Date: 2022-08-02T03:14:16+00:00

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    142:     /* clean up */
    143:     PetscSectionDestroy(&inverseSec);
    144:     PetscFree(inverse);
    145:     PetscFree(tmpAdjP);
    146:     PetscFree(tmpAdjQ);
    147:   }
    148:   else {
    149:     *anchorAdj = NULL;
    150:     PetscSectionSetUp(adjSec);
    151:   }
    152:   *anchorSectionAdj = adjSec;
    153:   return 0;
    154: }

    156: static PetscErrorCode DMPlexCreateAdjacencySection_Static(DM dm, PetscInt bs, PetscSF sfDof, PetscBool useCone, PetscBool useClosure, PetscBool useAnchors, PetscSection *sA, PetscInt **colIdx)
    157: {
    158:   MPI_Comm           comm;
    159:   PetscMPIInt        size;
    160:   PetscBool          doCommLocal, doComm, debug = PETSC_FALSE;
    161:   PetscSF            sf, sfAdj;
    162:   PetscSection       section, sectionGlobal, leafSectionAdj, rootSectionAdj, sectionAdj, anchorSectionAdj;
    163:   PetscInt           nroots, nleaves, l, p, r;
    164:   const PetscInt    *leaves;
    165:   const PetscSFNode *remotes;
    166:   PetscInt           dim, pStart, pEnd, numDof, globalOffStart, globalOffEnd, numCols;
    167:   PetscInt          *tmpAdj = NULL, *adj, *rootAdj, *anchorAdj = NULL, *cols, *remoteOffsets;
    168:   PetscInt           adjSize;

    170:   PetscObjectGetComm((PetscObject) dm, &comm);
    171:   PetscOptionsGetBool(NULL,NULL, "-dm_view_preallocation", &debug, NULL);
    172:   MPI_Comm_size(comm, &size);
    173:   DMGetDimension(dm, &dim);
    174:   DMGetPointSF(dm, &sf);
    175:   DMGetLocalSection(dm, &section);
    176:   DMGetGlobalSection(dm, &sectionGlobal);
    177:   PetscSFGetGraph(sf, &nroots, NULL, NULL, NULL);
    178:   doCommLocal = (size > 1) && (nroots >= 0) ? PETSC_TRUE : PETSC_FALSE;
    179:   MPIU_Allreduce(&doCommLocal, &doComm, 1, MPIU_BOOL, MPI_LAND, comm);
    180:   /* Create section for dof adjacency (dof ==> # adj dof) */
    181:   PetscSectionGetChart(section, &pStart, &pEnd);
    182:   PetscSectionGetStorageSize(section, &numDof);
    183:   PetscSectionCreate(comm, &leafSectionAdj);
    184:   PetscSectionSetChart(leafSectionAdj, 0, numDof);
    185:   PetscSectionCreate(comm, &rootSectionAdj);
    186:   PetscSectionSetChart(rootSectionAdj, 0, numDof);
    187:   /*   Fill in the ghost dofs on the interface */
    188:   PetscSFGetGraph(sf, NULL, &nleaves, &leaves, &remotes);
    189:   /*
    190:    section        - maps points to (# dofs, local dofs)
    191:    sectionGlobal  - maps points to (# dofs, global dofs)
    192:    leafSectionAdj - maps unowned local dofs to # adj dofs
    193:    rootSectionAdj - maps   owned local dofs to # adj dofs
    194:    adj            - adj global dofs indexed by leafSectionAdj
    195:    rootAdj        - adj global dofs indexed by rootSectionAdj
    196:    sf    - describes shared points across procs
    197:    sfDof - describes shared dofs across procs
    198:    sfAdj - describes shared adjacent dofs across procs
    199:    ** The bootstrapping process involves six rounds with similar structure of visiting neighbors of each point.
    200:   (0). If there are point-to-point constraints, add the adjacencies of constrained points to anchors in anchorAdj
    201:        (This is done in DMPlexComputeAnchorAdjacencies())
    202:     1. Visit unowned points on interface, count adjacencies placing in leafSectionAdj
    203:        Reduce those counts to rootSectionAdj (now redundantly counting some interface points)
    204:     2. Visit owned points on interface, count adjacencies placing in rootSectionAdj
    205:        Create sfAdj connecting rootSectionAdj and leafSectionAdj
    206:     3. Visit unowned points on interface, write adjacencies to adj
    207:        Gather adj to rootAdj (note that there is redundancy in rootAdj when multiple procs find the same adjacencies)
    208:     4. Visit owned points on interface, write adjacencies to rootAdj
    209:        Remove redundancy in rootAdj
    210:    ** The last two traversals use transitive closure
    211:     5. Visit all owned points in the subdomain, count dofs for each point (sectionAdj)
    212:        Allocate memory addressed by sectionAdj (cols)
    213:     6. Visit all owned points in the subdomain, insert dof adjacencies into cols
    214:    ** Knowing all the column adjacencies, check ownership and sum into dnz and onz
    215:   */
    216:   DMPlexComputeAnchorAdjacencies(dm, useCone, useClosure, &anchorSectionAdj, &anchorAdj);
    217:   for (l = 0; l < nleaves; ++l) {
    218:     PetscInt dof, off, d, q, anDof;
    219:     PetscInt p = leaves[l], numAdj = PETSC_DETERMINE;

    221:     if ((p < pStart) || (p >= pEnd)) continue;
    222:     PetscSectionGetDof(section, p, &dof);
    223:     PetscSectionGetOffset(section, p, &off);
    224:     DMPlexGetAdjacency_Internal(dm, p, useCone, useClosure, useAnchors, &numAdj, &tmpAdj);
    225:     for (q = 0; q < numAdj; ++q) {
    226:       const PetscInt padj = tmpAdj[q];
    227:       PetscInt ndof, ncdof;

    229:       if ((padj < pStart) || (padj >= pEnd)) continue;
    230:       PetscSectionGetDof(section, padj, &ndof);
    231:       PetscSectionGetConstraintDof(section, padj, &ncdof);
    232:       for (d = off; d < off+dof; ++d) {
    233:         PetscSectionAddDof(leafSectionAdj, d, ndof-ncdof);
    234:       }
    235:     }
    236:     PetscSectionGetDof(anchorSectionAdj, p, &anDof);
    237:     if (anDof) {
    238:       for (d = off; d < off+dof; ++d) {
    239:         PetscSectionAddDof(leafSectionAdj, d, anDof);
    240:       }
    241:     }
    242:   }
    243:   PetscSectionSetUp(leafSectionAdj);
    244:   if (debug) {
    245:     PetscPrintf(comm, "Adjacency Section for Preallocation on Leaves:\n");
    246:     PetscSectionView(leafSectionAdj, NULL);
    247:   }
    248:   /* Get maximum remote adjacency sizes for owned dofs on interface (roots) */
    249:   if (doComm) {
    250:     PetscSFReduceBegin(sfDof, MPIU_INT, leafSectionAdj->atlasDof, rootSectionAdj->atlasDof, MPI_SUM);
    251:     PetscSFReduceEnd(sfDof, MPIU_INT, leafSectionAdj->atlasDof, rootSectionAdj->atlasDof, MPI_SUM);
    252:     PetscSectionInvalidateMaxDof_Internal(rootSectionAdj);
    253:   }
    254:   if (debug) {
    255:     PetscPrintf(comm, "Adjancency Section for Preallocation on Roots:\n");
    256:     PetscSectionView(rootSectionAdj, NULL);
    257:   }
    258:   /* Add in local adjacency sizes for owned dofs on interface (roots) */
    259:   for (p = pStart; p < pEnd; ++p) {
    260:     PetscInt numAdj = PETSC_DETERMINE, adof, dof, off, d, q, anDof;

    262:     PetscSectionGetDof(section, p, &dof);
    263:     PetscSectionGetOffset(section, p, &off);
    264:     if (!dof) continue;
    265:     PetscSectionGetDof(rootSectionAdj, off, &adof);
    266:     if (adof <= 0) continue;
    267:     DMPlexGetAdjacency_Internal(dm, p, useCone, useClosure, useAnchors, &numAdj, &tmpAdj);
    268:     for (q = 0; q < numAdj; ++q) {
    269:       const PetscInt padj = tmpAdj[q];
    270:       PetscInt ndof, ncdof;

    272:       if ((padj < pStart) || (padj >= pEnd)) continue;
    273:       PetscSectionGetDof(section, padj, &ndof);
    274:       PetscSectionGetConstraintDof(section, padj, &ncdof);
    275:       for (d = off; d < off+dof; ++d) {
    276:         PetscSectionAddDof(rootSectionAdj, d, ndof-ncdof);
    277:       }
    278:     }
    279:     PetscSectionGetDof(anchorSectionAdj, p, &anDof);
    280:     if (anDof) {
    281:       for (d = off; d < off+dof; ++d) {
    282:         PetscSectionAddDof(rootSectionAdj, d, anDof);
    283:       }
    284:     }
    285:   }
    286:   PetscSectionSetUp(rootSectionAdj);
    287:   if (debug) {
    288:     PetscPrintf(comm, "Adjancency Section for Preallocation on Roots after local additions:\n");
    289:     PetscSectionView(rootSectionAdj, NULL);
    290:   }
    291:   /* Create adj SF based on dof SF */
    292:   PetscSFCreateRemoteOffsets(sfDof, rootSectionAdj, leafSectionAdj, &remoteOffsets);
    293:   PetscSFCreateSectionSF(sfDof, rootSectionAdj, remoteOffsets, leafSectionAdj, &sfAdj);
    294:   PetscFree(remoteOffsets);
    295:   if (debug && size > 1) {
    296:     PetscPrintf(comm, "Adjacency SF for Preallocation:\n");
    297:     PetscSFView(sfAdj, NULL);
    298:   }
    299:   /* Create leaf adjacency */
    300:   PetscSectionSetUp(leafSectionAdj);
    301:   PetscSectionGetStorageSize(leafSectionAdj, &adjSize);
    302:   PetscCalloc1(adjSize, &adj);
    303:   for (l = 0; l < nleaves; ++l) {
    304:     PetscInt dof, off, d, q, anDof, anOff;
    305:     PetscInt p = leaves[l], numAdj = PETSC_DETERMINE;

    307:     if ((p < pStart) || (p >= pEnd)) continue;
    308:     PetscSectionGetDof(section, p, &dof);
    309:     PetscSectionGetOffset(section, p, &off);
    310:     DMPlexGetAdjacency_Internal(dm, p, useCone, useClosure, useAnchors, &numAdj, &tmpAdj);
    311:     PetscSectionGetDof(anchorSectionAdj, p, &anDof);
    312:     PetscSectionGetOffset(anchorSectionAdj, p, &anOff);
    313:     for (d = off; d < off+dof; ++d) {
    314:       PetscInt aoff, i = 0;

    316:       PetscSectionGetOffset(leafSectionAdj, d, &aoff);
    317:       for (q = 0; q < numAdj; ++q) {
    318:         const PetscInt padj = tmpAdj[q];
    319:         PetscInt ndof, ncdof, ngoff, nd;

    321:         if ((padj < pStart) || (padj >= pEnd)) continue;
    322:         PetscSectionGetDof(section, padj, &ndof);
    323:         PetscSectionGetConstraintDof(section, padj, &ncdof);
    324:         PetscSectionGetOffset(sectionGlobal, padj, &ngoff);
    325:         for (nd = 0; nd < ndof-ncdof; ++nd) {
    326:           adj[aoff+i] = (ngoff < 0 ? -(ngoff+1) : ngoff) + nd;
    327:           ++i;
    328:         }
    329:       }
    330:       for (q = 0; q < anDof; q++) {
    331:         adj[aoff+i] = anchorAdj[anOff+q];
    332:         ++i;
    333:       }
    334:     }
    335:   }
    336:   /* Debugging */
    337:   if (debug) {
    338:     IS tmp;
    339:     PetscPrintf(comm, "Leaf adjacency indices\n");
    340:     ISCreateGeneral(comm, adjSize, adj, PETSC_USE_POINTER, &tmp);
    341:     ISView(tmp, NULL);
    342:     ISDestroy(&tmp);
    343:   }
    344:   /* Gather adjacent indices to root */
    345:   PetscSectionGetStorageSize(rootSectionAdj, &adjSize);
    346:   PetscMalloc1(adjSize, &rootAdj);
    347:   for (r = 0; r < adjSize; ++r) rootAdj[r] = -1;
    348:   if (doComm) {
    349:     const PetscInt *indegree;
    350:     PetscInt       *remoteadj, radjsize = 0;

    352:     PetscSFComputeDegreeBegin(sfAdj, &indegree);
    353:     PetscSFComputeDegreeEnd(sfAdj, &indegree);
    354:     for (p = 0; p < adjSize; ++p) radjsize += indegree[p];
    355:     PetscMalloc1(radjsize, &remoteadj);
    356:     PetscSFGatherBegin(sfAdj, MPIU_INT, adj, remoteadj);
    357:     PetscSFGatherEnd(sfAdj, MPIU_INT, adj, remoteadj);
    358:     for (p = 0, l = 0, r = 0; p < adjSize; ++p, l = PetscMax(p, l + indegree[p-1])) {
    359:       PetscInt s;
    360:       for (s = 0; s < indegree[p]; ++s, ++r) rootAdj[l+s] = remoteadj[r];
    361:     }
    364:     PetscFree(remoteadj);
    365:   }
    366:   PetscSFDestroy(&sfAdj);
    367:   PetscFree(adj);
    368:   /* Debugging */
    369:   if (debug) {
    370:     IS tmp;
    371:     PetscPrintf(comm, "Root adjacency indices after gather\n");
    372:     ISCreateGeneral(comm, adjSize, rootAdj, PETSC_USE_POINTER, &tmp);
    373:     ISView(tmp, NULL);
    374:     ISDestroy(&tmp);
    375:   }
    376:   /* Add in local adjacency indices for owned dofs on interface (roots) */
    377:   for (p = pStart; p < pEnd; ++p) {
    378:     PetscInt numAdj = PETSC_DETERMINE, adof, dof, off, d, q, anDof, anOff;

    380:     PetscSectionGetDof(section, p, &dof);
    381:     PetscSectionGetOffset(section, p, &off);
    382:     if (!dof) continue;
    383:     PetscSectionGetDof(rootSectionAdj, off, &adof);
    384:     if (adof <= 0) continue;
    385:     DMPlexGetAdjacency_Internal(dm, p, useCone, useClosure, useAnchors, &numAdj, &tmpAdj);
    386:     PetscSectionGetDof(anchorSectionAdj, p, &anDof);
    387:     PetscSectionGetOffset(anchorSectionAdj, p, &anOff);
    388:     for (d = off; d < off+dof; ++d) {
    389:       PetscInt adof, aoff, i;

    391:       PetscSectionGetDof(rootSectionAdj, d, &adof);
    392:       PetscSectionGetOffset(rootSectionAdj, d, &aoff);
    393:       i    = adof-1;
    394:       for (q = 0; q < anDof; q++) {
    395:         rootAdj[aoff+i] = anchorAdj[anOff+q];
    396:         --i;
    397:       }
    398:       for (q = 0; q < numAdj; ++q) {
    399:         const PetscInt padj = tmpAdj[q];
    400:         PetscInt ndof, ncdof, ngoff, nd;

    402:         if ((padj < pStart) || (padj >= pEnd)) continue;
    403:         PetscSectionGetDof(section, padj, &ndof);
    404:         PetscSectionGetConstraintDof(section, padj, &ncdof);
    405:         PetscSectionGetOffset(sectionGlobal, padj, &ngoff);
    406:         for (nd = 0; nd < ndof-ncdof; ++nd) {
    407:           rootAdj[aoff+i] = ngoff < 0 ? -(ngoff+1)+nd : ngoff+nd;
    408:           --i;
    409:         }
    410:       }
    411:     }
    412:   }
    413:   /* Debugging */
    414:   if (debug) {
    415:     IS tmp;
    416:     PetscPrintf(comm, "Root adjacency indices\n");
    417:     ISCreateGeneral(comm, adjSize, rootAdj, PETSC_USE_POINTER, &tmp);
    418:     ISView(tmp, NULL);
    419:     ISDestroy(&tmp);
    420:   }
    421:   /* Compress indices */
    422:   PetscSectionSetUp(rootSectionAdj);
    423:   for (p = pStart; p < pEnd; ++p) {
    424:     PetscInt dof, cdof, off, d;
    425:     PetscInt adof, aoff;

    427:     PetscSectionGetDof(section, p, &dof);
    428:     PetscSectionGetConstraintDof(section, p, &cdof);
    429:     PetscSectionGetOffset(section, p, &off);
    430:     if (!dof) continue;
    431:     PetscSectionGetDof(rootSectionAdj, off, &adof);
    432:     if (adof <= 0) continue;
    433:     for (d = off; d < off+dof-cdof; ++d) {
    434:       PetscSectionGetDof(rootSectionAdj, d, &adof);
    435:       PetscSectionGetOffset(rootSectionAdj, d, &aoff);
    436:       PetscSortRemoveDupsInt(&adof, &rootAdj[aoff]);
    437:       PetscSectionSetDof(rootSectionAdj, d, adof);
    438:     }
    439:   }
    440:   /* Debugging */
    441:   if (debug) {
    442:     IS tmp;
    443:     PetscPrintf(comm, "Adjancency Section for Preallocation on Roots after compression:\n");
    444:     PetscSectionView(rootSectionAdj, NULL);
    445:     PetscPrintf(comm, "Root adjacency indices after compression\n");
    446:     ISCreateGeneral(comm, adjSize, rootAdj, PETSC_USE_POINTER, &tmp);
    447:     ISView(tmp, NULL);
    448:     ISDestroy(&tmp);
    449:   }
    450:   /* Build adjacency section: Maps global indices to sets of adjacent global indices */
    451:   PetscSectionGetOffsetRange(sectionGlobal, &globalOffStart, &globalOffEnd);
    452:   PetscSectionCreate(comm, &sectionAdj);
    453:   PetscSectionSetChart(sectionAdj, globalOffStart, globalOffEnd);
    454:   for (p = pStart; p < pEnd; ++p) {
    455:     PetscInt  numAdj = PETSC_DETERMINE, dof, cdof, off, goff, d, q, anDof;
    456:     PetscBool found  = PETSC_TRUE;

    458:     PetscSectionGetDof(section, p, &dof);
    459:     PetscSectionGetConstraintDof(section, p, &cdof);
    460:     PetscSectionGetOffset(section, p, &off);
    461:     PetscSectionGetOffset(sectionGlobal, p, &goff);
    462:     for (d = 0; d < dof-cdof; ++d) {
    463:       PetscInt ldof, rdof;

    465:       PetscSectionGetDof(leafSectionAdj, off+d, &ldof);
    466:       PetscSectionGetDof(rootSectionAdj, off+d, &rdof);
    467:       if (ldof > 0) {
    468:         /* We do not own this point */
    469:       } else if (rdof > 0) {
    470:         PetscSectionSetDof(sectionAdj, goff+d, rdof);
    471:       } else {
    472:         found = PETSC_FALSE;
    473:       }
    474:     }
    475:     if (found) continue;
    476:     PetscSectionGetDof(section, p, &dof);
    477:     PetscSectionGetOffset(sectionGlobal, p, &goff);
    478:     DMPlexGetAdjacency_Internal(dm, p, useCone, useClosure, useAnchors, &numAdj, &tmpAdj);
    479:     for (q = 0; q < numAdj; ++q) {
    480:       const PetscInt padj = tmpAdj[q];
    481:       PetscInt ndof, ncdof, noff;

    483:       if ((padj < pStart) || (padj >= pEnd)) continue;
    484:       PetscSectionGetDof(section, padj, &ndof);
    485:       PetscSectionGetConstraintDof(section, padj, &ncdof);
    486:       PetscSectionGetOffset(section, padj, &noff);
    487:       for (d = goff; d < goff+dof-cdof; ++d) {
    488:         PetscSectionAddDof(sectionAdj, d, ndof-ncdof);
    489:       }
    490:     }
    491:     PetscSectionGetDof(anchorSectionAdj, p, &anDof);
    492:     if (anDof) {
    493:       for (d = goff; d < goff+dof-cdof; ++d) {
    494:         PetscSectionAddDof(sectionAdj, d, anDof);
    495:       }
    496:     }
    497:   }
    498:   PetscSectionSetUp(sectionAdj);
    499:   if (debug) {
    500:     PetscPrintf(comm, "Adjacency Section for Preallocation:\n");
    501:     PetscSectionView(sectionAdj, NULL);
    502:   }
    503:   /* Get adjacent indices */
    504:   PetscSectionGetStorageSize(sectionAdj, &numCols);
    505:   PetscMalloc1(numCols, &cols);
    506:   for (p = pStart; p < pEnd; ++p) {
    507:     PetscInt  numAdj = PETSC_DETERMINE, dof, cdof, off, goff, d, q, anDof, anOff;
    508:     PetscBool found  = PETSC_TRUE;

    510:     PetscSectionGetDof(section, p, &dof);
    511:     PetscSectionGetConstraintDof(section, p, &cdof);
    512:     PetscSectionGetOffset(section, p, &off);
    513:     PetscSectionGetOffset(sectionGlobal, p, &goff);
    514:     for (d = 0; d < dof-cdof; ++d) {
    515:       PetscInt ldof, rdof;

    517:       PetscSectionGetDof(leafSectionAdj, off+d, &ldof);
    518:       PetscSectionGetDof(rootSectionAdj, off+d, &rdof);
    519:       if (ldof > 0) {
    520:         /* We do not own this point */
    521:       } else if (rdof > 0) {
    522:         PetscInt aoff, roff;

    524:         PetscSectionGetOffset(sectionAdj, goff+d, &aoff);
    525:         PetscSectionGetOffset(rootSectionAdj, off+d, &roff);
    526:         PetscArraycpy(&cols[aoff], &rootAdj[roff], rdof);
    527:       } else {
    528:         found = PETSC_FALSE;
    529:       }
    530:     }
    531:     if (found) continue;
    532:     DMPlexGetAdjacency_Internal(dm, p, useCone, useClosure, useAnchors, &numAdj, &tmpAdj);
    533:     PetscSectionGetDof(anchorSectionAdj, p, &anDof);
    534:     PetscSectionGetOffset(anchorSectionAdj, p, &anOff);
    535:     for (d = goff; d < goff+dof-cdof; ++d) {
    536:       PetscInt adof, aoff, i = 0;

    538:       PetscSectionGetDof(sectionAdj, d, &adof);
    539:       PetscSectionGetOffset(sectionAdj, d, &aoff);
    540:       for (q = 0; q < numAdj; ++q) {
    541:         const PetscInt  padj = tmpAdj[q];
    542:         PetscInt        ndof, ncdof, ngoff, nd;
    543:         const PetscInt *ncind;

    545:         /* Adjacent points may not be in the section chart */
    546:         if ((padj < pStart) || (padj >= pEnd)) continue;
    547:         PetscSectionGetDof(section, padj, &ndof);
    548:         PetscSectionGetConstraintDof(section, padj, &ncdof);
    549:         PetscSectionGetConstraintIndices(section, padj, &ncind);
    550:         PetscSectionGetOffset(sectionGlobal, padj, &ngoff);
    551:         for (nd = 0; nd < ndof-ncdof; ++nd, ++i) {
    552:           cols[aoff+i] = ngoff < 0 ? -(ngoff+1)+nd : ngoff+nd;
    553:         }
    554:       }
    555:       for (q = 0; q < anDof; q++, i++) {
    556:         cols[aoff+i] = anchorAdj[anOff + q];
    557:       }
    559:     }
    560:   }
    561:   PetscSectionDestroy(&anchorSectionAdj);
    562:   PetscSectionDestroy(&leafSectionAdj);
    563:   PetscSectionDestroy(&rootSectionAdj);
    564:   PetscFree(anchorAdj);
    565:   PetscFree(rootAdj);
    566:   PetscFree(tmpAdj);
    567:   /* Debugging */
    568:   if (debug) {
    569:     IS tmp;
    570:     PetscPrintf(comm, "Column indices\n");
    571:     ISCreateGeneral(comm, numCols, cols, PETSC_USE_POINTER, &tmp);
    572:     ISView(tmp, NULL);
    573:     ISDestroy(&tmp);
    574:   }

    576:   *sA     = sectionAdj;
    577:   *colIdx = cols;
    578:   return 0;
    579: }

    581: 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[])
    582: {
    583:   PetscSection   section;
    584:   PetscInt       rStart, rEnd, r, pStart, pEnd, p;

    586:   /* This loop needs to change to a loop over points, then field dofs, which means we need to look both sections */
    587:   PetscLayoutGetRange(rLayout, &rStart, &rEnd);
    589:   if (f >= 0 && bs == 1) {
    590:     DMGetLocalSection(dm, &section);
    591:     PetscSectionGetChart(section, &pStart, &pEnd);
    592:     for (p = pStart; p < pEnd; ++p) {
    593:       PetscInt rS, rE;

    595:       DMGetGlobalFieldOffset_Private(dm, p, f, &rS, &rE);
    596:       for (r = rS; r < rE; ++r) {
    597:         PetscInt numCols, cStart, c;

    599:         PetscSectionGetDof(sectionAdj, r, &numCols);
    600:         PetscSectionGetOffset(sectionAdj, r, &cStart);
    601:         for (c = cStart; c < cStart+numCols; ++c) {
    602:           if ((cols[c] >= rStart) && (cols[c] < rEnd)) {
    603:             ++dnz[r-rStart];
    604:             if (cols[c] >= r) ++dnzu[r-rStart];
    605:           } else {
    606:             ++onz[r-rStart];
    607:             if (cols[c] >= r) ++onzu[r-rStart];
    608:           }
    609:         }
    610:       }
    611:     }
    612:   } else {
    613:     /* Only loop over blocks of rows */
    614:     for (r = rStart/bs; r < rEnd/bs; ++r) {
    615:       const PetscInt row = r*bs;
    616:       PetscInt       numCols, cStart, c;

    618:       PetscSectionGetDof(sectionAdj, row, &numCols);
    619:       PetscSectionGetOffset(sectionAdj, row, &cStart);
    620:       for (c = cStart; c < cStart+numCols; ++c) {
    621:         if ((cols[c] >= rStart) && (cols[c] < rEnd)) {
    622:           ++dnz[r-rStart/bs];
    623:           if (cols[c] >= row) ++dnzu[r-rStart/bs];
    624:         } else {
    625:           ++onz[r-rStart/bs];
    626:           if (cols[c] >= row) ++onzu[r-rStart/bs];
    627:         }
    628:       }
    629:     }
    630:     for (r = 0; r < (rEnd - rStart)/bs; ++r) {
    631:       dnz[r]  /= bs;
    632:       onz[r]  /= bs;
    633:       dnzu[r] /= bs;
    634:       onzu[r] /= bs;
    635:     }
    636:   }
    637:   return 0;
    638: }

    640: static PetscErrorCode DMPlexFillMatrix_Static(DM dm, PetscLayout rLayout, PetscInt bs, PetscInt f, PetscSection sectionAdj, const PetscInt cols[], Mat A)
    641: {
    642:   PetscSection   section;
    643:   PetscScalar   *values;
    644:   PetscInt       rStart, rEnd, r, pStart, pEnd, p, len, maxRowLen = 0;

    646:   PetscLayoutGetRange(rLayout, &rStart, &rEnd);
    647:   for (r = rStart; r < rEnd; ++r) {
    648:     PetscSectionGetDof(sectionAdj, r, &len);
    649:     maxRowLen = PetscMax(maxRowLen, len);
    650:   }
    651:   PetscCalloc1(maxRowLen, &values);
    652:   if (f >=0 && bs == 1) {
    653:     DMGetLocalSection(dm, &section);
    654:     PetscSectionGetChart(section, &pStart, &pEnd);
    655:     for (p = pStart; p < pEnd; ++p) {
    656:       PetscInt rS, rE;

    658:       DMGetGlobalFieldOffset_Private(dm, p, f, &rS, &rE);
    659:       for (r = rS; r < rE; ++r) {
    660:         PetscInt numCols, cStart;

    662:         PetscSectionGetDof(sectionAdj, r, &numCols);
    663:         PetscSectionGetOffset(sectionAdj, r, &cStart);
    664:         MatSetValues(A, 1, &r, numCols, &cols[cStart], values, INSERT_VALUES);
    665:       }
    666:     }
    667:   } else {
    668:     for (r = rStart; r < rEnd; ++r) {
    669:       PetscInt numCols, cStart;

    671:       PetscSectionGetDof(sectionAdj, r, &numCols);
    672:       PetscSectionGetOffset(sectionAdj, r, &cStart);
    673:       MatSetValues(A, 1, &r, numCols, &cols[cStart], values, INSERT_VALUES);
    674:     }
    675:   }
    676:   PetscFree(values);
    677:   return 0;
    678: }

    680: /*@C
    681:   DMPlexPreallocateOperator - Calculate the matrix nonzero pattern based upon the information in the DM,
    682:   the PetscDS it contains, and the default PetscSection.

    684:   Collective

    686:   Input Parameters:
    687: + dm   - The DMPlex
    688: . bs   - The matrix blocksize
    689: . dnz  - An array to hold the number of nonzeros in the diagonal block
    690: . onz  - An array to hold the number of nonzeros in the off-diagonal block
    691: . dnzu - An array to hold the number of nonzeros in the upper triangle of the diagonal block
    692: . onzu - An array to hold the number of nonzeros in the upper triangle of the off-diagonal block
    693: - fillMatrix - If PETSC_TRUE, fill the matrix with zeros

    695:   Output Parameter:
    696: . A - The preallocated matrix

    698:   Level: advanced

    700: .seealso: DMCreateMatrix()
    701: @*/
    702: PetscErrorCode DMPlexPreallocateOperator(DM dm, PetscInt bs, PetscInt dnz[], PetscInt onz[], PetscInt dnzu[], PetscInt onzu[], Mat A, PetscBool fillMatrix)
    703: {
    704:   MPI_Comm       comm;
    705:   PetscDS        prob;
    706:   MatType        mtype;
    707:   PetscSF        sf, sfDof;
    708:   PetscSection   section;
    709:   PetscInt      *remoteOffsets;
    710:   PetscSection   sectionAdj[4] = {NULL, NULL, NULL, NULL};
    711:   PetscInt      *cols[4]       = {NULL, NULL, NULL, NULL};
    712:   PetscBool      useCone, useClosure;
    713:   PetscInt       Nf, f, idx, locRows;
    714:   PetscLayout    rLayout;
    715:   PetscBool      isSymBlock, isSymSeqBlock, isSymMPIBlock, debug = PETSC_FALSE;
    716:   PetscMPIInt    size;

    724:   DMGetDS(dm, &prob);
    725:   DMGetPointSF(dm, &sf);
    726:   DMGetLocalSection(dm, &section);
    727:   PetscOptionsGetBool(NULL,NULL, "-dm_view_preallocation", &debug, NULL);
    728:   PetscObjectGetComm((PetscObject) dm, &comm);
    729:   MPI_Comm_size(comm, &size);
    730:   PetscLogEventBegin(DMPLEX_Preallocate,dm,0,0,0);
    731:   /* Create dof SF based on point SF */
    732:   if (debug) {
    733:     PetscSection section, sectionGlobal;
    734:     PetscSF      sf;

    736:     DMGetPointSF(dm, &sf);
    737:     DMGetLocalSection(dm, &section);
    738:     DMGetGlobalSection(dm, &sectionGlobal);
    739:     PetscPrintf(comm, "Input Section for Preallocation:\n");
    740:     PetscSectionView(section, NULL);
    741:     PetscPrintf(comm, "Input Global Section for Preallocation:\n");
    742:     PetscSectionView(sectionGlobal, NULL);
    743:     if (size > 1) {
    744:       PetscPrintf(comm, "Input SF for Preallocation:\n");
    745:       PetscSFView(sf, NULL);
    746:     }
    747:   }
    748:   PetscSFCreateRemoteOffsets(sf, section, section, &remoteOffsets);
    749:   PetscSFCreateSectionSF(sf, section, remoteOffsets, section, &sfDof);
    750:   PetscFree(remoteOffsets);
    751:   if (debug && size > 1) {
    752:     PetscPrintf(comm, "Dof SF for Preallocation:\n");
    753:     PetscSFView(sfDof, NULL);
    754:   }
    755:   /* Create allocation vectors from adjacency graph */
    756:   MatGetLocalSize(A, &locRows, NULL);
    757:   PetscLayoutCreate(comm, &rLayout);
    758:   PetscLayoutSetLocalSize(rLayout, locRows);
    759:   PetscLayoutSetBlockSize(rLayout, 1);
    760:   PetscLayoutSetUp(rLayout);
    761:   /* There are 4 types of adjacency */
    762:   PetscSectionGetNumFields(section, &Nf);
    763:   if (Nf < 1 || bs > 1) {
    764:     DMGetBasicAdjacency(dm, &useCone, &useClosure);
    765:     idx  = (useCone ? 1 : 0) + (useClosure ? 2 : 0);
    766:     DMPlexCreateAdjacencySection_Static(dm, bs, sfDof, useCone, useClosure, PETSC_TRUE, &sectionAdj[idx], &cols[idx]);
    767:     DMPlexUpdateAllocation_Static(dm, rLayout, bs, -1, sectionAdj[idx], cols[idx], dnz, onz, dnzu, onzu);
    768:   } else {
    769:     for (f = 0; f < Nf; ++f) {
    770:       DMGetAdjacency(dm, f, &useCone, &useClosure);
    771:       idx  = (useCone ? 1 : 0) + (useClosure ? 2 : 0);
    772:       if (!sectionAdj[idx]) DMPlexCreateAdjacencySection_Static(dm, bs, sfDof, useCone, useClosure, PETSC_TRUE, &sectionAdj[idx], &cols[idx]);
    773:       DMPlexUpdateAllocation_Static(dm, rLayout, bs, f, sectionAdj[idx], cols[idx], dnz, onz, dnzu, onzu);
    774:     }
    775:   }
    776:   PetscSFDestroy(&sfDof);
    777:   /* Set matrix pattern */
    778:   MatXAIJSetPreallocation(A, bs, dnz, onz, dnzu, onzu);
    779:   MatSetOption(A, MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_TRUE);
    780:   /* Check for symmetric storage */
    781:   MatGetType(A, &mtype);
    782:   PetscStrcmp(mtype, MATSBAIJ, &isSymBlock);
    783:   PetscStrcmp(mtype, MATSEQSBAIJ, &isSymSeqBlock);
    784:   PetscStrcmp(mtype, MATMPISBAIJ, &isSymMPIBlock);
    785:   if (isSymBlock || isSymSeqBlock || isSymMPIBlock) MatSetOption(A, MAT_IGNORE_LOWER_TRIANGULAR, PETSC_TRUE);
    786:   /* Fill matrix with zeros */
    787:   if (fillMatrix) {
    788:     if (Nf < 1 || bs > 1) {
    789:       DMGetBasicAdjacency(dm, &useCone, &useClosure);
    790:       idx  = (useCone ? 1 : 0) + (useClosure ? 2 : 0);
    791:       DMPlexFillMatrix_Static(dm, rLayout, bs, -1, sectionAdj[idx], cols[idx], A);
    792:     } else {
    793:       for (f = 0; f < Nf; ++f) {
    794:         DMGetAdjacency(dm, f, &useCone, &useClosure);
    795:         idx  = (useCone ? 1 : 0) + (useClosure ? 2 : 0);
    796:         DMPlexFillMatrix_Static(dm, rLayout, bs, f, sectionAdj[idx], cols[idx], A);
    797:       }
    798:     }
    799:     MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);
    800:     MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);
    801:   }
    802:   PetscLayoutDestroy(&rLayout);
    803:   for (idx = 0; idx < 4; ++idx) {PetscSectionDestroy(&sectionAdj[idx])); PetscCall(PetscFree(cols[idx]);}
    804:   PetscLogEventEnd(DMPLEX_Preallocate,dm,0,0,0);
    805:   return 0;
    806: }

    808: #if 0
    809: PetscErrorCode DMPlexPreallocateOperator_2(DM dm, PetscInt bs, PetscSection section, PetscSection sectionGlobal, PetscInt dnz[], PetscInt onz[], PetscInt dnzu[], PetscInt onzu[], Mat A, PetscBool fillMatrix)
    810: {
    811:   PetscInt       *tmpClosure,*tmpAdj,*visits;
    812:   PetscInt        c,cStart,cEnd,pStart,pEnd;

    814:   DMGetDimension(dm, &dim);
    815:   DMPlexGetDepth(dm, &depth);
    816:   DMPlexGetMaxSizes(dm, &maxConeSize, &maxSupportSize);

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

    820:   PetscSectionGetChart(section, &pStart, &pEnd);
    821:   npoints = pEnd - pStart;

    823:   PetscMalloc3(maxClosureSize,&tmpClosure,npoints,&lvisits,npoints,&visits);
    824:   PetscArrayzero(lvisits,pEnd-pStart);
    825:   PetscArrayzero(visits,pEnd-pStart);
    826:   DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);
    827:   for (c=cStart; c<cEnd; c++) {
    828:     PetscInt *support = tmpClosure;
    829:     DMPlexGetTransitiveClosure(dm, c, PETSC_FALSE, &supportSize, (PetscInt**)&support);
    830:     for (p=0; p<supportSize; p++) lvisits[support[p]]++;
    831:   }
    832:   PetscSFReduceBegin(sf,MPIU_INT,lvisits,visits,MPI_SUM);
    833:   PetscSFReduceEnd  (sf,MPIU_INT,lvisits,visits,MPI_SUM);
    834:   PetscSFBcastBegin(sf,MPIU_INT,visits,lvisits,MPI_REPLACE);
    835:   PetscSFBcastEnd  (sf,MPIU_INT,visits,lvisits);

    837:   PetscSFGetRootRanks();

    839:   PetscMalloc2(maxClosureSize*maxClosureSize,&cellmat,npoints,&owner);
    840:   for (c=cStart; c<cEnd; c++) {
    841:     PetscArrayzero(cellmat,maxClosureSize*maxClosureSize);
    842:     /*
    843:      Depth-first walk of transitive closure.
    844:      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.
    845:      This contribution is added to dnz if owning ranks of p and q match, to onz otherwise.
    846:      */
    847:   }

    849:   PetscSFReduceBegin(sf,MPIU_INT,ldnz,dnz,MPI_SUM);
    850:   PetscSFReduceEnd  (sf,MPIU_INT,lonz,onz,MPI_SUM);
    851:   return 0;
    852: }
    853: #endif