Date: 2016-07-24T17:00:07+00:00

Actual source code: plexdistribute.c
petsc-3.7.3 2016-07-24
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      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(comm, &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: }