetscPrintf(comm, "Serial Parent Section: \n");
1199:       PetscSectionView(origParentSection, PETSC_VIEWER_STDOUT_WORLD);
1200:       PetscPrintf(comm, "Parallel Parent Section: \n");
1201:       PetscSectionView(newParentSection, PETSC_VIEWER_STDOUT_WORLD);
1202:       PetscSFView(parentSF, NULL);
1203:     }
1204:     DMPlexSetTree(dmParallel,newParentSection,newParents,newChildIDs);
1205:     PetscSectionDestroy(&newParentSection);
1206:     PetscFree2(newParents,newChildIDs);
1207:     PetscSFDestroy(&parentSF);
1208:   }
1209:   pmesh->useAnchors = mesh->useAnchors;
1210:   return(0);
1211: }

1215: PetscErrorCode DMPlexDistributeSF(DM dm, PetscSF migrationSF, DM dmParallel)
1216: {
1217:   DM_Plex               *mesh  = (DM_Plex*) dm->data;
1218:   DM_Plex               *pmesh = (DM_Plex*) (dmParallel)->data;
1219:   PetscMPIInt            rank, numProcs;
1220:   MPI_Comm               comm;
1221:   PetscErrorCode         ierr;


1227:   /* Create point SF for parallel mesh */
1228:   PetscLogEventBegin(DMPLEX_DistributeSF,dm,0,0,0);
1229:   PetscObjectGetComm((PetscObject)dm, &comm);
1230:   MPI_Comm_rank(comm, &rank);
1231:   MPI_Comm_size(comm, &numProcs);
1232:   {
1233:     const PetscInt *leaves;
1234:     PetscSFNode    *remotePoints, *rowners, *lowners;
1235:     PetscInt        numRoots, numLeaves, numGhostPoints = 0, p, gp, *ghostPoints;
1236:     PetscInt        pStart, pEnd;

1238:     DMPlexGetChart(dmParallel, &pStart, &pEnd);
1239:     PetscSFGetGraph(migrationSF, &numRoots, &numLeaves, &leaves, NULL);
1240:     PetscMalloc2(numRoots,&rowners,numLeaves,&lowners);
1241:     for (p=0; p<numRoots; p++) {
1242:       rowners[p].rank  = -1;
1243:       rowners[p].index = -1;
1244:     }
1245:     PetscSFBcastBegin(migrationSF, MPIU_2INT, rowners, lowners);
1246:     PetscSFBcastEnd(migrationSF, MPIU_2INT, rowners, lowners);
1247:     for (p = 0; p < numLeaves; ++p) {
1248:       if (lowners[p].rank < 0 || lowners[p].rank == rank) { /* Either put in a bid or we know we own it */
1249:         lowners[p].rank  = rank;
1250:         lowners[p].index = leaves ? leaves[p] : p;
1251:       } else if (lowners[p].rank >= 0) { /* Point already claimed so flag so that MAXLOC does not listen to us */
1252:         lowners[p].rank  = -2;
1253:         lowners[p].index = -2;
1254:       }
1255:     }
1256:     for (p=0; p<numRoots; p++) { /* Root must not participate in the rediction, flag so that MAXLOC does not use */
1257:       rowners[p].rank  = -3;
1258:       rowners[p].index = -3;
1259:     }
1260:     PetscSFReduceBegin(migrationSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);
1261:     PetscSFReduceEnd(migrationSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);
1262:     PetscSFBcastBegin(migrationSF, MPIU_2INT, rowners, lowners);
1263:     PetscSFBcastEnd(migrationSF, MPIU_2INT, rowners, lowners);
1264:     for (p = 0; p < numLeaves; ++p) {
1265:       if (lowners[p].rank < 0 || lowners[p].index < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Cell partition corrupt: point not claimed");
1266:       if (lowners[p].rank != rank) ++numGhostPoints;
1267:     }
1268:     PetscMalloc1(numGhostPoints, &ghostPoints);
1269:     PetscMalloc1(numGhostPoints, &remotePoints);
1270:     for (p = 0, gp = 0; p < numLeaves; ++p) {
1271:       if (lowners[p].rank != rank) {
1272:         ghostPoints[gp]        = leaves ? leaves[p] : p;
1273:         remotePoints[gp].rank  = lowners[p].rank;
1274:         remotePoints[gp].index = lowners[p].index;
1275:         ++gp;
1276:       }
1277:     }
1278:     PetscFree2(rowners,lowners);
1279:     PetscSFSetGraph((dmParallel)->sf, pEnd - pStart, numGhostPoints, ghostPoints, PETSC_OWN_POINTER, remotePoints, PETSC_OWN_POINTER);
1280:     PetscSFSetFromOptions((dmParallel)->sf);
1281:   }
1282:   pmesh->useCone    = mesh->useCone;
1283:   pmesh->useClosure = mesh->useClosure;
1284:   PetscLogEventEnd(DMPLEX_DistributeSF,dm,0,0,0);
1285:   return(0);
1286: }

1290: /*@C
1291:   DMPlexDerivePointSF - Build a point SF from an SF describing a point migration

1293:   Input Parameter:
1294: + dm          - The source DMPlex object
1295: . migrationSF - The star forest that describes the parallel point remapping
1296: . ownership   - Flag causing a vote to determine point ownership

1298:   Output Parameter:
1299: - pointSF     - The star forest describing the point overlap in the remapped DM

1301:   Level: developer

1303: .seealso: DMPlexDistribute(), DMPlexDistributeOverlap()
1304: @*/
1305: PetscErrorCode DMPlexCreatePointSF(DM dm, PetscSF migrationSF, PetscBool ownership, PetscSF *pointSF)
1306: {
1307:   PetscMPIInt        rank;
1308:   PetscInt           p, nroots, nleaves, idx, npointLeaves;
1309:   PetscInt          *pointLocal;
1310:   const PetscInt    *leaves;
1311:   const PetscSFNode *roots;
1312:   PetscSFNode       *rootNodes, *leafNodes, *pointRemote;
1313:   PetscErrorCode     ierr;

1317:   MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);

1319:   PetscSFGetGraph(migrationSF, &nroots, &nleaves, &leaves, &roots);
1320:   PetscMalloc2(nroots, &rootNodes, nleaves, &leafNodes);
1321:   if (ownership) {
1322:     /* Point ownership vote: Process with highest rank ownes shared points */
1323:     for (p = 0; p < nleaves; ++p) {
1324:       /* Either put in a bid or we know we own it */
1325:       leafNodes[p].rank  = rank;
1326:       leafNodes[p].index = p;
1327:     }
1328:     for (p = 0; p < nroots; p++) {
1329:       /* Root must not participate in the reduction, flag so that MAXLOC does not use */
1330:       rootNodes[p].rank  = -3;
1331:       rootNodes[p].index = -3;
1332:     }
1333:     PetscSFReduceBegin(migrationSF, MPIU_2INT, leafNodes, rootNodes, MPI_MAXLOC);
1334:     PetscSFReduceEnd(migrationSF, MPIU_2INT, leafNodes, rootNodes, MPI_MAXLOC);
1335:   } else {
1336:     for (p = 0; p < nroots; p++) {
1337:       rootNodes[p].index = -1;
1338:       rootNodes[p].rank = rank;
1339:     };
1340:     for (p = 0; p < nleaves; p++) {
1341:       /* Write new local id into old location */
1342:       if (roots[p].rank == rank) {
1343:         rootNodes[roots[p].index].index = leaves[p];
1344:       }
1345:     }
1346:   }
1347:   PetscSFBcastBegin(migrationSF, MPIU_2INT, rootNodes, leafNodes);
1348:   PetscSFBcastEnd(migrationSF, MPIU_2INT, rootNodes, leafNodes);

1350:   for (npointLeaves = 0, p = 0; p < nleaves; p++) {if (leafNodes[p].rank != rank) npointLeaves++;}
1351:   PetscMalloc1(npointLeaves, &pointLocal);
1352:   PetscMalloc1(npointLeaves, &pointRemote);
1353:   for (idx = 0, p = 0; p < nleaves; p++) {
1354:     if (leafNodes[p].rank != rank) {
1355:       pointLocal[idx] = p;
1356:       pointRemote[idx] = leafNodes[p];
1357:       idx++;
1358:     }
1359:   }
1360:   PetscSFCreate(PetscObjectComm((PetscObject) dm), pointSF);
1361:   PetscSFSetFromOptions(*pointSF);
1362:   PetscSFSetGraph(*pointSF, nleaves, npointLeaves, pointLocal, PETSC_OWN_POINTER, pointRemote, PETSC_OWN_POINTER);
1363:   PetscFree2(rootNodes, leafNodes);
1364:   return(0);
1365: }

1369: /*@C
1370:   DMPlexMigrate  - Migrates internal DM data over the supplied star forest

1372:   Input Parameter:
1373: + dm       - The source DMPlex object
1374: . sf       - The star forest communication context describing the migration pattern

1376:   Output Parameter:
1377: - targetDM - The target DMPlex object

1379:   Level: intermediate

1381: .seealso: DMPlexDistribute(), DMPlexDistributeOverlap()
1382: @*/
1383: PetscErrorCode DMPlexMigrate(DM dm, PetscSF sf, DM targetDM)
1384: {
1385:   MPI_Comm               comm;
1386:   PetscInt               dim, nroots;
1387:   PetscSF                sfPoint;
1388:   ISLocalToGlobalMapping ltogMigration;
1389:   PetscBool              flg;
1390:   PetscErrorCode         ierr;

1394:   PetscLogEventBegin(DMPLEX_Migrate, dm, 0, 0, 0);
1395:   PetscObjectGetComm((PetscObject) dm, &comm);
1396:   DMGetDimension(dm, &dim);
1397:   DMSetDimension(targetDM, dim);

1399:   /* Check for a one-to-all distribution pattern */
1400:   DMGetPointSF(dm, &sfPoint);
1401:   PetscSFGetGraph(sfPoint, &nroots, NULL, NULL, NULL);
1402:   if (nroots >= 0) {
1403:     IS                     isOriginal;
1404:     ISLocalToGlobalMapping ltogOriginal;
1405:     PetscInt               n, size, nleaves, conesSize;
1406:     PetscInt              *numbering_orig, *numbering_new, *cones;
1407:     PetscSection           coneSection;
1408:     /* Get the original point numbering */
1409:     DMPlexCreatePointNumbering(dm, &isOriginal);
1410:     ISLocalToGlobalMappingCreateIS(isOriginal, &ltogOriginal);
1411:     ISLocalToGlobalMappingGetSize(ltogOriginal, &size);
1412:     ISLocalToGlobalMappingGetBlockIndices(ltogOriginal, (const PetscInt**)&numbering_orig);
1413:     /* Convert to positive global numbers */
1414:     for (n=0; n<size; n++) {if (numbering_orig[n] < 0) numbering_orig[n] = -(numbering_orig[n]+1);}
1415:     /* Derive the new local-to-global mapping from the old one */
1416:     PetscSFGetGraph(sf, NULL, &nleaves, NULL, NULL);
1417:     PetscMalloc1(nleaves, &numbering_new);
1418:     PetscSFBcastBegin(sf, MPIU_INT, (PetscInt *) numbering_orig, numbering_new);
1419:     PetscSFBcastEnd(sf, MPIU_INT, (PetscInt *) numbering_orig, numbering_new);
1420:     ISLocalToGlobalMappingCreate(comm, 1, nleaves, (const PetscInt*) numbering_new, PETSC_OWN_POINTER, &ltogMigration);
1421:     ISLocalToGlobalMappingRestoreIndices(ltogOriginal, (const PetscInt**)&numbering_orig);
1422:     /* Convert cones to global numbering before migrating them */
1423:     DMPlexGetConeSection(dm, &coneSection);
1424:     PetscSectionGetStorageSize(coneSection, &conesSize);
1425:     DMPlexGetCones(dm, &cones);
1426:     ISLocalToGlobalMappingApplyBlock(ltogOriginal, conesSize, cones, cones);
1427:     ISDestroy(&isOriginal);
1428:     ISLocalToGlobalMappingDestroy(&ltogOriginal);
1429:   } else {
1430:     /* One-to-all distribution pattern: We can derive LToG from SF */
1431:     ISLocalToGlobalMappingCreateSF(sf, 0, &ltogMigration);
1432:   }
1433:   PetscOptionsHasName(((PetscObject) dm)->prefix, "-partition_view", &flg);
1434:   if (flg) {
1435:     PetscPrintf(comm, "Point renumbering for DM migration:\n");
1436:     ISLocalToGlobalMappingView(ltogMigration, NULL);
1437:   }
1438:   /* Migrate DM data to target DM */
1439:   DMPlexDistributeCones(dm, sf, ltogMigration, targetDM);
1440:   DMPlexDistributeCoordinates(dm, sf, targetDM);
1441:   DMPlexDistributeLabels(dm, sf, targetDM);
1442:   DMPlexDistributeSetupHybrid(dm, sf, ltogMigration, targetDM);
1443:   DMPlexDistributeSetupTree(dm, sf, ltogMigration, targetDM);
1444:   ISLocalToGlobalMappingDestroy(&ltogMigration);
1445:   PetscLogEventEnd(DMPLEX_Migrate, dm, 0, 0, 0);
1446:   return(0);
1447: }

1451: /*@C
1452:   DMPlexDistribute - Distributes the mesh and any associated sections.

1454:   Not Collective

1456:   Input Parameter:
1457: + dm  - The original DMPlex object
1458: - overlap - The overlap of partitions, 0 is the default

1460:   Output Parameter:
1461: + sf - The PetscSF used for point distribution
1462: - parallelMesh - The distributed DMPlex object, or NULL

1464:   Note: If the mesh was not distributed, the return value is NULL.

1466:   The user can control the definition of adjacency for the mesh using DMPlexGetAdjacencyUseCone() and
1467:   DMPlexSetAdjacencyUseClosure(). They should choose the combination appropriate for the function
1468:   representation on the mesh.

1470:   Level: intermediate

1472: .keywords: mesh, elements
1473: .seealso: DMPlexCreate(), DMPlexDistributeByFace(), DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure()
1474: @*/
1475: PetscErrorCode DMPlexDistribute(DM dm, PetscInt overlap, PetscSF *sf, DM *dmParallel)
1476: {
1477:   MPI_Comm               comm;
1478:   PetscPartitioner       partitioner;
1479:   IS                     cellPart;
1480:   PetscSection           cellPartSection;
1481:   DM                     dmCoord;
1482:   DMLabel                lblPartition, lblMigration;
1483:   PetscSF                sfProcess, sfMigration, sfStratified, sfPoint;
1484:   PetscBool              flg;
1485:   PetscMPIInt            rank, numProcs, p;
1486:   PetscErrorCode         ierr;


1493:   PetscLogEventBegin(DMPLEX_Distribute,dm,0,0,0);
1494:   PetscObjectGetComm((PetscObject)dm,&comm);
1495:   MPI_Comm_rank(comm, &rank);
1496:   MPI_Comm_size(comm, &numProcs);

1498:   *dmParallel = NULL;
1499:   if (numProcs == 1) return(0);

1501:   /* Create cell partition */
1502:   PetscLogEventBegin(PETSCPARTITIONER_Partition,dm,0,0,0);
1503:   PetscSectionCreate(comm, &cellPartSection);
1504:   DMPlexGetPartitioner(dm, &partitioner);
1505:   PetscPartitionerPartition(partitioner, dm, cellPartSection, &cellPart);
1506:   {
1507:     /* Convert partition to DMLabel */
1508:     PetscInt proc, pStart, pEnd, npoints, poffset;
1509:     const PetscInt *points;
1510:     DMLabelCreate("Point Partition", &lblPartition);
1511:     ISGetIndices(cellPart, &points);
1512:     PetscSectionGetChart(cellPartSection, &pStart, &pEnd);
1513:     for (proc = pStart; proc < pEnd; proc++) {
1514:       PetscSectionGetDof(cellPartSection, proc, &npoints);
1515:       PetscSectionGetOffset(cellPartSection, proc, &poffset);
1516:       for (p = poffset; p < poffset+npoints; p++) {
1517:         DMLabelSetValue(lblPartition, points[p], proc);
1518:       }
1519:     }
1520:     ISRestoreIndices(cellPart, &points);
1521:   }
1522:   DMPlexPartitionLabelClosure(dm, lblPartition);
1523:   {
1524:     /* Build a global process SF */
1525:     PetscSFNode *remoteProc;
1526:     PetscMalloc1(numProcs, &remoteProc);
1527:     for (p = 0; p < numProcs; ++p) {
1528:       remoteProc[p].rank  = p;
1529:       remoteProc[p].index = rank;
1530:     }
1531:     PetscSFCreate(comm, &sfProcess);
1532:     PetscObjectSetName((PetscObject) sfProcess, "Process SF");
1533:     PetscSFSetGraph(sfProcess, numProcs, numProcs, NULL, PETSC_OWN_POINTER, remoteProc, PETSC_OWN_POINTER);
1534:   }
1535:   DMLabelCreate("Point migration", &lblMigration);
1536:   DMPlexPartitionLabelInvert(dm, lblPartition, sfProcess, lblMigration);
1537:   DMPlexPartitionLabelCreateSF(dm, lblMigration, &sfMigration);
1538:   /* Stratify the SF in case we are migrating an already parallel plex */
1539:   DMPlexStratifyMigrationSF(dm, sfMigration, &sfStratified);
1540:   PetscSFDestroy(&sfMigration);
1541:   sfMigration = sfStratified;
1542:   PetscLogEventEnd(PETSCPARTITIONER_Partition,dm,0,0,0);
1543:   PetscOptionsHasName(((PetscObject) dm)->prefix, "-partition_view", &flg);
1544:   if (flg) {
1545:     PetscViewerASCIISynchronizedAllow(PETSC_VIEWER_STDOUT_WORLD, PETSC_TRUE);
1546:     DMLabelView(lblPartition, PETSC_VIEWER_STDOUT_WORLD);
1547:     PetscSFView(sfMigration, PETSC_VIEWER_STDOUT_WORLD);
1548:   }

1550:   /* Create non-overlapping parallel DM and migrate internal data */
1551:   DMPlexCreate(comm, dmParallel);
1552:   PetscObjectSetName((PetscObject) *dmParallel, "Parallel Mesh");
1553:   DMPlexMigrate(dm, sfMigration, *dmParallel);

1555:   /* Build the point SF without overlap */
1556:   DMPlexCreatePointSF(*dmParallel, sfMigration, PETSC_TRUE, &sfPoint);
1557:   DMSetPointSF(*dmParallel, sfPoint);
1558:   DMGetCoordinateDM(*dmParallel, &dmCoord);
1559:   if (dmCoord) {DMSetPointSF(dmCoord, sfPoint);}
1560:   if (flg) {PetscSFView(sfPoint, PETSC_VIEWER_STDOUT_WORLD);}

1562:   if (overlap > 0) {
1563:     DM                 dmOverlap;
1564:     PetscInt           nroots, nleaves;
1565:     PetscSFNode       *newRemote;
1566:     const PetscSFNode *oldRemote;
1567:     PetscSF            sfOverlap, sfOverlapPoint;
1568:     /* Add the partition overlap to the distributed DM */
1569:     DMPlexDistributeOverlap(*dmParallel, overlap, &sfOverlap, &dmOverlap);
1570:     DMDestroy(dmParallel);
1571:     *dmParallel = dmOverlap;
1572:     if (flg) {
1573:       PetscPrintf(comm, "Overlap Migration SF:\n");
1574:       PetscSFView(sfOverlap, NULL);
1575:     }

1577:     /* Re-map the migration SF to establish the full migration pattern */
1578:     PetscSFGetGraph(sfMigration, &nroots, NULL, NULL, &oldRemote);
1579:     PetscSFGetGraph(sfOverlap, NULL, &nleaves, NULL, NULL);
1580:     PetscMalloc1(nleaves, &newRemote);
1581:     PetscSFBcastBegin(sfOverlap, MPIU_2INT, oldRemote, newRemote);
1582:     PetscSFBcastEnd(sfOverlap, MPIU_2INT, oldRemote, newRemote);
1583:     PetscSFCreate(comm, &sfOverlapPoint);
1584:     PetscSFSetGraph(sfOverlapPoint, nroots, nleaves, NULL, PETSC_OWN_POINTER, newRemote, PETSC_OWN_POINTER);
1585:     PetscSFDestroy(&sfOverlap);
1586:     PetscSFDestroy(&sfMigration);
1587:     sfMigration = sfOverlapPoint;
1588:   }
1589:   /* Cleanup Partition */
1590:   PetscSFDestroy(&sfProcess);
1591:   DMLabelDestroy(&lblPartition);
1592:   DMLabelDestroy(&lblMigration);
1593:   PetscSectionDestroy(&cellPartSection);
1594:   ISDestroy(&cellPart);
1595:   /* Copy BC */
1596:   DMPlexCopyBoundary(dm, *dmParallel);
1597:   /* Cleanup */
1598:   if (sf) {*sf = sfMigration;}
1599:   else    {PetscSFDestroy(&sfMigration);}
1600:   PetscSFDestroy(&sfPoint);
1601:   PetscLogEventEnd(DMPLEX_Distribute,dm,0,0,0);
1602:   return(0);
1603: }

1607: /*@C
1608:   DMPlexDistribute - Add partition overlap to a distributed non-overlapping DM.

1610:   Not Collective

1612:   Input Parameter:
1613: + dm  - The non-overlapping distrbuted DMPlex object
1614: - overlap - The overlap of partitions, 0 is the default

1616:   Output Parameter:
1617: + sf - The PetscSF used for point distribution
1618: - dmOverlap - The overlapping distributed DMPlex object, or NULL

1620:   Note: If the mesh was not distributed, the return value is NULL.

1622:   The user can control the definition of adjacency for the mesh using DMPlexGetAdjacencyUseCone() and
1623:   DMPlexSetAdjacencyUseClosure(). They should choose the combination appropriate for the function
1624:   representation on the mesh.

1626:   Level: intermediate

1628: .keywords: mesh, elements
1629: .seealso: DMPlexCreate(), DMPlexDistributeByFace(), DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure()
1630: @*/
1631: PetscErrorCode DMPlexDistributeOverlap(DM dm, PetscInt overlap, PetscSF *sf, DM *dmOverlap)
1632: {
1633:   MPI_Comm               comm;
1634:   PetscMPIInt            rank;
1635:   PetscSection           rootSection, leafSection;
1636:   IS                     rootrank, leafrank;
1637:   DM                     dmCoord;
1638:   DMLabel                lblOverlap;
1639:   PetscSF                sfOverlap, sfStratified, sfPoint;
1640:   PetscErrorCode         ierr;


1647:   PetscLogEventBegin(DMPLEX_DistributeOverlap, dm, 0, 0, 0);
1648:   PetscObjectGetComm((PetscObject)dm,&comm);
1649:   MPI_Comm_rank(comm, &rank);

1651:   /* Compute point overlap with neighbouring processes on the distributed DM */
1652:   PetscLogEventBegin(PETSCPARTITIONER_Partition,dm,0,0,0);
1653:   PetscSectionCreate(comm, &rootSection);
1654:   PetscSectionCreate(comm, &leafSection);
1655:   DMPlexDistributeOwnership(dm, rootSection, &rootrank, leafSection, &leafrank);
1656:   DMPlexCreateOverlap(dm, overlap, rootSection, rootrank, leafSection, leafrank, &lblOverlap);
1657:   /* Convert overlap label to stratified migration SF */
1658:   DMPlexPartitionLabelCreateSF(dm, lblOverlap, &sfOverlap);
1659:   DMPlexStratifyMigrationSF(dm, sfOverlap, &sfStratified);
1660:   PetscSFDestroy(&sfOverlap);
1661:   sfOverlap = sfStratified;
1662:   PetscObjectSetName((PetscObject) sfOverlap, "Overlap SF");
1663:   PetscSFSetFromOptions(sfOverlap);

1665:   PetscSectionDestroy(&rootSection);
1666:   PetscSectionDestroy(&leafSection);
1667:   ISDestroy(&rootrank);
1668:   ISDestroy(&leafrank);
1669:   PetscLogEventEnd(PETSCPARTITIONER_Partition,dm,0,0,0);

1671:   /* Build the overlapping DM */
1672:   DMPlexCreate(comm, dmOverlap);
1673:   PetscObjectSetName((PetscObject) *dmOverlap, "Parallel Mesh");
1674:   DMPlexMigrate(dm, sfOverlap, *dmOverlap);
1675:   /* Build the new point SF */
1676:   DMPlexCreatePointSF(*dmOverlap, sfOverlap, PETSC_FALSE, &sfPoint);
1677:   DMSetPointSF(*dmOverlap, sfPoint);
1678:   DMGetCoordinateDM(*dmOverlap, &dmCoord);
1679:   if (dmCoord) {DMSetPointSF(dmCoord, sfPoint);}
1680:   PetscSFDestroy(&sfPoint);
1681:   /* Cleanup overlap partition */
1682:   DMLabelDestroy(&lblOverlap);
1683:   if (sf) *sf = sfOverlap;
1684:   else    {PetscSFDestroy(&sfOverlap);}
1685:   PetscLogEventEnd(DMPLEX_DistributeOverlap, dm, 0, 0, 0);
1686:   return(0);
1687: }