impls/pmetis/pmetis.c

#include <../src/mat/impls/adj/mpi/mpiadj.h> /*I "petscmat.h" I*/

/*
   Currently using ParMetis-4.0.2
*/

#include <parmetis.h>

/*
      The first 5 elements of this structure are the input control array to Metis
*/
typedef struct {
  PetscInt  cuts; /* number of cuts made (output) */
  PetscInt  foldfactor;
  PetscInt  parallel; /* use parallel partitioner for coarse problem */
  PetscInt  indexing; /* 0 indicates C indexing, 1 Fortran */
  PetscInt  printout; /* indicates if one wishes Metis to print info */
  PetscBool repartition;
} MatPartitioning_Parmetis;

#define PetscCallPARMETIS(n, func) \
  do { \
    PetscCheck(n != METIS_ERROR_INPUT, PETSC_COMM_SELF, PETSC_ERR_LIB, "ParMETIS error due to wrong inputs and/or options for %s", func); \
    PetscCheck(n != METIS_ERROR_MEMORY, PETSC_COMM_SELF, PETSC_ERR_LIB, "ParMETIS error due to insufficient memory in %s", func); \
    PetscCheck(n != METIS_ERROR, PETSC_COMM_SELF, PETSC_ERR_LIB, "ParMETIS general error in %s", func); \
  } while (0)

#define PetscCallParmetis_(name, func, args) \
  do { \
    PetscStackPushExternal(name); \
    int status = func args; \
    PetscStackPop; \
    PetscCallPARMETIS(status, name); \
  } while (0)

#define PetscCallParmetis(func, args) PetscCallParmetis_(PetscStringize(func), func, args)

static PetscErrorCode MatPartitioningApply_Parmetis_Private(MatPartitioning part, PetscBool useND, PetscBool isImprove, IS *partitioning)
{
  MatPartitioning_Parmetis *pmetis = (MatPartitioning_Parmetis *)part->data;
  PetscInt                 *locals = NULL;
  Mat                       mat    = part->adj, amat, pmat;
  PetscBool                 flg;
  PetscInt                  bs = 1;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(part, MAT_PARTITIONING_CLASSID, 1);
  PetscAssertPointer(partitioning, 4);
  PetscCall(PetscObjectTypeCompare((PetscObject)mat, MATMPIADJ, &flg));
  if (flg) {
    amat = mat;
    PetscCall(PetscObjectReference((PetscObject)amat));
  } else {
    /* bs indicates if the converted matrix is "reduced" from the original and hence the
       resulting partition results need to be stretched to match the original matrix */
    PetscCall(MatConvert(mat, MATMPIADJ, MAT_INITIAL_MATRIX, &amat));
    if (amat->rmap->n > 0) bs = mat->rmap->n / amat->rmap->n;
  }
  PetscCall(MatMPIAdjCreateNonemptySubcommMat(amat, &pmat));
  PetscCallMPI(MPI_Barrier(PetscObjectComm((PetscObject)part)));

  if (pmat) {
    MPI_Comm    pcomm, comm;
    Mat_MPIAdj *adj     = (Mat_MPIAdj *)pmat->data;
    PetscInt   *vtxdist = pmat->rmap->range;
    PetscInt   *xadj    = adj->i;
    PetscInt   *adjncy  = adj->j;
    PetscInt   *NDorder = NULL;
    PetscInt    itmp = 0, wgtflag = 0, numflag = 0, ncon = part->ncon, nparts = part->n, options[24], i, j;
    real_t     *tpwgts, *ubvec, itr = (real_t)0.1;

    PetscCall(PetscObjectGetComm((PetscObject)pmat, &pcomm));
    if (PetscDefined(USE_DEBUG)) {
      /* check that matrix has no diagonal entries */
      PetscInt rstart;
      PetscCall(MatGetOwnershipRange(pmat, &rstart, NULL));
      for (i = 0; i < pmat->rmap->n; i++) {
        for (j = xadj[i]; j < xadj[i + 1]; j++) PetscCheck(adjncy[j] != i + rstart, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Row %" PetscInt_FMT " has diagonal entry; Parmetis forbids diagonal entry", i + rstart);
      }
    }

    PetscCall(PetscMalloc1(pmat->rmap->n, &locals));

    if (isImprove) {
      PetscInt        i;
      const PetscInt *part_indices;
      PetscValidHeaderSpecific(*partitioning, IS_CLASSID, 4);
      PetscCall(ISGetIndices(*partitioning, &part_indices));
      for (i = 0; i < pmat->rmap->n; i++) locals[i] = part_indices[i * bs];
      PetscCall(ISRestoreIndices(*partitioning, &part_indices));
      PetscCall(ISDestroy(partitioning));
    }

    if (adj->values && part->use_edge_weights && !part->vertex_weights) wgtflag = 1;
    if (part->vertex_weights && !adj->values) wgtflag = 2;
    if (part->vertex_weights && adj->values && part->use_edge_weights) wgtflag = 3;

    if (PetscLogPrintInfo) {
      itmp             = pmetis->printout;
      pmetis->printout = 127;
    }
    PetscCall(PetscMalloc1(ncon * nparts, &tpwgts));
    for (i = 0; i < ncon; i++) {
      for (j = 0; j < nparts; j++) {
        if (part->part_weights) {
          tpwgts[i * nparts + j] = (real_t)part->part_weights[i * nparts + j];
        } else {
          tpwgts[i * nparts + j] = (real_t)1. / nparts;
        }
      }
    }
    PetscCall(PetscMalloc1(ncon, &ubvec));
    for (i = 0; i < ncon; i++) ubvec[i] = (real_t)1.05;
    /* This sets the defaults */
    options[0] = 1;
    for (i = 1; i < 24; i++) options[i] = -1;
    options[1] = 0; /* no verbosity */
    options[2] = 0;
    options[3] = PARMETIS_PSR_COUPLED; /* Seed */
    /* Duplicate the communicator to be sure that ParMETIS attribute caching does not interfere with PETSc. */
    PetscCallMPI(MPI_Comm_dup(pcomm, &comm));
    if (useND) {
      PetscInt   *sizes, *seps, log2size, subd, *level;
      PetscMPIInt size;
      idx_t       mtype = PARMETIS_MTYPE_GLOBAL, rtype = PARMETIS_SRTYPE_2PHASE, p_nseps = 1, s_nseps = 1;
      real_t      ubfrac = (real_t)1.05;

      PetscCallMPI(MPI_Comm_size(comm, &size));
      PetscCall(PetscMalloc1(pmat->rmap->n, &NDorder));
      PetscCall(PetscMalloc3(2 * size, &sizes, 4 * size, &seps, size, &level));
      PetscCallParmetis(ParMETIS_V32_NodeND, ((idx_t *)vtxdist, (idx_t *)xadj, (idx_t *)adjncy, (idx_t *)part->vertex_weights, (idx_t *)&numflag, &mtype, &rtype, &p_nseps, &s_nseps, &ubfrac, NULL /* seed */, NULL /* dbglvl */, (idx_t *)NDorder, (idx_t *)(sizes), &comm));
      log2size = PetscLog2Real(size);
      subd     = PetscPowInt(2, log2size);
      PetscCall(MatPartitioningSizesToSep_Private(subd, sizes, seps, level));
      for (i = 0; i < pmat->rmap->n; i++) {
        PetscInt loc;

        PetscCall(PetscFindInt(NDorder[i], 2 * subd, seps, &loc));
        if (loc < 0) {
          loc = -(loc + 1);
          if (loc % 2) { /* part of subdomain */
            locals[i] = loc / 2;
          } else {
            PetscCall(PetscFindInt(NDorder[i], 2 * (subd - 1), seps + 2 * subd, &loc));
            loc       = loc < 0 ? -(loc + 1) / 2 : loc / 2;
            locals[i] = level[loc];
          }
        } else locals[i] = loc / 2;
      }
      PetscCall(PetscFree3(sizes, seps, level));
    } else {
      if (pmetis->repartition) {
        PetscCallParmetis(ParMETIS_V3_AdaptiveRepart, ((idx_t *)vtxdist, (idx_t *)xadj, (idx_t *)adjncy, (idx_t *)part->vertex_weights, (idx_t *)part->vertex_weights, (idx_t *)adj->values, (idx_t *)&wgtflag, (idx_t *)&numflag, (idx_t *)&ncon, (idx_t *)&nparts, tpwgts, ubvec, &itr, (idx_t *)options,
                                                       (idx_t *)&pmetis->cuts, (idx_t *)locals, &comm));
      } else if (isImprove) {
        PetscCallParmetis(ParMETIS_V3_RefineKway, ((idx_t *)vtxdist, (idx_t *)xadj, (idx_t *)adjncy, (idx_t *)part->vertex_weights, (idx_t *)adj->values, (idx_t *)&wgtflag, (idx_t *)&numflag, (idx_t *)&ncon, (idx_t *)&nparts, tpwgts, ubvec, (idx_t *)options,
                                                   (idx_t *)&pmetis->cuts, (idx_t *)locals, &comm));
      } else {
        PetscCallParmetis(ParMETIS_V3_PartKway, ((idx_t *)vtxdist, (idx_t *)xadj, (idx_t *)adjncy, (idx_t *)part->vertex_weights, (idx_t *)adj->values, (idx_t *)&wgtflag, (idx_t *)&numflag, (idx_t *)&ncon, (idx_t *)&nparts, tpwgts, ubvec, (idx_t *)options,
                                                 (idx_t *)&pmetis->cuts, (idx_t *)locals, &comm));
      }
    }
    PetscCallMPI(MPI_Comm_free(&comm));

    PetscCall(PetscFree(tpwgts));
    PetscCall(PetscFree(ubvec));
    if (PetscLogPrintInfo) pmetis->printout = itmp;

    if (bs > 1) {
      PetscInt i, j, *newlocals;
      PetscCall(PetscMalloc1(bs * pmat->rmap->n, &newlocals));
      for (i = 0; i < pmat->rmap->n; i++) {
        for (j = 0; j < bs; j++) newlocals[bs * i + j] = locals[i];
      }
      PetscCall(PetscFree(locals));
      PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)part), bs * pmat->rmap->n, newlocals, PETSC_OWN_POINTER, partitioning));
    } else {
      PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)part), pmat->rmap->n, locals, PETSC_OWN_POINTER, partitioning));
    }
    if (useND) {
      IS ndis;

      if (bs > 1) {
        PetscCall(ISCreateBlock(PetscObjectComm((PetscObject)part), bs, pmat->rmap->n, NDorder, PETSC_OWN_POINTER, &ndis));
      } else {
        PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)part), pmat->rmap->n, NDorder, PETSC_OWN_POINTER, &ndis));
      }
      PetscCall(ISSetPermutation(ndis));
      PetscCall(PetscObjectCompose((PetscObject)*partitioning, "_petsc_matpartitioning_ndorder", (PetscObject)ndis));
      PetscCall(ISDestroy(&ndis));
    }
  } else {
    PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)part), 0, NULL, PETSC_COPY_VALUES, partitioning));
    if (useND) {
      IS ndis;

      if (bs > 1) {
        PetscCall(ISCreateBlock(PetscObjectComm((PetscObject)part), bs, 0, NULL, PETSC_COPY_VALUES, &ndis));
      } else {
        PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)part), 0, NULL, PETSC_COPY_VALUES, &ndis));
      }
      PetscCall(ISSetPermutation(ndis));
      PetscCall(PetscObjectCompose((PetscObject)*partitioning, "_petsc_matpartitioning_ndorder", (PetscObject)ndis));
      PetscCall(ISDestroy(&ndis));
    }
  }
  PetscCall(MatDestroy(&pmat));
  PetscCall(MatDestroy(&amat));
  PetscFunctionReturn(PETSC_SUCCESS);
}

/*
   Uses the ParMETIS parallel matrix partitioner to compute a nested dissection ordering of the matrix in parallel
*/
static PetscErrorCode MatPartitioningApplyND_Parmetis(MatPartitioning part, IS *partitioning)
{
  PetscFunctionBegin;
  PetscCall(MatPartitioningApply_Parmetis_Private(part, PETSC_TRUE, PETSC_FALSE, partitioning));
  PetscFunctionReturn(PETSC_SUCCESS);
}

/*
   Uses the ParMETIS parallel matrix partitioner to partition the matrix in parallel
*/
static PetscErrorCode MatPartitioningApply_Parmetis(MatPartitioning part, IS *partitioning)
{
  PetscFunctionBegin;
  PetscCall(MatPartitioningApply_Parmetis_Private(part, PETSC_FALSE, PETSC_FALSE, partitioning));
  PetscFunctionReturn(PETSC_SUCCESS);
}

/*
   Uses the ParMETIS to improve the quality  of a partition
*/
static PetscErrorCode MatPartitioningImprove_Parmetis(MatPartitioning part, IS *partitioning)
{
  PetscFunctionBegin;
  PetscCall(MatPartitioningApply_Parmetis_Private(part, PETSC_FALSE, PETSC_TRUE, partitioning));
  PetscFunctionReturn(PETSC_SUCCESS);
}

static PetscErrorCode MatPartitioningView_Parmetis(MatPartitioning part, PetscViewer viewer)
{
  MatPartitioning_Parmetis *pmetis = (MatPartitioning_Parmetis *)part->data;
  PetscMPIInt               rank;
  PetscBool                 isascii;

  PetscFunctionBegin;
  PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)part), &rank));
  PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERASCII, &isascii));
  if (isascii) {
    if (pmetis->parallel == 2) {
      PetscCall(PetscViewerASCIIPrintf(viewer, "  Using parallel coarse grid partitioner\n"));
    } else {
      PetscCall(PetscViewerASCIIPrintf(viewer, "  Using sequential coarse grid partitioner\n"));
    }
    PetscCall(PetscViewerASCIIPrintf(viewer, "  Using %" PetscInt_FMT " fold factor\n", pmetis->foldfactor));
    PetscCall(PetscViewerASCIIPushSynchronized(viewer));
    PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "  [%d]Number of cuts found %" PetscInt_FMT "\n", rank, pmetis->cuts));
    PetscCall(PetscViewerFlush(viewer));
    PetscCall(PetscViewerASCIIPopSynchronized(viewer));
  }
  PetscFunctionReturn(PETSC_SUCCESS);
}

/*@
  MatPartitioningParmetisSetCoarseSequential - Use the sequential code to
  do the partitioning of the coarse grid.

  Logically Collective

  Input Parameter:
. part - the partitioning context

  Level: advanced

.seealso: `MATPARTITIONINGPARMETIS`
@*/
PetscErrorCode MatPartitioningParmetisSetCoarseSequential(MatPartitioning part)
{
  MatPartitioning_Parmetis *pmetis = (MatPartitioning_Parmetis *)part->data;

  PetscFunctionBegin;
  pmetis->parallel = 1;
  PetscFunctionReturn(PETSC_SUCCESS);
}

/*@
  MatPartitioningParmetisSetRepartition - Repartition
  current mesh to rebalance computation.

  Logically Collective

  Input Parameter:
. part - the partitioning context

  Level: advanced

.seealso: `MATPARTITIONINGPARMETIS`
@*/
PetscErrorCode MatPartitioningParmetisSetRepartition(MatPartitioning part)
{
  MatPartitioning_Parmetis *pmetis = (MatPartitioning_Parmetis *)part->data;

  PetscFunctionBegin;
  pmetis->repartition = PETSC_TRUE;
  PetscFunctionReturn(PETSC_SUCCESS);
}

/*@
  MatPartitioningParmetisGetEdgeCut - Returns the number of edge cuts in the vertex partition.

  Input Parameter:
. part - the partitioning context

  Output Parameter:
. cut - the edge cut

  Level: advanced

.seealso: `MATPARTITIONINGPARMETIS`
@*/
PetscErrorCode MatPartitioningParmetisGetEdgeCut(MatPartitioning part, PetscInt *cut)
{
  MatPartitioning_Parmetis *pmetis = (MatPartitioning_Parmetis *)part->data;

  PetscFunctionBegin;
  *cut = pmetis->cuts;
  PetscFunctionReturn(PETSC_SUCCESS);
}

static PetscErrorCode MatPartitioningSetFromOptions_Parmetis(MatPartitioning part, PetscOptionItems PetscOptionsObject)
{
  PetscBool flag = PETSC_FALSE;

  PetscFunctionBegin;
  PetscOptionsHeadBegin(PetscOptionsObject, "Set ParMeTiS partitioning options");
  PetscCall(PetscOptionsBool("-mat_partitioning_parmetis_coarse_sequential", "Use sequential coarse partitioner", "MatPartitioningParmetisSetCoarseSequential", flag, &flag, NULL));
  if (flag) PetscCall(MatPartitioningParmetisSetCoarseSequential(part));
  PetscCall(PetscOptionsBool("-mat_partitioning_parmetis_repartition", "", "MatPartitioningParmetisSetRepartition", flag, &flag, NULL));
  if (flag) PetscCall(MatPartitioningParmetisSetRepartition(part));
  PetscOptionsHeadEnd();
  PetscFunctionReturn(PETSC_SUCCESS);
}

static PetscErrorCode MatPartitioningDestroy_Parmetis(MatPartitioning part)
{
  MatPartitioning_Parmetis *pmetis = (MatPartitioning_Parmetis *)part->data;

  PetscFunctionBegin;
  PetscCall(PetscFree(pmetis));
  PetscFunctionReturn(PETSC_SUCCESS);
}

/*MC
   MATPARTITIONINGPARMETIS - Creates a partitioning context via the external package PARMETIS.

   Collective

   Input Parameter:
.  part - the partitioning context

   Options Database Key:
.  -mat_partitioning_parmetis_coarse_sequential - use sequential PARMETIS coarse partitioner

   Level: beginner

   Note:
    See https://www-users.cs.umn.edu/~karypis/metis/

.seealso: `MatPartitioningSetType()`, `MatPartitioningType`, `MatPartitioningParmetisSetCoarseSequential()`, `MatPartitioningParmetisSetRepartition()`,
          `MatPartitioningParmetisGetEdgeCut()`
M*/

PETSC_EXTERN PetscErrorCode MatPartitioningCreate_Parmetis(MatPartitioning part)
{
  MatPartitioning_Parmetis *pmetis;

  PetscFunctionBegin;
  PetscCall(PetscNew(&pmetis));
  part->data = (void *)pmetis;

  pmetis->cuts        = 0;   /* output variable */
  pmetis->foldfactor  = 150; /*folding factor */
  pmetis->parallel    = 2;   /* use parallel partitioner for coarse grid */
  pmetis->indexing    = 0;   /* index numbering starts from 0 */
  pmetis->printout    = 0;   /* print no output while running */
  pmetis->repartition = PETSC_FALSE;

  part->ops->apply          = MatPartitioningApply_Parmetis;
  part->ops->applynd        = MatPartitioningApplyND_Parmetis;
  part->ops->improve        = MatPartitioningImprove_Parmetis;
  part->ops->view           = MatPartitioningView_Parmetis;
  part->ops->destroy        = MatPartitioningDestroy_Parmetis;
  part->ops->setfromoptions = MatPartitioningSetFromOptions_Parmetis;
  PetscFunctionReturn(PETSC_SUCCESS);
}

/*@
  MatMeshToCellGraph - Convert a mesh to a cell graph.

  Collective

  Input Parameters:
+ mesh         - the graph that represents the coupling of the vertices of the mesh
- ncommonnodes - mesh elements that share this number of common nodes are considered neighbors, use 2 for triangles and
                     quadrilaterials, 3 for tetrahedrals and 4 for hexahedrals

  Output Parameter:
. dual - the dual graph

  Level: advanced

  Notes:
  Uses the ParMETIS package to convert a `Mat` that represents coupling of vertices of a mesh
  to a `Mat` the represents the graph of the coupling between cells (the "dual" graph) and is
  suitable for partitioning with the `MatPartitioning` object. Use this to partition cells of a
  mesh.

  Currently requires ParMetis to be installed and uses ParMETIS_V3_Mesh2Dual()

  Each row of the mesh object represents a single cell in the mesh. For triangles it has 3 entries, quadrilaterials 4 entries,
  tetrahedrals 4 entries and hexahedrals 8 entries. You can mix triangles and quadrilaterals in the same mesh, but cannot
  mix  tetrahedrals and hexahedrals
  The columns of each row of the `Mat` mesh are the global vertex numbers of the vertices of that row's cell.
  The number of rows in mesh is number of cells, the number of columns is the number of vertices.

.seealso: `MatCreateMPIAdj()`, `MatPartitioningCreate()`
@*/
PetscErrorCode MatMeshToCellGraph(Mat mesh, PetscInt ncommonnodes, Mat *dual)
{
  PetscInt   *newxadj, *newadjncy;
  PetscInt    numflag = 0;
  Mat_MPIAdj *adj     = (Mat_MPIAdj *)mesh->data, *newadj;
  PetscBool   flg;
  MPI_Comm    comm;

  PetscFunctionBegin;
  PetscCall(PetscObjectTypeCompare((PetscObject)mesh, MATMPIADJ, &flg));
  PetscCheck(flg, PETSC_COMM_SELF, PETSC_ERR_SUP, "Must use MPIAdj matrix type");

  PetscCall(PetscObjectGetComm((PetscObject)mesh, &comm));
  PetscCallParmetis(ParMETIS_V3_Mesh2Dual, ((idx_t *)mesh->rmap->range, (idx_t *)adj->i, (idx_t *)adj->j, (idx_t *)&numflag, (idx_t *)&ncommonnodes, (idx_t **)&newxadj, (idx_t **)&newadjncy, &comm));
  PetscCall(MatCreateMPIAdj(PetscObjectComm((PetscObject)mesh), mesh->rmap->n, mesh->rmap->N, newxadj, newadjncy, NULL, dual));
  newadj = (Mat_MPIAdj *)(*dual)->data;

  newadj->freeaijwithfree = PETSC_TRUE; /* signal the matrix should be freed with system free since space was allocated by ParMETIS */
  PetscFunctionReturn(PETSC_SUCCESS);
}