Actual source code: plexpreallocate.c

      1: #include <petsc/private/dmpleximpl.h>
      2: #include <petsc/private/isimpl.h>
      3: #include <petscsf.h>
      4: #include <petscds.h>

      6: /* get adjacencies due to point-to-point constraints that can't be found with DMPlexGetAdjacency() */
      7: static PetscErrorCode DMPlexComputeAnchorAdjacencies(DM dm, PetscBool useCone, PetscBool useClosure, PetscSection *anchorSectionAdj, PetscInt *anchorAdj[])
      8: {
      9:   PetscInt     pStart, pEnd;
     10:   PetscSection section, sectionGlobal, adjSec, aSec;
     11:   IS           aIS;

     13:   PetscFunctionBegin;
     14:   PetscCall(DMGetLocalSection(dm, &section));
     15:   PetscCall(DMGetGlobalSection(dm, &sectionGlobal));
     16:   PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)section), &adjSec));
     17:   PetscCall(PetscSectionGetChart(section, &pStart, &pEnd));
     18:   PetscCall(PetscSectionSetChart(adjSec, pStart, pEnd));

     20:   PetscCall(DMPlexGetAnchors(dm, &aSec, &aIS));
     21:   if (aSec) {
     22:     const PetscInt *anchors;
     23:     PetscInt        p, q, a, aSize, *offsets, aStart, aEnd, *inverse, iSize, *adj, adjSize;
     24:     PetscInt       *tmpAdjP = NULL, *tmpAdjQ = NULL;
     25:     PetscSection    inverseSec;

     27:     /* invert the constraint-to-anchor map */
     28:     PetscCall(PetscSectionCreate(PetscObjectComm((PetscObject)aSec), &inverseSec));
     29:     PetscCall(PetscSectionSetChart(inverseSec, pStart, pEnd));
     30:     PetscCall(ISGetLocalSize(aIS, &aSize));
     31:     PetscCall(ISGetIndices(aIS, &anchors));

     33:     for (p = 0; p < aSize; p++) {
     34:       PetscInt a = anchors[p];

     36:       PetscCall(PetscSectionAddDof(inverseSec, a, 1));
     37:     }
     38:     PetscCall(PetscSectionSetUp(inverseSec));
     39:     PetscCall(PetscSectionGetStorageSize(inverseSec, &iSize));
     40:     PetscCall(PetscMalloc1(iSize, &inverse));
     41:     PetscCall(PetscCalloc1(pEnd - pStart, &offsets));
     42:     PetscCall(PetscSectionGetChart(aSec, &aStart, &aEnd));
     43:     for (p = aStart; p < aEnd; p++) {
     44:       PetscInt dof, off;

     46:       PetscCall(PetscSectionGetDof(aSec, p, &dof));
     47:       PetscCall(PetscSectionGetOffset(aSec, p, &off));

     49:       for (q = 0; q < dof; q++) {
     50:         PetscInt iOff;

     52:         a = anchors[off + q];
     53:         PetscCall(PetscSectionGetOffset(inverseSec, a, &iOff));
     54:         inverse[iOff + offsets[a - pStart]++] = p;
     55:       }
     56:     }
     57:     PetscCall(ISRestoreIndices(aIS, &anchors));
     58:     PetscCall(PetscFree(offsets));

     60:     /* construct anchorAdj and adjSec
     61:      *
     62:      * loop over anchors:
     63:      *   construct anchor adjacency
     64:      *   loop over constrained:
     65:      *     construct constrained adjacency
     66:      *     if not in anchor adjacency, add to dofs
     67:      * setup adjSec, allocate anchorAdj
     68:      * loop over anchors:
     69:      *   construct anchor adjacency
     70:      *   loop over constrained:
     71:      *     construct constrained adjacency
     72:      *     if not in anchor adjacency
     73:      *       if not already in list, put in list
     74:      *   sort, unique, reduce dof count
     75:      * optional: compactify
     76:      */
     77:     for (p = pStart; p < pEnd; p++) {
     78:       PetscInt iDof, iOff, i, r, s, numAdjP = PETSC_DETERMINE;

     80:       PetscCall(PetscSectionGetDof(inverseSec, p, &iDof));
     81:       if (!iDof) continue;
     82:       PetscCall(PetscSectionGetOffset(inverseSec, p, &iOff));
     83:       PetscCall(DMPlexGetAdjacency_Internal(dm, p, useCone, useClosure, PETSC_TRUE, &numAdjP, &tmpAdjP));
     84:       for (i = 0; i < iDof; i++) {
     85:         PetscInt iNew = 0, qAdj, qAdjDof, qAdjCDof, numAdjQ = PETSC_DETERMINE;

     87:         q = inverse[iOff + i];
     88:         PetscCall(DMPlexGetAdjacency_Internal(dm, q, useCone, useClosure, PETSC_TRUE, &numAdjQ, &tmpAdjQ));
     89:         for (r = 0; r < numAdjQ; r++) {
     90:           qAdj = tmpAdjQ[r];
     91:           if ((qAdj < pStart) || (qAdj >= pEnd)) continue;
     92:           for (s = 0; s < numAdjP; s++) {
     93:             if (qAdj == tmpAdjP[s]) break;
     94:           }
     95:           if (s < numAdjP) continue;
     96:           PetscCall(PetscSectionGetDof(section, qAdj, &qAdjDof));
     97:           PetscCall(PetscSectionGetConstraintDof(section, qAdj, &qAdjCDof));
     98:           iNew += qAdjDof - qAdjCDof;
     99:         }
    100:         PetscCall(PetscSectionAddDof(adjSec, p, iNew));
    101:       }
    102:     }

    104:     PetscCall(PetscSectionSetUp(adjSec));
    105:     PetscCall(PetscSectionGetStorageSize(adjSec, &adjSize));
    106:     PetscCall(PetscMalloc1(adjSize, &adj));

    108:     for (p = pStart; p < pEnd; p++) {
    109:       PetscInt iDof, iOff, i, r, s, aOff, aOffOrig, aDof, numAdjP = PETSC_DETERMINE;

    111:       PetscCall(PetscSectionGetDof(inverseSec, p, &iDof));
    112:       if (!iDof) continue;
    113:       PetscCall(PetscSectionGetOffset(inverseSec, p, &iOff));
    114:       PetscCall(DMPlexGetAdjacency_Internal(dm, p, useCone, useClosure, PETSC_TRUE, &numAdjP, &tmpAdjP));
    115:       PetscCall(PetscSectionGetDof(adjSec, p, &aDof));
    116:       PetscCall(PetscSectionGetOffset(adjSec, p, &aOff));
    117:       aOffOrig = aOff;
    118:       for (i = 0; i < iDof; i++) {
    119:         PetscInt qAdj, qAdjDof, qAdjCDof, qAdjOff, nd, numAdjQ = PETSC_DETERMINE;

    121:         q = inverse[iOff + i];
    122:         PetscCall(DMPlexGetAdjacency_Internal(dm, q, useCone, useClosure, PETSC_TRUE, &numAdjQ, &tmpAdjQ));
    123:         for (r = 0; r < numAdjQ; r++) {
    124:           qAdj = tmpAdjQ[r];
    125:           if ((qAdj < pStart) || (qAdj >= pEnd)) continue;
    126:           for (s = 0; s < numAdjP; s++) {
    127:             if (qAdj == tmpAdjP[s]) break;
    128:           }
    129:           if (s < numAdjP) continue;
    130:           PetscCall(PetscSectionGetDof(section, qAdj, &qAdjDof));
    131:           PetscCall(PetscSectionGetConstraintDof(section, qAdj, &qAdjCDof));
    132:           PetscCall(PetscSectionGetOffset(sectionGlobal, qAdj, &qAdjOff));
    133:           for (nd = 0; nd < qAdjDof - qAdjCDof; ++nd) adj[aOff++] = (qAdjOff < 0 ? -(qAdjOff + 1) : qAdjOff) + nd;
    134:         }
    135:       }
    136:       PetscCall(PetscSortRemoveDupsInt(&aDof, PetscSafePointerPlusOffset(adj, aOffOrig)));
    137:       PetscCall(PetscSectionSetDof(adjSec, p, aDof));
    138:     }
    139:     *anchorAdj = adj;

    141:     /* clean up */
    142:     PetscCall(PetscSectionDestroy(&inverseSec));
    143:     PetscCall(PetscFree(inverse));
    144:     PetscCall(PetscFree(tmpAdjP));
    145:     PetscCall(PetscFree(tmpAdjQ));
    146:   } else {
    147:     *anchorAdj = NULL;
    148:     PetscCall(PetscSectionSetUp(adjSec));
    149:   }
    150:   *anchorSectionAdj = adjSec;
    151:   PetscFunctionReturn(PETSC_SUCCESS);
    152: }

    154: // Based off of `PetscIntViewNumColumns()`
    155: static PetscErrorCode PetscIntViewPairs(PetscInt N, PetscInt Ncol, const PetscInt idx1[], const PetscInt idx2[], PetscViewer viewer)
    156: {
    157:   PetscMPIInt rank, size;
    158:   PetscInt    j, i, n = N / Ncol, p = N % Ncol;
    159:   PetscBool   isascii;
    160:   MPI_Comm    comm;

    162:   PetscFunctionBegin;
    163:   if (!viewer) viewer = PETSC_VIEWER_STDOUT_SELF;
    164:   if (N) PetscAssertPointer(idx1, 3);
    165:   if (N) PetscAssertPointer(idx2, 4);
    167:   PetscCall(PetscObjectGetComm((PetscObject)viewer, &comm));
    168:   PetscCallMPI(MPI_Comm_size(comm, &size));
    169:   PetscCallMPI(MPI_Comm_rank(comm, &rank));

    171:   PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERASCII, &isascii));
    172:   if (isascii) {
    173:     PetscCall(PetscViewerASCIIPushSynchronized(viewer));
    174:     for (i = 0; i < n; i++) {
    175:       if (size > 1) {
    176:         PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "[%d] %" PetscInt_FMT ":", rank, Ncol * i));
    177:       } else {
    178:         PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "%" PetscInt_FMT ":", Ncol * i));
    179:       }
    180:       for (j = 0; j < Ncol; j++) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " (%" PetscInt_FMT ", %" PetscInt_FMT ")", idx1[i * Ncol + j], idx2[i * Ncol + j]));
    181:       PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "\n"));
    182:     }
    183:     if (p) {
    184:       if (size > 1) {
    185:         PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "[%d] %" PetscInt_FMT ":", rank, Ncol * n));
    186:       } else {
    187:         PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "%" PetscInt_FMT ":", Ncol * n));
    188:       }
    189:       for (i = 0; i < p; i++) PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, " (%" PetscInt_FMT ", %" PetscInt_FMT ")", idx1[Ncol * n + i], idx2[Ncol * n + i]));
    190:       PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "\n"));
    191:     }
    192:     PetscCall(PetscViewerFlush(viewer));
    193:     PetscCall(PetscViewerASCIIPopSynchronized(viewer));
    194:   } else {
    195:     const char *tname;
    196:     PetscCall(PetscObjectGetName((PetscObject)viewer, &tname));
    197:     SETERRQ(PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot handle that PetscViewer of type %s", tname);
    198:   }
    199:   PetscFunctionReturn(PETSC_SUCCESS);
    200: }

    202: // Determine if any of the local adjacencies match a leaf and root of the pointSF.
    203: // When using isoperiodic boundary conditions, it is possible for periodic (leaf) and donor (root) pairs to be on the same rank.
    204: // This check is done to ensure the adjacency in these cases is only counted for one of the mesh points rather than both.
    205: static inline PetscErrorCode AdjancencyContainsLeafRootPair(PetscSection myRankPairSection, const PetscInt leaves[], const PetscInt roots[], PetscInt numAdj, const PetscInt tmpAdj[], PetscInt *num_leaves_found, PetscInt leaves_found[])
    206: {
    207:   PetscInt root_index = -1, leaf_, num_roots, num_leaves;

    209:   PetscFunctionBeginUser;
    210:   PetscCall(PetscSectionGetChart(myRankPairSection, NULL, &num_roots));
    211:   PetscCall(PetscSectionGetStorageSize(myRankPairSection, &num_leaves));
    212:   *num_leaves_found = 0;
    213:   for (PetscInt q = 0; q < numAdj; q++) {
    214:     const PetscInt padj = tmpAdj[q];
    215:     PetscCall(PetscFindInt(padj, num_roots, roots, &root_index));
    216:     if (root_index >= 0) {
    217:       PetscInt dof, offset;

    219:       PetscCall(PetscSectionGetDof(myRankPairSection, root_index, &dof));
    220:       PetscCall(PetscSectionGetOffset(myRankPairSection, root_index, &offset));

    222:       for (PetscInt l = 0; l < dof; l++) {
    223:         leaf_ = leaves[offset + l];
    224:         for (PetscInt q = 0; q < numAdj; q++) {
    225:           if (tmpAdj[q] == leaf_) {
    226:             leaves_found[*num_leaves_found] = leaf_;
    227:             (*num_leaves_found)++;
    228:             break;
    229:           }
    230:         }
    231:       }
    232:     }
    233:   }

    235:   PetscCall(PetscIntSortSemiOrdered(*num_leaves_found, leaves_found));
    236:   PetscFunctionReturn(PETSC_SUCCESS);
    237: }

    239: static PetscErrorCode DMPlexCreateAdjacencySection_Static(DM dm, PetscInt bs, PetscSF sfDof, PetscBool useCone, PetscBool useClosure, PetscBool useAnchors, PetscSection *sA, PetscInt **colIdx)
    240: {
    241:   MPI_Comm           comm;
    242:   PetscMPIInt        myrank;
    243:   PetscBool          doCommLocal, doComm, debug = PETSC_FALSE;
    244:   PetscSF            sf, sfAdj;
    245:   PetscSection       section, sectionGlobal, leafSectionAdj, rootSectionAdj, sectionAdj, anchorSectionAdj, myRankPairSection;
    246:   PetscInt           nroots, nleaves, l, p, r;
    247:   const PetscInt    *leaves;
    248:   const PetscSFNode *remotes;
    249:   PetscInt           dim, pStart, pEnd, numDof, globalOffStart, globalOffEnd, numCols, adjSize;
    250:   PetscInt          *tmpAdj = NULL, *adj, *rootAdj, *anchorAdj = NULL, *cols, *remoteOffsets, *myRankPairRoots = NULL, *myRankPairLeaves = NULL;

    252:   PetscFunctionBegin;
    253:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
    254:   PetscCall(PetscOptionsGetBool(NULL, NULL, "-dm_view_preallocation", &debug, NULL));
    255:   PetscCallMPI(MPI_Comm_rank(comm, &myrank));
    256:   PetscCall(DMGetDimension(dm, &dim));
    257:   PetscCall(DMGetIsoperiodicPointSF_Internal(dm, &sf));
    258:   PetscCall(DMGetLocalSection(dm, &section));
    259:   PetscCall(DMGetGlobalSection(dm, &sectionGlobal));
    260:   PetscCall(PetscSFGetGraph(sf, &nroots, NULL, NULL, NULL));
    261:   doCommLocal = nroots >= 0 ? PETSC_TRUE : PETSC_FALSE;
    262:   PetscCallMPI(MPIU_Allreduce(&doCommLocal, &doComm, 1, MPI_C_BOOL, MPI_LAND, comm));
    263:   /* Create section for dof adjacency (dof ==> # adj dof) */
    264:   PetscCall(PetscSectionGetChart(section, &pStart, &pEnd));
    265:   PetscCall(PetscSectionGetStorageSize(section, &numDof));
    266:   PetscCall(PetscSectionCreate(comm, &leafSectionAdj));
    267:   PetscCall(PetscSectionSetChart(leafSectionAdj, 0, numDof));
    268:   PetscCall(PetscSectionCreate(comm, &rootSectionAdj));
    269:   PetscCall(PetscSectionSetChart(rootSectionAdj, 0, numDof));
    270:   PetscCall(PetscSFGetGraph(sf, NULL, &nleaves, &leaves, &remotes));

    272:   // Store leaf-root pairs if the leaf and root are both located on current rank.
    273:   // The point in myRankPairSection is an index into myRankPairRoots.
    274:   // The section then defines the number of pairs for that root and the offset into myRankPairLeaves to access them.
    275:   {
    276:     PetscSegBuffer seg_roots, seg_leaves;
    277:     PetscCount     buffer_size;
    278:     PetscInt      *roots_with_dups, num_non_dups, num_pairs = 0;

    280:     PetscCall(PetscSegBufferCreate(sizeof(PetscInt), 32, &seg_roots));
    281:     PetscCall(PetscSegBufferCreate(sizeof(PetscInt), 32, &seg_leaves));
    282:     for (PetscInt l = 0; l < nleaves; l++) {
    283:       if (remotes[l].rank == myrank) {
    284:         PetscInt *slot;
    285:         PetscCall(PetscSegBufferGetInts(seg_roots, 1, &slot));
    286:         *slot = remotes[l].index;
    287:         PetscCall(PetscSegBufferGetInts(seg_leaves, 1, &slot));
    288:         *slot = leaves[l];
    289:       }
    290:     }
    291:     PetscCall(PetscSegBufferGetSize(seg_roots, &buffer_size));
    292:     PetscCall(PetscIntCast(buffer_size, &num_pairs));
    293:     PetscCall(PetscSegBufferExtractAlloc(seg_roots, &roots_with_dups));
    294:     PetscCall(PetscSegBufferExtractAlloc(seg_leaves, &myRankPairLeaves));
    295:     PetscCall(PetscSegBufferDestroy(&seg_roots));
    296:     PetscCall(PetscSegBufferDestroy(&seg_leaves));

    298:     PetscCall(PetscIntSortSemiOrderedWithArray(num_pairs, roots_with_dups, myRankPairLeaves));
    299:     if (debug) {
    300:       PetscCall(PetscPrintf(comm, "Root/leaf pairs on the same rank:\n"));
    301:       PetscCall(PetscIntViewPairs(num_pairs, 5, roots_with_dups, myRankPairLeaves, NULL));
    302:     }
    303:     PetscCall(PetscMalloc1(num_pairs, &myRankPairRoots));
    304:     PetscCall(PetscArraycpy(myRankPairRoots, roots_with_dups, num_pairs));

    306:     num_non_dups = num_pairs;
    307:     PetscCall(PetscSortedRemoveDupsInt(&num_non_dups, myRankPairRoots));
    308:     PetscCall(PetscSectionCreate(comm, &myRankPairSection));
    309:     PetscCall(PetscSectionSetChart(myRankPairSection, 0, num_non_dups));
    310:     for (PetscInt p = 0; p < num_pairs; p++) {
    311:       PetscInt root = roots_with_dups[p], index;
    312:       PetscCall(PetscFindInt(root, num_non_dups, myRankPairRoots, &index));
    313:       PetscAssert(index >= 0, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Root not found after removal of duplicates");
    314:       PetscCall(PetscSectionAddDof(myRankPairSection, index, 1));
    315:     }
    316:     PetscCall(PetscSectionSetUp(myRankPairSection));

    318:     if (debug) {
    319:       PetscCall(PetscPrintf(comm, "Root/leaf pair section on the same rank:\n"));
    320:       PetscCall(PetscIntView(num_non_dups, myRankPairRoots, NULL));
    321:       PetscCall(PetscSectionArrayView(myRankPairSection, myRankPairLeaves, PETSC_INT, NULL));
    322:     }
    323:     PetscCall(PetscFree(roots_with_dups));
    324:   }

    326:   /*
    327:    section        - maps points to (# dofs, local dofs)
    328:    sectionGlobal  - maps points to (# dofs, global dofs)
    329:    leafSectionAdj - maps unowned local dofs to # adj dofs
    330:    rootSectionAdj - maps   owned local dofs to # adj dofs
    331:    adj            - adj global dofs indexed by leafSectionAdj
    332:    rootAdj        - adj global dofs indexed by rootSectionAdj
    333:    sf    - describes shared points across procs
    334:    sfDof - describes shared dofs across procs
    335:    sfAdj - describes shared adjacent dofs across procs
    336:    ** The bootstrapping process involves six rounds with similar structure of visiting neighbors of each point.
    337:   (0). If there are point-to-point constraints, add the adjacencies of constrained points to anchors in anchorAdj
    338:        (This is done in DMPlexComputeAnchorAdjacencies())
    339:     1. Visit unowned points on interface, count adjacencies placing in leafSectionAdj
    340:        Reduce those counts to rootSectionAdj (now redundantly counting some interface points)
    341:     2. Visit owned points on interface, count adjacencies placing in rootSectionAdj
    342:        Create sfAdj connecting rootSectionAdj and leafSectionAdj
    343:     3. Visit unowned points on interface, write adjacencies to adj
    344:        Gather adj to rootAdj (note that there is redundancy in rootAdj when multiple procs find the same adjacencies)
    345:     4. Visit owned points on interface, write adjacencies to rootAdj
    346:        Remove redundancy in rootAdj
    347:    ** The last two traversals use transitive closure
    348:     5. Visit all owned points in the subdomain, count dofs for each point (sectionAdj)
    349:        Allocate memory addressed by sectionAdj (cols)
    350:     6. Visit all owned points in the subdomain, insert dof adjacencies into cols
    351:    ** Knowing all the column adjacencies, check ownership and sum into dnz and onz
    352:   */
    353:   PetscCall(DMPlexComputeAnchorAdjacencies(dm, useCone, useClosure, &anchorSectionAdj, &anchorAdj));
    354:   for (l = 0; l < nleaves; ++l) {
    355:     PetscInt dof, off, d, q, anDof;
    356:     PetscInt p = leaves[l], numAdj = PETSC_DETERMINE;

    358:     if ((p < pStart) || (p >= pEnd)) continue;
    359:     PetscCall(PetscSectionGetDof(section, p, &dof));
    360:     PetscCall(PetscSectionGetOffset(section, p, &off));
    361:     PetscCall(DMPlexGetAdjacency_Internal(dm, p, useCone, useClosure, useAnchors, &numAdj, &tmpAdj));
    362:     for (q = 0; q < numAdj; ++q) {
    363:       const PetscInt padj = tmpAdj[q];
    364:       PetscInt       ndof, ncdof;

    366:       if ((padj < pStart) || (padj >= pEnd)) continue;
    367:       PetscCall(PetscSectionGetDof(section, padj, &ndof));
    368:       PetscCall(PetscSectionGetConstraintDof(section, padj, &ncdof));
    369:       for (d = off; d < off + dof; ++d) PetscCall(PetscSectionAddDof(leafSectionAdj, d, ndof - ncdof));
    370:     }
    371:     PetscCall(PetscSectionGetDof(anchorSectionAdj, p, &anDof));
    372:     if (anDof) {
    373:       for (d = off; d < off + dof; ++d) PetscCall(PetscSectionAddDof(leafSectionAdj, d, anDof));
    374:     }
    375:   }
    376:   PetscCall(PetscSectionSetUp(leafSectionAdj));
    377:   if (debug) {
    378:     PetscCall(PetscPrintf(comm, "Adjacency Section for Preallocation on Leaves:\n"));
    379:     PetscCall(PetscSectionView(leafSectionAdj, NULL));
    380:   }
    381:   /* Get maximum remote adjacency sizes for owned dofs on interface (roots) */
    382:   if (doComm) {
    383:     PetscCall(PetscSFReduceBegin(sfDof, MPIU_INT, leafSectionAdj->atlasDof, rootSectionAdj->atlasDof, MPI_SUM));
    384:     PetscCall(PetscSFReduceEnd(sfDof, MPIU_INT, leafSectionAdj->atlasDof, rootSectionAdj->atlasDof, MPI_SUM));
    385:     PetscCall(PetscSectionInvalidateMaxDof_Internal(rootSectionAdj));
    386:   }
    387:   if (debug) {
    388:     PetscCall(PetscPrintf(comm, "Adjacency Section for Preallocation on Roots:\n"));
    389:     PetscCall(PetscSectionView(rootSectionAdj, NULL));
    390:   }
    391:   /* Add in local adjacency sizes for owned dofs on interface (roots) */
    392:   for (p = pStart; p < pEnd; ++p) {
    393:     PetscInt numAdj = PETSC_DETERMINE, adof, dof, off, d, q, anDof;

    395:     PetscCall(PetscSectionGetDof(section, p, &dof));
    396:     PetscCall(PetscSectionGetOffset(section, p, &off));
    397:     if (!dof) continue;
    398:     PetscCall(PetscSectionGetDof(rootSectionAdj, off, &adof));
    399:     if (adof <= 0) continue;
    400:     PetscCall(DMPlexGetAdjacency_Internal(dm, p, useCone, useClosure, useAnchors, &numAdj, &tmpAdj));
    401:     for (q = 0; q < numAdj; ++q) {
    402:       const PetscInt padj = tmpAdj[q];
    403:       PetscInt       ndof, ncdof;

    405:       if ((padj < pStart) || (padj >= pEnd)) continue;
    406:       PetscCall(PetscSectionGetDof(section, padj, &ndof));
    407:       PetscCall(PetscSectionGetConstraintDof(section, padj, &ncdof));
    408:       for (d = off; d < off + dof; ++d) PetscCall(PetscSectionAddDof(rootSectionAdj, d, ndof - ncdof));
    409:     }
    410:     PetscCall(PetscSectionGetDof(anchorSectionAdj, p, &anDof));
    411:     if (anDof) {
    412:       for (d = off; d < off + dof; ++d) PetscCall(PetscSectionAddDof(rootSectionAdj, d, anDof));
    413:     }
    414:   }
    415:   PetscCall(PetscSectionSetUp(rootSectionAdj));
    416:   if (debug) {
    417:     PetscCall(PetscPrintf(comm, "Adjacency Section for Preallocation on Roots after local additions:\n"));
    418:     PetscCall(PetscSectionView(rootSectionAdj, NULL));
    419:   }
    420:   /* Create adj SF based on dof SF */
    421:   PetscCall(PetscSFCreateRemoteOffsets(sfDof, rootSectionAdj, leafSectionAdj, &remoteOffsets));
    422:   PetscCall(PetscSFCreateSectionSF(sfDof, rootSectionAdj, remoteOffsets, leafSectionAdj, &sfAdj));
    423:   PetscCall(PetscFree(remoteOffsets));
    424:   if (debug) {
    425:     PetscCall(PetscPrintf(comm, "Adjacency SF for Preallocation:\n"));
    426:     PetscCall(PetscSFView(sfAdj, NULL));
    427:   }
    428:   /* Create leaf adjacency */
    429:   PetscCall(PetscSectionSetUp(leafSectionAdj));
    430:   PetscCall(PetscSectionGetStorageSize(leafSectionAdj, &adjSize));
    431:   PetscCall(PetscCalloc1(adjSize, &adj));
    432:   for (l = 0; l < nleaves; ++l) {
    433:     PetscInt dof, off, d, q, anDof, anOff;
    434:     PetscInt p = leaves[l], numAdj = PETSC_DETERMINE;

    436:     if ((p < pStart) || (p >= pEnd)) continue;
    437:     PetscCall(PetscSectionGetDof(section, p, &dof));
    438:     PetscCall(PetscSectionGetOffset(section, p, &off));
    439:     PetscCall(DMPlexGetAdjacency_Internal(dm, p, useCone, useClosure, useAnchors, &numAdj, &tmpAdj));
    440:     PetscCall(PetscSectionGetDof(anchorSectionAdj, p, &anDof));
    441:     PetscCall(PetscSectionGetOffset(anchorSectionAdj, p, &anOff));
    442:     for (d = off; d < off + dof; ++d) {
    443:       PetscInt aoff, i = 0;

    445:       PetscCall(PetscSectionGetOffset(leafSectionAdj, d, &aoff));
    446:       for (q = 0; q < numAdj; ++q) {
    447:         const PetscInt padj = tmpAdj[q];
    448:         PetscInt       ndof, ncdof, ngoff, nd;

    450:         if ((padj < pStart) || (padj >= pEnd)) continue;
    451:         PetscCall(PetscSectionGetDof(section, padj, &ndof));
    452:         PetscCall(PetscSectionGetConstraintDof(section, padj, &ncdof));
    453:         PetscCall(PetscSectionGetOffset(sectionGlobal, padj, &ngoff));
    454:         for (nd = 0; nd < ndof - ncdof; ++nd) {
    455:           adj[aoff + i] = (ngoff < 0 ? -(ngoff + 1) : ngoff) + nd;
    456:           ++i;
    457:         }
    458:       }
    459:       for (q = 0; q < anDof; q++) {
    460:         adj[aoff + i] = anchorAdj[anOff + q];
    461:         ++i;
    462:       }
    463:     }
    464:   }
    465:   /* Debugging */
    466:   if (debug) {
    467:     PetscCall(PetscPrintf(comm, "Leaf adjacency indices\n"));
    468:     PetscCall(PetscSectionArrayView(leafSectionAdj, adj, PETSC_INT, NULL));
    469:   }
    470:   /* Gather adjacent indices to root */
    471:   PetscCall(PetscSectionGetStorageSize(rootSectionAdj, &adjSize));
    472:   PetscCall(PetscMalloc1(adjSize, &rootAdj));
    473:   for (r = 0; r < adjSize; ++r) rootAdj[r] = -1;
    474:   if (doComm) {
    475:     const PetscInt *indegree;
    476:     PetscInt       *remoteadj, radjsize = 0;

    478:     PetscCall(PetscSFComputeDegreeBegin(sfAdj, &indegree));
    479:     PetscCall(PetscSFComputeDegreeEnd(sfAdj, &indegree));
    480:     for (p = 0; p < adjSize; ++p) radjsize += indegree[p];
    481:     PetscCall(PetscMalloc1(radjsize, &remoteadj));
    482:     PetscCall(PetscSFGatherBegin(sfAdj, MPIU_INT, adj, remoteadj));
    483:     PetscCall(PetscSFGatherEnd(sfAdj, MPIU_INT, adj, remoteadj));
    484:     for (p = 0, l = 0, r = 0; p < adjSize; ++p, l = PetscMax(p, l + indegree[p - 1])) {
    485:       PetscInt s;
    486:       for (s = 0; s < indegree[p]; ++s, ++r) rootAdj[l + s] = remoteadj[r];
    487:     }
    488:     PetscCheck(r == radjsize, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Inconsistency in communication %" PetscInt_FMT " != %" PetscInt_FMT, r, radjsize);
    489:     PetscCheck(l == adjSize, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Inconsistency in communication %" PetscInt_FMT " != %" PetscInt_FMT, l, adjSize);
    490:     PetscCall(PetscFree(remoteadj));
    491:   }
    492:   PetscCall(PetscSFDestroy(&sfAdj));
    493:   PetscCall(PetscFree(adj));
    494:   /* Debugging */
    495:   if (debug) {
    496:     PetscCall(PetscPrintf(comm, "Root adjacency indices after gather\n"));
    497:     PetscCall(PetscSectionArrayView(rootSectionAdj, rootAdj, PETSC_INT, NULL));
    498:   }
    499:   /* Add in local adjacency indices for owned dofs on interface (roots) */
    500:   for (p = pStart; p < pEnd; ++p) {
    501:     PetscInt numAdj = PETSC_DETERMINE, adof, dof, off, d, q, anDof, anOff;

    503:     PetscCall(PetscSectionGetDof(section, p, &dof));
    504:     PetscCall(PetscSectionGetOffset(section, p, &off));
    505:     if (!dof) continue;
    506:     PetscCall(PetscSectionGetDof(rootSectionAdj, off, &adof));
    507:     if (adof <= 0) continue;
    508:     PetscCall(DMPlexGetAdjacency_Internal(dm, p, useCone, useClosure, useAnchors, &numAdj, &tmpAdj));
    509:     PetscCall(PetscSectionGetDof(anchorSectionAdj, p, &anDof));
    510:     PetscCall(PetscSectionGetOffset(anchorSectionAdj, p, &anOff));
    511:     for (d = off; d < off + dof; ++d) {
    512:       PetscInt adof, aoff, i;

    514:       PetscCall(PetscSectionGetDof(rootSectionAdj, d, &adof));
    515:       PetscCall(PetscSectionGetOffset(rootSectionAdj, d, &aoff));
    516:       i = adof - 1;
    517:       for (q = 0; q < anDof; q++) {
    518:         rootAdj[aoff + i] = anchorAdj[anOff + q];
    519:         --i;
    520:       }
    521:       for (q = 0; q < numAdj; ++q) {
    522:         const PetscInt padj = tmpAdj[q];
    523:         PetscInt       ndof, ncdof, ngoff, nd;

    525:         if ((padj < pStart) || (padj >= pEnd)) continue;
    526:         PetscCall(PetscSectionGetDof(section, padj, &ndof));
    527:         PetscCall(PetscSectionGetConstraintDof(section, padj, &ncdof));
    528:         PetscCall(PetscSectionGetOffset(sectionGlobal, padj, &ngoff));
    529:         for (nd = 0; nd < ndof - ncdof; ++nd) {
    530:           rootAdj[aoff + i] = ngoff < 0 ? -(ngoff + 1) + nd : ngoff + nd;
    531:           --i;
    532:         }
    533:       }
    534:     }
    535:   }
    536:   /* Debugging */
    537:   if (debug) {
    538:     PetscCall(PetscPrintf(comm, "Adjacency Section for Preallocation on Roots before compression:\n"));
    539:     PetscCall(PetscSectionArrayView(rootSectionAdj, rootAdj, PETSC_INT, NULL));
    540:   }
    541:   /* Compress indices */
    542:   PetscCall(PetscSectionSetUp(rootSectionAdj));
    543:   for (p = pStart; p < pEnd; ++p) {
    544:     PetscInt dof, cdof, off, d;
    545:     PetscInt adof, aoff;

    547:     PetscCall(PetscSectionGetDof(section, p, &dof));
    548:     PetscCall(PetscSectionGetConstraintDof(section, p, &cdof));
    549:     PetscCall(PetscSectionGetOffset(section, p, &off));
    550:     if (!dof) continue;
    551:     PetscCall(PetscSectionGetDof(rootSectionAdj, off, &adof));
    552:     if (adof <= 0) continue;
    553:     for (d = off; d < off + dof - cdof; ++d) {
    554:       PetscCall(PetscSectionGetDof(rootSectionAdj, d, &adof));
    555:       PetscCall(PetscSectionGetOffset(rootSectionAdj, d, &aoff));
    556:       PetscCall(PetscSortRemoveDupsInt(&adof, &rootAdj[aoff]));
    557:       PetscCall(PetscSectionSetDof(rootSectionAdj, d, adof));
    558:     }
    559:   }
    560:   /* Debugging */
    561:   if (debug) {
    562:     PetscCall(PetscPrintf(comm, "Adjacency Section for Preallocation on Roots after compression:\n"));
    563:     PetscCall(PetscSectionArrayView(rootSectionAdj, rootAdj, PETSC_INT, NULL));
    564:   }
    565:   /* Build adjacency section: Maps global indices to sets of adjacent global indices */
    566:   PetscCall(PetscSectionGetOffsetRange(sectionGlobal, &globalOffStart, &globalOffEnd));
    567:   PetscCall(PetscSectionCreate(comm, &sectionAdj));
    568:   PetscCall(PetscSectionSetChart(sectionAdj, globalOffStart, globalOffEnd));

    570:   PetscInt *exclude_leaves, num_exclude_leaves = 0, max_adjacency_size = 0;
    571:   PetscCall(DMPlexGetMaxAdjacencySize_Internal(dm, useAnchors, &max_adjacency_size));
    572:   PetscCall(PetscMalloc1(max_adjacency_size, &exclude_leaves));

    574:   for (p = pStart; p < pEnd; ++p) {
    575:     PetscInt  numAdj = PETSC_DETERMINE, dof, cdof, off, goff, d, q, anDof;
    576:     PetscBool found  = PETSC_TRUE;

    578:     PetscCall(PetscSectionGetDof(section, p, &dof));
    579:     PetscCall(PetscSectionGetConstraintDof(section, p, &cdof));
    580:     PetscCall(PetscSectionGetOffset(section, p, &off));
    581:     PetscCall(PetscSectionGetOffset(sectionGlobal, p, &goff));
    582:     for (d = 0; d < dof - cdof; ++d) {
    583:       PetscInt ldof, rdof;

    585:       PetscCall(PetscSectionGetDof(leafSectionAdj, off + d, &ldof));
    586:       PetscCall(PetscSectionGetDof(rootSectionAdj, off + d, &rdof));
    587:       if (ldof > 0) {
    588:         /* We do not own this point */
    589:       } else if (rdof > 0) {
    590:         PetscCall(PetscSectionSetDof(sectionAdj, goff + d, rdof));
    591:       } else {
    592:         found = PETSC_FALSE;
    593:       }
    594:     }
    595:     if (found) continue;
    596:     PetscCall(PetscSectionGetDof(section, p, &dof));
    597:     PetscCall(PetscSectionGetOffset(sectionGlobal, p, &goff));
    598:     PetscCall(DMPlexGetAdjacency_Internal(dm, p, useCone, useClosure, useAnchors, &numAdj, &tmpAdj));
    599:     PetscCall(AdjancencyContainsLeafRootPair(myRankPairSection, myRankPairLeaves, myRankPairRoots, numAdj, tmpAdj, &num_exclude_leaves, exclude_leaves));
    600:     for (q = 0; q < numAdj; ++q) {
    601:       const PetscInt padj = tmpAdj[q];
    602:       PetscInt       ndof, ncdof, noff, count;

    604:       if ((padj < pStart) || (padj >= pEnd)) continue;
    605:       PetscCall(PetscSectionGetDof(section, padj, &ndof));
    606:       PetscCall(PetscSectionGetConstraintDof(section, padj, &ncdof));
    607:       PetscCall(PetscSectionGetOffset(section, padj, &noff));
    608:       // If leaf-root pair are both on this rank, only count root
    609:       PetscCall(PetscFindInt(padj, num_exclude_leaves, exclude_leaves, &count));
    610:       if (count >= 0) continue;
    611:       for (d = goff; d < goff + dof - cdof; ++d) PetscCall(PetscSectionAddDof(sectionAdj, d, ndof - ncdof));
    612:     }
    613:     PetscCall(PetscSectionGetDof(anchorSectionAdj, p, &anDof));
    614:     if (anDof) {
    615:       for (d = goff; d < goff + dof - cdof; ++d) PetscCall(PetscSectionAddDof(sectionAdj, d, anDof));
    616:     }
    617:   }
    618:   PetscCall(PetscSectionSetUp(sectionAdj));
    619:   if (debug) {
    620:     PetscCall(PetscPrintf(comm, "Adjacency Section for Preallocation:\n"));
    621:     PetscCall(PetscSectionView(sectionAdj, NULL));
    622:   }
    623:   /* Get adjacent indices */
    624:   PetscCall(PetscSectionGetStorageSize(sectionAdj, &numCols));
    625:   PetscCall(PetscMalloc1(numCols, &cols));
    626:   for (p = pStart; p < pEnd; ++p) {
    627:     PetscInt  numAdj = PETSC_DETERMINE, dof, cdof, off, goff, d, q, anDof, anOff;
    628:     PetscBool found  = PETSC_TRUE;

    630:     PetscCall(PetscSectionGetDof(section, p, &dof));
    631:     PetscCall(PetscSectionGetConstraintDof(section, p, &cdof));
    632:     PetscCall(PetscSectionGetOffset(section, p, &off));
    633:     PetscCall(PetscSectionGetOffset(sectionGlobal, p, &goff));
    634:     for (d = 0; d < dof - cdof; ++d) {
    635:       PetscInt ldof, rdof;

    637:       PetscCall(PetscSectionGetDof(leafSectionAdj, off + d, &ldof));
    638:       PetscCall(PetscSectionGetDof(rootSectionAdj, off + d, &rdof));
    639:       if (ldof > 0) {
    640:         /* We do not own this point */
    641:       } else if (rdof > 0) {
    642:         PetscInt aoff, roff;

    644:         PetscCall(PetscSectionGetOffset(sectionAdj, goff + d, &aoff));
    645:         PetscCall(PetscSectionGetOffset(rootSectionAdj, off + d, &roff));
    646:         PetscCall(PetscArraycpy(&cols[aoff], &rootAdj[roff], rdof));
    647:       } else {
    648:         found = PETSC_FALSE;
    649:       }
    650:     }
    651:     if (found) continue;
    652:     PetscCall(DMPlexGetAdjacency_Internal(dm, p, useCone, useClosure, useAnchors, &numAdj, &tmpAdj));
    653:     PetscCall(AdjancencyContainsLeafRootPair(myRankPairSection, myRankPairLeaves, myRankPairRoots, numAdj, tmpAdj, &num_exclude_leaves, exclude_leaves));
    654:     PetscCall(PetscSectionGetDof(anchorSectionAdj, p, &anDof));
    655:     PetscCall(PetscSectionGetOffset(anchorSectionAdj, p, &anOff));
    656:     for (d = goff; d < goff + dof - cdof; ++d) {
    657:       PetscInt adof, aoff, i = 0;

    659:       PetscCall(PetscSectionGetDof(sectionAdj, d, &adof));
    660:       PetscCall(PetscSectionGetOffset(sectionAdj, d, &aoff));
    661:       for (q = 0; q < numAdj; ++q) {
    662:         const PetscInt padj = tmpAdj[q], *ncind;
    663:         PetscInt       ndof, ncdof, ngoff, nd, count;

    665:         /* Adjacent points may not be in the section chart */
    666:         if ((padj < pStart) || (padj >= pEnd)) continue;
    667:         PetscCall(PetscSectionGetDof(section, padj, &ndof));
    668:         PetscCall(PetscSectionGetConstraintDof(section, padj, &ncdof));
    669:         PetscCall(PetscSectionGetConstraintIndices(section, padj, &ncind));
    670:         PetscCall(PetscSectionGetOffset(sectionGlobal, padj, &ngoff));
    671:         // If leaf-root pair are both on this rank, only count root
    672:         PetscCall(PetscFindInt(padj, num_exclude_leaves, exclude_leaves, &count));
    673:         if (count >= 0) continue;
    674:         for (nd = 0; nd < ndof - ncdof; ++nd, ++i) cols[aoff + i] = ngoff < 0 ? -(ngoff + 1) + nd : ngoff + nd;
    675:       }
    676:       for (q = 0; q < anDof; q++, i++) cols[aoff + i] = anchorAdj[anOff + q];
    677:       PetscCheck(i == adof, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid number of entries %" PetscInt_FMT " != %" PetscInt_FMT " for dof %" PetscInt_FMT " (point %" PetscInt_FMT ")", i, adof, d, p);
    678:     }
    679:   }
    680:   PetscCall(PetscSectionDestroy(&anchorSectionAdj));
    681:   PetscCall(PetscSectionDestroy(&leafSectionAdj));
    682:   PetscCall(PetscSectionDestroy(&rootSectionAdj));
    683:   PetscCall(PetscSectionDestroy(&myRankPairSection));
    684:   PetscCall(PetscFree(exclude_leaves));
    685:   PetscCall(PetscFree(myRankPairLeaves));
    686:   PetscCall(PetscFree(myRankPairRoots));
    687:   PetscCall(PetscFree(anchorAdj));
    688:   PetscCall(PetscFree(rootAdj));
    689:   PetscCall(PetscFree(tmpAdj));
    690:   /* Debugging */
    691:   if (debug) {
    692:     PetscCall(PetscPrintf(comm, "Column indices\n"));
    693:     PetscCall(PetscSectionArrayView(sectionAdj, cols, PETSC_INT, NULL));
    694:   }

    696:   *sA     = sectionAdj;
    697:   *colIdx = cols;
    698:   PetscFunctionReturn(PETSC_SUCCESS);
    699: }

    701: static PetscErrorCode DMPlexUpdateAllocation_Static(DM dm, PetscLayout rLayout, PetscInt bs, PetscInt f, PetscSection sectionAdj, const PetscInt cols[], PetscInt dnz[], PetscInt onz[], PetscInt dnzu[], PetscInt onzu[])
    702: {
    703:   PetscSection section;
    704:   PetscInt     rStart, rEnd, r, pStart, pEnd, p;

    706:   PetscFunctionBegin;
    707:   /* This loop needs to change to a loop over points, then field dofs, which means we need to look both sections */
    708:   PetscCall(PetscLayoutGetRange(rLayout, &rStart, &rEnd));
    709:   PetscCheck((rStart % bs) == 0 && (rEnd % bs) == 0, PetscObjectComm((PetscObject)rLayout), PETSC_ERR_ARG_WRONG, "Invalid layout [%" PetscInt_FMT ", %" PetscInt_FMT ") for matrix, must be divisible by block size %" PetscInt_FMT, rStart, rEnd, bs);
    710:   if (f >= 0 && bs == 1) {
    711:     PetscCall(DMGetLocalSection(dm, &section));
    712:     PetscCall(PetscSectionGetChart(section, &pStart, &pEnd));
    713:     for (p = pStart; p < pEnd; ++p) {
    714:       PetscInt rS, rE;

    716:       PetscCall(DMGetGlobalFieldOffset_Private(dm, p, f, &rS, &rE));
    717:       for (r = rS; r < rE; ++r) {
    718:         PetscInt numCols, cStart, c;

    720:         PetscCall(PetscSectionGetDof(sectionAdj, r, &numCols));
    721:         PetscCall(PetscSectionGetOffset(sectionAdj, r, &cStart));
    722:         for (c = cStart; c < cStart + numCols; ++c) {
    723:           if ((cols[c] >= rStart) && (cols[c] < rEnd)) {
    724:             ++dnz[r - rStart];
    725:             if (cols[c] >= r) ++dnzu[r - rStart];
    726:           } else {
    727:             ++onz[r - rStart];
    728:             if (cols[c] >= r) ++onzu[r - rStart];
    729:           }
    730:         }
    731:       }
    732:     }
    733:   } else {
    734:     /* Only loop over blocks of rows */
    735:     for (r = rStart / bs; r < rEnd / bs; ++r) {
    736:       const PetscInt row = r * bs;
    737:       PetscInt       numCols, cStart, c;

    739:       PetscCall(PetscSectionGetDof(sectionAdj, row, &numCols));
    740:       PetscCall(PetscSectionGetOffset(sectionAdj, row, &cStart));
    741:       for (c = cStart; c < cStart + numCols; ++c) {
    742:         if ((cols[c] >= rStart) && (cols[c] < rEnd)) {
    743:           ++dnz[r - rStart / bs];
    744:           if (cols[c] >= row) ++dnzu[r - rStart / bs];
    745:         } else {
    746:           ++onz[r - rStart / bs];
    747:           if (cols[c] >= row) ++onzu[r - rStart / bs];
    748:         }
    749:       }
    750:     }
    751:     for (r = 0; r < (rEnd - rStart) / bs; ++r) {
    752:       dnz[r] /= bs;
    753:       onz[r] /= bs;
    754:       dnzu[r] /= bs;
    755:       onzu[r] /= bs;
    756:     }
    757:   }
    758:   PetscFunctionReturn(PETSC_SUCCESS);
    759: }

    761: static PetscErrorCode DMPlexFillMatrix_Static(DM dm, PetscLayout rLayout, PetscInt bs, PetscInt f, PetscSection sectionAdj, const PetscInt cols[], Mat A)
    762: {
    763:   PetscSection section;
    764:   PetscScalar *values;
    765:   PetscInt     rStart, rEnd, r, pStart, pEnd, p, len, maxRowLen = 0;

    767:   PetscFunctionBegin;
    768:   PetscCall(PetscLayoutGetRange(rLayout, &rStart, &rEnd));
    769:   for (r = rStart; r < rEnd; ++r) {
    770:     PetscCall(PetscSectionGetDof(sectionAdj, r, &len));
    771:     maxRowLen = PetscMax(maxRowLen, len);
    772:   }
    773:   PetscCall(PetscCalloc1(maxRowLen, &values));
    774:   if (f >= 0 && bs == 1) {
    775:     PetscCall(DMGetLocalSection(dm, &section));
    776:     PetscCall(PetscSectionGetChart(section, &pStart, &pEnd));
    777:     for (p = pStart; p < pEnd; ++p) {
    778:       PetscInt rS, rE;

    780:       PetscCall(DMGetGlobalFieldOffset_Private(dm, p, f, &rS, &rE));
    781:       for (r = rS; r < rE; ++r) {
    782:         PetscInt numCols, cStart;

    784:         PetscCall(PetscSectionGetDof(sectionAdj, r, &numCols));
    785:         PetscCall(PetscSectionGetOffset(sectionAdj, r, &cStart));
    786:         PetscCall(MatSetValues(A, 1, &r, numCols, &cols[cStart], values, INSERT_VALUES));
    787:       }
    788:     }
    789:   } else {
    790:     for (r = rStart; r < rEnd; ++r) {
    791:       PetscInt numCols, cStart;

    793:       PetscCall(PetscSectionGetDof(sectionAdj, r, &numCols));
    794:       PetscCall(PetscSectionGetOffset(sectionAdj, r, &cStart));
    795:       PetscCall(MatSetValues(A, 1, &r, numCols, &cols[cStart], values, INSERT_VALUES));
    796:     }
    797:   }
    798:   PetscCall(PetscFree(values));
    799:   PetscFunctionReturn(PETSC_SUCCESS);
    800: }

    802: /*@
    803:   DMPlexPreallocateOperator - Calculate the matrix nonzero pattern based upon the information in the `DM`,
    804:   the `PetscDS` it contains, and the default `PetscSection`.

    806:   Collective

    808:   Input Parameters:
    809: + dm         - The `DMPLEX`
    810: . bs         - The matrix blocksize
    811: . dnz        - An array to hold the number of nonzeros in the diagonal block
    812: . onz        - An array to hold the number of nonzeros in the off-diagonal block
    813: . dnzu       - An array to hold the number of nonzeros in the upper triangle of the diagonal block
    814: . onzu       - An array to hold the number of nonzeros in the upper triangle of the off-diagonal block
    815: - fillMatrix - If `PETSC_TRUE`, fill the matrix with zeros

    817:   Output Parameter:
    818: . A - The preallocated matrix

    820:   Level: advanced

    822: .seealso: [](ch_unstructured), `DM`, `DMPLEX`, `DMCreateMatrix()`
    823: @*/
    824: PetscErrorCode DMPlexPreallocateOperator(DM dm, PetscInt bs, PetscInt dnz[], PetscInt onz[], PetscInt dnzu[], PetscInt onzu[], Mat A, PetscBool fillMatrix)
    825: {
    826:   MPI_Comm     comm;
    827:   MatType      mtype;
    828:   PetscSF      sf, sfDof;
    829:   PetscSection section;
    830:   PetscInt    *remoteOffsets;
    831:   PetscSection sectionAdj[4] = {NULL, NULL, NULL, NULL};
    832:   PetscInt    *cols[4]       = {NULL, NULL, NULL, NULL};
    833:   PetscBool    useCone, useClosure;
    834:   PetscInt     Nf, f, idx, locRows;
    835:   PetscLayout  rLayout;
    836:   PetscBool    isSymBlock, isSymSeqBlock, isSymMPIBlock, debug = PETSC_FALSE;

    838:   PetscFunctionBegin;
    841:   if (dnz) PetscAssertPointer(dnz, 3);
    842:   if (onz) PetscAssertPointer(onz, 4);
    843:   if (dnzu) PetscAssertPointer(dnzu, 5);
    844:   if (onzu) PetscAssertPointer(onzu, 6);
    845:   PetscCall(DMGetIsoperiodicPointSF_Internal(dm, &sf));
    846:   PetscCall(DMGetLocalSection(dm, &section));
    847:   PetscCall(PetscOptionsGetBool(NULL, NULL, "-dm_view_preallocation", &debug, NULL));
    848:   PetscCall(PetscObjectGetComm((PetscObject)dm, &comm));
    849:   PetscCall(PetscLogEventBegin(DMPLEX_Preallocate, dm, 0, 0, 0));
    850:   /* Create dof SF based on point SF */
    851:   if (debug) {
    852:     PetscSection section, sectionGlobal;
    853:     PetscSF      sf;

    855:     PetscCall(DMGetIsoperiodicPointSF_Internal(dm, &sf));
    856:     PetscCall(DMGetLocalSection(dm, &section));
    857:     PetscCall(DMGetGlobalSection(dm, &sectionGlobal));
    858:     PetscCall(PetscPrintf(comm, "Input Section for Preallocation:\n"));
    859:     PetscCall(PetscSectionView(section, NULL));
    860:     PetscCall(PetscPrintf(comm, "Input Global Section for Preallocation:\n"));
    861:     PetscCall(PetscSectionView(sectionGlobal, NULL));
    862:     PetscCall(PetscPrintf(comm, "Input SF for Preallocation:\n"));
    863:     PetscCall(PetscSFView(sf, NULL));
    864:   }
    865:   PetscCall(PetscSFCreateRemoteOffsets(sf, section, section, &remoteOffsets));
    866:   PetscCall(PetscSFCreateSectionSF(sf, section, remoteOffsets, section, &sfDof));
    867:   PetscCall(PetscFree(remoteOffsets));
    868:   if (debug) {
    869:     PetscCall(PetscPrintf(comm, "Dof SF for Preallocation:\n"));
    870:     PetscCall(PetscSFView(sfDof, NULL));
    871:   }
    872:   /* Create allocation vectors from adjacency graph */
    873:   PetscCall(MatGetLocalSize(A, &locRows, NULL));
    874:   PetscCall(PetscLayoutCreate(comm, &rLayout));
    875:   PetscCall(PetscLayoutSetLocalSize(rLayout, locRows));
    876:   PetscCall(PetscLayoutSetBlockSize(rLayout, 1));
    877:   PetscCall(PetscLayoutSetUp(rLayout));
    878:   /* There are 4 types of adjacency */
    879:   PetscCall(PetscSectionGetNumFields(section, &Nf));
    880:   if (Nf < 1 || bs > 1) {
    881:     PetscCall(DMGetBasicAdjacency(dm, &useCone, &useClosure));
    882:     idx = (useCone ? 1 : 0) + (useClosure ? 2 : 0);
    883:     PetscCall(DMPlexCreateAdjacencySection_Static(dm, bs, sfDof, useCone, useClosure, PETSC_TRUE, &sectionAdj[idx], &cols[idx]));
    884:     PetscCall(DMPlexUpdateAllocation_Static(dm, rLayout, bs, -1, sectionAdj[idx], cols[idx], dnz, onz, dnzu, onzu));
    885:   } else {
    886:     for (f = 0; f < Nf; ++f) {
    887:       PetscCall(DMGetAdjacency(dm, f, &useCone, &useClosure));
    888:       idx = (useCone ? 1 : 0) + (useClosure ? 2 : 0);
    889:       if (!sectionAdj[idx]) PetscCall(DMPlexCreateAdjacencySection_Static(dm, bs, sfDof, useCone, useClosure, PETSC_TRUE, &sectionAdj[idx], &cols[idx]));
    890:       PetscCall(DMPlexUpdateAllocation_Static(dm, rLayout, bs, f, sectionAdj[idx], cols[idx], dnz, onz, dnzu, onzu));
    891:     }
    892:   }
    893:   PetscCall(PetscSFDestroy(&sfDof));
    894:   /* Set matrix pattern */
    895:   PetscCall(MatXAIJSetPreallocation(A, bs, dnz, onz, dnzu, onzu));
    896:   PetscCall(MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE));
    897:   /* Check for symmetric storage */
    898:   PetscCall(MatGetType(A, &mtype));
    899:   PetscCall(PetscStrcmp(mtype, MATSBAIJ, &isSymBlock));
    900:   PetscCall(PetscStrcmp(mtype, MATSEQSBAIJ, &isSymSeqBlock));
    901:   PetscCall(PetscStrcmp(mtype, MATMPISBAIJ, &isSymMPIBlock));
    902:   if (isSymBlock || isSymSeqBlock || isSymMPIBlock) PetscCall(MatSetOption(A, MAT_IGNORE_LOWER_TRIANGULAR, PETSC_TRUE));
    903:   /* Fill matrix with zeros */
    904:   if (fillMatrix) {
    905:     if (Nf < 1 || bs > 1) {
    906:       PetscCall(DMGetBasicAdjacency(dm, &useCone, &useClosure));
    907:       idx = (useCone ? 1 : 0) + (useClosure ? 2 : 0);
    908:       PetscCall(DMPlexFillMatrix_Static(dm, rLayout, bs, -1, sectionAdj[idx], cols[idx], A));
    909:     } else {
    910:       for (f = 0; f < Nf; ++f) {
    911:         PetscCall(DMGetAdjacency(dm, f, &useCone, &useClosure));
    912:         idx = (useCone ? 1 : 0) + (useClosure ? 2 : 0);
    913:         PetscCall(DMPlexFillMatrix_Static(dm, rLayout, bs, f, sectionAdj[idx], cols[idx], A));
    914:       }
    915:     }
    916:     PetscCall(MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY));
    917:     PetscCall(MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY));
    918:   }
    919:   PetscCall(PetscLayoutDestroy(&rLayout));
    920:   for (idx = 0; idx < 4; ++idx) {
    921:     PetscCall(PetscSectionDestroy(&sectionAdj[idx]));
    922:     PetscCall(PetscFree(cols[idx]));
    923:   }
    924:   PetscCall(PetscLogEventEnd(DMPLEX_Preallocate, dm, 0, 0, 0));
    925:   PetscFunctionReturn(PETSC_SUCCESS);
    926: }

    928: #if 0
    929: PetscErrorCode DMPlexPreallocateOperator_2(DM dm, PetscInt bs, PetscSection section, PetscSection sectionGlobal, PetscInt dnz[], PetscInt onz[], PetscInt dnzu[], PetscInt onzu[], Mat A, PetscBool fillMatrix)
    930: {
    931:   PetscInt       *tmpClosure,*tmpAdj,*visits;
    932:   PetscInt        c,cStart,cEnd,pStart,pEnd;

    934:   PetscFunctionBegin;
    935:   PetscCall(DMGetDimension(dm, &dim));
    936:   PetscCall(DMPlexGetDepth(dm, &depth));
    937:   PetscCall(DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize));

    939:   maxClosureSize = 2*PetscMax(PetscPowInt(mesh->maxConeSize,depth+1),PetscPowInt(mesh->maxSupportSize,depth+1));

    941:   PetscCall(PetscSectionGetChart(section, &pStart, &pEnd));
    942:   npoints = pEnd - pStart;

    944:   PetscCall(PetscMalloc3(maxClosureSize,&tmpClosure,npoints,&lvisits,npoints,&visits));
    945:   PetscCall(PetscArrayzero(lvisits,pEnd-pStart));
    946:   PetscCall(PetscArrayzero(visits,pEnd-pStart));
    947:   PetscCall(DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd));
    948:   for (c=cStart; c<cEnd; c++) {
    949:     PetscInt *support = tmpClosure;
    950:     PetscCall(DMPlexGetTransitiveClosure(dm, c, PETSC_FALSE, &supportSize, (PetscInt**)&support));
    951:     for (p=0; p<supportSize; p++) lvisits[support[p]]++;
    952:   }
    953:   PetscCall(PetscSFReduceBegin(sf,MPIU_INT,lvisits,visits,MPI_SUM));
    954:   PetscCall(PetscSFReduceEnd  (sf,MPIU_INT,lvisits,visits,MPI_SUM));
    955:   PetscCall(PetscSFBcastBegin(sf,MPIU_INT,visits,lvisits,MPI_REPLACE));
    956:   PetscCall(PetscSFBcastEnd  (sf,MPIU_INT,visits,lvisits));

    958:   PetscCall(PetscSFGetRootRanks());

    960:   PetscCall(PetscMalloc2(maxClosureSize*maxClosureSize,&cellmat,npoints,&owner));
    961:   for (c=cStart; c<cEnd; c++) {
    962:     PetscCall(PetscArrayzero(cellmat,maxClosureSize*maxClosureSize));
    963:     /*
    964:      Depth-first walk of transitive closure.
    965:      At each leaf frame f of transitive closure that we see, add 1/visits[f] to each pair (p,q) not marked as done in cellmat.
    966:      This contribution is added to dnz if owning ranks of p and q match, to onz otherwise.
    967:      */
    968:   }

    970:   PetscCall(PetscSFReduceBegin(sf,MPIU_INT,ldnz,dnz,MPI_SUM));
    971:   PetscCall(PetscSFReduceEnd  (sf,MPIU_INT,lonz,onz,MPI_SUM));
    972:   PetscFunctionReturn(PETSC_SUCCESS);
    973: }
    974: #endif