Actual source code: plexdistribute.c

petsc-3.7.4 2016-10-02
Report Typos and Errors
  1: #include <petsc/private/dmpleximpl.h>    /*I      "petscdmplex.h"   I*/
  2: #include <petsc/private/dmlabelimpl.h>   /*I      "petscdmlabel.h"  I*/

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

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

 13:   Level: intermediate

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

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

 28:   mesh->useCone = useCone;
 29:   return(0);
 30: }

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

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

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

 43:   Level: intermediate

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

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

 59:   *useCone = mesh->useCone;
 60:   return(0);
 61: }

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

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

 72:   Level: intermediate

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

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

 87:   mesh->useClosure = useClosure;
 88:   return(0);
 89: }

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

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

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

102:   Level: intermediate

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

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

118:   *useClosure = mesh->useClosure;
119:   return(0);
120: }

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

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

131:   Level: intermediate

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

141:   mesh->useAnchors = useAnchors;
142:   return(0);
143: }

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

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

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

156:   Level: intermediate

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

167:   *useAnchors = mesh->useAnchors;
168:   return(0);
169: }

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

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

187:     DMPlexGetSupportSize(dm, point, &supportSize);
188:     DMPlexGetSupport(dm, point, &support);
189:     for (s = 0; s < supportSize; ++s) {
190:       for (q = 0; q < numAdj || (adj[numAdj++] = support[s],0); ++q) {
191:         if (support[s] == adj[q]) break;
192:       }
193:       if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize);
194:     }
195:   }
196:   *adjSize = numAdj;
197:   return(0);
198: }

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

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

216:     DMPlexGetConeSize(dm, point, &coneSize);
217:     DMPlexGetCone(dm, point, &cone);
218:     for (c = 0; c < coneSize; ++c) {
219:       for (q = 0; q < numAdj || (adj[numAdj++] = cone[c],0); ++q) {
220:         if (cone[c] == adj[q]) break;
221:       }
222:       if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize);
223:     }
224:   }
225:   *adjSize = numAdj;
226:   return(0);
227: }

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

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

243:     DMPlexGetTransitiveClosure(dm, star[s], (PetscBool)!useClosure, &closureSize, (PetscInt**) &closure);
244:     for (c = 0; c < closureSize*2; c += 2) {
245:       for (q = 0; q < numAdj || (adj[numAdj++] = closure[c],0); ++q) {
246:         if (closure[c] == adj[q]) break;
247:       }
248:       if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize);
249:     }
250:     DMPlexRestoreTransitiveClosure(dm, star[s], (PetscBool)!useClosure, &closureSize, (PetscInt**) &closure);
251:   }
252:   DMPlexRestoreTransitiveClosure(dm, p, useClosure, &starSize, &star);
253:   *adjSize = numAdj;
254:   return(0);
255: }

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

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

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

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

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

319:         for (j = i + 1; j < numAdj; j++) {
320:           orig[j - 1] = orig[j];
321:         }
322:         origSize--;
323:         numAdj--;
324:         PetscSectionGetOffset(aSec,p,&aOff);
325:         for (s = 0; s < aDof; ++s) {
326:           for (q = 0; q < numAdj || (orig[numAdj++] = anchors[aOff+s],0); ++q) {
327:             if (anchors[aOff+s] == orig[q]) break;
328:           }
329:           if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize);
330:         }
331:       }
332:       else {
333:         i++;
334:       }
335:     }
336:     *adjSize = numAdj;
337:     ISRestoreIndices(aIS,&anchors);
338:   }
339:   return(0);
340: }

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

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

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

357:   Level: advanced

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

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

372:   DMPlexGetAdjacency_Internal(dm, p, mesh->useCone, mesh->useClosure, mesh->useAnchors, adjSize, adj);
373:   return(0);
374: }

378: /*@
379:   DMPlexCreateTwoSidedProcessSF - Create an SF which just has process connectivity

381:   Collective on DM

383:   Input Parameters:
384: + dm      - The DM
385: - sfPoint - The PetscSF which encodes point connectivity

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

391:   Level: developer

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

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

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

434:     PetscSectionGetDof(leafRankSection, p, &ndof);
435:     PetscSectionGetOffset(leafRankSection, p, &noff);
436:     for (n = 0; n < ndof; ++n) {PetscBTSet(neighbors, nranks[noff+n]);}
437:   }
438:   ISRestoreIndices(leafRanks, &nranks);
439:   /* Compute leaf-to-root process connectivity */
440:   for (l = 0; l < numLeaves; ++l) {PetscBTSet(neighbors, remotePoints[l].rank);}
441:   /* Calculate edges */
442:   PetscBTClear(neighbors, rank);
443:   for(proc = 0, numNeighbors = 0; proc < numProcs; ++proc) {if (PetscBTLookup(neighbors, proc)) ++numNeighbors;}
444:   PetscMalloc1(numNeighbors, &ranksNew);
445:   PetscMalloc1(numNeighbors, &localPointsNew);
446:   PetscMalloc1(numNeighbors, &remotePointsNew);
447:   for(proc = 0, n = 0; proc < numProcs; ++proc) {
448:     if (PetscBTLookup(neighbors, proc)) {
449:       ranksNew[n]              = proc;
450:       localPointsNew[n]        = proc;
451:       remotePointsNew[n].index = rank;
452:       remotePointsNew[n].rank  = proc;
453:       ++n;
454:     }
455:   }
456:   PetscBTDestroy(&neighbors);
457:   if (processRanks) {ISCreateGeneral(PetscObjectComm((PetscObject)dm), numNeighbors, ranksNew, PETSC_OWN_POINTER, processRanks);}
458:   else              {PetscFree(ranksNew);}
459:   if (sfProcess) {
460:     PetscSFCreate(PetscObjectComm((PetscObject)dm), sfProcess);
461:     PetscObjectSetName((PetscObject) *sfProcess, "Two-Sided Process SF");
462:     PetscSFSetFromOptions(*sfProcess);
463:     PetscSFSetGraph(*sfProcess, numProcs, numNeighbors, localPointsNew, PETSC_OWN_POINTER, remotePointsNew, PETSC_OWN_POINTER);
464:   }
465:   return(0);
466: }

470: /*@
471:   DMPlexDistributeOwnership - Compute owner information for shared points. This basically gets two-sided for an SF.

473:   Collective on DM

475:   Input Parameter:
476: . dm - The DM

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

484:   Level: developer

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

499:   PetscObjectGetComm((PetscObject) dm, &comm);
500:   MPI_Comm_rank(comm, &rank);
501:   DMPlexGetChart(dm, &pStart, &pEnd);
502:   DMGetPointSF(dm, &sfPoint);
503:   /* Compute number of leaves for each root */
504:   PetscObjectSetName((PetscObject) rootSection, "Root Section");
505:   PetscSectionSetChart(rootSection, pStart, pEnd);
506:   PetscSFComputeDegreeBegin(sfPoint, &rootdegree);
507:   PetscSFComputeDegreeEnd(sfPoint, &rootdegree);
508:   for (p = pStart; p < pEnd; ++p) {PetscSectionSetDof(rootSection, p, rootdegree[p-pStart]);}
509:   PetscSectionSetUp(rootSection);
510:   /* Gather rank of each leaf to root */
511:   PetscSectionGetStorageSize(rootSection, &nedges);
512:   PetscMalloc1(pEnd-pStart, &myrank);
513:   PetscMalloc1(nedges,  &remoterank);
514:   for (p = 0; p < pEnd-pStart; ++p) myrank[p] = rank;
515:   PetscSFGatherBegin(sfPoint, MPIU_INT, myrank, remoterank);
516:   PetscSFGatherEnd(sfPoint, MPIU_INT, myrank, remoterank);
517:   PetscFree(myrank);
518:   ISCreateGeneral(comm, nedges, remoterank, PETSC_OWN_POINTER, rootrank);
519:   /* Distribute remote ranks to leaves */
520:   PetscObjectSetName((PetscObject) leafSection, "Leaf Section");
521:   DMPlexDistributeFieldIS(dm, sfPoint, rootSection, *rootrank, leafSection, leafrank);
522:   return(0);
523: }

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

530:   Collective on DM

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

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

543:   Level: developer

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

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

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

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

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

605:       if (remoteRank == rank) continue;
606:       for (a = 0; a < adjSize; ++a) {DMLabelSetValue(ovAdjByRank, adj[a], remoteRank);}
607:     }
608:   }
609:   PetscFree(adj);
610:   ISRestoreIndices(rootrank, &rrank);
611:   ISRestoreIndices(leafrank, &nrank);
612:   /* Add additional overlap levels */
613:   for (l = 1; l < levels; l++) {
614:     /* Propagate point donations over SF to capture remote connections */
615:     DMPlexPartitionLabelPropagate(dm, ovAdjByRank);
616:     /* Add next level of point donations to the label */
617:     DMPlexPartitionLabelAdjacency(dm, ovAdjByRank);
618:   }
619:   /* We require the closure in the overlap */
620:   DMPlexGetAdjacencyUseCone(dm, &useCone);
621:   DMPlexGetAdjacencyUseClosure(dm, &useClosure);
622:   if (useCone || !useClosure) {
623:     DMPlexPartitionLabelClosure(dm, ovAdjByRank);
624:   }
625:   PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-overlap_view", &flg);
626:   if (flg) {
627:     DMLabelView(ovAdjByRank, PETSC_VIEWER_STDOUT_WORLD);
628:   }
629:   /* Make global process SF and invert sender to receiver label */
630:   {
631:     /* Build a global process SF */
632:     PetscSFNode *remoteProc;
633:     PetscMalloc1(numProcs, &remoteProc);
634:     for (p = 0; p < numProcs; ++p) {
635:       remoteProc[p].rank  = p;
636:       remoteProc[p].index = rank;
637:     }
638:     PetscSFCreate(comm, &sfProc);
639:     PetscObjectSetName((PetscObject) sfProc, "Process SF");
640:     PetscSFSetGraph(sfProc, numProcs, numProcs, NULL, PETSC_OWN_POINTER, remoteProc, PETSC_OWN_POINTER);
641:   }
642:   DMLabelCreate("Overlap label", ovLabel);
643:   DMPlexPartitionLabelInvert(dm, ovAdjByRank, sfProc, *ovLabel);
644:   /* Add owned points, except for shared local points */
645:   for (p = pStart; p < pEnd; ++p) {DMLabelSetValue(*ovLabel, p, rank);}
646:   for (l = 0; l < nleaves; ++l) {
647:     DMLabelClearValue(*ovLabel, local[l], rank);
648:     DMLabelSetValue(*ovLabel, remote[l].index, remote[l].rank);
649:   }
650:   /* Clean up */
651:   DMLabelDestroy(&ovAdjByRank);
652:   PetscSFDestroy(&sfProc);
653:   return(0);
654: }

658: PetscErrorCode DMPlexCreateOverlapMigrationSF(DM dm, PetscSF overlapSF, PetscSF *migrationSF)
659: {
660:   MPI_Comm           comm;
661:   PetscMPIInt        rank, numProcs;
662:   PetscInt           d, dim, p, pStart, pEnd, nroots, nleaves, newLeaves, point, numSharedPoints;
663:   PetscInt          *pointDepths, *remoteDepths, *ilocal;
664:   PetscInt          *depthRecv, *depthShift, *depthIdx;
665:   PetscSFNode       *iremote;
666:   PetscSF            pointSF;
667:   const PetscInt    *sharedLocal;
668:   const PetscSFNode *overlapRemote, *sharedRemote;
669:   PetscErrorCode     ierr;

673:   PetscObjectGetComm((PetscObject)dm, &comm);
674:   MPI_Comm_rank(comm, &rank);
675:   MPI_Comm_size(comm, &numProcs);
676:   DMGetDimension(dm, &dim);

678:   /* Before building the migration SF we need to know the new stratum offsets */
679:   PetscSFGetGraph(overlapSF, &nroots, &nleaves, NULL, &overlapRemote);
680:   PetscMalloc2(nroots, &pointDepths, nleaves, &remoteDepths);
681:   for (d=0; d<dim+1; d++) {
682:     DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
683:     for (p=pStart; p<pEnd; p++) pointDepths[p] = d;
684:   }
685:   for (p=0; p<nleaves; p++) remoteDepths[p] = -1;
686:   PetscSFBcastBegin(overlapSF, MPIU_INT, pointDepths, remoteDepths);
687:   PetscSFBcastEnd(overlapSF, MPIU_INT, pointDepths, remoteDepths);

689:   /* Count recevied points in each stratum and compute the internal strata shift */
690:   PetscMalloc3(dim+1, &depthRecv, dim+1, &depthShift, dim+1, &depthIdx);
691:   for (d=0; d<dim+1; d++) depthRecv[d]=0;
692:   for (p=0; p<nleaves; p++) depthRecv[remoteDepths[p]]++;
693:   depthShift[dim] = 0;
694:   for (d=0; d<dim; d++) depthShift[d] = depthRecv[dim];
695:   for (d=1; d<dim; d++) depthShift[d] += depthRecv[0];
696:   for (d=dim-2; d>0; d--) depthShift[d] += depthRecv[d+1];
697:   for (d=0; d<dim+1; d++) {
698:     DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
699:     depthIdx[d] = pStart + depthShift[d];
700:   }

702:   /* Form the overlap SF build an SF that describes the full overlap migration SF */
703:   DMPlexGetChart(dm, &pStart, &pEnd);
704:   newLeaves = pEnd - pStart + nleaves;
705:   PetscMalloc1(newLeaves, &ilocal);
706:   PetscMalloc1(newLeaves, &iremote);
707:   /* First map local points to themselves */
708:   for (d=0; d<dim+1; d++) {
709:     DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
710:     for (p=pStart; p<pEnd; p++) {
711:       point = p + depthShift[d];
712:       ilocal[point] = point;
713:       iremote[point].index = p;
714:       iremote[point].rank = rank;
715:       depthIdx[d]++;
716:     }
717:   }

719:   /* Add in the remote roots for currently shared points */
720:   DMGetPointSF(dm, &pointSF);
721:   PetscSFGetGraph(pointSF, NULL, &numSharedPoints, &sharedLocal, &sharedRemote);
722:   for (d=0; d<dim+1; d++) {
723:     DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
724:     for (p=0; p<numSharedPoints; p++) {
725:       if (pStart <= sharedLocal[p] && sharedLocal[p] < pEnd) {
726:         point = sharedLocal[p] + depthShift[d];
727:         iremote[point].index = sharedRemote[p].index;
728:         iremote[point].rank = sharedRemote[p].rank;
729:       }
730:     }
731:   }

733:   /* Now add the incoming overlap points */
734:   for (p=0; p<nleaves; p++) {
735:     point = depthIdx[remoteDepths[p]];
736:     ilocal[point] = point;
737:     iremote[point].index = overlapRemote[p].index;
738:     iremote[point].rank = overlapRemote[p].rank;
739:     depthIdx[remoteDepths[p]]++;
740:   }
741:   PetscFree2(pointDepths,remoteDepths);

743:   PetscSFCreate(comm, migrationSF);
744:   PetscObjectSetName((PetscObject) *migrationSF, "Overlap Migration SF");
745:   PetscSFSetFromOptions(*migrationSF);
746:   DMPlexGetChart(dm, &pStart, &pEnd);
747:   PetscSFSetGraph(*migrationSF, pEnd-pStart, newLeaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER);

749:   PetscFree3(depthRecv, depthShift, depthIdx);
750:   return(0);
751: }

755: /*@
756:   DMPlexStratifyMigrationSF - Add partition overlap to a distributed non-overlapping DM.

758:   Input Parameter:
759: + dm          - The DM
760: - sf          - A star forest with non-ordered leaves, usually defining a DM point migration

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

765:   Level: developer

767: .seealso: DMPlexPartitionLabelCreateSF(), DMPlexDistribute(), DMPlexDistributeOverlap()
768: @*/
769: PetscErrorCode DMPlexStratifyMigrationSF(DM dm, PetscSF sf, PetscSF *migrationSF)
770: {
771:   MPI_Comm           comm;
772:   PetscMPIInt        rank, numProcs;
773:   PetscInt           d, ldepth, depth, p, pStart, pEnd, nroots, nleaves;
774:   PetscInt          *pointDepths, *remoteDepths, *ilocal;
775:   PetscInt          *depthRecv, *depthShift, *depthIdx;
776:   const PetscSFNode *iremote;
777:   PetscErrorCode     ierr;

781:   PetscObjectGetComm((PetscObject) dm, &comm);
782:   MPI_Comm_rank(comm, &rank);
783:   MPI_Comm_size(comm, &numProcs);
784:   DMPlexGetDepth(dm, &ldepth);
785:   MPIU_Allreduce(&ldepth, &depth, 1, MPIU_INT, MPI_MAX, comm);
786:   if ((ldepth >= 0) && (depth != ldepth)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Inconsistent Plex depth %d != %d", ldepth, depth);

788:   /* Before building the migration SF we need to know the new stratum offsets */
789:   PetscSFGetGraph(sf, &nroots, &nleaves, NULL, &iremote);
790:   PetscMalloc2(nroots, &pointDepths, nleaves, &remoteDepths);
791:   for (d = 0; d < depth+1; ++d) {
792:     DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);
793:     for (p = pStart; p < pEnd; ++p) pointDepths[p] = d;
794:   }
795:   for (p = 0; p < nleaves; ++p) remoteDepths[p] = -1;
796:   PetscSFBcastBegin(sf, MPIU_INT, pointDepths, remoteDepths);
797:   PetscSFBcastEnd(sf, MPIU_INT, pointDepths, remoteDepths);
798:   /* Count recevied points in each stratum and compute the internal strata shift */
799:   PetscMalloc3(depth+1, &depthRecv, depth+1, &depthShift, depth+1, &depthIdx);
800:   for (d = 0; d < depth+1; ++d) depthRecv[d] = 0;
801:   for (p = 0; p < nleaves; ++p) depthRecv[remoteDepths[p]]++;
802:   depthShift[depth] = 0;
803:   for (d = 0; d < depth; ++d) depthShift[d] = depthRecv[depth];
804:   for (d = 1; d < depth; ++d) depthShift[d] += depthRecv[0];
805:   for (d = depth-2; d > 0; --d) depthShift[d] += depthRecv[d+1];
806:   for (d = 0; d < depth+1; ++d) {depthIdx[d] = 0;}
807:   /* Derive a new local permutation based on stratified indices */
808:   PetscMalloc1(nleaves, &ilocal);
809:   for (p = 0; p < nleaves; ++p) {
810:     const PetscInt dep = remoteDepths[p];

812:     ilocal[p] = depthShift[dep] + depthIdx[dep];
813:     depthIdx[dep]++;
814:   }
815:   PetscSFCreate(comm, migrationSF);
816:   PetscObjectSetName((PetscObject) *migrationSF, "Migration SF");
817:   PetscSFSetGraph(*migrationSF, nroots, nleaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_COPY_VALUES);
818:   PetscFree2(pointDepths,remoteDepths);
819:   PetscFree3(depthRecv, depthShift, depthIdx);
820:   return(0);
821: }

825: /*@
826:   DMPlexDistributeField - Distribute field data to match a given PetscSF, usually the SF from mesh distribution

828:   Collective on DM

830:   Input Parameters:
831: + dm - The DMPlex object
832: . pointSF - The PetscSF describing the communication pattern
833: . originalSection - The PetscSection for existing data layout
834: - originalVec - The existing data

836:   Output Parameters:
837: + newSection - The PetscSF describing the new data layout
838: - newVec - The new data

840:   Level: developer

842: .seealso: DMPlexDistribute(), DMPlexDistributeFieldIS(), DMPlexDistributeData()
843: @*/
844: PetscErrorCode DMPlexDistributeField(DM dm, PetscSF pointSF, PetscSection originalSection, Vec originalVec, PetscSection newSection, Vec newVec)
845: {
846:   PetscSF        fieldSF;
847:   PetscInt      *remoteOffsets, fieldSize;
848:   PetscScalar   *originalValues, *newValues;

852:   PetscLogEventBegin(DMPLEX_DistributeField,dm,0,0,0);
853:   PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);

855:   PetscSectionGetStorageSize(newSection, &fieldSize);
856:   VecSetSizes(newVec, fieldSize, PETSC_DETERMINE);
857:   VecSetType(newVec,dm->vectype);

859:   VecGetArray(originalVec, &originalValues);
860:   VecGetArray(newVec, &newValues);
861:   PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);
862:   PetscFree(remoteOffsets);
863:   PetscSFBcastBegin(fieldSF, MPIU_SCALAR, originalValues, newValues);
864:   PetscSFBcastEnd(fieldSF, MPIU_SCALAR, originalValues, newValues);
865:   PetscSFDestroy(&fieldSF);
866:   VecRestoreArray(newVec, &newValues);
867:   VecRestoreArray(originalVec, &originalValues);
868:   PetscLogEventEnd(DMPLEX_DistributeField,dm,0,0,0);
869:   return(0);
870: }

874: /*@
875:   DMPlexDistributeFieldIS - Distribute field data to match a given PetscSF, usually the SF from mesh distribution

877:   Collective on DM

879:   Input Parameters:
880: + dm - The DMPlex object
881: . pointSF - The PetscSF describing the communication pattern
882: . originalSection - The PetscSection for existing data layout
883: - originalIS - The existing data

885:   Output Parameters:
886: + newSection - The PetscSF describing the new data layout
887: - newIS - The new data

889:   Level: developer

891: .seealso: DMPlexDistribute(), DMPlexDistributeField(), DMPlexDistributeData()
892: @*/
893: PetscErrorCode DMPlexDistributeFieldIS(DM dm, PetscSF pointSF, PetscSection originalSection, IS originalIS, PetscSection newSection, IS *newIS)
894: {
895:   PetscSF         fieldSF;
896:   PetscInt       *newValues, *remoteOffsets, fieldSize;
897:   const PetscInt *originalValues;
898:   PetscErrorCode  ierr;

901:   PetscLogEventBegin(DMPLEX_DistributeField,dm,0,0,0);
902:   PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);

904:   PetscSectionGetStorageSize(newSection, &fieldSize);
905:   PetscMalloc1(fieldSize, &newValues);

907:   ISGetIndices(originalIS, &originalValues);
908:   PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);
909:   PetscFree(remoteOffsets);
910:   PetscSFBcastBegin(fieldSF, MPIU_INT, (PetscInt *) originalValues, newValues);
911:   PetscSFBcastEnd(fieldSF, MPIU_INT, (PetscInt *) originalValues, newValues);
912:   PetscSFDestroy(&fieldSF);
913:   ISRestoreIndices(originalIS, &originalValues);
914:   ISCreateGeneral(PetscObjectComm((PetscObject) pointSF), fieldSize, newValues, PETSC_OWN_POINTER, newIS);
915:   PetscLogEventEnd(DMPLEX_DistributeField,dm,0,0,0);
916:   return(0);
917: }

921: /*@
922:   DMPlexDistributeData - Distribute field data to match a given PetscSF, usually the SF from mesh distribution

924:   Collective on DM

926:   Input Parameters:
927: + dm - The DMPlex object
928: . pointSF - The PetscSF describing the communication pattern
929: . originalSection - The PetscSection for existing data layout
930: . datatype - The type of data
931: - originalData - The existing data

933:   Output Parameters:
934: + newSection - The PetscSection describing the new data layout
935: - newData - The new data

937:   Level: developer

939: .seealso: DMPlexDistribute(), DMPlexDistributeField()
940: @*/
941: PetscErrorCode DMPlexDistributeData(DM dm, PetscSF pointSF, PetscSection originalSection, MPI_Datatype datatype, void *originalData, PetscSection newSection, void **newData)
942: {
943:   PetscSF        fieldSF;
944:   PetscInt      *remoteOffsets, fieldSize;
945:   PetscMPIInt    dataSize;

949:   PetscLogEventBegin(DMPLEX_DistributeData,dm,0,0,0);
950:   PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);

952:   PetscSectionGetStorageSize(newSection, &fieldSize);
953:   MPI_Type_size(datatype, &dataSize);
954:   PetscMalloc(fieldSize * dataSize, newData);

956:   PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);
957:   PetscFree(remoteOffsets);
958:   PetscSFBcastBegin(fieldSF, datatype, originalData, *newData);
959:   PetscSFBcastEnd(fieldSF, datatype, originalData, *newData);
960:   PetscSFDestroy(&fieldSF);
961:   PetscLogEventEnd(DMPLEX_DistributeData,dm,0,0,0);
962:   return(0);
963: }

967: PetscErrorCode DMPlexDistributeCones(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping original, ISLocalToGlobalMapping renumbering, DM dmParallel)
968: {
969:   DM_Plex               *mesh  = (DM_Plex*) dm->data;
970:   DM_Plex               *pmesh = (DM_Plex*) (dmParallel)->data;
971:   MPI_Comm               comm;
972:   PetscSF                coneSF;
973:   PetscSection           originalConeSection, newConeSection;
974:   PetscInt              *remoteOffsets, *cones, *globCones, *newCones, newConesSize;
975:   PetscBool              flg;
976:   PetscErrorCode         ierr;

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

983:   /* Distribute cone section */
984:   PetscObjectGetComm((PetscObject)dm, &comm);
985:   DMPlexGetConeSection(dm, &originalConeSection);
986:   DMPlexGetConeSection(dmParallel, &newConeSection);
987:   PetscSFDistributeSection(migrationSF, originalConeSection, &remoteOffsets, newConeSection);
988:   DMSetUp(dmParallel);
989:   {
990:     PetscInt pStart, pEnd, p;

992:     PetscSectionGetChart(newConeSection, &pStart, &pEnd);
993:     for (p = pStart; p < pEnd; ++p) {
994:       PetscInt coneSize;
995:       PetscSectionGetDof(newConeSection, p, &coneSize);
996:       pmesh->maxConeSize = PetscMax(pmesh->maxConeSize, coneSize);
997:     }
998:   }
999:   /* Communicate and renumber cones */
1000:   PetscSFCreateSectionSF(migrationSF, originalConeSection, remoteOffsets, newConeSection, &coneSF);
1001:   PetscFree(remoteOffsets);
1002:   DMPlexGetCones(dm, &cones);
1003:   if (original) {
1004:     PetscInt numCones;

1006:     PetscSectionGetStorageSize(originalConeSection,&numCones); PetscMalloc1(numCones,&globCones);
1007:     ISLocalToGlobalMappingApplyBlock(original, numCones, cones, globCones);
1008:   }
1009:   else {
1010:     globCones = cones;
1011:   }
1012:   DMPlexGetCones(dmParallel, &newCones);
1013:   PetscSFBcastBegin(coneSF, MPIU_INT, globCones, newCones);
1014:   PetscSFBcastEnd(coneSF, MPIU_INT, globCones, newCones);
1015:   if (original) {
1016:     PetscFree(globCones);
1017:   }
1018:   PetscSectionGetStorageSize(newConeSection, &newConesSize);
1019:   ISGlobalToLocalMappingApplyBlock(renumbering, IS_GTOLM_MASK, newConesSize, newCones, NULL, newCones);
1020: #if PETSC_USE_DEBUG
1021:   {
1022:     PetscInt  p;
1023:     PetscBool valid = PETSC_TRUE;
1024:     for (p = 0; p < newConesSize; ++p) {
1025:       if (newCones[p] < 0) {valid = PETSC_FALSE; PetscPrintf(PETSC_COMM_SELF, "Point %d not in overlap SF\n", p);}
1026:     }
1027:     if (!valid) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid global to local map");
1028:   }
1029: #endif
1030:   PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-cones_view", &flg);
1031:   if (flg) {
1032:     PetscPrintf(comm, "Serial Cone Section:\n");
1033:     PetscSectionView(originalConeSection, PETSC_VIEWER_STDOUT_WORLD);
1034:     PetscPrintf(comm, "Parallel Cone Section:\n");
1035:     PetscSectionView(newConeSection, PETSC_VIEWER_STDOUT_WORLD);
1036:     PetscSFView(coneSF, NULL);
1037:   }
1038:   DMPlexGetConeOrientations(dm, &cones);
1039:   DMPlexGetConeOrientations(dmParallel, &newCones);
1040:   PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones);
1041:   PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones);
1042:   PetscSFDestroy(&coneSF);
1043:   PetscLogEventEnd(DMPLEX_DistributeCones,dm,0,0,0);
1044:   /* Create supports and stratify sieve */
1045:   {
1046:     PetscInt pStart, pEnd;

1048:     PetscSectionGetChart(pmesh->coneSection, &pStart, &pEnd);
1049:     PetscSectionSetChart(pmesh->supportSection, pStart, pEnd);
1050:   }
1051:   DMPlexSymmetrize(dmParallel);
1052:   DMPlexStratify(dmParallel);
1053:   pmesh->useCone    = mesh->useCone;
1054:   pmesh->useClosure = mesh->useClosure;
1055:   return(0);
1056: }

1060: PetscErrorCode DMPlexDistributeCoordinates(DM dm, PetscSF migrationSF, DM dmParallel)
1061: {
1062:   MPI_Comm         comm;
1063:   PetscSection     originalCoordSection, newCoordSection;
1064:   Vec              originalCoordinates, newCoordinates;
1065:   PetscInt         bs;
1066:   const char      *name;
1067:   const PetscReal *maxCell, *L;
1068:   const DMBoundaryType *bd;
1069:   PetscErrorCode   ierr;


1075:   PetscObjectGetComm((PetscObject)dm, &comm);
1076:   DMGetCoordinateSection(dm, &originalCoordSection);
1077:   DMGetCoordinateSection(dmParallel, &newCoordSection);
1078:   DMGetCoordinatesLocal(dm, &originalCoordinates);
1079:   if (originalCoordinates) {
1080:     VecCreate(PETSC_COMM_SELF, &newCoordinates);
1081:     PetscObjectGetName((PetscObject) originalCoordinates, &name);
1082:     PetscObjectSetName((PetscObject) newCoordinates, name);

1084:     DMPlexDistributeField(dm, migrationSF, originalCoordSection, originalCoordinates, newCoordSection, newCoordinates);
1085:     DMSetCoordinatesLocal(dmParallel, newCoordinates);
1086:     VecGetBlockSize(originalCoordinates, &bs);
1087:     VecSetBlockSize(newCoordinates, bs);
1088:     VecDestroy(&newCoordinates);
1089:   }
1090:   DMGetPeriodicity(dm, &maxCell, &L, &bd);
1091:   if (L) {DMSetPeriodicity(dmParallel, maxCell, L, bd);}
1092:   return(0);
1093: }

1097: /* Here we are assuming that process 0 always has everything */
1098: PetscErrorCode DMPlexDistributeLabels(DM dm, PetscSF migrationSF, DM dmParallel)
1099: {
1100:   DM_Plex         *mesh = (DM_Plex*) dm->data;
1101:   MPI_Comm         comm;
1102:   DMLabel          depthLabel;
1103:   PetscMPIInt      rank;
1104:   PetscInt         depth, d, numLabels, numLocalLabels, l;
1105:   PetscBool        hasLabels = PETSC_FALSE, lsendDepth, sendDepth;
1106:   PetscObjectState depthState = -1;
1107:   PetscErrorCode   ierr;

1112:   PetscLogEventBegin(DMPLEX_DistributeLabels,dm,0,0,0);
1113:   PetscObjectGetComm((PetscObject)dm, &comm);
1114:   MPI_Comm_rank(comm, &rank);

1116:   /* If the user has changed the depth label, communicate it instead */
1117:   DMPlexGetDepth(dm, &depth);
1118:   DMPlexGetDepthLabel(dm, &depthLabel);
1119:   if (depthLabel) {DMLabelGetState(depthLabel, &depthState);}
1120:   lsendDepth = mesh->depthState != depthState ? PETSC_TRUE : PETSC_FALSE;
1121:   MPIU_Allreduce(&lsendDepth, &sendDepth, 1, MPIU_BOOL, MPI_LOR, comm);
1122:   if (sendDepth) {
1123:     DMRemoveLabel(dmParallel, "depth", &depthLabel);
1124:     DMLabelDestroy(&depthLabel);
1125:   }
1126:   /* Everyone must have either the same number of labels, or none */
1127:   DMGetNumLabels(dm, &numLocalLabels);
1128:   numLabels = numLocalLabels;
1129:   MPI_Bcast(&numLabels, 1, MPIU_INT, 0, comm);
1130:   if (numLabels == numLocalLabels) hasLabels = PETSC_TRUE;
1131:   for (l = numLabels-1; l >= 0; --l) {
1132:     DMLabel     label = NULL, labelNew = NULL;
1133:     PetscBool   isdepth;

1135:     if (hasLabels) {
1136:       DMGetLabelByNum(dm, l, &label);
1137:       /* Skip "depth" because it is recreated */
1138:       PetscStrcmp(label->name, "depth", &isdepth);
1139:     }
1140:     MPI_Bcast(&isdepth, 1, MPIU_BOOL, 0, comm);
1141:     if (isdepth && !sendDepth) continue;
1142:     DMLabelDistribute(label, migrationSF, &labelNew);
1143:     if (isdepth) {
1144:       /* Put in any missing strata which can occur if users are managing the depth label themselves */
1145:       PetscInt gdepth;

1147:       MPIU_Allreduce(&depth, &gdepth, 1, MPIU_INT, MPI_MAX, comm);
1148:       if ((depth >= 0) && (gdepth != depth)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Inconsistent Plex depth %d != %d", depth, gdepth);
1149:       for (d = 0; d <= gdepth; ++d) {
1150:         PetscBool has;

1152:         DMLabelHasStratum(labelNew, d, &has);
1153:         if (!has) DMLabelAddStratum(labelNew, d);
1154:       }
1155:     }
1156:     DMAddLabel(dmParallel, labelNew);
1157:   }
1158:   PetscLogEventEnd(DMPLEX_DistributeLabels,dm,0,0,0);
1159:   return(0);
1160: }

1164: PetscErrorCode DMPlexDistributeSetupHybrid(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping renumbering, DM dmParallel)
1165: {
1166:   DM_Plex        *mesh  = (DM_Plex*) dm->data;
1167:   DM_Plex        *pmesh = (DM_Plex*) (dmParallel)->data;
1168:   MPI_Comm        comm;
1169:   const PetscInt *gpoints;
1170:   PetscInt        dim, depth, n, d;
1171:   PetscErrorCode  ierr;


1177:   PetscObjectGetComm((PetscObject)dm, &comm);
1178:   DMGetDimension(dm, &dim);

1180:   /* Setup hybrid structure */
1181:   for (d = 0; d <= dim; ++d) {pmesh->hybridPointMax[d] = mesh->hybridPointMax[d];}
1182:   MPI_Bcast(pmesh->hybridPointMax, dim+1, MPIU_INT, 0, comm);
1183:   ISLocalToGlobalMappingGetSize(renumbering, &n);
1184:   ISLocalToGlobalMappingGetIndices(renumbering, &gpoints);
1185:   DMPlexGetDepth(dm, &depth);
1186:   for (d = 0; d <= dim; ++d) {
1187:     PetscInt pmax = pmesh->hybridPointMax[d], newmax = 0, pEnd, stratum[2], p;

1189:     if (pmax < 0) continue;
1190:     DMPlexGetDepthStratum(dm, d > depth ? depth : d, &stratum[0], &stratum[1]);
1191:     DMPlexGetDepthStratum(dmParallel, d, NULL, &pEnd);
1192:     MPI_Bcast(stratum, 2, MPIU_INT, 0, comm);
1193:     for (p = 0; p < n; ++p) {
1194:       const PetscInt point = gpoints[p];

1196:       if ((point >= stratum[0]) && (point < stratum[1]) && (point >= pmax)) ++newmax;
1197:     }
1198:     if (newmax > 0) pmesh->hybridPointMax[d] = pEnd - newmax;
1199:     else            pmesh->hybridPointMax[d] = -1;
1200:   }
1201:   ISLocalToGlobalMappingRestoreIndices(renumbering, &gpoints);
1202:   return(0);
1203: }

1207: PetscErrorCode DMPlexDistributeSetupTree(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping original, ISLocalToGlobalMapping renumbering, DM dmParallel)
1208: {
1209:   DM_Plex        *mesh  = (DM_Plex*) dm->data;
1210:   DM_Plex        *pmesh = (DM_Plex*) (dmParallel)->data;
1211:   MPI_Comm        comm;
1212:   DM              refTree;
1213:   PetscSection    origParentSection, newParentSection;
1214:   PetscInt        *origParents, *origChildIDs;
1215:   PetscBool       flg;
1216:   PetscErrorCode  ierr;

1221:   PetscObjectGetComm((PetscObject)dm, &comm);

1223:   /* Set up tree */
1224:   DMPlexGetReferenceTree(dm,&refTree);
1225:   DMPlexSetReferenceTree(dmParallel,refTree);
1226:   DMPlexGetTree(dm,&origParentSection,&origParents,&origChildIDs,NULL,NULL);
1227:   if (origParentSection) {
1228:     PetscInt        pStart, pEnd;
1229:     PetscInt        *newParents, *newChildIDs, *globParents;
1230:     PetscInt        *remoteOffsetsParents, newParentSize;
1231:     PetscSF         parentSF;

1233:     DMPlexGetChart(dmParallel, &pStart, &pEnd);
1234:     PetscSectionCreate(PetscObjectComm((PetscObject)dmParallel),&newParentSection);
1235:     PetscSectionSetChart(newParentSection,pStart,pEnd);
1236:     PetscSFDistributeSection(migrationSF, origParentSection, &remoteOffsetsParents, newParentSection);
1237:     PetscSFCreateSectionSF(migrationSF, origParentSection, remoteOffsetsParents, newParentSection, &parentSF);
1238:     PetscFree(remoteOffsetsParents);
1239:     PetscSectionGetStorageSize(newParentSection,&newParentSize);
1240:     PetscMalloc2(newParentSize,&newParents,newParentSize,&newChildIDs);
1241:     if (original) {
1242:       PetscInt numParents;

1244:       PetscSectionGetStorageSize(origParentSection,&numParents);
1245:       PetscMalloc1(numParents,&globParents);
1246:       ISLocalToGlobalMappingApplyBlock(original, numParents, origParents, globParents);
1247:     }
1248:     else {
1249:       globParents = origParents;
1250:     }
1251:     PetscSFBcastBegin(parentSF, MPIU_INT, globParents, newParents);
1252:     PetscSFBcastEnd(parentSF, MPIU_INT, globParents, newParents);
1253:     if (original) {
1254:       PetscFree(globParents);
1255:     }
1256:     PetscSFBcastBegin(parentSF, MPIU_INT, origChildIDs, newChildIDs);
1257:     PetscSFBcastEnd(parentSF, MPIU_INT, origChildIDs, newChildIDs);
1258:     ISGlobalToLocalMappingApplyBlock(renumbering,IS_GTOLM_MASK, newParentSize, newParents, NULL, newParents);
1259: #if PETSC_USE_DEBUG
1260:     {
1261:       PetscInt  p;
1262:       PetscBool valid = PETSC_TRUE;
1263:       for (p = 0; p < newParentSize; ++p) {
1264:         if (newParents[p] < 0) {valid = PETSC_FALSE; PetscPrintf(PETSC_COMM_SELF, "Point %d not in overlap SF\n", p);}
1265:       }
1266:       if (!valid) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid global to local map");
1267:     }
1268: #endif
1269:     PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-parents_view", &flg);
1270:     if (flg) {
1271:       PetscPrintf(comm, "Serial Parent Section: \n");
1272:       PetscSectionView(origParentSection, PETSC_VIEWER_STDOUT_WORLD);
1273:       PetscPrintf(comm, "Parallel Parent Section: \n");
1274:       PetscSectionView(newParentSection, PETSC_VIEWER_STDOUT_WORLD);
1275:       PetscSFView(parentSF, NULL);
1276:     }
1277:     DMPlexSetTree(dmParallel,newParentSection,newParents,newChildIDs);
1278:     PetscSectionDestroy(&newParentSection);
1279:     PetscFree2(newParents,newChildIDs);
1280:     PetscSFDestroy(&parentSF);
1281:   }
1282:   pmesh->useAnchors = mesh->useAnchors;
1283:   return(0);
1284: }

1288: PetscErrorCode DMPlexDistributeSF(DM dm, PetscSF migrationSF, DM dmParallel)
1289: {
1290:   DM_Plex               *mesh  = (DM_Plex*) dm->data;
1291:   DM_Plex               *pmesh = (DM_Plex*) (dmParallel)->data;
1292:   PetscMPIInt            rank, numProcs;
1293:   MPI_Comm               comm;
1294:   PetscErrorCode         ierr;


1300:   /* Create point SF for parallel mesh */
1301:   PetscLogEventBegin(DMPLEX_DistributeSF,dm,0,0,0);
1302:   PetscObjectGetComm((PetscObject)dm, &comm);
1303:   MPI_Comm_rank(comm, &rank);
1304:   MPI_Comm_size(comm, &numProcs);
1305:   {
1306:     const PetscInt *leaves;
1307:     PetscSFNode    *remotePoints, *rowners, *lowners;
1308:     PetscInt        numRoots, numLeaves, numGhostPoints = 0, p, gp, *ghostPoints;
1309:     PetscInt        pStart, pEnd;

1311:     DMPlexGetChart(dmParallel, &pStart, &pEnd);
1312:     PetscSFGetGraph(migrationSF, &numRoots, &numLeaves, &leaves, NULL);
1313:     PetscMalloc2(numRoots,&rowners,numLeaves,&lowners);
1314:     for (p=0; p<numRoots; p++) {
1315:       rowners[p].rank  = -1;
1316:       rowners[p].index = -1;
1317:     }
1318:     PetscSFBcastBegin(migrationSF, MPIU_2INT, rowners, lowners);
1319:     PetscSFBcastEnd(migrationSF, MPIU_2INT, rowners, lowners);
1320:     for (p = 0; p < numLeaves; ++p) {
1321:       if (lowners[p].rank < 0 || lowners[p].rank == rank) { /* Either put in a bid or we know we own it */
1322:         lowners[p].rank  = rank;
1323:         lowners[p].index = leaves ? leaves[p] : p;
1324:       } else if (lowners[p].rank >= 0) { /* Point already claimed so flag so that MAXLOC does not listen to us */
1325:         lowners[p].rank  = -2;
1326:         lowners[p].index = -2;
1327:       }
1328:     }
1329:     for (p=0; p<numRoots; p++) { /* Root must not participate in the rediction, flag so that MAXLOC does not use */
1330:       rowners[p].rank  = -3;
1331:       rowners[p].index = -3;
1332:     }
1333:     PetscSFReduceBegin(migrationSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);
1334:     PetscSFReduceEnd(migrationSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);
1335:     PetscSFBcastBegin(migrationSF, MPIU_2INT, rowners, lowners);
1336:     PetscSFBcastEnd(migrationSF, MPIU_2INT, rowners, lowners);
1337:     for (p = 0; p < numLeaves; ++p) {
1338:       if (lowners[p].rank < 0 || lowners[p].index < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Cell partition corrupt: point not claimed");
1339:       if (lowners[p].rank != rank) ++numGhostPoints;
1340:     }
1341:     PetscMalloc1(numGhostPoints, &ghostPoints);
1342:     PetscMalloc1(numGhostPoints, &remotePoints);
1343:     for (p = 0, gp = 0; p < numLeaves; ++p) {
1344:       if (lowners[p].rank != rank) {
1345:         ghostPoints[gp]        = leaves ? leaves[p] : p;
1346:         remotePoints[gp].rank  = lowners[p].rank;
1347:         remotePoints[gp].index = lowners[p].index;
1348:         ++gp;
1349:       }
1350:     }
1351:     PetscFree2(rowners,lowners);
1352:     PetscSFSetGraph((dmParallel)->sf, pEnd - pStart, numGhostPoints, ghostPoints, PETSC_OWN_POINTER, remotePoints, PETSC_OWN_POINTER);
1353:     PetscSFSetFromOptions((dmParallel)->sf);
1354:   }
1355:   pmesh->useCone    = mesh->useCone;
1356:   pmesh->useClosure = mesh->useClosure;
1357:   PetscLogEventEnd(DMPLEX_DistributeSF,dm,0,0,0);
1358:   return(0);
1359: }

1363: /*@C
1364:   DMPlexDerivePointSF - Build a point SF from an SF describing a point migration

1366:   Input Parameter:
1367: + dm          - The source DMPlex object
1368: . migrationSF - The star forest that describes the parallel point remapping
1369: . ownership   - Flag causing a vote to determine point ownership

1371:   Output Parameter:
1372: - pointSF     - The star forest describing the point overlap in the remapped DM

1374:   Level: developer

1376: .seealso: DMPlexDistribute(), DMPlexDistributeOverlap()
1377: @*/
1378: PetscErrorCode DMPlexCreatePointSF(DM dm, PetscSF migrationSF, PetscBool ownership, PetscSF *pointSF)
1379: {
1380:   PetscMPIInt        rank;
1381:   PetscInt           p, nroots, nleaves, idx, npointLeaves;
1382:   PetscInt          *pointLocal;
1383:   const PetscInt    *leaves;
1384:   const PetscSFNode *roots;
1385:   PetscSFNode       *rootNodes, *leafNodes, *pointRemote;
1386:   PetscErrorCode     ierr;

1390:   MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);

1392:   PetscSFGetGraph(migrationSF, &nroots, &nleaves, &leaves, &roots);
1393:   PetscMalloc2(nroots, &rootNodes, nleaves, &leafNodes);
1394:   if (ownership) {
1395:     /* Point ownership vote: Process with highest rank ownes shared points */
1396:     for (p = 0; p < nleaves; ++p) {
1397:       /* Either put in a bid or we know we own it */
1398:       leafNodes[p].rank  = rank;
1399:       leafNodes[p].index = p;
1400:     }
1401:     for (p = 0; p < nroots; p++) {
1402:       /* Root must not participate in the reduction, flag so that MAXLOC does not use */
1403:       rootNodes[p].rank  = -3;
1404:       rootNodes[p].index = -3;
1405:     }
1406:     PetscSFReduceBegin(migrationSF, MPIU_2INT, leafNodes, rootNodes, MPI_MAXLOC);
1407:     PetscSFReduceEnd(migrationSF, MPIU_2INT, leafNodes, rootNodes, MPI_MAXLOC);
1408:   } else {
1409:     for (p = 0; p < nroots; p++) {
1410:       rootNodes[p].index = -1;
1411:       rootNodes[p].rank = rank;
1412:     };
1413:     for (p = 0; p < nleaves; p++) {
1414:       /* Write new local id into old location */
1415:       if (roots[p].rank == rank) {
1416:         rootNodes[roots[p].index].index = leaves ? leaves[p] : p;
1417:       }
1418:     }
1419:   }
1420:   PetscSFBcastBegin(migrationSF, MPIU_2INT, rootNodes, leafNodes);
1421:   PetscSFBcastEnd(migrationSF, MPIU_2INT, rootNodes, leafNodes);

1423:   for (npointLeaves = 0, p = 0; p < nleaves; p++) {if (leafNodes[p].rank != rank) npointLeaves++;}
1424:   PetscMalloc1(npointLeaves, &pointLocal);
1425:   PetscMalloc1(npointLeaves, &pointRemote);
1426:   for (idx = 0, p = 0; p < nleaves; p++) {
1427:     if (leafNodes[p].rank != rank) {
1428:       pointLocal[idx] = p;
1429:       pointRemote[idx] = leafNodes[p];
1430:       idx++;
1431:     }
1432:   }
1433:   PetscSFCreate(PetscObjectComm((PetscObject) dm), pointSF);
1434:   PetscSFSetFromOptions(*pointSF);
1435:   PetscSFSetGraph(*pointSF, nleaves, npointLeaves, pointLocal, PETSC_OWN_POINTER, pointRemote, PETSC_OWN_POINTER);
1436:   PetscFree2(rootNodes, leafNodes);
1437:   return(0);
1438: }

1442: /*@C
1443:   DMPlexMigrate  - Migrates internal DM data over the supplied star forest

1445:   Input Parameter:
1446: + dm       - The source DMPlex object
1447: . sf       - The star forest communication context describing the migration pattern

1449:   Output Parameter:
1450: - targetDM - The target DMPlex object

1452:   Level: intermediate

1454: .seealso: DMPlexDistribute(), DMPlexDistributeOverlap()
1455: @*/
1456: PetscErrorCode DMPlexMigrate(DM dm, PetscSF sf, DM targetDM)
1457: {
1458:   MPI_Comm               comm;
1459:   PetscInt               dim, nroots;
1460:   PetscSF                sfPoint;
1461:   ISLocalToGlobalMapping ltogMigration;
1462:   ISLocalToGlobalMapping ltogOriginal = NULL;
1463:   PetscBool              flg;
1464:   PetscErrorCode         ierr;

1468:   PetscLogEventBegin(DMPLEX_Migrate, dm, 0, 0, 0);
1469:   PetscObjectGetComm((PetscObject) dm, &comm);
1470:   DMGetDimension(dm, &dim);
1471:   DMSetDimension(targetDM, dim);

1473:   /* Check for a one-to-all distribution pattern */
1474:   DMGetPointSF(dm, &sfPoint);
1475:   PetscSFGetGraph(sfPoint, &nroots, NULL, NULL, NULL);
1476:   if (nroots >= 0) {
1477:     IS                     isOriginal;
1478:     PetscInt               n, size, nleaves;
1479:     PetscInt              *numbering_orig, *numbering_new;
1480:     /* Get the original point numbering */
1481:     DMPlexCreatePointNumbering(dm, &isOriginal);
1482:     ISLocalToGlobalMappingCreateIS(isOriginal, &ltogOriginal);
1483:     ISLocalToGlobalMappingGetSize(ltogOriginal, &size);
1484:     ISLocalToGlobalMappingGetBlockIndices(ltogOriginal, (const PetscInt**)&numbering_orig);
1485:     /* Convert to positive global numbers */
1486:     for (n=0; n<size; n++) {if (numbering_orig[n] < 0) numbering_orig[n] = -(numbering_orig[n]+1);}
1487:     /* Derive the new local-to-global mapping from the old one */
1488:     PetscSFGetGraph(sf, NULL, &nleaves, NULL, NULL);
1489:     PetscMalloc1(nleaves, &numbering_new);
1490:     PetscSFBcastBegin(sf, MPIU_INT, (PetscInt *) numbering_orig, numbering_new);
1491:     PetscSFBcastEnd(sf, MPIU_INT, (PetscInt *) numbering_orig, numbering_new);
1492:     ISLocalToGlobalMappingCreate(comm, 1, nleaves, (const PetscInt*) numbering_new, PETSC_OWN_POINTER, &ltogMigration);
1493:     ISLocalToGlobalMappingRestoreIndices(ltogOriginal, (const PetscInt**)&numbering_orig);
1494:     ISDestroy(&isOriginal);
1495:   } else {
1496:     /* One-to-all distribution pattern: We can derive LToG from SF */
1497:     ISLocalToGlobalMappingCreateSF(sf, 0, &ltogMigration);
1498:   }
1499:   PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-partition_view", &flg);
1500:   if (flg) {
1501:     PetscPrintf(comm, "Point renumbering for DM migration:\n");
1502:     ISLocalToGlobalMappingView(ltogMigration, NULL);
1503:   }
1504:   /* Migrate DM data to target DM */
1505:   DMPlexDistributeCones(dm, sf, ltogOriginal, ltogMigration, targetDM);
1506:   DMPlexDistributeCoordinates(dm, sf, targetDM);
1507:   DMPlexDistributeLabels(dm, sf, targetDM);
1508:   DMPlexDistributeSetupHybrid(dm, sf, ltogMigration, targetDM);
1509:   DMPlexDistributeSetupTree(dm, sf, ltogOriginal, ltogMigration, targetDM);
1510:   ISLocalToGlobalMappingDestroy(&ltogOriginal);
1511:   ISLocalToGlobalMappingDestroy(&ltogMigration);
1512:   PetscLogEventEnd(DMPLEX_Migrate, dm, 0, 0, 0);
1513:   return(0);
1514: }

1518: /*@C
1519:   DMPlexDistribute - Distributes the mesh and any associated sections.

1521:   Not Collective

1523:   Input Parameter:
1524: + dm  - The original DMPlex object
1525: - overlap - The overlap of partitions, 0 is the default

1527:   Output Parameter:
1528: + sf - The PetscSF used for point distribution
1529: - parallelMesh - The distributed DMPlex object, or NULL

1531:   Note: If the mesh was not distributed, the return value is NULL.

1533:   The user can control the definition of adjacency for the mesh using DMPlexGetAdjacencyUseCone() and
1534:   DMPlexSetAdjacencyUseClosure(). They should choose the combination appropriate for the function
1535:   representation on the mesh.

1537:   Level: intermediate

1539: .keywords: mesh, elements
1540: .seealso: DMPlexCreate(), DMPlexDistributeByFace(), DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure()
1541: @*/
1542: PetscErrorCode DMPlexDistribute(DM dm, PetscInt overlap, PetscSF *sf, DM *dmParallel)
1543: {
1544:   MPI_Comm               comm;
1545:   PetscPartitioner       partitioner;
1546:   IS                     cellPart;
1547:   PetscSection           cellPartSection;
1548:   DM                     dmCoord;
1549:   DMLabel                lblPartition, lblMigration;
1550:   PetscSF                sfProcess, sfMigration, sfStratified, sfPoint;
1551:   PetscBool              flg;
1552:   PetscMPIInt            rank, numProcs, p;
1553:   PetscErrorCode         ierr;


1560:   PetscLogEventBegin(DMPLEX_Distribute,dm,0,0,0);
1561:   PetscObjectGetComm((PetscObject)dm,&comm);
1562:   MPI_Comm_rank(comm, &rank);
1563:   MPI_Comm_size(comm, &numProcs);

1565:   *dmParallel = NULL;
1566:   if (numProcs == 1) return(0);

1568:   /* Create cell partition */
1569:   PetscLogEventBegin(PETSCPARTITIONER_Partition,dm,0,0,0);
1570:   PetscSectionCreate(comm, &cellPartSection);
1571:   DMPlexGetPartitioner(dm, &partitioner);
1572:   PetscPartitionerPartition(partitioner, dm, cellPartSection, &cellPart);
1573:   {
1574:     /* Convert partition to DMLabel */
1575:     PetscInt proc, pStart, pEnd, npoints, poffset;
1576:     const PetscInt *points;
1577:     DMLabelCreate("Point Partition", &lblPartition);
1578:     ISGetIndices(cellPart, &points);
1579:     PetscSectionGetChart(cellPartSection, &pStart, &pEnd);
1580:     for (proc = pStart; proc < pEnd; proc++) {
1581:       PetscSectionGetDof(cellPartSection, proc, &npoints);
1582:       PetscSectionGetOffset(cellPartSection, proc, &poffset);
1583:       for (p = poffset; p < poffset+npoints; p++) {
1584:         DMLabelSetValue(lblPartition, points[p], proc);
1585:       }
1586:     }
1587:     ISRestoreIndices(cellPart, &points);
1588:   }
1589:   DMPlexPartitionLabelClosure(dm, lblPartition);
1590:   {
1591:     /* Build a global process SF */
1592:     PetscSFNode *remoteProc;
1593:     PetscMalloc1(numProcs, &remoteProc);
1594:     for (p = 0; p < numProcs; ++p) {
1595:       remoteProc[p].rank  = p;
1596:       remoteProc[p].index = rank;
1597:     }
1598:     PetscSFCreate(comm, &sfProcess);
1599:     PetscObjectSetName((PetscObject) sfProcess, "Process SF");
1600:     PetscSFSetGraph(sfProcess, numProcs, numProcs, NULL, PETSC_OWN_POINTER, remoteProc, PETSC_OWN_POINTER);
1601:   }
1602:   DMLabelCreate("Point migration", &lblMigration);
1603:   DMPlexPartitionLabelInvert(dm, lblPartition, sfProcess, lblMigration);
1604:   DMPlexPartitionLabelCreateSF(dm, lblMigration, &sfMigration);
1605:   /* Stratify the SF in case we are migrating an already parallel plex */
1606:   DMPlexStratifyMigrationSF(dm, sfMigration, &sfStratified);
1607:   PetscSFDestroy(&sfMigration);
1608:   sfMigration = sfStratified;
1609:   PetscLogEventEnd(PETSCPARTITIONER_Partition,dm,0,0,0);
1610:   PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-partition_view", &flg);
1611:   if (flg) {
1612:     DMLabelView(lblPartition, PETSC_VIEWER_STDOUT_WORLD);
1613:     PetscSFView(sfMigration, PETSC_VIEWER_STDOUT_WORLD);
1614:   }

1616:   /* Create non-overlapping parallel DM and migrate internal data */
1617:   DMPlexCreate(comm, dmParallel);
1618:   PetscObjectSetName((PetscObject) *dmParallel, "Parallel Mesh");
1619:   DMPlexMigrate(dm, sfMigration, *dmParallel);

1621:   /* Build the point SF without overlap */
1622:   DMPlexCreatePointSF(*dmParallel, sfMigration, PETSC_TRUE, &sfPoint);
1623:   DMSetPointSF(*dmParallel, sfPoint);
1624:   DMGetCoordinateDM(*dmParallel, &dmCoord);
1625:   if (dmCoord) {DMSetPointSF(dmCoord, sfPoint);}
1626:   if (flg) {PetscSFView(sfPoint, PETSC_VIEWER_STDOUT_WORLD);}

1628:   if (overlap > 0) {
1629:     DM                 dmOverlap;
1630:     PetscInt           nroots, nleaves;
1631:     PetscSFNode       *newRemote;
1632:     const PetscSFNode *oldRemote;
1633:     PetscSF            sfOverlap, sfOverlapPoint;
1634:     /* Add the partition overlap to the distributed DM */
1635:     DMPlexDistributeOverlap(*dmParallel, overlap, &sfOverlap, &dmOverlap);
1636:     DMDestroy(dmParallel);
1637:     *dmParallel = dmOverlap;
1638:     if (flg) {
1639:       PetscPrintf(comm, "Overlap Migration SF:\n");
1640:       PetscSFView(sfOverlap, NULL);
1641:     }

1643:     /* Re-map the migration SF to establish the full migration pattern */
1644:     PetscSFGetGraph(sfMigration, &nroots, NULL, NULL, &oldRemote);
1645:     PetscSFGetGraph(sfOverlap, NULL, &nleaves, NULL, NULL);
1646:     PetscMalloc1(nleaves, &newRemote);
1647:     PetscSFBcastBegin(sfOverlap, MPIU_2INT, oldRemote, newRemote);
1648:     PetscSFBcastEnd(sfOverlap, MPIU_2INT, oldRemote, newRemote);
1649:     PetscSFCreate(comm, &sfOverlapPoint);
1650:     PetscSFSetGraph(sfOverlapPoint, nroots, nleaves, NULL, PETSC_OWN_POINTER, newRemote, PETSC_OWN_POINTER);
1651:     PetscSFDestroy(&sfOverlap);
1652:     PetscSFDestroy(&sfMigration);
1653:     sfMigration = sfOverlapPoint;
1654:   }
1655:   /* Cleanup Partition */
1656:   PetscSFDestroy(&sfProcess);
1657:   DMLabelDestroy(&lblPartition);
1658:   DMLabelDestroy(&lblMigration);
1659:   PetscSectionDestroy(&cellPartSection);
1660:   ISDestroy(&cellPart);
1661:   /* Copy BC */
1662:   DMCopyBoundary(dm, *dmParallel);
1663:   /* Create sfNatural */
1664:   if (dm->useNatural) {
1665:     PetscSection section;

1667:     DMGetDefaultSection(dm, &section);
1668:     DMPlexCreateGlobalToNaturalSF(*dmParallel, section, sfMigration, &(*dmParallel)->sfNatural);
1669:   }
1670:   /* Cleanup */
1671:   if (sf) {*sf = sfMigration;}
1672:   else    {PetscSFDestroy(&sfMigration);}
1673:   PetscSFDestroy(&sfPoint);
1674:   PetscLogEventEnd(DMPLEX_Distribute,dm,0,0,0);
1675:   return(0);
1676: }

1680: /*@C
1681:   DMPlexDistribute - Add partition overlap to a distributed non-overlapping DM.

1683:   Not Collective

1685:   Input Parameter:
1686: + dm  - The non-overlapping distrbuted DMPlex object
1687: - overlap - The overlap of partitions, 0 is the default

1689:   Output Parameter:
1690: + sf - The PetscSF used for point distribution
1691: - dmOverlap - The overlapping distributed DMPlex object, or NULL

1693:   Note: If the mesh was not distributed, the return value is NULL.

1695:   The user can control the definition of adjacency for the mesh using DMPlexGetAdjacencyUseCone() and
1696:   DMPlexSetAdjacencyUseClosure(). They should choose the combination appropriate for the function
1697:   representation on the mesh.

1699:   Level: intermediate

1701: .keywords: mesh, elements
1702: .seealso: DMPlexCreate(), DMPlexDistributeByFace(), DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure()
1703: @*/
1704: PetscErrorCode DMPlexDistributeOverlap(DM dm, PetscInt overlap, PetscSF *sf, DM *dmOverlap)
1705: {
1706:   MPI_Comm               comm;
1707:   PetscMPIInt            rank;
1708:   PetscSection           rootSection, leafSection;
1709:   IS                     rootrank, leafrank;
1710:   DM                     dmCoord;
1711:   DMLabel                lblOverlap;
1712:   PetscSF                sfOverlap, sfStratified, sfPoint;
1713:   PetscErrorCode         ierr;


1720:   PetscLogEventBegin(DMPLEX_DistributeOverlap, dm, 0, 0, 0);
1721:   PetscObjectGetComm((PetscObject)dm,&comm);
1722:   MPI_Comm_rank(comm, &rank);

1724:   /* Compute point overlap with neighbouring processes on the distributed DM */
1725:   PetscLogEventBegin(PETSCPARTITIONER_Partition,dm,0,0,0);
1726:   PetscSectionCreate(comm, &rootSection);
1727:   PetscSectionCreate(comm, &leafSection);
1728:   DMPlexDistributeOwnership(dm, rootSection, &rootrank, leafSection, &leafrank);
1729:   DMPlexCreateOverlap(dm, overlap, rootSection, rootrank, leafSection, leafrank, &lblOverlap);
1730:   /* Convert overlap label to stratified migration SF */
1731:   DMPlexPartitionLabelCreateSF(dm, lblOverlap, &sfOverlap);
1732:   DMPlexStratifyMigrationSF(dm, sfOverlap, &sfStratified);
1733:   PetscSFDestroy(&sfOverlap);
1734:   sfOverlap = sfStratified;
1735:   PetscObjectSetName((PetscObject) sfOverlap, "Overlap SF");
1736:   PetscSFSetFromOptions(sfOverlap);

1738:   PetscSectionDestroy(&rootSection);
1739:   PetscSectionDestroy(&leafSection);
1740:   ISDestroy(&rootrank);
1741:   ISDestroy(&leafrank);
1742:   PetscLogEventEnd(PETSCPARTITIONER_Partition,dm,0,0,0);

1744:   /* Build the overlapping DM */
1745:   DMPlexCreate(comm, dmOverlap);
1746:   PetscObjectSetName((PetscObject) *dmOverlap, "Parallel Mesh");
1747:   DMPlexMigrate(dm, sfOverlap, *dmOverlap);
1748:   /* Build the new point SF */
1749:   DMPlexCreatePointSF(*dmOverlap, sfOverlap, PETSC_FALSE, &sfPoint);
1750:   DMSetPointSF(*dmOverlap, sfPoint);
1751:   DMGetCoordinateDM(*dmOverlap, &dmCoord);
1752:   if (dmCoord) {DMSetPointSF(dmCoord, sfPoint);}
1753:   PetscSFDestroy(&sfPoint);
1754:   /* Cleanup overlap partition */
1755:   DMLabelDestroy(&lblOverlap);
1756:   if (sf) *sf = sfOverlap;
1757:   else    {PetscSFDestroy(&sfOverlap);}
1758:   PetscLogEventEnd(DMPLEX_DistributeOverlap, dm, 0, 0, 0);
1759:   return(0);
1760: }

1764: /*@C
1765:   DMPlexGetGatherDM - Get a copy of the DMPlex that gathers all points on the
1766:   root process of the original's communicator.

1768:   Input Parameters:
1769: . dm - the original DMPlex object

1771:   Output Parameters:
1772: . gatherMesh - the gathered DM object, or NULL

1774:   Level: intermediate

1776: .keywords: mesh
1777: .seealso: DMPlexDistribute(), DMPlexGetRedundantDM()
1778: @*/
1779: PetscErrorCode DMPlexGetGatherDM(DM dm, DM * gatherMesh)
1780: {
1781:   MPI_Comm       comm;
1782:   PetscMPIInt    size;
1783:   PetscPartitioner oldPart, gatherPart;

1788:   comm = PetscObjectComm((PetscObject)dm);
1789:   MPI_Comm_size(comm,&size);
1790:   *gatherMesh = NULL;
1791:   if (size == 1) return(0);
1792:   DMPlexGetPartitioner(dm,&oldPart);
1793:   PetscObjectReference((PetscObject)oldPart);
1794:   PetscPartitionerCreate(comm,&gatherPart);
1795:   PetscPartitionerSetType(gatherPart,PETSCPARTITIONERGATHER);
1796:   DMPlexSetPartitioner(dm,gatherPart);
1797:   DMPlexDistribute(dm,0,NULL,gatherMesh);
1798:   DMPlexSetPartitioner(dm,oldPart);
1799:   PetscPartitionerDestroy(&gatherPart);
1800:   PetscPartitionerDestroy(&oldPart);
1801:   return(0);
1802: }

1806: /*@C
1807:   DMPlexGetRedundantDM - Get a copy of the DMPlex that is completely copied on each process.

1809:   Input Parameters:
1810: . dm - the original DMPlex object

1812:   Output Parameters:
1813: . redundantMesh - the redundant DM object, or NULL

1815:   Level: intermediate

1817: .keywords: mesh
1818: .seealso: DMPlexDistribute(), DMPlexGetGatherDM()
1819: @*/
1820: PetscErrorCode DMPlexGetRedundantDM(DM dm, DM * redundantMesh)
1821: {
1822:   MPI_Comm       comm;
1823:   PetscMPIInt    size, rank;
1824:   PetscInt       pStart, pEnd, p;
1825:   PetscInt       numPoints = -1;
1826:   PetscSF        migrationSF, sfPoint;
1827:   DM             gatherDM, dmCoord;
1828:   PetscSFNode    *points;

1833:   comm = PetscObjectComm((PetscObject)dm);
1834:   MPI_Comm_size(comm,&size);
1835:   *redundantMesh = NULL;
1836:   if (size == 1) return(0);
1837:   DMPlexGetGatherDM(dm,&gatherDM);
1838:   if (!gatherDM) return(0);
1839:   MPI_Comm_rank(comm,&rank);
1840:   DMPlexGetChart(gatherDM,&pStart,&pEnd);
1841:   numPoints = pEnd - pStart;
1842:   MPI_Bcast(&numPoints,1,MPIU_INT,0,comm);
1843:   PetscMalloc1(numPoints,&points);
1844:   PetscSFCreate(comm,&migrationSF);
1845:   for (p = 0; p < numPoints; p++) {
1846:     points[p].index = p;
1847:     points[p].rank  = 0;
1848:   }
1849:   PetscSFSetGraph(migrationSF,pEnd-pStart,numPoints,NULL,PETSC_OWN_POINTER,points,PETSC_OWN_POINTER);
1850:   DMPlexCreate(comm, redundantMesh);
1851:   PetscObjectSetName((PetscObject) *redundantMesh, "Redundant Mesh");
1852:   DMPlexMigrate(gatherDM, migrationSF, *redundantMesh);
1853:   DMPlexCreatePointSF(*redundantMesh, migrationSF, PETSC_FALSE, &sfPoint);
1854:   DMSetPointSF(*redundantMesh, sfPoint);
1855:   DMGetCoordinateDM(*redundantMesh, &dmCoord);
1856:   if (dmCoord) {DMSetPointSF(dmCoord, sfPoint);}
1857:   PetscSFDestroy(&sfPoint);
1858:   PetscSFDestroy(&migrationSF);
1859:   DMDestroy(&gatherDM);
1860:   return(0);
1861: }