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

  Collective on DM

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

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

  Level: developer

.seealso: DMPlexDistribute(), DMPlexDistributeData()
@*/
PetscErrorCode DMPlexDistributeField(DM dm, PetscSF pointSF, PetscSection originalSection, Vec originalVec, PetscSection newSection, Vec newVec)
{
  PetscSF        fieldSF;
  PetscInt      *remoteOffsets, fieldSize;
  PetscScalar   *originalValues, *newValues;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = PetscLogEventBegin(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr);
  ierr = PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);CHKERRQ(ierr);

  ierr = PetscSectionGetStorageSize(newSection, &fieldSize);CHKERRQ(ierr);
  ierr = VecSetSizes(newVec, fieldSize, PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = VecSetType(newVec,dm->vectype);CHKERRQ(ierr);

  ierr = VecGetArray(originalVec, &originalValues);CHKERRQ(ierr);
  ierr = VecGetArray(newVec, &newValues);CHKERRQ(ierr);
  ierr = PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);CHKERRQ(ierr);
  ierr = PetscSFBcastBegin(fieldSF, MPIU_SCALAR, originalValues, newValues);CHKERRQ(ierr);
  ierr = PetscSFBcastEnd(fieldSF, MPIU_SCALAR, originalValues, newValues);CHKERRQ(ierr);
  ierr = PetscSFDestroy(&fieldSF);CHKERRQ(ierr);
  ierr = VecRestoreArray(newVec, &newValues);CHKERRQ(ierr);
  ierr = VecRestoreArray(originalVec, &originalValues);CHKERRQ(ierr);
  ierr = PetscLogEventEnd(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
示例#2
0
文件: ex3.c 项目: erdc-cm/petsc-dev
PetscErrorCode DistributeCoordinates(DM dm, PetscSF pointSF, DM parallelDM)
{
  PetscSF        coordSF;
  PetscSection   originalCoordSection, newCoordSection;
  Vec            coordinates, newCoordinates;
  PetscScalar   *coords,     *newCoords;
  PetscInt      *remoteOffsets, coordSize;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMMeshGetCoordinateSection(dm, &originalCoordSection);CHKERRQ(ierr);
  ierr = DMMeshGetCoordinateSection(parallelDM, &newCoordSection);CHKERRQ(ierr);
  ierr = PetscSFDistributeSection(pointSF, originalCoordSection, &remoteOffsets, newCoordSection);CHKERRQ(ierr);

  ierr = DMMeshGetCoordinateVec(dm, &coordinates);CHKERRQ(ierr);
  ierr = DMMeshGetCoordinateVec(parallelDM, &newCoordinates);CHKERRQ(ierr);
  ierr = PetscSectionGetStorageSize(newCoordSection, &coordSize);CHKERRQ(ierr);
  ierr = VecSetSizes(newCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = VecSetFromOptions(newCoordinates);CHKERRQ(ierr);

  ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
  ierr = VecGetArray(newCoordinates, &newCoords);CHKERRQ(ierr);
  ierr = PetscSFCreateSectionSF(pointSF, originalCoordSection, remoteOffsets, newCoordSection, &coordSF);CHKERRQ(ierr);
  ierr = PetscSFBcastBegin(coordSF, MPIU_SCALAR, coords, newCoords);CHKERRQ(ierr);
  ierr = PetscSFBcastEnd(coordSF, MPIU_SCALAR, coords, newCoords);CHKERRQ(ierr);
  ierr = PetscSFDestroy(&coordSF);CHKERRQ(ierr);
  ierr = VecRestoreArray(newCoordinates, &newCoords);CHKERRQ(ierr);
  ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
示例#3
0
文件: dmlabel.c 项目: plguhur/petsc
PetscErrorCode DMLabelDistribute_Internal(DMLabel label, PetscSF sf, PetscSection *leafSection, PetscInt **leafStrata)
{
  MPI_Comm       comm;
  PetscInt       s, l, nroots, nleaves, dof, offset, size;
  PetscInt      *remoteOffsets, *rootStrata, *rootIdx;
  PetscSection   rootSection;
  PetscSF        labelSF;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (label) {ierr = DMLabelMakeAllValid_Private(label);CHKERRQ(ierr);}
  ierr = PetscObjectGetComm((PetscObject)sf, &comm);CHKERRQ(ierr);
  /* Build a section of stratum values per point, generate the according SF
     and distribute point-wise stratum values to leaves. */
  ierr = PetscSFGetGraph(sf, &nroots, &nleaves, NULL, NULL);CHKERRQ(ierr);
  ierr = PetscSectionCreate(comm, &rootSection);CHKERRQ(ierr);
  ierr = PetscSectionSetChart(rootSection, 0, nroots);CHKERRQ(ierr);
  if (label) {
    for (s = 0; s < label->numStrata; ++s) {
      for (l = 0; l < label->stratumSizes[s]; l++) {
        ierr = PetscSectionGetDof(rootSection, label->points[s][l], &dof);CHKERRQ(ierr);
        ierr = PetscSectionSetDof(rootSection, label->points[s][l], dof+1);CHKERRQ(ierr);
      }
    }
  }
  ierr = PetscSectionSetUp(rootSection);CHKERRQ(ierr);
  /* Create a point-wise array of stratum values */
  ierr = PetscSectionGetStorageSize(rootSection, &size);CHKERRQ(ierr);
  ierr = PetscMalloc1(size, &rootStrata);CHKERRQ(ierr);
  ierr = PetscCalloc1(nroots, &rootIdx);CHKERRQ(ierr);
  if (label) {
    for (s = 0; s < label->numStrata; ++s) {
      for (l = 0; l < label->stratumSizes[s]; l++) {
        const PetscInt p = label->points[s][l];
        ierr = PetscSectionGetOffset(rootSection, p, &offset);CHKERRQ(ierr);
        rootStrata[offset+rootIdx[p]++] = label->stratumValues[s];
      }
    }
  }
  /* Build SF that maps label points to remote processes */
  ierr = PetscSectionCreate(comm, leafSection);CHKERRQ(ierr);
  ierr = PetscSFDistributeSection(sf, rootSection, &remoteOffsets, *leafSection);CHKERRQ(ierr);
  ierr = PetscSFCreateSectionSF(sf, rootSection, remoteOffsets, *leafSection, &labelSF);CHKERRQ(ierr);
  ierr = PetscFree(remoteOffsets);CHKERRQ(ierr);
  /* Send the strata for each point over the derived SF */
  ierr = PetscSectionGetStorageSize(*leafSection, &size);CHKERRQ(ierr);
  ierr = PetscMalloc1(size, leafStrata);CHKERRQ(ierr);
  ierr = PetscSFBcastBegin(labelSF, MPIU_INT, rootStrata, *leafStrata);CHKERRQ(ierr);
  ierr = PetscSFBcastEnd(labelSF, MPIU_INT, rootStrata, *leafStrata);CHKERRQ(ierr);
  /* Clean up */
  ierr = PetscFree(rootStrata);CHKERRQ(ierr);
  ierr = PetscFree(rootIdx);CHKERRQ(ierr);
  ierr = PetscSectionDestroy(&rootSection);CHKERRQ(ierr);
  ierr = PetscSFDestroy(&labelSF);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
示例#4
0
int main(int argc, char *argv[])
{
    MPI_Comm       comm;
    DM             dm;
    PetscSF        sf;
    AppCtx         user;
    PetscErrorCode ierr;

    PetscFunctionBegin;
    ierr = PetscInitialize(&argc, &argv, (char*) 0, help);
    CHKERRQ(ierr);
    comm = PETSC_COMM_WORLD;
    ierr = ProcessOptions(comm, &user);
    CHKERRQ(ierr);
    ierr = CreateMesh(comm, &user, &dm);
    CHKERRQ(ierr);
    ierr = DMMeshConvertOverlapToSF(dm, &sf);
    CHKERRQ(ierr);
    {
        PetscSection section;
        PetscSF      sectionSF;

        ierr = DMMeshGetCoordinateSection(dm, &section);
        CHKERRQ(ierr);
        ierr = PetscSectionView(section, PETSC_VIEWER_STDOUT_SELF);
        CHKERRQ(ierr);
        ierr = PetscSFCreateSectionSF(sf, section, &sectionSF);
        CHKERRQ(ierr);
        ierr = PetscSFDestroy(&sectionSF);
        CHKERRQ(ierr);
        ierr = PetscSectionDestroy(&section);
        CHKERRQ(ierr);
    }
    ierr = PetscSFDestroy(&sf);
    CHKERRQ(ierr);
    ierr = DMDestroy(&dm);
    CHKERRQ(ierr);
    ierr = PetscFinalize();
    PetscFunctionReturn(0);
}
/*@
  DMPlexDistributeData - Distribute field data to match a given PetscSF, usually the SF from mesh distribution

  Collective on DM

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

  Output Parameters:
+ newSection - The PetscSF describing the new data layout
- newData - The new data

  Level: developer

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

  PetscFunctionBegin;
  ierr = PetscLogEventBegin(DMPLEX_DistributeData,dm,0,0,0);CHKERRQ(ierr);
  ierr = PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);CHKERRQ(ierr);

  ierr = PetscSectionGetStorageSize(newSection, &fieldSize);CHKERRQ(ierr);
  ierr = MPI_Type_size(datatype, &dataSize);CHKERRQ(ierr);
  ierr = PetscMalloc(fieldSize * dataSize, newData);CHKERRQ(ierr);

  ierr = PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);CHKERRQ(ierr);
  ierr = PetscSFBcastBegin(fieldSF, datatype, originalData, *newData);CHKERRQ(ierr);
  ierr = PetscSFBcastEnd(fieldSF, datatype, originalData, *newData);CHKERRQ(ierr);
  ierr = PetscSFDestroy(&fieldSF);CHKERRQ(ierr);
  ierr = PetscLogEventEnd(DMPLEX_DistributeData,dm,0,0,0);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
示例#6
0
PetscErrorCode DMPlexPreallocateOperator(DM dm, PetscInt bs, PetscSection section, PetscSection sectionGlobal, PetscInt dnz[], PetscInt onz[], PetscInt dnzu[], PetscInt onzu[], Mat A, PetscBool fillMatrix)
{
  MPI_Comm           comm;
  MatType            mtype;
  PetscSF            sf, sfDof, sfAdj;
  PetscSection       leafSectionAdj, rootSectionAdj, sectionAdj, anchorSectionAdj;
  PetscInt           nroots, nleaves, l, p;
  const PetscInt    *leaves;
  const PetscSFNode *remotes;
  PetscInt           dim, pStart, pEnd, numDof, globalOffStart, globalOffEnd, numCols;
  PetscInt          *tmpAdj = NULL, *adj, *rootAdj, *anchorAdj = NULL, *cols, *remoteOffsets;
  PetscInt           adjSize;
  PetscLayout        rLayout;
  PetscInt           locRows, rStart, rEnd, r;
  PetscMPIInt        size;
  PetscBool          doCommLocal, doComm, debug = PETSC_FALSE, isSymBlock, isSymSeqBlock, isSymMPIBlock;
  PetscBool          useAnchors;
  PetscErrorCode     ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  PetscValidHeaderSpecific(section, PETSC_SECTION_CLASSID, 3);
  PetscValidHeaderSpecific(sectionGlobal, PETSC_SECTION_CLASSID, 4);
  PetscValidHeaderSpecific(A, MAT_CLASSID, 9);
  if (dnz)  PetscValidPointer(dnz,5);
  if (onz)  PetscValidPointer(onz,6);
  if (dnzu) PetscValidPointer(dnzu,7);
  if (onzu) PetscValidPointer(onzu,8);
  ierr = PetscLogEventBegin(DMPLEX_Preallocate,dm,0,0,0);CHKERRQ(ierr);
  ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
  ierr = PetscOptionsGetBool(NULL, "-dm_view_preallocation", &debug, NULL);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr);
  ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
  ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr);
  ierr = PetscSFGetGraph(sf, &nroots, NULL, NULL, NULL);CHKERRQ(ierr);
  doCommLocal = (size > 1) && (nroots >= 0) ? PETSC_TRUE : PETSC_FALSE;
  ierr = MPI_Allreduce(&doCommLocal, &doComm, 1, MPIU_BOOL, MPI_LAND, comm);CHKERRQ(ierr);
  /* Create dof SF based on point SF */
  if (debug) {
    ierr = PetscPrintf(comm, "Input Section for Preallocation:\n");CHKERRQ(ierr);
    ierr = PetscSectionView(section, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
    ierr = PetscPrintf(comm, "Input Global Section for Preallocation:\n");CHKERRQ(ierr);
    ierr = PetscSectionView(sectionGlobal, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
    ierr = PetscPrintf(comm, "Input SF for Preallocation:\n");CHKERRQ(ierr);
    ierr = PetscSFView(sf, NULL);CHKERRQ(ierr);
  }
  ierr = PetscSFCreateRemoteOffsets(sf, section, section, &remoteOffsets);CHKERRQ(ierr);
  ierr = PetscSFCreateSectionSF(sf, section, remoteOffsets, section, &sfDof);CHKERRQ(ierr);
  if (debug) {
    ierr = PetscPrintf(comm, "Dof SF for Preallocation:\n");CHKERRQ(ierr);
    ierr = PetscSFView(sfDof, NULL);CHKERRQ(ierr);
  }
  /* Create section for dof adjacency (dof ==> # adj dof) */
  ierr = PetscSectionGetChart(section, &pStart, &pEnd);CHKERRQ(ierr);
  ierr = PetscSectionGetStorageSize(section, &numDof);CHKERRQ(ierr);
  ierr = PetscSectionCreate(comm, &leafSectionAdj);CHKERRQ(ierr);
  ierr = PetscSectionSetChart(leafSectionAdj, 0, numDof);CHKERRQ(ierr);
  ierr = PetscSectionCreate(comm, &rootSectionAdj);CHKERRQ(ierr);
  ierr = PetscSectionSetChart(rootSectionAdj, 0, numDof);CHKERRQ(ierr);
  /*   Fill in the ghost dofs on the interface */
  ierr = PetscSFGetGraph(sf, NULL, &nleaves, &leaves, &remotes);CHKERRQ(ierr);
  /* use constraints in finding adjacency in this routine */
  ierr = DMPlexGetAdjacencyUseAnchors(dm,&useAnchors);CHKERRQ(ierr);
  ierr = DMPlexSetAdjacencyUseAnchors(dm,PETSC_TRUE);CHKERRQ(ierr);

  /*
   section        - maps points to (# dofs, local dofs)
   sectionGlobal  - maps points to (# dofs, global dofs)
   leafSectionAdj - maps unowned local dofs to # adj dofs
   rootSectionAdj - maps   owned local dofs to # adj dofs
   adj            - adj global dofs indexed by leafSectionAdj
   rootAdj        - adj global dofs indexed by rootSectionAdj
   sf    - describes shared points across procs
   sfDof - describes shared dofs across procs
   sfAdj - describes shared adjacent dofs across procs
   ** The bootstrapping process involves six rounds with similar structure of visiting neighbors of each point.
  (0). If there are point-to-point constraints, add the adjacencies of constrained points to anchors in anchorAdj
       (This is done in DMPlexComputeAnchorAdjacencies())
    1. Visit unowned points on interface, count adjacencies placing in leafSectionAdj
       Reduce those counts to rootSectionAdj (now redundantly counting some interface points)
    2. Visit owned points on interface, count adjacencies placing in rootSectionAdj
       Create sfAdj connecting rootSectionAdj and leafSectionAdj
    3. Visit unowned points on interface, write adjacencies to adj
       Gather adj to rootAdj (note that there is redundancy in rootAdj when multiple procs find the same adjacencies)
    4. Visit owned points on interface, write adjacencies to rootAdj
       Remove redundancy in rootAdj
   ** The last two traversals use transitive closure
    5. Visit all owned points in the subdomain, count dofs for each point (sectionAdj)
       Allocate memory addressed by sectionAdj (cols)
    6. Visit all owned points in the subdomain, insert dof adjacencies into cols
   ** Knowing all the column adjacencies, check ownership and sum into dnz and onz
  */

  ierr = DMPlexComputeAnchorAdjacencies(dm,section,sectionGlobal,&anchorSectionAdj,&anchorAdj);CHKERRQ(ierr);

  for (l = 0; l < nleaves; ++l) {
    PetscInt dof, off, d, q, anDof;
    PetscInt p = leaves[l], numAdj = PETSC_DETERMINE;

    if ((p < pStart) || (p >= pEnd)) continue;
    ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
    ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
    ierr = DMPlexGetAdjacency(dm, p, &numAdj, &tmpAdj);CHKERRQ(ierr);
    for (q = 0; q < numAdj; ++q) {
      const PetscInt padj = tmpAdj[q];
      PetscInt ndof, ncdof;

      if ((padj < pStart) || (padj >= pEnd)) continue;
      ierr = PetscSectionGetDof(section, padj, &ndof);CHKERRQ(ierr);
      ierr = PetscSectionGetConstraintDof(section, padj, &ncdof);CHKERRQ(ierr);
      for (d = off; d < off+dof; ++d) {
        ierr = PetscSectionAddDof(leafSectionAdj, d, ndof-ncdof);CHKERRQ(ierr);
      }
    }
    ierr = PetscSectionGetDof(anchorSectionAdj, p, &anDof);CHKERRQ(ierr);
    if (anDof) {
      for (d = off; d < off+dof; ++d) {
        ierr = PetscSectionAddDof(leafSectionAdj, d, anDof);CHKERRQ(ierr);
      }
    }
  }
  ierr = PetscSectionSetUp(leafSectionAdj);CHKERRQ(ierr);
  if (debug) {
    ierr = PetscPrintf(comm, "Adjacency Section for Preallocation on Leaves:\n");CHKERRQ(ierr);
    ierr = PetscSectionView(leafSectionAdj, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  }
  /* Get maximum remote adjacency sizes for owned dofs on interface (roots) */
  if (doComm) {
    ierr = PetscSFReduceBegin(sfDof, MPIU_INT, leafSectionAdj->atlasDof, rootSectionAdj->atlasDof, MPI_SUM);CHKERRQ(ierr);
    ierr = PetscSFReduceEnd(sfDof, MPIU_INT, leafSectionAdj->atlasDof, rootSectionAdj->atlasDof, MPI_SUM);CHKERRQ(ierr);
  }
  if (debug) {
    ierr = PetscPrintf(comm, "Adjancency Section for Preallocation on Roots:\n");CHKERRQ(ierr);
    ierr = PetscSectionView(rootSectionAdj, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  }
  /* Add in local adjacency sizes for owned dofs on interface (roots) */
  for (p = pStart; p < pEnd; ++p) {
    PetscInt numAdj = PETSC_DETERMINE, adof, dof, off, d, q, anDof;

    ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
    ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
    if (!dof) continue;
    ierr = PetscSectionGetDof(rootSectionAdj, off, &adof);CHKERRQ(ierr);
    if (adof <= 0) continue;
    ierr = DMPlexGetAdjacency(dm, p, &numAdj, &tmpAdj);CHKERRQ(ierr);
    for (q = 0; q < numAdj; ++q) {
      const PetscInt padj = tmpAdj[q];
      PetscInt ndof, ncdof;

      if ((padj < pStart) || (padj >= pEnd)) continue;
      ierr = PetscSectionGetDof(section, padj, &ndof);CHKERRQ(ierr);
      ierr = PetscSectionGetConstraintDof(section, padj, &ncdof);CHKERRQ(ierr);
      for (d = off; d < off+dof; ++d) {
        ierr = PetscSectionAddDof(rootSectionAdj, d, ndof-ncdof);CHKERRQ(ierr);
      }
    }
    ierr = PetscSectionGetDof(anchorSectionAdj, p, &anDof);CHKERRQ(ierr);
    if (anDof) {
      for (d = off; d < off+dof; ++d) {
        ierr = PetscSectionAddDof(rootSectionAdj, d, anDof);CHKERRQ(ierr);
      }
    }
  }
  ierr = PetscSectionSetUp(rootSectionAdj);CHKERRQ(ierr);
  if (debug) {
    ierr = PetscPrintf(comm, "Adjancency Section for Preallocation on Roots after local additions:\n");CHKERRQ(ierr);
    ierr = PetscSectionView(rootSectionAdj, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  }
  /* Create adj SF based on dof SF */
  ierr = PetscSFCreateRemoteOffsets(sfDof, rootSectionAdj, leafSectionAdj, &remoteOffsets);CHKERRQ(ierr);
  ierr = PetscSFCreateSectionSF(sfDof, rootSectionAdj, remoteOffsets, leafSectionAdj, &sfAdj);CHKERRQ(ierr);
  if (debug) {
    ierr = PetscPrintf(comm, "Adjacency SF for Preallocation:\n");CHKERRQ(ierr);
    ierr = PetscSFView(sfAdj, NULL);CHKERRQ(ierr);
  }
  ierr = PetscSFDestroy(&sfDof);CHKERRQ(ierr);
  /* Create leaf adjacency */
  ierr = PetscSectionSetUp(leafSectionAdj);CHKERRQ(ierr);
  ierr = PetscSectionGetStorageSize(leafSectionAdj, &adjSize);CHKERRQ(ierr);
  ierr = PetscCalloc1(adjSize, &adj);CHKERRQ(ierr);
  for (l = 0; l < nleaves; ++l) {
    PetscInt dof, off, d, q, anDof, anOff;
    PetscInt p = leaves[l], numAdj = PETSC_DETERMINE;

    if ((p < pStart) || (p >= pEnd)) continue;
    ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
    ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
    ierr = DMPlexGetAdjacency(dm, p, &numAdj, &tmpAdj);CHKERRQ(ierr);
    ierr = PetscSectionGetDof(anchorSectionAdj, p, &anDof);CHKERRQ(ierr);
    ierr = PetscSectionGetOffset(anchorSectionAdj, p, &anOff);CHKERRQ(ierr);
    for (d = off; d < off+dof; ++d) {
      PetscInt aoff, i = 0;

      ierr = PetscSectionGetOffset(leafSectionAdj, d, &aoff);CHKERRQ(ierr);
      for (q = 0; q < numAdj; ++q) {
        const PetscInt padj = tmpAdj[q];
        PetscInt ndof, ncdof, ngoff, nd;

        if ((padj < pStart) || (padj >= pEnd)) continue;
        ierr = PetscSectionGetDof(section, padj, &ndof);CHKERRQ(ierr);
        ierr = PetscSectionGetConstraintDof(section, padj, &ncdof);CHKERRQ(ierr);
        ierr = PetscSectionGetOffset(sectionGlobal, padj, &ngoff);CHKERRQ(ierr);
        for (nd = 0; nd < ndof-ncdof; ++nd) {
          adj[aoff+i] = (ngoff < 0 ? -(ngoff+1) : ngoff) + nd;
          ++i;
        }
      }
      for (q = 0; q < anDof; q++) {
        adj[aoff+i] = anchorAdj[anOff+q];
        ++i;
      }
    }
  }
  /* Debugging */
  if (debug) {
    IS tmp;
    ierr = PetscPrintf(comm, "Leaf adjacency indices\n");CHKERRQ(ierr);
    ierr = ISCreateGeneral(comm, adjSize, adj, PETSC_USE_POINTER, &tmp);CHKERRQ(ierr);
    ierr = ISView(tmp, NULL);CHKERRQ(ierr);
    ierr = ISDestroy(&tmp);CHKERRQ(ierr);
  }
  /* Gather adjacenct indices to root */
  ierr = PetscSectionGetStorageSize(rootSectionAdj, &adjSize);CHKERRQ(ierr);
  ierr = PetscMalloc1(adjSize, &rootAdj);CHKERRQ(ierr);
  for (r = 0; r < adjSize; ++r) rootAdj[r] = -1;
  if (doComm) {
    ierr = PetscSFGatherBegin(sfAdj, MPIU_INT, adj, rootAdj);CHKERRQ(ierr);
    ierr = PetscSFGatherEnd(sfAdj, MPIU_INT, adj, rootAdj);CHKERRQ(ierr);
  }
  ierr = PetscSFDestroy(&sfAdj);CHKERRQ(ierr);
  ierr = PetscFree(adj);CHKERRQ(ierr);
  /* Debugging */
  if (debug) {
    IS tmp;
    ierr = PetscPrintf(comm, "Root adjacency indices after gather\n");CHKERRQ(ierr);
    ierr = ISCreateGeneral(comm, adjSize, rootAdj, PETSC_USE_POINTER, &tmp);CHKERRQ(ierr);
    ierr = ISView(tmp, NULL);CHKERRQ(ierr);
    ierr = ISDestroy(&tmp);CHKERRQ(ierr);
  }
  /* Add in local adjacency indices for owned dofs on interface (roots) */
  for (p = pStart; p < pEnd; ++p) {
    PetscInt numAdj = PETSC_DETERMINE, adof, dof, off, d, q, anDof, anOff;

    ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
    ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
    if (!dof) continue;
    ierr = PetscSectionGetDof(rootSectionAdj, off, &adof);CHKERRQ(ierr);
    if (adof <= 0) continue;
    ierr = DMPlexGetAdjacency(dm, p, &numAdj, &tmpAdj);CHKERRQ(ierr);
    ierr = PetscSectionGetDof(anchorSectionAdj, p, &anDof);CHKERRQ(ierr);
    ierr = PetscSectionGetOffset(anchorSectionAdj, p, &anOff);CHKERRQ(ierr);
    for (d = off; d < off+dof; ++d) {
      PetscInt adof, aoff, i;

      ierr = PetscSectionGetDof(rootSectionAdj, d, &adof);CHKERRQ(ierr);
      ierr = PetscSectionGetOffset(rootSectionAdj, d, &aoff);CHKERRQ(ierr);
      i    = adof-1;
      for (q = 0; q < anDof; q++) {
        rootAdj[aoff+i] = anchorAdj[anOff+q];
        --i;
      }
      for (q = 0; q < numAdj; ++q) {
        const PetscInt padj = tmpAdj[q];
        PetscInt ndof, ncdof, ngoff, nd;

        if ((padj < pStart) || (padj >= pEnd)) continue;
        ierr = PetscSectionGetDof(section, padj, &ndof);CHKERRQ(ierr);
        ierr = PetscSectionGetConstraintDof(section, padj, &ncdof);CHKERRQ(ierr);
        ierr = PetscSectionGetOffset(sectionGlobal, padj, &ngoff);CHKERRQ(ierr);
        for (nd = 0; nd < ndof-ncdof; ++nd) {
          rootAdj[aoff+i] = ngoff < 0 ? -(ngoff+1)+nd : ngoff+nd;
          --i;
        }
      }
    }
  }
  /* Debugging */
  if (debug) {
    IS tmp;
    ierr = PetscPrintf(comm, "Root adjacency indices\n");CHKERRQ(ierr);
    ierr = ISCreateGeneral(comm, adjSize, rootAdj, PETSC_USE_POINTER, &tmp);CHKERRQ(ierr);
    ierr = ISView(tmp, NULL);CHKERRQ(ierr);
    ierr = ISDestroy(&tmp);CHKERRQ(ierr);
  }
  /* Compress indices */
  ierr = PetscSectionSetUp(rootSectionAdj);CHKERRQ(ierr);
  for (p = pStart; p < pEnd; ++p) {
    PetscInt dof, cdof, off, d;
    PetscInt adof, aoff;

    ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
    ierr = PetscSectionGetConstraintDof(section, p, &cdof);CHKERRQ(ierr);
    ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
    if (!dof) continue;
    ierr = PetscSectionGetDof(rootSectionAdj, off, &adof);CHKERRQ(ierr);
    if (adof <= 0) continue;
    for (d = off; d < off+dof-cdof; ++d) {
      ierr = PetscSectionGetDof(rootSectionAdj, d, &adof);CHKERRQ(ierr);
      ierr = PetscSectionGetOffset(rootSectionAdj, d, &aoff);CHKERRQ(ierr);
      ierr = PetscSortRemoveDupsInt(&adof, &rootAdj[aoff]);CHKERRQ(ierr);
      ierr = PetscSectionSetDof(rootSectionAdj, d, adof);CHKERRQ(ierr);
    }
  }
  /* Debugging */
  if (debug) {
    IS tmp;
    ierr = PetscPrintf(comm, "Adjancency Section for Preallocation on Roots after compression:\n");CHKERRQ(ierr);
    ierr = PetscSectionView(rootSectionAdj, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
    ierr = PetscPrintf(comm, "Root adjacency indices after compression\n");CHKERRQ(ierr);
    ierr = ISCreateGeneral(comm, adjSize, rootAdj, PETSC_USE_POINTER, &tmp);CHKERRQ(ierr);
    ierr = ISView(tmp, NULL);CHKERRQ(ierr);
    ierr = ISDestroy(&tmp);CHKERRQ(ierr);
  }
  /* Build adjacency section: Maps global indices to sets of adjacent global indices */
  ierr = PetscSectionGetOffsetRange(sectionGlobal, &globalOffStart, &globalOffEnd);CHKERRQ(ierr);
  ierr = PetscSectionCreate(comm, &sectionAdj);CHKERRQ(ierr);
  ierr = PetscSectionSetChart(sectionAdj, globalOffStart, globalOffEnd);CHKERRQ(ierr);
  for (p = pStart; p < pEnd; ++p) {
    PetscInt  numAdj = PETSC_DETERMINE, dof, cdof, off, goff, d, q, anDof;
    PetscBool found  = PETSC_TRUE;

    ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
    ierr = PetscSectionGetConstraintDof(section, p, &cdof);CHKERRQ(ierr);
    ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
    ierr = PetscSectionGetOffset(sectionGlobal, p, &goff);CHKERRQ(ierr);
    for (d = 0; d < dof-cdof; ++d) {
      PetscInt ldof, rdof;

      ierr = PetscSectionGetDof(leafSectionAdj, off+d, &ldof);CHKERRQ(ierr);
      ierr = PetscSectionGetDof(rootSectionAdj, off+d, &rdof);CHKERRQ(ierr);
      if (ldof > 0) {
        /* We do not own this point */
      } else if (rdof > 0) {
        ierr = PetscSectionSetDof(sectionAdj, goff+d, rdof);CHKERRQ(ierr);
      } else {
        found = PETSC_FALSE;
      }
    }
    if (found) continue;
    ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
    ierr = PetscSectionGetOffset(sectionGlobal, p, &goff);CHKERRQ(ierr);
    ierr = DMPlexGetAdjacency(dm, p, &numAdj, &tmpAdj);CHKERRQ(ierr);
    for (q = 0; q < numAdj; ++q) {
      const PetscInt padj = tmpAdj[q];
      PetscInt ndof, ncdof, noff;

      if ((padj < pStart) || (padj >= pEnd)) continue;
      ierr = PetscSectionGetDof(section, padj, &ndof);CHKERRQ(ierr);
      ierr = PetscSectionGetConstraintDof(section, padj, &ncdof);CHKERRQ(ierr);
      ierr = PetscSectionGetOffset(section, padj, &noff);CHKERRQ(ierr);
      for (d = goff; d < goff+dof-cdof; ++d) {
        ierr = PetscSectionAddDof(sectionAdj, d, ndof-ncdof);CHKERRQ(ierr);
      }
    }
    ierr = PetscSectionGetDof(anchorSectionAdj, p, &anDof);CHKERRQ(ierr);
    if (anDof) {
      for (d = goff; d < goff+dof-cdof; ++d) {
        ierr = PetscSectionAddDof(sectionAdj, d, anDof);CHKERRQ(ierr);
      }
    }
  }
  ierr = PetscSectionSetUp(sectionAdj);CHKERRQ(ierr);
  if (debug) {
    ierr = PetscPrintf(comm, "Adjacency Section for Preallocation:\n");CHKERRQ(ierr);
    ierr = PetscSectionView(sectionAdj, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  }
  /* Get adjacent indices */
  ierr = PetscSectionGetStorageSize(sectionAdj, &numCols);CHKERRQ(ierr);
  ierr = PetscMalloc1(numCols, &cols);CHKERRQ(ierr);
  for (p = pStart; p < pEnd; ++p) {
    PetscInt  numAdj = PETSC_DETERMINE, dof, cdof, off, goff, d, q, anDof, anOff;
    PetscBool found  = PETSC_TRUE;

    ierr = PetscSectionGetDof(section, p, &dof);CHKERRQ(ierr);
    ierr = PetscSectionGetConstraintDof(section, p, &cdof);CHKERRQ(ierr);
    ierr = PetscSectionGetOffset(section, p, &off);CHKERRQ(ierr);
    ierr = PetscSectionGetOffset(sectionGlobal, p, &goff);CHKERRQ(ierr);
    for (d = 0; d < dof-cdof; ++d) {
      PetscInt ldof, rdof;

      ierr = PetscSectionGetDof(leafSectionAdj, off+d, &ldof);CHKERRQ(ierr);
      ierr = PetscSectionGetDof(rootSectionAdj, off+d, &rdof);CHKERRQ(ierr);
      if (ldof > 0) {
        /* We do not own this point */
      } else if (rdof > 0) {
        PetscInt aoff, roff;

        ierr = PetscSectionGetOffset(sectionAdj, goff+d, &aoff);CHKERRQ(ierr);
        ierr = PetscSectionGetOffset(rootSectionAdj, off+d, &roff);CHKERRQ(ierr);
        ierr = PetscMemcpy(&cols[aoff], &rootAdj[roff], rdof * sizeof(PetscInt));CHKERRQ(ierr);
      } else {
        found = PETSC_FALSE;
      }
    }
    if (found) continue;
    ierr = DMPlexGetAdjacency(dm, p, &numAdj, &tmpAdj);CHKERRQ(ierr);
    ierr = PetscSectionGetDof(anchorSectionAdj, p, &anDof);CHKERRQ(ierr);
    ierr = PetscSectionGetOffset(anchorSectionAdj, p, &anOff);CHKERRQ(ierr);
    for (d = goff; d < goff+dof-cdof; ++d) {
      PetscInt adof, aoff, i = 0;

      ierr = PetscSectionGetDof(sectionAdj, d, &adof);CHKERRQ(ierr);
      ierr = PetscSectionGetOffset(sectionAdj, d, &aoff);CHKERRQ(ierr);
      for (q = 0; q < numAdj; ++q) {
        const PetscInt  padj = tmpAdj[q];
        PetscInt        ndof, ncdof, ngoff, nd;
        const PetscInt *ncind;

        /* Adjacent points may not be in the section chart */
        if ((padj < pStart) || (padj >= pEnd)) continue;
        ierr = PetscSectionGetDof(section, padj, &ndof);CHKERRQ(ierr);
        ierr = PetscSectionGetConstraintDof(section, padj, &ncdof);CHKERRQ(ierr);
        ierr = PetscSectionGetConstraintIndices(section, padj, &ncind);CHKERRQ(ierr);
        ierr = PetscSectionGetOffset(sectionGlobal, padj, &ngoff);CHKERRQ(ierr);
        for (nd = 0; nd < ndof-ncdof; ++nd, ++i) {
          cols[aoff+i] = ngoff < 0 ? -(ngoff+1)+nd : ngoff+nd;
        }
      }
      for (q = 0; q < anDof; q++, i++) {
        cols[aoff+i] = anchorAdj[anOff + q];
      }
      if (i != adof) SETERRQ4(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of entries %D != %D for dof %D (point %D)", i, adof, d, p);
    }
  }
  ierr = PetscSectionDestroy(&anchorSectionAdj);CHKERRQ(ierr);
  ierr = PetscSectionDestroy(&leafSectionAdj);CHKERRQ(ierr);
  ierr = PetscSectionDestroy(&rootSectionAdj);CHKERRQ(ierr);
  ierr = PetscFree(anchorAdj);CHKERRQ(ierr);
  ierr = PetscFree(rootAdj);CHKERRQ(ierr);
  ierr = PetscFree(tmpAdj);CHKERRQ(ierr);
  /* Debugging */
  if (debug) {
    IS tmp;
    ierr = PetscPrintf(comm, "Column indices\n");CHKERRQ(ierr);
    ierr = ISCreateGeneral(comm, numCols, cols, PETSC_USE_POINTER, &tmp);CHKERRQ(ierr);
    ierr = ISView(tmp, NULL);CHKERRQ(ierr);
    ierr = ISDestroy(&tmp);CHKERRQ(ierr);
  }
  /* Create allocation vectors from adjacency graph */
  ierr = MatGetLocalSize(A, &locRows, NULL);CHKERRQ(ierr);
  ierr = PetscLayoutCreate(PetscObjectComm((PetscObject)A), &rLayout);CHKERRQ(ierr);
  ierr = PetscLayoutSetLocalSize(rLayout, locRows);CHKERRQ(ierr);
  ierr = PetscLayoutSetBlockSize(rLayout, 1);CHKERRQ(ierr);
  ierr = PetscLayoutSetUp(rLayout);CHKERRQ(ierr);
  ierr = PetscLayoutGetRange(rLayout, &rStart, &rEnd);CHKERRQ(ierr);
  ierr = PetscLayoutDestroy(&rLayout);CHKERRQ(ierr);
  /* Only loop over blocks of rows */
  if (rStart%bs || rEnd%bs) SETERRQ3(PetscObjectComm((PetscObject)A), PETSC_ERR_ARG_WRONG, "Invalid layout [%d, %d) for matrix, must be divisible by block size %d", rStart, rEnd, bs);
  for (r = rStart/bs; r < rEnd/bs; ++r) {
    const PetscInt row = r*bs;
    PetscInt       numCols, cStart, c;

    ierr = PetscSectionGetDof(sectionAdj, row, &numCols);CHKERRQ(ierr);
    ierr = PetscSectionGetOffset(sectionAdj, row, &cStart);CHKERRQ(ierr);
    for (c = cStart; c < cStart+numCols; ++c) {
      if ((cols[c] >= rStart*bs) && (cols[c] < rEnd*bs)) {
        ++dnz[r-rStart];
        if (cols[c] >= row) ++dnzu[r-rStart];
      } else {
        ++onz[r-rStart];
        if (cols[c] >= row) ++onzu[r-rStart];
      }
    }
  }
  if (bs > 1) {
    for (r = 0; r < locRows/bs; ++r) {
      dnz[r]  /= bs;
      onz[r]  /= bs;
      dnzu[r] /= bs;
      onzu[r] /= bs;
    }
  }
  /* Set matrix pattern */
  ierr = MatXAIJSetPreallocation(A, bs, dnz, onz, dnzu, onzu);CHKERRQ(ierr);
  ierr = MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);CHKERRQ(ierr);
  /* Check for symmetric storage */
  ierr = MatGetType(A, &mtype);CHKERRQ(ierr);
  ierr = PetscStrcmp(mtype, MATSBAIJ, &isSymBlock);CHKERRQ(ierr);
  ierr = PetscStrcmp(mtype, MATSEQSBAIJ, &isSymSeqBlock);CHKERRQ(ierr);
  ierr = PetscStrcmp(mtype, MATMPISBAIJ, &isSymMPIBlock);CHKERRQ(ierr);
  if (isSymBlock || isSymSeqBlock || isSymMPIBlock) {ierr = MatSetOption(A, MAT_IGNORE_LOWER_TRIANGULAR, PETSC_TRUE);CHKERRQ(ierr);}
  /* Fill matrix with zeros */
  if (fillMatrix) {
    PetscScalar *values;
    PetscInt     maxRowLen = 0;

    for (r = rStart; r < rEnd; ++r) {
      PetscInt len;

      ierr      = PetscSectionGetDof(sectionAdj, r, &len);CHKERRQ(ierr);
      maxRowLen = PetscMax(maxRowLen, len);
    }
    ierr = PetscCalloc1(maxRowLen, &values);CHKERRQ(ierr);
    for (r = rStart; r < rEnd; ++r) {
      PetscInt numCols, cStart;

      ierr = PetscSectionGetDof(sectionAdj, r, &numCols);CHKERRQ(ierr);
      ierr = PetscSectionGetOffset(sectionAdj, r, &cStart);CHKERRQ(ierr);
      ierr = MatSetValues(A, 1, &r, numCols, &cols[cStart], values, INSERT_VALUES);CHKERRQ(ierr);
    }
    ierr = PetscFree(values);CHKERRQ(ierr);
    ierr = MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
    ierr = MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  }
  /* restore original useAnchors */
  ierr = DMPlexSetAdjacencyUseAnchors(dm,useAnchors);CHKERRQ(ierr);
  ierr = PetscSectionDestroy(&sectionAdj);CHKERRQ(ierr);
  ierr = PetscFree(cols);CHKERRQ(ierr);
  ierr = PetscLogEventEnd(DMPLEX_Preallocate,dm,0,0,0);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
/*@C
  DMPlexDistribute - Distributes the mesh and any associated sections.

  Not Collective

  Input Parameter:
+ dm  - The original DMPlex object
. partitioner - The partitioning package, or NULL for the default
- overlap - The overlap of partitions, 0 is the default

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

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

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

  Level: intermediate

.keywords: mesh, elements
.seealso: DMPlexCreate(), DMPlexDistributeByFace(), DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure()
@*/
PetscErrorCode DMPlexDistribute(DM dm, const char partitioner[], PetscInt overlap, PetscSF *sf, DM *dmParallel)
{
  DM_Plex               *mesh   = (DM_Plex*) dm->data, *pmesh;
  MPI_Comm               comm;
  const PetscInt         height = 0;
  PetscInt               dim, numRemoteRanks;
  IS                     origCellPart,        origPart,        cellPart,        part;
  PetscSection           origCellPartSection, origPartSection, cellPartSection, partSection;
  PetscSFNode           *remoteRanks;
  PetscSF                partSF, pointSF, coneSF;
  ISLocalToGlobalMapping renumbering;
  PetscSection           originalConeSection, newConeSection;
  PetscInt              *remoteOffsets;
  PetscInt              *cones, *newCones, newConesSize;
  PetscBool              flg;
  PetscMPIInt            rank, numProcs, p;
  PetscErrorCode         ierr;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(dm, DM_CLASSID, 1);
  if (sf) PetscValidPointer(sf,4);
  PetscValidPointer(dmParallel,5);

  ierr = PetscLogEventBegin(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr);
  ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr);

  *dmParallel = NULL;
  if (numProcs == 1) PetscFunctionReturn(0);

  ierr = DMPlexGetDimension(dm, &dim);CHKERRQ(ierr);
  /* Create cell partition - We need to rewrite to use IS, use the MatPartition stuff */
  ierr = PetscLogEventBegin(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr);
  if (overlap > 1) SETERRQ(PetscObjectComm((PetscObject)dm), PETSC_ERR_SUP, "Overlap > 1 not yet implemented");
  ierr = DMPlexCreatePartition(dm, partitioner, height, overlap > 0 ? PETSC_TRUE : PETSC_FALSE, &cellPartSection, &cellPart, &origCellPartSection, &origCellPart);CHKERRQ(ierr);
  /* Create SF assuming a serial partition for all processes: Could check for IS length here */
  if (!rank) numRemoteRanks = numProcs;
  else       numRemoteRanks = 0;
  ierr = PetscMalloc1(numRemoteRanks, &remoteRanks);CHKERRQ(ierr);
  for (p = 0; p < numRemoteRanks; ++p) {
    remoteRanks[p].rank  = p;
    remoteRanks[p].index = 0;
  }
  ierr = PetscSFCreate(comm, &partSF);CHKERRQ(ierr);
  ierr = PetscSFSetGraph(partSF, 1, numRemoteRanks, NULL, PETSC_OWN_POINTER, remoteRanks, PETSC_OWN_POINTER);CHKERRQ(ierr);
  ierr = PetscOptionsHasName(((PetscObject) dm)->prefix, "-partition_view", &flg);CHKERRQ(ierr);
  if (flg) {
    ierr = PetscPrintf(comm, "Cell Partition:\n");CHKERRQ(ierr);
    ierr = PetscSectionView(cellPartSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
    ierr = ISView(cellPart, NULL);CHKERRQ(ierr);
    if (origCellPart) {
      ierr = PetscPrintf(comm, "Original Cell Partition:\n");CHKERRQ(ierr);
      ierr = PetscSectionView(origCellPartSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
      ierr = ISView(origCellPart, NULL);CHKERRQ(ierr);
    }
    ierr = PetscSFView(partSF, NULL);CHKERRQ(ierr);
  }
  /* Close the partition over the mesh */
  ierr = DMPlexCreatePartitionClosure(dm, cellPartSection, cellPart, &partSection, &part);CHKERRQ(ierr);
  ierr = ISDestroy(&cellPart);CHKERRQ(ierr);
  ierr = PetscSectionDestroy(&cellPartSection);CHKERRQ(ierr);
  /* Create new mesh */
  ierr  = DMPlexCreate(comm, dmParallel);CHKERRQ(ierr);
  ierr  = DMPlexSetDimension(*dmParallel, dim);CHKERRQ(ierr);
  ierr  = PetscObjectSetName((PetscObject) *dmParallel, "Parallel Mesh");CHKERRQ(ierr);
  pmesh = (DM_Plex*) (*dmParallel)->data;
  /* Distribute sieve points and the global point numbering (replaces creating remote bases) */
  ierr = PetscSFConvertPartition(partSF, partSection, part, &renumbering, &pointSF);CHKERRQ(ierr);
  if (flg) {
    ierr = PetscPrintf(comm, "Point Partition:\n");CHKERRQ(ierr);
    ierr = PetscSectionView(partSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
    ierr = ISView(part, NULL);CHKERRQ(ierr);
    ierr = PetscSFView(pointSF, NULL);CHKERRQ(ierr);
    ierr = PetscPrintf(comm, "Point Renumbering after partition:\n");CHKERRQ(ierr);
    ierr = ISLocalToGlobalMappingView(renumbering, NULL);CHKERRQ(ierr);
  }
  ierr = PetscLogEventEnd(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr);
  ierr = PetscLogEventBegin(DMPLEX_DistributeCones,dm,0,0,0);CHKERRQ(ierr);
  /* Distribute cone section */
  ierr = DMPlexGetConeSection(dm, &originalConeSection);CHKERRQ(ierr);
  ierr = DMPlexGetConeSection(*dmParallel, &newConeSection);CHKERRQ(ierr);
  ierr = PetscSFDistributeSection(pointSF, originalConeSection, &remoteOffsets, newConeSection);CHKERRQ(ierr);
  ierr = DMSetUp(*dmParallel);CHKERRQ(ierr);
  {
    PetscInt pStart, pEnd, p;

    ierr = PetscSectionGetChart(newConeSection, &pStart, &pEnd);CHKERRQ(ierr);
    for (p = pStart; p < pEnd; ++p) {
      PetscInt coneSize;
      ierr               = PetscSectionGetDof(newConeSection, p, &coneSize);CHKERRQ(ierr);
      pmesh->maxConeSize = PetscMax(pmesh->maxConeSize, coneSize);
    }
  }
  /* Communicate and renumber cones */
  ierr = PetscSFCreateSectionSF(pointSF, originalConeSection, remoteOffsets, newConeSection, &coneSF);CHKERRQ(ierr);
  ierr = DMPlexGetCones(dm, &cones);CHKERRQ(ierr);
  ierr = DMPlexGetCones(*dmParallel, &newCones);CHKERRQ(ierr);
  ierr = PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr);
  ierr = PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr);
  ierr = PetscSectionGetStorageSize(newConeSection, &newConesSize);CHKERRQ(ierr);
  ierr = ISGlobalToLocalMappingApplyBlock(renumbering, IS_GTOLM_MASK, newConesSize, newCones, NULL, newCones);CHKERRQ(ierr);
  ierr = PetscOptionsHasName(((PetscObject) dm)->prefix, "-cones_view", &flg);CHKERRQ(ierr);
  if (flg) {
    ierr = PetscPrintf(comm, "Serial Cone Section:\n");CHKERRQ(ierr);
    ierr = PetscSectionView(originalConeSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
    ierr = PetscPrintf(comm, "Parallel Cone Section:\n");CHKERRQ(ierr);
    ierr = PetscSectionView(newConeSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
    ierr = PetscSFView(coneSF, NULL);CHKERRQ(ierr);
  }
  ierr = DMPlexGetConeOrientations(dm, &cones);CHKERRQ(ierr);
  ierr = DMPlexGetConeOrientations(*dmParallel, &newCones);CHKERRQ(ierr);
  ierr = PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr);
  ierr = PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr);
  ierr = PetscSFDestroy(&coneSF);CHKERRQ(ierr);
  ierr = PetscLogEventEnd(DMPLEX_DistributeCones,dm,0,0,0);CHKERRQ(ierr);
  /* Create supports and stratify sieve */
  {
    PetscInt pStart, pEnd;

    ierr = PetscSectionGetChart(pmesh->coneSection, &pStart, &pEnd);CHKERRQ(ierr);
    ierr = PetscSectionSetChart(pmesh->supportSection, pStart, pEnd);CHKERRQ(ierr);
  }
  ierr = DMPlexSymmetrize(*dmParallel);CHKERRQ(ierr);
  ierr = DMPlexStratify(*dmParallel);CHKERRQ(ierr);
  /* Distribute Coordinates */
  {
    PetscSection originalCoordSection, newCoordSection;
    Vec          originalCoordinates, newCoordinates;
    PetscInt     bs;
    const char  *name;

    ierr = DMGetCoordinateSection(dm, &originalCoordSection);CHKERRQ(ierr);
    ierr = DMGetCoordinateSection(*dmParallel, &newCoordSection);CHKERRQ(ierr);
    ierr = DMGetCoordinatesLocal(dm, &originalCoordinates);CHKERRQ(ierr);
    ierr = VecCreate(comm, &newCoordinates);CHKERRQ(ierr);
    ierr = PetscObjectGetName((PetscObject) originalCoordinates, &name);CHKERRQ(ierr);
    ierr = PetscObjectSetName((PetscObject) newCoordinates, name);CHKERRQ(ierr);

    ierr = DMPlexDistributeField(dm, pointSF, originalCoordSection, originalCoordinates, newCoordSection, newCoordinates);CHKERRQ(ierr);
    ierr = DMSetCoordinatesLocal(*dmParallel, newCoordinates);CHKERRQ(ierr);
    ierr = VecGetBlockSize(originalCoordinates, &bs);CHKERRQ(ierr);
    ierr = VecSetBlockSize(newCoordinates, bs);CHKERRQ(ierr);
    ierr = VecDestroy(&newCoordinates);CHKERRQ(ierr);
  }
  /* Distribute labels */
  ierr = PetscLogEventBegin(DMPLEX_DistributeLabels,dm,0,0,0);CHKERRQ(ierr);
  {
    DMLabel  next      = mesh->labels, newNext = pmesh->labels;
    PetscInt numLabels = 0, l;

    /* Bcast number of labels */
    while (next) {++numLabels; next = next->next;}
    ierr = MPI_Bcast(&numLabels, 1, MPIU_INT, 0, comm);CHKERRQ(ierr);
    next = mesh->labels;
    for (l = 0; l < numLabels; ++l) {
      DMLabel   labelNew;
      PetscBool isdepth;

      /* Skip "depth" because it is recreated */
      if (!rank) {ierr = PetscStrcmp(next->name, "depth", &isdepth);CHKERRQ(ierr);}
      ierr = MPI_Bcast(&isdepth, 1, MPIU_BOOL, 0, comm);CHKERRQ(ierr);
      if (isdepth) {if (!rank) next = next->next; continue;}
      ierr = DMLabelDistribute(next, partSection, part, renumbering, &labelNew);CHKERRQ(ierr);
      /* Insert into list */
      if (newNext) newNext->next = labelNew;
      else         pmesh->labels = labelNew;
      newNext = labelNew;
      if (!rank) next = next->next;
    }
  }
  ierr = PetscLogEventEnd(DMPLEX_DistributeLabels,dm,0,0,0);CHKERRQ(ierr);
  /* Setup hybrid structure */
  {
    const PetscInt *gpoints;
    PetscInt        depth, n, d;

    for (d = 0; d <= dim; ++d) {pmesh->hybridPointMax[d] = mesh->hybridPointMax[d];}
    ierr = MPI_Bcast(pmesh->hybridPointMax, dim+1, MPIU_INT, 0, comm);CHKERRQ(ierr);
    ierr = ISLocalToGlobalMappingGetSize(renumbering, &n);CHKERRQ(ierr);
    ierr = ISLocalToGlobalMappingGetIndices(renumbering, &gpoints);CHKERRQ(ierr);
    ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr);
    for (d = 0; d <= dim; ++d) {
      PetscInt pmax = pmesh->hybridPointMax[d], newmax = 0, pEnd, stratum[2], p;

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

        if ((point >= stratum[0]) && (point < stratum[1]) && (point >= pmax)) ++newmax;
      }
      if (newmax > 0) pmesh->hybridPointMax[d] = pEnd - newmax;
      else            pmesh->hybridPointMax[d] = -1;
    }
    ierr = ISLocalToGlobalMappingRestoreIndices(renumbering, &gpoints);CHKERRQ(ierr);
  }
  /* Cleanup Partition */
  ierr = ISLocalToGlobalMappingDestroy(&renumbering);CHKERRQ(ierr);
  ierr = PetscSFDestroy(&partSF);CHKERRQ(ierr);
  ierr = PetscSectionDestroy(&partSection);CHKERRQ(ierr);
  ierr = ISDestroy(&part);CHKERRQ(ierr);
  /* Create point SF for parallel mesh */
  ierr = PetscLogEventBegin(DMPLEX_DistributeSF,dm,0,0,0);CHKERRQ(ierr);
  {
    const PetscInt *leaves;
    PetscSFNode    *remotePoints, *rowners, *lowners;
    PetscInt        numRoots, numLeaves, numGhostPoints = 0, p, gp, *ghostPoints;
    PetscInt        pStart, pEnd;

    ierr = DMPlexGetChart(*dmParallel, &pStart, &pEnd);CHKERRQ(ierr);
    ierr = PetscSFGetGraph(pointSF, &numRoots, &numLeaves, &leaves, NULL);CHKERRQ(ierr);
    ierr = PetscMalloc2(numRoots,&rowners,numLeaves,&lowners);CHKERRQ(ierr);
    for (p=0; p<numRoots; p++) {
      rowners[p].rank  = -1;
      rowners[p].index = -1;
    }
    if (origCellPart) {
      /* Make sure points in the original partition are not assigned to other procs */
      const PetscInt *origPoints;

      ierr = DMPlexCreatePartitionClosure(dm, origCellPartSection, origCellPart, &origPartSection, &origPart);CHKERRQ(ierr);
      ierr = ISGetIndices(origPart, &origPoints);CHKERRQ(ierr);
      for (p = 0; p < numProcs; ++p) {
        PetscInt dof, off, d;

        ierr = PetscSectionGetDof(origPartSection, p, &dof);CHKERRQ(ierr);
        ierr = PetscSectionGetOffset(origPartSection, p, &off);CHKERRQ(ierr);
        for (d = off; d < off+dof; ++d) {
          rowners[origPoints[d]].rank = p;
        }
      }
      ierr = ISRestoreIndices(origPart, &origPoints);CHKERRQ(ierr);
      ierr = ISDestroy(&origPart);CHKERRQ(ierr);
      ierr = PetscSectionDestroy(&origPartSection);CHKERRQ(ierr);
    }
    ierr = ISDestroy(&origCellPart);CHKERRQ(ierr);
    ierr = PetscSectionDestroy(&origCellPartSection);CHKERRQ(ierr);

    ierr = PetscSFBcastBegin(pointSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr);
    ierr = PetscSFBcastEnd(pointSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr);
    for (p = 0; p < numLeaves; ++p) {
      if (lowners[p].rank < 0 || lowners[p].rank == rank) { /* Either put in a bid or we know we own it */
        lowners[p].rank  = rank;
        lowners[p].index = leaves ? leaves[p] : p;
      } else if (lowners[p].rank >= 0) { /* Point already claimed so flag so that MAXLOC does not listen to us */
        lowners[p].rank  = -2;
        lowners[p].index = -2;
      }
    }
    for (p=0; p<numRoots; p++) { /* Root must not participate in the rediction, flag so that MAXLOC does not use */
      rowners[p].rank  = -3;
      rowners[p].index = -3;
    }
    ierr = PetscSFReduceBegin(pointSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);CHKERRQ(ierr);
    ierr = PetscSFReduceEnd(pointSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);CHKERRQ(ierr);
    ierr = PetscSFBcastBegin(pointSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr);
    ierr = PetscSFBcastEnd(pointSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr);
    for (p = 0; p < numLeaves; ++p) {
      if (lowners[p].rank < 0 || lowners[p].index < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Cell partition corrupt: point not claimed");
      if (lowners[p].rank != rank) ++numGhostPoints;
    }
    ierr = PetscMalloc1(numGhostPoints,    &ghostPoints);CHKERRQ(ierr);
    ierr = PetscMalloc1(numGhostPoints, &remotePoints);CHKERRQ(ierr);
    for (p = 0, gp = 0; p < numLeaves; ++p) {
      if (lowners[p].rank != rank) {
        ghostPoints[gp]        = leaves ? leaves[p] : p;
        remotePoints[gp].rank  = lowners[p].rank;
        remotePoints[gp].index = lowners[p].index;
        ++gp;
      }
    }
    ierr = PetscFree2(rowners,lowners);CHKERRQ(ierr);
    ierr = PetscSFSetGraph((*dmParallel)->sf, pEnd - pStart, numGhostPoints, ghostPoints, PETSC_OWN_POINTER, remotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr);
    ierr = PetscSFSetFromOptions((*dmParallel)->sf);CHKERRQ(ierr);
  }
  pmesh->useCone    = mesh->useCone;
  pmesh->useClosure = mesh->useClosure;
  ierr = PetscLogEventEnd(DMPLEX_DistributeSF,dm,0,0,0);CHKERRQ(ierr);
  /* Copy BC */
  ierr = DMPlexCopyBoundary(dm, *dmParallel);CHKERRQ(ierr);
  /* Cleanup */
  if (sf) {*sf = pointSF;}
  else    {ierr = PetscSFDestroy(&pointSF);CHKERRQ(ierr);}
  ierr = DMSetFromOptions(*dmParallel);CHKERRQ(ierr);
  ierr = PetscLogEventEnd(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
示例#8
0
PetscErrorCode DMLabelDistribute(DMLabel label, PetscSF sf, DMLabel *labelNew)
{
  MPI_Comm       comm;
  PetscSection   rootSection, leafSection;
  PetscSF        labelSF;
  PetscInt       p, pStart, pEnd, l, lStart, lEnd, s, nroots, nleaves, size, dof, offset, stratum;
  PetscInt      *remoteOffsets, *rootStrata, *rootIdx, *leafStrata, *strataIdx;
  char          *name;
  PetscInt       nameSize;
  size_t         len = 0;
  PetscMPIInt    rank, numProcs;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  if (label) {ierr = DMLabelMakeAllValid_Private(label);CHKERRQ(ierr);}
  ierr = PetscObjectGetComm((PetscObject)sf, &comm);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
  ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr);
  /* Bcast name */
  if (!rank) {ierr = PetscStrlen(label->name, &len);CHKERRQ(ierr);}
  nameSize = len;
  ierr = MPI_Bcast(&nameSize, 1, MPIU_INT, 0, comm);CHKERRQ(ierr);
  ierr = PetscMalloc1(nameSize+1, &name);CHKERRQ(ierr);
  if (!rank) {ierr = PetscMemcpy(name, label->name, nameSize+1);CHKERRQ(ierr);}
  ierr = MPI_Bcast(name, nameSize+1, MPI_CHAR, 0, comm);CHKERRQ(ierr);
  ierr = DMLabelCreate(name, labelNew);CHKERRQ(ierr);
  ierr = PetscFree(name);CHKERRQ(ierr);
  /* Bcast numStrata */
  if (!rank) (*labelNew)->numStrata = label->numStrata;
  ierr = MPI_Bcast(&(*labelNew)->numStrata, 1, MPIU_INT, 0, comm);CHKERRQ(ierr);
  /* Bcast stratumValues */
  ierr = PetscMalloc1((*labelNew)->numStrata, &(*labelNew)->stratumValues);CHKERRQ(ierr);
  if (!rank) {ierr = PetscMemcpy((*labelNew)->stratumValues, label->stratumValues, label->numStrata * sizeof(PetscInt));CHKERRQ(ierr);}
  ierr = MPI_Bcast((*labelNew)->stratumValues, (*labelNew)->numStrata, MPIU_INT, 0, comm);CHKERRQ(ierr);
  ierr = PetscMalloc1((*labelNew)->numStrata, &(*labelNew)->arrayValid);CHKERRQ(ierr);
  for (s = 0; s < (*labelNew)->numStrata; ++s) (*labelNew)->arrayValid[s] = PETSC_TRUE;

  /* Build a section detailing strata-per-point, distribute and build SF
     from that and then send our points. */
  ierr = PetscSFGetGraph(sf, &nroots, &nleaves, NULL, NULL);CHKERRQ(ierr);
  ierr = PetscSectionCreate(comm, &rootSection);CHKERRQ(ierr);
  ierr = PetscSectionSetChart(rootSection, 0, nroots);CHKERRQ(ierr);
  if (label) {
    for (s = 0; s < label->numStrata; ++s) {
      lStart = 0;
      lEnd = label->stratumSizes[s];
      for (l=lStart; l<lEnd; l++) {
        ierr = PetscSectionGetDof(rootSection, label->points[s][l], &dof);CHKERRQ(ierr);
        ierr = PetscSectionSetDof(rootSection, label->points[s][l], dof+1);CHKERRQ(ierr);
      }
    }
  }
  ierr = PetscSectionSetUp(rootSection);CHKERRQ(ierr);

  /* Create a point-wise array of point strata */
  ierr = PetscSectionGetStorageSize(rootSection, &size);CHKERRQ(ierr);
  ierr = PetscMalloc1(size, &rootStrata);CHKERRQ(ierr);
  ierr = PetscCalloc1(nroots, &rootIdx);CHKERRQ(ierr);
  if (label) {
    for (s = 0; s < label->numStrata; ++s) {
      lStart = 0;
      lEnd = label->stratumSizes[s];
      for (l=lStart; l<lEnd; l++) {
        p = label->points[s][l];
        ierr = PetscSectionGetOffset(rootSection, p, &offset);CHKERRQ(ierr);
        rootStrata[offset+rootIdx[p]++] = s;
      }
    }
  }

  /* Build SF that maps label points to remote processes */
  ierr = PetscSectionCreate(comm, &leafSection);CHKERRQ(ierr);
  ierr = PetscSFDistributeSection(sf, rootSection, &remoteOffsets, leafSection);CHKERRQ(ierr);
  ierr = PetscSFCreateSectionSF(sf, rootSection, remoteOffsets, leafSection, &labelSF);CHKERRQ(ierr);

  /* Send the strata for each point over the derived SF */
  ierr = PetscSectionGetStorageSize(leafSection, &size);CHKERRQ(ierr);
  ierr = PetscMalloc1(size, &leafStrata);CHKERRQ(ierr);
  ierr = PetscSFBcastBegin(labelSF, MPIU_INT, rootStrata, leafStrata);CHKERRQ(ierr);
  ierr = PetscSFBcastEnd(labelSF, MPIU_INT, rootStrata, leafStrata);CHKERRQ(ierr);

  /* Rebuild the point strata on the receiver */
  ierr = PetscCalloc1((*labelNew)->numStrata,&(*labelNew)->stratumSizes);CHKERRQ(ierr);
  ierr = PetscSectionGetChart(leafSection, &pStart, &pEnd);CHKERRQ(ierr);
  for (p=pStart; p<pEnd; p++) {
    ierr = PetscSectionGetDof(leafSection, p, &dof);CHKERRQ(ierr);
    ierr = PetscSectionGetOffset(leafSection, p, &offset);CHKERRQ(ierr);
    for (s=0; s<dof; s++) {
      (*labelNew)->stratumSizes[leafStrata[offset+s]]++;
    }
  }
  ierr = PetscCalloc1((*labelNew)->numStrata,&(*labelNew)->ht);CHKERRQ(ierr);
  ierr = PetscMalloc1((*labelNew)->numStrata,&(*labelNew)->points);CHKERRQ(ierr);
  for (s = 0; s < (*labelNew)->numStrata; ++s) {
    PetscHashICreate((*labelNew)->ht[s]);
    ierr = PetscMalloc1((*labelNew)->stratumSizes[s], &(*labelNew)->points[s]);CHKERRQ(ierr);
  }

  /* Insert points into new strata */
  ierr = PetscCalloc1((*labelNew)->numStrata, &strataIdx);CHKERRQ(ierr);
  ierr = PetscSectionGetChart(leafSection, &pStart, &pEnd);CHKERRQ(ierr);
  for (p=pStart; p<pEnd; p++) {
    ierr = PetscSectionGetDof(leafSection, p, &dof);CHKERRQ(ierr);
    ierr = PetscSectionGetOffset(leafSection, p, &offset);CHKERRQ(ierr);
    for (s=0; s<dof; s++) {
      stratum = leafStrata[offset+s];
      (*labelNew)->points[stratum][strataIdx[stratum]++] = p;
    }
  }
  ierr = PetscFree(rootStrata);CHKERRQ(ierr);
  ierr = PetscFree(leafStrata);CHKERRQ(ierr);
  ierr = PetscFree(rootIdx);CHKERRQ(ierr);
  ierr = PetscFree(strataIdx);CHKERRQ(ierr);
  ierr = PetscSectionDestroy(&rootSection);CHKERRQ(ierr);
  ierr = PetscSectionDestroy(&leafSection);CHKERRQ(ierr);
  ierr = PetscSFDestroy(&labelSF);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
示例#9
0
文件: ex3.c 项目: erdc-cm/petsc-dev
/* Distribute cones
   - Partitioning:         input partition point map and naive sf, output sf with inverse of map, distribute points
   - Distribute section:   input current sf, communicate sizes and offsets, output local section and offsets (only use for new sf)
   - Create SF for values: input current sf and offsets, output new sf
   - Distribute values:    input new sf, communicate values
 */
PetscErrorCode DistributeMesh(DM dm, AppCtx *user, PetscSF *pointSF, DM *parallelDM)
{
  MPI_Comm       comm   = ((PetscObject) dm)->comm;
  const PetscInt height = 0;
  PetscInt       dim, numRemoteRanks;
  IS             cellPart,        part;
  PetscSection   cellPartSection, partSection;
  PetscSFNode   *remoteRanks;
  PetscSF        partSF;
  ISLocalToGlobalMapping renumbering;
  PetscSF        coneSF;
  PetscSection   originalConeSection, newConeSection;
  PetscInt      *remoteOffsets, newConesSize;
  PetscInt      *cones, *newCones;
  PetscMPIInt    numProcs, rank, p;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr);
  ierr = DMMeshGetDimension(dm, &dim);CHKERRQ(ierr);
  /* Create cell partition - We need to rewrite to use IS, use the MatPartition stuff */
  ierr = DMMeshCreatePartition(dm, &cellPartSection, &cellPart, height);CHKERRQ(ierr);
  /* Create SF assuming a serial partition for all processes: Could check for IS length here */
  if (!rank) {
    numRemoteRanks = numProcs;
  } else {
    numRemoteRanks = 0;
  }
  ierr = PetscMalloc(numRemoteRanks * sizeof(PetscSFNode), &remoteRanks);CHKERRQ(ierr);
  for(p = 0; p < numRemoteRanks; ++p) {
    remoteRanks[p].rank  = p;
    remoteRanks[p].index = 0;
  }
  ierr = PetscSFCreate(comm, &partSF);CHKERRQ(ierr);
  ierr = PetscSFSetGraph(partSF, 1, numRemoteRanks, PETSC_NULL, PETSC_OWN_POINTER, remoteRanks, PETSC_OWN_POINTER);CHKERRQ(ierr);
  /* Debugging */
  ierr = PetscPrintf(comm, "Cell Partition:\n");CHKERRQ(ierr);
  ierr = PetscSectionView(cellPartSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  ierr = ISView(cellPart, PETSC_NULL);CHKERRQ(ierr);
  ierr = PetscSFView(partSF, PETSC_NULL);CHKERRQ(ierr);
  /* Close the partition over the mesh */
  ierr = DMMeshCreatePartitionClosure(dm, cellPartSection, cellPart, &partSection, &part);CHKERRQ(ierr);
  ierr = ISDestroy(&cellPart);CHKERRQ(ierr);
  ierr = PetscSectionDestroy(&cellPartSection);CHKERRQ(ierr);
  /* Create new mesh */
  ierr = DMMeshCreate(comm, parallelDM);CHKERRQ(ierr);
  ierr = DMMeshSetDimension(*parallelDM, dim);CHKERRQ(ierr);
  ierr = PetscObjectSetName((PetscObject) *parallelDM, "Parallel Mesh");CHKERRQ(ierr);
  /* Distribute sieve points and the global point numbering (replaces creating remote bases) */
  ierr = PetscSFConvertPartition(partSF, partSection, part, &renumbering, pointSF);CHKERRQ(ierr);
  /* Debugging */
  ierr = PetscPrintf(comm, "Point Partition:\n");CHKERRQ(ierr);
  ierr = PetscSectionView(partSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  ierr = ISView(part, PETSC_NULL);CHKERRQ(ierr);
  ierr = PetscSFView(*pointSF, PETSC_NULL);CHKERRQ(ierr);
  ierr = PetscPrintf(comm, "Point Renumbering after partition:\n");CHKERRQ(ierr);
  ierr = ISLocalToGlobalMappingView(renumbering, PETSC_NULL);CHKERRQ(ierr);
  /* Cleanup */
  ierr = PetscSFDestroy(&partSF);CHKERRQ(ierr);
  ierr = PetscSectionDestroy(&partSection);CHKERRQ(ierr);
  ierr = ISDestroy(&part);CHKERRQ(ierr);
  /* Distribute cone section */
  ierr = DMMeshGetConeSection(dm, &originalConeSection);CHKERRQ(ierr);
  ierr = DMMeshGetConeSection(*parallelDM, &newConeSection);CHKERRQ(ierr);
  ierr = PetscSFDistributeSection(*pointSF, originalConeSection, &remoteOffsets, newConeSection);CHKERRQ(ierr);
  ierr = DMMeshSetUp(*parallelDM);CHKERRQ(ierr);
  /* Communicate and renumber cones */
  ierr = PetscSFCreateSectionSF(*pointSF, originalConeSection, remoteOffsets, newConeSection, &coneSF);CHKERRQ(ierr);
  ierr = DMMeshGetCones(dm, &cones);CHKERRQ(ierr);
  ierr = DMMeshGetCones(*parallelDM, &newCones);CHKERRQ(ierr);
  ierr = PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr);
  ierr = PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr);
  ierr = PetscSectionGetStorageSize(newConeSection, &newConesSize);CHKERRQ(ierr);
  ierr = ISGlobalToLocalMappingApply(renumbering, IS_GTOLM_MASK, newConesSize, newCones, PETSC_NULL, newCones);CHKERRQ(ierr);
  ierr = ISLocalToGlobalMappingDestroy(&renumbering);CHKERRQ(ierr);
  /* Debugging */
  ierr = PetscPrintf(comm, "Serial Cone Section:\n");CHKERRQ(ierr);
  ierr = PetscSectionView(originalConeSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  ierr = PetscPrintf(comm, "Parallel Cone Section:\n");CHKERRQ(ierr);
  ierr = PetscSectionView(newConeSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  ierr = PetscSFView(coneSF, PETSC_NULL);CHKERRQ(ierr);
  ierr = PetscSFDestroy(&coneSF);CHKERRQ(ierr);
  /* Create supports and stratify sieve */
  ierr = DMMeshSymmetrize(*parallelDM);CHKERRQ(ierr);
  ierr = DMMeshStratify(*parallelDM);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
示例#10
0
/* This interpolates the PointSF in parallel following local interpolation */
static PetscErrorCode DMPlexInterpolatePointSF(DM dm, PetscSF pointSF, PetscInt depth)
{
  PetscMPIInt        numProcs, rank;
  PetscInt           p, c, d, dof, offset;
  PetscInt           numLeaves, numRoots, candidatesSize, candidatesRemoteSize;
  const PetscInt    *localPoints;
  const PetscSFNode *remotePoints;
  PetscSFNode       *candidates, *candidatesRemote, *claims;
  PetscSection       candidateSection, candidateSectionRemote, claimSection;
  PetscHashI         leafhash;
  PetscHashIJ        roothash;
  PetscHashIJKey     key;
  PetscErrorCode     ierr;

  PetscFunctionBegin;
  ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &numProcs);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr);
  ierr = PetscSFGetGraph(pointSF, &numRoots, &numLeaves, &localPoints, &remotePoints);CHKERRQ(ierr);
  if (numProcs < 2 || numRoots < 0) PetscFunctionReturn(0);
  /* Build hashes of points in the SF for efficient lookup */
  PetscHashICreate(leafhash);
  PetscHashIJCreate(&roothash);
  ierr = PetscHashIJSetMultivalued(roothash, PETSC_FALSE);CHKERRQ(ierr);
  for (p = 0; p < numLeaves; ++p) {
    PetscHashIAdd(leafhash, localPoints[p], p);
    key.i = remotePoints[p].index; key.j = remotePoints[p].rank;
    PetscHashIJAdd(roothash, key, p);
  }
  /* Build a section / SFNode array of candidate points in the single-level adjacency of leaves,
     where each candidate is defined by the root entry for the other vertex that defines the edge. */
  ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), &candidateSection);CHKERRQ(ierr);
  ierr = PetscSectionSetChart(candidateSection, 0, numRoots);CHKERRQ(ierr);
  {
    PetscInt leaf, root, idx, a, *adj = NULL;
    for (p = 0; p < numLeaves; ++p) {
      PetscInt adjSize = PETSC_DETERMINE;
      ierr = DMPlexGetAdjacency_Internal(dm, localPoints[p], PETSC_FALSE, PETSC_FALSE, PETSC_FALSE, &adjSize, &adj);CHKERRQ(ierr);
      for (a = 0; a < adjSize; ++a) {
        PetscHashIMap(leafhash, adj[a], leaf);
        if (leaf >= 0) {ierr = PetscSectionAddDof(candidateSection, localPoints[p], 1);CHKERRQ(ierr);}
      }
    }
    ierr = PetscSectionSetUp(candidateSection);CHKERRQ(ierr);
    ierr = PetscSectionGetStorageSize(candidateSection, &candidatesSize);CHKERRQ(ierr);
    ierr = PetscMalloc1(candidatesSize, &candidates);CHKERRQ(ierr);
    for (p = 0; p < numLeaves; ++p) {
      PetscInt adjSize = PETSC_DETERMINE;
      ierr = PetscSectionGetOffset(candidateSection, localPoints[p], &offset);CHKERRQ(ierr);
      ierr = DMPlexGetAdjacency_Internal(dm, localPoints[p], PETSC_FALSE, PETSC_FALSE, PETSC_FALSE, &adjSize, &adj);CHKERRQ(ierr);
      for (idx = 0, a = 0; a < adjSize; ++a) {
        PetscHashIMap(leafhash, adj[a], root);
        if (root >= 0) candidates[offset+idx++] = remotePoints[root];
      }
    }
    ierr = PetscFree(adj);CHKERRQ(ierr);
  }
  /* Gather candidate section / array pair into the root partition via inverse(multi(pointSF)). */
  {
    PetscSF   sfMulti, sfInverse, sfCandidates;
    PetscInt *remoteOffsets;
    ierr = PetscSFGetMultiSF(pointSF, &sfMulti);CHKERRQ(ierr);
    ierr = PetscSFCreateInverseSF(sfMulti, &sfInverse);CHKERRQ(ierr);
    ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), &candidateSectionRemote);CHKERRQ(ierr);
    ierr = PetscSFDistributeSection(sfInverse, candidateSection, &remoteOffsets, candidateSectionRemote);CHKERRQ(ierr);
    ierr = PetscSFCreateSectionSF(sfInverse, candidateSection, remoteOffsets, candidateSectionRemote, &sfCandidates);CHKERRQ(ierr);
    ierr = PetscSectionGetStorageSize(candidateSectionRemote, &candidatesRemoteSize);CHKERRQ(ierr);
    ierr = PetscMalloc1(candidatesRemoteSize, &candidatesRemote);CHKERRQ(ierr);
    ierr = PetscSFBcastBegin(sfCandidates, MPIU_2INT, candidates, candidatesRemote);CHKERRQ(ierr);
    ierr = PetscSFBcastEnd(sfCandidates, MPIU_2INT, candidates, candidatesRemote);CHKERRQ(ierr);
    ierr = PetscSFDestroy(&sfInverse);CHKERRQ(ierr);
    ierr = PetscSFDestroy(&sfCandidates);CHKERRQ(ierr);
    ierr = PetscFree(remoteOffsets);CHKERRQ(ierr);
  }
  /* Walk local roots and check for each remote candidate whether we know all required points,
     either from owning it or having a root entry in the point SF. If we do we place a claim
     by replacing the vertex number with our edge ID. */
  {
    PetscInt        idx, root, joinSize, vertices[2];
    const PetscInt *rootdegree, *join = NULL;
    ierr = PetscSFComputeDegreeBegin(pointSF, &rootdegree);CHKERRQ(ierr);
    ierr = PetscSFComputeDegreeEnd(pointSF, &rootdegree);CHKERRQ(ierr);
    /* Loop remote edge connections and put in a claim if both vertices are known */
    for (idx = 0, p = 0; p < numRoots; ++p) {
      for (d = 0; d < rootdegree[p]; ++d) {
        ierr = PetscSectionGetDof(candidateSectionRemote, idx, &dof);CHKERRQ(ierr);
        ierr = PetscSectionGetOffset(candidateSectionRemote, idx, &offset);CHKERRQ(ierr);
        for (c = 0; c < dof; ++c) {
          /* We own both vertices, so we claim the edge by replacing vertex with edge */
          if (candidatesRemote[offset+c].rank == rank) {
            vertices[0] = p; vertices[1] = candidatesRemote[offset+c].index;
            ierr = DMPlexGetJoin(dm, 2, vertices, &joinSize, &join);CHKERRQ(ierr);
            if (joinSize == 1) candidatesRemote[offset+c].index = join[0];
            ierr = DMPlexRestoreJoin(dm, 2, vertices, &joinSize, &join);CHKERRQ(ierr);
            continue;
          }
          /* If we own one vertex and share a root with the other, we claim it */
          key.i = candidatesRemote[offset+c].index; key.j = candidatesRemote[offset+c].rank;
          PetscHashIJGet(roothash, key, &root);
          if (root >= 0) {
            vertices[0] = p; vertices[1] = localPoints[root];
            ierr = DMPlexGetJoin(dm, 2, vertices, &joinSize, &join);CHKERRQ(ierr);
            if (joinSize == 1) {
              candidatesRemote[offset+c].index = join[0];
              candidatesRemote[offset+c].rank = rank;
            }
            ierr = DMPlexRestoreJoin(dm, 2, vertices, &joinSize, &join);CHKERRQ(ierr);
          }
        }
        idx++;
      }
    }
  }
  /* Push claims back to receiver via the MultiSF and derive new pointSF mapping on receiver */
  {
    PetscSF         sfMulti, sfClaims, sfPointNew;
    PetscHashI      claimshash;
    PetscInt        size, pStart, pEnd, root, joinSize, numLocalNew;
    PetscInt       *remoteOffsets, *localPointsNew, vertices[2];
    const PetscInt *join = NULL;
    PetscSFNode    *remotePointsNew;
    ierr = PetscSFGetMultiSF(pointSF, &sfMulti);CHKERRQ(ierr);
    ierr = PetscSectionCreate(PetscObjectComm((PetscObject) dm), &claimSection);CHKERRQ(ierr);
    ierr = PetscSFDistributeSection(sfMulti, candidateSectionRemote, &remoteOffsets, claimSection);CHKERRQ(ierr);
    ierr = PetscSFCreateSectionSF(sfMulti, candidateSectionRemote, remoteOffsets, claimSection, &sfClaims);CHKERRQ(ierr);
    ierr = PetscSectionGetStorageSize(claimSection, &size);CHKERRQ(ierr);
    ierr = PetscMalloc1(size, &claims);CHKERRQ(ierr);
    ierr = PetscSFBcastBegin(sfClaims, MPIU_2INT, candidatesRemote, claims);CHKERRQ(ierr);
    ierr = PetscSFBcastEnd(sfClaims, MPIU_2INT, candidatesRemote, claims);CHKERRQ(ierr);
    ierr = PetscSFDestroy(&sfClaims);CHKERRQ(ierr);
    ierr = PetscFree(remoteOffsets);CHKERRQ(ierr);
    /* Walk the original section of local supports and add an SF entry for each updated item */
    PetscHashICreate(claimshash);
    for (p = 0; p < numRoots; ++p) {
      ierr = PetscSectionGetDof(candidateSection, p, &dof);CHKERRQ(ierr);
      ierr = PetscSectionGetOffset(candidateSection, p, &offset);CHKERRQ(ierr);
      for (d = 0; d < dof; ++d) {
        if (candidates[offset+d].index != claims[offset+d].index) {
          key.i = candidates[offset+d].index; key.j = candidates[offset+d].rank;
          PetscHashIJGet(roothash, key, &root);
          if (root >= 0) {
            vertices[0] = p; vertices[1] = localPoints[root];
            ierr = DMPlexGetJoin(dm, 2, vertices, &joinSize, &join);CHKERRQ(ierr);
            if (joinSize == 1) PetscHashIAdd(claimshash, join[0], offset+d);
            ierr = DMPlexRestoreJoin(dm, 2, vertices, &joinSize, &join);CHKERRQ(ierr);
          }
        }
      }
    }
    /* Create new pointSF from hashed claims */
    PetscHashISize(claimshash, numLocalNew);
    ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr);
    ierr = PetscMalloc1(numLeaves + numLocalNew, &localPointsNew);CHKERRQ(ierr);
    ierr = PetscMalloc1(numLeaves + numLocalNew, &remotePointsNew);CHKERRQ(ierr);
    for (p = 0; p < numLeaves; ++p) {
      localPointsNew[p] = localPoints[p];
      remotePointsNew[p].index = remotePoints[p].index;
      remotePointsNew[p].rank = remotePoints[p].rank;
    }
    p = numLeaves; ierr = PetscHashIGetKeys(claimshash, &p, localPointsNew);CHKERRQ(ierr);
    for (p = numLeaves; p < numLeaves + numLocalNew; ++p) {
      PetscHashIMap(claimshash, localPointsNew[p], offset);
      remotePointsNew[p] = claims[offset];
    }
    ierr = PetscSFCreate(PetscObjectComm((PetscObject) dm), &sfPointNew);CHKERRQ(ierr);
    ierr = PetscSFSetGraph(sfPointNew, pEnd-pStart, numLeaves+numLocalNew, localPointsNew, PETSC_OWN_POINTER, remotePointsNew, PETSC_OWN_POINTER);CHKERRQ(ierr);
    ierr = DMSetPointSF(dm, sfPointNew);CHKERRQ(ierr);
    ierr = PetscSFDestroy(&sfPointNew);CHKERRQ(ierr);
    PetscHashIDestroy(claimshash);
  }
  PetscHashIDestroy(leafhash);
  ierr = PetscHashIJDestroy(&roothash);CHKERRQ(ierr);
  ierr = PetscSectionDestroy(&candidateSection);CHKERRQ(ierr);
  ierr = PetscSectionDestroy(&candidateSectionRemote);CHKERRQ(ierr);
  ierr = PetscSectionDestroy(&claimSection);CHKERRQ(ierr);
  ierr = PetscFree(candidates);CHKERRQ(ierr);
  ierr = PetscFree(candidatesRemote);CHKERRQ(ierr);
  ierr = PetscFree(claims);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}