Actual source code: bddcgraph.c

      1: #include <petsc/private/petscimpl.h>
      2: #include <../src/ksp/pc/impls/bddc/bddcprivate.h>
      3: #include <../src/ksp/pc/impls/bddc/bddcstructs.h>

      5: PetscErrorCode PCBDDCGraphGetDirichletDofsB(PCBDDCGraph graph, IS* dirdofs)
      6: {

     10:   if (graph->dirdofsB) {
     11:     PetscObjectReference((PetscObject)graph->dirdofsB);
     12:   } else if (graph->has_dirichlet) {
     13:     PetscInt i,size;
     14:     PetscInt *dirdofs_idxs;

     16:     size = 0;
     17:     for (i=0;i<graph->nvtxs;i++) {
     18:       if (graph->count[i] && graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) size++;
     19:     }

     21:     PetscMalloc1(size,&dirdofs_idxs);
     22:     size = 0;
     23:     for (i=0;i<graph->nvtxs;i++) {
     24:       if (graph->count[i] && graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) dirdofs_idxs[size++] = i;
     25:     }
     26:     ISCreateGeneral(PETSC_COMM_SELF,size,dirdofs_idxs,PETSC_OWN_POINTER,&graph->dirdofsB);
     27:     PetscObjectReference((PetscObject)graph->dirdofsB);
     28:   }
     29:   *dirdofs = graph->dirdofsB;
     30:   return(0);
     31: }

     33: PetscErrorCode PCBDDCGraphGetDirichletDofs(PCBDDCGraph graph, IS* dirdofs)
     34: {

     38:   if (graph->dirdofs) {
     39:     PetscObjectReference((PetscObject)graph->dirdofs);
     40:   } else if (graph->has_dirichlet) {
     41:     PetscInt i,size;
     42:     PetscInt *dirdofs_idxs;

     44:     size = 0;
     45:     for (i=0;i<graph->nvtxs;i++) {
     46:       if (graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) size++;
     47:     }

     49:     PetscMalloc1(size,&dirdofs_idxs);
     50:     size = 0;
     51:     for (i=0;i<graph->nvtxs;i++) {
     52:       if (graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) dirdofs_idxs[size++] = i;
     53:     }
     54:     ISCreateGeneral(PetscObjectComm((PetscObject)graph->l2gmap),size,dirdofs_idxs,PETSC_OWN_POINTER,&graph->dirdofs);
     55:     PetscObjectReference((PetscObject)graph->dirdofs);
     56:   }
     57:   *dirdofs = graph->dirdofs;
     58:   return(0);
     59: }

     61: PetscErrorCode PCBDDCGraphASCIIView(PCBDDCGraph graph, PetscInt verbosity_level, PetscViewer viewer)
     62: {
     63:   PetscInt       i,j,tabs;
     64:   PetscInt*      queue_in_global_numbering;

     68:   PetscViewerASCIIPushSynchronized(viewer);
     69:   PetscViewerASCIIGetTab(viewer,&tabs);
     70:   PetscViewerASCIIPrintf(viewer,"--------------------------------------------------\n");
     71:   PetscViewerFlush(viewer);
     72:   PetscViewerASCIISynchronizedPrintf(viewer,"Local BDDC graph for subdomain %04d\n",PetscGlobalRank);
     73:   PetscViewerASCIISynchronizedPrintf(viewer,"Number of vertices %d\n",graph->nvtxs);
     74:   PetscViewerASCIISynchronizedPrintf(viewer,"Custom minimal size %d\n",graph->custom_minimal_size);
     75:   if (graph->maxcount != PETSC_MAX_INT) {
     76:     PetscViewerASCIISynchronizedPrintf(viewer,"Max count %d\n",graph->maxcount);
     77:   }
     78:   PetscViewerASCIISynchronizedPrintf(viewer,"Topological two dim? %d (set %d)\n",graph->twodim,graph->twodimset);
     79:   if (verbosity_level > 2) {
     80:     for (i=0;i<graph->nvtxs;i++) {
     81:       PetscViewerASCIISynchronizedPrintf(viewer,"%d:\n",i);
     82:       PetscViewerASCIISynchronizedPrintf(viewer,"   which_dof: %d\n",graph->which_dof[i]);
     83:       PetscViewerASCIISynchronizedPrintf(viewer,"   special_dof: %d\n",graph->special_dof[i]);
     84:       PetscViewerASCIISynchronizedPrintf(viewer,"   neighbours: %d\n",graph->count[i]);
     85:       PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
     86:       if (graph->count[i]) {
     87:         PetscViewerASCIISynchronizedPrintf(viewer,"     set of neighbours:");
     88:         for (j=0;j<graph->count[i];j++) {
     89:           PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->neighbours_set[i][j]);
     90:         }
     91:         PetscViewerASCIISynchronizedPrintf(viewer,"\n");
     92:       }
     93:       PetscViewerASCIISetTab(viewer,tabs);
     94:       PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
     95:       if (graph->mirrors) {
     96:         PetscViewerASCIISynchronizedPrintf(viewer,"   mirrors: %d\n",graph->mirrors[i]);
     97:         if (graph->mirrors[i]) {
     98:           PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
     99:           PetscViewerASCIISynchronizedPrintf(viewer,"     set of mirrors:");
    100:           for (j=0;j<graph->mirrors[i];j++) {
    101:             PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->mirrors_set[i][j]);
    102:           }
    103:           PetscViewerASCIISynchronizedPrintf(viewer,"\n");
    104:           PetscViewerASCIISetTab(viewer,tabs);
    105:           PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
    106:         }
    107:       }
    108:       if (verbosity_level > 3) {
    109:         if (graph->xadj) {
    110:           PetscViewerASCIISynchronizedPrintf(viewer,"   local adj list:");
    111:           PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
    112:           for (j=graph->xadj[i];j<graph->xadj[i+1];j++) {
    113:             PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->adjncy[j]);
    114:           }
    115:           PetscViewerASCIISynchronizedPrintf(viewer,"\n");
    116:           PetscViewerASCIISetTab(viewer,tabs);
    117:           PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
    118:         } else {
    119:           PetscViewerASCIISynchronizedPrintf(viewer,"   no adj info\n");
    120:         }
    121:       }
    122:       if (graph->n_local_subs) {
    123:         PetscViewerASCIISynchronizedPrintf(viewer,"   local sub id: %d\n",graph->local_subs[i]);
    124:       }
    125:       PetscViewerASCIISynchronizedPrintf(viewer,"   interface subset id: %d\n",graph->subset[i]);
    126:       if (graph->subset[i] && graph->subset_ncc) {
    127:         PetscViewerASCIISynchronizedPrintf(viewer,"   ncc for subset: %d\n",graph->subset_ncc[graph->subset[i]-1]);
    128:       }
    129:     }
    130:   }
    131:   PetscViewerASCIISynchronizedPrintf(viewer,"Total number of connected components %d\n",graph->ncc);
    132:   PetscMalloc1(graph->cptr[graph->ncc],&queue_in_global_numbering);
    133:   ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_in_global_numbering);
    134:   for (i=0;i<graph->ncc;i++) {
    135:     PetscInt node_num=graph->queue[graph->cptr[i]];
    136:     PetscBool printcc = PETSC_FALSE;
    137:     PetscViewerASCIISynchronizedPrintf(viewer,"  cc %d (size %d, fid %d, neighs:",i,graph->cptr[i+1]-graph->cptr[i],graph->which_dof[node_num]);
    138:     PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);
    139:     for (j=0;j<graph->count[node_num];j++) {
    140:       PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->neighbours_set[node_num][j]);
    141:     }
    142:     if (verbosity_level > 1) {
    143:       PetscViewerASCIISynchronizedPrintf(viewer,"):");
    144:       if (verbosity_level > 2 || graph->twodim || graph->count[node_num] > 1 || (graph->count[node_num] == 1 && graph->special_dof[node_num] == PCBDDCGRAPH_NEUMANN_MARK)) {
    145:         printcc = PETSC_TRUE;
    146:       }
    147:       if (printcc) {
    148:         for (j=graph->cptr[i];j<graph->cptr[i+1];j++) {
    149:           PetscViewerASCIISynchronizedPrintf(viewer," %d (%d)",graph->queue[j],queue_in_global_numbering[j]);
    150:         }
    151:       }
    152:     } else {
    153:       PetscViewerASCIISynchronizedPrintf(viewer,")");
    154:     }
    155:     PetscViewerASCIISynchronizedPrintf(viewer,"\n");
    156:     PetscViewerASCIISetTab(viewer,tabs);
    157:     PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);
    158:   }
    159:   PetscFree(queue_in_global_numbering);
    160:   PetscViewerFlush(viewer);
    161:   return(0);
    162: }

    164: PetscErrorCode PCBDDCGraphRestoreCandidatesIS(PCBDDCGraph graph, PetscInt *n_faces, IS *FacesIS[], PetscInt *n_edges, IS *EdgesIS[], IS *VerticesIS)
    165: {
    166:   PetscInt       i;

    170:   if (n_faces) {
    171:     if (FacesIS) {
    172:       for (i=0;i<*n_faces;i++) {
    173:         ISDestroy(&((*FacesIS)[i]));
    174:       }
    175:       PetscFree(*FacesIS);
    176:     }
    177:     *n_faces = 0;
    178:   }
    179:   if (n_edges) {
    180:     if (EdgesIS) {
    181:       for (i=0;i<*n_edges;i++) {
    182:         ISDestroy(&((*EdgesIS)[i]));
    183:       }
    184:       PetscFree(*EdgesIS);
    185:     }
    186:     *n_edges = 0;
    187:   }
    188:   if (VerticesIS) {
    189:     ISDestroy(VerticesIS);
    190:   }
    191:   return(0);
    192: }

    194: PetscErrorCode PCBDDCGraphGetCandidatesIS(PCBDDCGraph graph, PetscInt *n_faces, IS *FacesIS[], PetscInt *n_edges, IS *EdgesIS[], IS *VerticesIS)
    195: {
    196:   IS             *ISForFaces,*ISForEdges,ISForVertices;
    197:   PetscInt       i,nfc,nec,nvc,*idx,*mark;

    201:   PetscCalloc1(graph->ncc,&mark);
    202:   /* loop on ccs to evalute number of faces, edges and vertices */
    203:   nfc = 0;
    204:   nec = 0;
    205:   nvc = 0;
    206:   for (i=0;i<graph->ncc;i++) {
    207:     PetscInt repdof = graph->queue[graph->cptr[i]];
    208:     if (graph->cptr[i+1]-graph->cptr[i] > graph->custom_minimal_size && graph->count[repdof] < graph->maxcount) {
    209:       if (!graph->twodim && graph->count[repdof] == 1 && graph->special_dof[repdof] != PCBDDCGRAPH_NEUMANN_MARK) {
    210:         nfc++;
    211:         mark[i] = 2;
    212:       } else {
    213:         nec++;
    214:         mark[i] = 1;
    215:       }
    216:     } else {
    217:       nvc += graph->cptr[i+1]-graph->cptr[i];
    218:     }
    219:   }

    221:   /* allocate IS arrays for faces, edges. Vertices need a single index set. */
    222:   if (FacesIS) {
    223:     PetscMalloc1(nfc,&ISForFaces);
    224:   }
    225:   if (EdgesIS) {
    226:     PetscMalloc1(nec,&ISForEdges);
    227:   }
    228:   if (VerticesIS) {
    229:     PetscMalloc1(nvc,&idx);
    230:   }

    232:   /* loop on ccs to compute index sets for faces and edges */
    233:   if (!graph->queue_sorted) {
    234:     PetscInt *queue_global;

    236:     PetscMalloc1(graph->cptr[graph->ncc],&queue_global);
    237:     ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_global);
    238:     for (i=0;i<graph->ncc;i++) {
    239:       PetscSortIntWithArray(graph->cptr[i+1]-graph->cptr[i],&queue_global[graph->cptr[i]],&graph->queue[graph->cptr[i]]);
    240:     }
    241:     PetscFree(queue_global);
    242:     graph->queue_sorted = PETSC_TRUE;
    243:   }
    244:   nfc = 0;
    245:   nec = 0;
    246:   for (i=0;i<graph->ncc;i++) {
    247:     if (mark[i] == 2) {
    248:       if (FacesIS) {
    249:         ISCreateGeneral(PETSC_COMM_SELF,graph->cptr[i+1]-graph->cptr[i],&graph->queue[graph->cptr[i]],PETSC_USE_POINTER,&ISForFaces[nfc]);
    250:       }
    251:       nfc++;
    252:     } else if (mark[i] == 1) {
    253:       if (EdgesIS) {
    254:         ISCreateGeneral(PETSC_COMM_SELF,graph->cptr[i+1]-graph->cptr[i],&graph->queue[graph->cptr[i]],PETSC_USE_POINTER,&ISForEdges[nec]);
    255:       }
    256:       nec++;
    257:     }
    258:   }

    260:   /* index set for vertices */
    261:   if (VerticesIS) {
    262:     nvc = 0;
    263:     for (i=0;i<graph->ncc;i++) {
    264:       if (!mark[i]) {
    265:         PetscInt j;

    267:         for (j=graph->cptr[i];j<graph->cptr[i+1];j++) {
    268:           idx[nvc]=graph->queue[j];
    269:           nvc++;
    270:         }
    271:       }
    272:     }
    273:     /* sort vertex set (by local ordering) */
    274:     PetscSortInt(nvc,idx);
    275:     ISCreateGeneral(PETSC_COMM_SELF,nvc,idx,PETSC_OWN_POINTER,&ISForVertices);
    276:   }
    277:   PetscFree(mark);

    279:   /* get back info */
    280:   if (n_faces)       *n_faces = nfc;
    281:   if (FacesIS)       *FacesIS = ISForFaces;
    282:   if (n_edges)       *n_edges = nec;
    283:   if (EdgesIS)       *EdgesIS = ISForEdges;
    284:   if (VerticesIS) *VerticesIS = ISForVertices;
    285:   return(0);
    286: }

    288: PetscErrorCode PCBDDCGraphComputeConnectedComponents(PCBDDCGraph graph)
    289: {
    290:   PetscBool      adapt_interface_reduced;
    291:   MPI_Comm       interface_comm;
    292:   PetscMPIInt    size;
    293:   PetscInt       i;
    294:   PetscBT        cornerp;

    298:   /* compute connected components locally */
    299:   PetscObjectGetComm((PetscObject)(graph->l2gmap),&interface_comm);
    300:   PCBDDCGraphComputeConnectedComponentsLocal(graph);

    302:   cornerp = NULL;
    303:   if (graph->active_coords) { /* face based corner selection */
    304:     PetscBT   excluded;
    305:     PetscReal *wdist;
    306:     PetscInt  n_neigh,*neigh,*n_shared,**shared;
    307:     PetscInt  maxc, ns;

    309:     PetscBTCreate(graph->nvtxs,&cornerp);
    310:     ISLocalToGlobalMappingGetInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);
    311:     for (ns = 1, maxc = 0; ns < n_neigh; ns++) maxc = PetscMax(maxc,n_shared[ns]);
    312:     PetscMalloc1(maxc*graph->cdim,&wdist);
    313:     PetscBTCreate(maxc,&excluded);

    315:     for (ns = 1; ns < n_neigh; ns++) { /* first proc is self */
    316:       PetscReal *anchor,mdist;
    317:       PetscInt  fst,j,k,d,cdim = graph->cdim,n = n_shared[ns];
    318:       PetscInt  point1,point2,point3;

    320:       /* import coordinates on shared interface */
    321:       PetscBTMemzero(n,excluded);
    322:       for (j=0,fst=-1,k=0;j<n;j++) {
    323:         PetscBool skip = PETSC_FALSE;
    324:         for (d=0;d<cdim;d++) {
    325:           PetscReal c = graph->coords[shared[ns][j]*cdim+d];
    326:           skip = (PetscBool)(skip || c == PETSC_MAX_REAL);
    327:           wdist[k++] = c;
    328:         }
    329:         if (skip) {
    330:           PetscBTSet(excluded,j);
    331:         } else if (fst == -1) fst = j;
    332:       }
    333:       if (fst == -1) continue;

    335:       /* the dofs are sorted by global numbering, so each rank start from the same id and will detect the same corners from the given set */
    336:       anchor = wdist + fst*cdim;

    338:       /* find the farthest point from the starting one */
    339:       mdist  = -1.0;
    340:       point1 = fst;
    341:       for (j=fst;j<n;j++) {
    342:         PetscReal dist = 0.0;

    344:         if (PetscUnlikely(PetscBTLookup(excluded,j))) continue;
    345:         for (d=0;d<cdim;d++) dist += (wdist[j*cdim+d]-anchor[d])*(wdist[j*cdim+d]-anchor[d]);
    346:         if (dist > mdist) { mdist = dist; point1 = j; }
    347:       }

    349:       /* find the farthest point from point1 */
    350:       anchor = wdist + point1*cdim;
    351:       mdist  = -1.0;
    352:       point2 = point1;
    353:       for (j=fst;j<n;j++) {
    354:         PetscReal dist = 0.0;

    356:         if (PetscUnlikely(PetscBTLookup(excluded,j))) continue;
    357:         for (d=0;d<cdim;d++) dist += (wdist[j*cdim+d]-anchor[d])*(wdist[j*cdim+d]-anchor[d]);
    358:         if (dist > mdist) { mdist = dist; point2 = j; }
    359:       }

    362:       /* find the third point maximizing the triangle area */
    363:       point3 = point2;
    364:       if (cdim > 2) {
    365:         PetscReal a = 0.0;

    367:         for (d=0;d<cdim;d++) a += (wdist[point1*cdim+d]-wdist[point2*cdim+d])*(wdist[point1*cdim+d]-wdist[point2*cdim+d]);
    368:         a = PetscSqrtReal(a);
    369:         mdist = -1.0;
    370:         for (j=fst;j<n;j++) {
    371:           PetscReal area,b = 0.0, c = 0.0,s;

    373:           if (PetscUnlikely(PetscBTLookup(excluded,j))) continue;
    374:           for (d=0;d<cdim;d++) {
    375:             b += (wdist[point1*cdim+d]-wdist[j*cdim+d])*(wdist[point1*cdim+d]-wdist[j*cdim+d]);
    376:             c += (wdist[point2*cdim+d]-wdist[j*cdim+d])*(wdist[point2*cdim+d]-wdist[j*cdim+d]);
    377:           }
    378:           b = PetscSqrtReal(b);
    379:           c = PetscSqrtReal(c);
    380:           s = 0.5*(a+b+c);

    382:           /* Heron's formula, area squared */
    383:           area = s*(s-a)*(s-b)*(s-c);
    384:           if (area > mdist) { mdist = area; point3 = j; }
    385:         }
    386:       }

    388:       PetscBTSet(cornerp,shared[ns][point1]);
    389:       PetscBTSet(cornerp,shared[ns][point2]);
    390:       PetscBTSet(cornerp,shared[ns][point3]);

    392:       /* all dofs having the same coordinates will be primal */
    393:       for (j=fst;j<n;j++) {
    394:         PetscBool same[3] = {PETSC_TRUE,PETSC_TRUE,PETSC_TRUE};

    396:         if (PetscUnlikely(PetscBTLookup(excluded,j))) continue;
    397:         for (d=0;d<cdim;d++) {
    398:           same[0] = (PetscBool)(same[0] && (PetscAbsReal(wdist[j*cdim + d]-wdist[point1*cdim+d]) < PETSC_SMALL));
    399:           same[1] = (PetscBool)(same[1] && (PetscAbsReal(wdist[j*cdim + d]-wdist[point2*cdim+d]) < PETSC_SMALL));
    400:           same[2] = (PetscBool)(same[2] && (PetscAbsReal(wdist[j*cdim + d]-wdist[point3*cdim+d]) < PETSC_SMALL));
    401:         }
    402:         if (same[0] || same[1] || same[2]) {
    403:           PetscBTSet(cornerp,shared[ns][j]);
    404:         }
    405:       }
    406:     }
    407:     PetscBTDestroy(&excluded);
    408:     PetscFree(wdist);
    409:     ISLocalToGlobalMappingRestoreInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);
    410:   }

    412:   /* check consistency of connected components among neighbouring subdomains -> it adapt them in case it is needed */
    413:   MPI_Comm_size(interface_comm,&size);
    414:   adapt_interface_reduced = PETSC_FALSE;
    415:   if (size > 1) {
    416:     PetscInt i;
    417:     PetscBool adapt_interface = cornerp ? PETSC_TRUE : PETSC_FALSE;
    418:     for (i=0;i<graph->n_subsets && !adapt_interface;i++) {
    419:       /* We are not sure that on a given subset of the local interface,
    420:          with two connected components, the latters be the same among sharing subdomains */
    421:       if (graph->subset_ncc[i] > 1) adapt_interface = PETSC_TRUE;
    422:     }
    423:     MPIU_Allreduce(&adapt_interface,&adapt_interface_reduced,1,MPIU_BOOL,MPI_LOR,interface_comm);
    424:   }

    426:   if (graph->n_subsets && adapt_interface_reduced) {
    427:     PetscBT     subset_cc_adapt;
    428:     MPI_Request *send_requests,*recv_requests;
    429:     PetscInt    *send_buffer,*recv_buffer;
    430:     PetscInt    sum_requests,start_of_recv,start_of_send;
    431:     PetscInt    *cum_recv_counts;
    432:     PetscInt    *labels;
    433:     PetscInt    ncc,cum_queue,mss,mns,j,k,s;
    434:     PetscInt    **refine_buffer=NULL,*private_labels = NULL;
    435:     PetscBool   *subset_has_corn,*recv_buffer_bool,*send_buffer_bool;

    437:     PetscCalloc1(graph->n_subsets,&subset_has_corn);
    438:     if (cornerp) {
    439:       for (i=0;i<graph->n_subsets;i++) {
    440:         for (j=0;j<graph->subset_size[i];j++) {
    441:           if (PetscBTLookup(cornerp,graph->subset_idxs[i][j])) {
    442:             subset_has_corn[i] = PETSC_TRUE;
    443:             break;
    444:           }
    445:         }
    446:       }
    447:     }
    448:     PetscMalloc1(graph->nvtxs,&labels);
    449:     PetscArrayzero(labels,graph->nvtxs);
    450:     for (i=0,k=0;i<graph->ncc;i++) {
    451:       PetscInt s = 1;
    452:       for (j=graph->cptr[i];j<graph->cptr[i+1];j++) {
    453:         if (cornerp && PetscBTLookup(cornerp,graph->queue[j])) {
    454:           labels[graph->queue[j]] = k+s;
    455:           s += 1;
    456:         } else {
    457:           labels[graph->queue[j]] = k;
    458:         }
    459:       }
    460:       k += s;
    461:     }

    463:     /* allocate some space */
    464:     PetscMalloc1(graph->n_subsets+1,&cum_recv_counts);
    465:     PetscArrayzero(cum_recv_counts,graph->n_subsets+1);

    467:     /* first count how many neighbours per connected component I will receive from */
    468:     cum_recv_counts[0] = 0;
    469:     for (i=0;i<graph->n_subsets;i++) cum_recv_counts[i+1] = cum_recv_counts[i]+graph->count[graph->subset_idxs[i][0]];
    470:     PetscMalloc1(graph->n_subsets,&send_buffer_bool);
    471:     PetscMalloc1(cum_recv_counts[graph->n_subsets],&recv_buffer_bool);
    472:     PetscMalloc2(cum_recv_counts[graph->n_subsets],&send_requests,cum_recv_counts[graph->n_subsets],&recv_requests);
    473:     for (i=0;i<cum_recv_counts[graph->n_subsets];i++) {
    474:       send_requests[i] = MPI_REQUEST_NULL;
    475:       recv_requests[i] = MPI_REQUEST_NULL;
    476:     }

    478:     /* exchange with my neighbours the number of my connected components on the subset of interface */
    479:     sum_requests = 0;
    480:     for (i=0;i<graph->n_subsets;i++) {
    481:       send_buffer_bool[i] = (PetscBool)(graph->subset_ncc[i] > 1 || subset_has_corn[i]);
    482:     }
    483:     for (i=0;i<graph->n_subsets;i++) {
    484:       PetscMPIInt neigh,tag;
    485:       PetscInt    count,*neighs;

    487:       count  = graph->count[graph->subset_idxs[i][0]];
    488:       neighs = graph->neighbours_set[graph->subset_idxs[i][0]];
    489:       PetscMPIIntCast(2*graph->subset_ref_node[i],&tag);
    490:       for (k=0;k<count;k++) {

    492:         PetscMPIIntCast(neighs[k],&neigh);
    493:         MPI_Isend(send_buffer_bool + i,           1,MPIU_BOOL,neigh,tag,interface_comm,&send_requests[sum_requests]);
    494:         MPI_Irecv(recv_buffer_bool + sum_requests,1,MPIU_BOOL,neigh,tag,interface_comm,&recv_requests[sum_requests]);
    495:         sum_requests++;
    496:       }
    497:     }
    498:     MPI_Waitall(sum_requests,recv_requests,MPI_STATUSES_IGNORE);
    499:     MPI_Waitall(sum_requests,send_requests,MPI_STATUSES_IGNORE);

    501:     /* determine the subsets I have to adapt (those having more than 1 cc) */
    502:     PetscBTCreate(graph->n_subsets,&subset_cc_adapt);
    503:     PetscBTMemzero(graph->n_subsets,subset_cc_adapt);
    504:     for (i=0;i<graph->n_subsets;i++) {
    505:       if (graph->subset_ncc[i] > 1 || subset_has_corn[i]) {
    506:         PetscBTSet(subset_cc_adapt,i);
    507:         continue;
    508:       }
    509:       for (j=cum_recv_counts[i];j<cum_recv_counts[i+1];j++){
    510:          if (recv_buffer_bool[j]) {
    511:           PetscBTSet(subset_cc_adapt,i);
    512:           break;
    513:         }
    514:       }
    515:     }
    516:     PetscFree(send_buffer_bool);
    517:     PetscFree(recv_buffer_bool);
    518:     PetscFree(subset_has_corn);

    520:     /* determine send/recv buffers sizes */
    521:     j = 0;
    522:     mss = 0;
    523:     for (i=0;i<graph->n_subsets;i++) {
    524:       if (PetscBTLookup(subset_cc_adapt,i)) {
    525:         j  += graph->subset_size[i];
    526:         mss = PetscMax(graph->subset_size[i],mss);
    527:       }
    528:     }
    529:     k = 0;
    530:     mns = 0;
    531:     for (i=0;i<graph->n_subsets;i++) {
    532:       if (PetscBTLookup(subset_cc_adapt,i)) {
    533:         k  += (cum_recv_counts[i+1]-cum_recv_counts[i])*graph->subset_size[i];
    534:         mns = PetscMax(cum_recv_counts[i+1]-cum_recv_counts[i],mns);
    535:       }
    536:     }
    537:     PetscMalloc2(j,&send_buffer,k,&recv_buffer);

    539:     /* fill send buffer (order matters: subset_idxs ordered by global ordering) */
    540:     j = 0;
    541:     for (i=0;i<graph->n_subsets;i++)
    542:       if (PetscBTLookup(subset_cc_adapt,i))
    543:         for (k=0;k<graph->subset_size[i];k++)
    544:           send_buffer[j++] = labels[graph->subset_idxs[i][k]];

    546:     /* now exchange the data */
    547:     start_of_recv = 0;
    548:     start_of_send = 0;
    549:     sum_requests  = 0;
    550:     for (i=0;i<graph->n_subsets;i++) {
    551:       if (PetscBTLookup(subset_cc_adapt,i)) {
    552:         PetscMPIInt neigh,tag;
    553:         PetscInt    size_of_send = graph->subset_size[i];

    555:         j    = graph->subset_idxs[i][0];
    556:         PetscMPIIntCast(2*graph->subset_ref_node[i]+1,&tag);
    557:         for (k=0;k<graph->count[j];k++) {
    558:           PetscMPIIntCast(graph->neighbours_set[j][k],&neigh);
    559:           MPI_Isend(&send_buffer[start_of_send],size_of_send,MPIU_INT,neigh,tag,interface_comm,&send_requests[sum_requests]);
    560:           MPI_Irecv(&recv_buffer[start_of_recv],size_of_send,MPIU_INT,neigh,tag,interface_comm,&recv_requests[sum_requests]);
    561:           start_of_recv += size_of_send;
    562:           sum_requests++;
    563:         }
    564:         start_of_send += size_of_send;
    565:       }
    566:     }
    567:     MPI_Waitall(sum_requests,recv_requests,MPI_STATUSES_IGNORE);

    569:     /* refine connected components */
    570:     start_of_recv = 0;
    571:     /* allocate some temporary space */
    572:     if (mss) {
    573:       PetscMalloc1(mss,&refine_buffer);
    574:       PetscMalloc2(mss*(mns+1),&refine_buffer[0],mss,&private_labels);
    575:     }
    576:     ncc = 0;
    577:     cum_queue = 0;
    578:     graph->cptr[0] = 0;
    579:     for (i=0;i<graph->n_subsets;i++) {
    580:       if (PetscBTLookup(subset_cc_adapt,i)) {
    581:         PetscInt subset_counter = 0;
    582:         PetscInt sharingprocs = cum_recv_counts[i+1]-cum_recv_counts[i]+1; /* count myself */
    583:         PetscInt buffer_size = graph->subset_size[i];

    585:         /* compute pointers */
    586:         for (j=1;j<buffer_size;j++) refine_buffer[j] = refine_buffer[j-1] + sharingprocs;
    587:         /* analyze contributions from subdomains that share the i-th subset
    588:            The structure of refine_buffer is suitable to find intersections of ccs among sharingprocs.
    589:            supposing the current subset is shared by 3 processes and has dimension 5 with global dofs 0,1,2,3,4 (local 0,4,3,1,2)
    590:            sharing procs connected components:
    591:              neigh 0: [0 1 4], [2 3], labels [4,7]  (2 connected components)
    592:              neigh 1: [0 1], [2 3 4], labels [3 2]  (2 connected components)
    593:              neigh 2: [0 4], [1], [2 3], labels [1 5 6] (3 connected components)
    594:            refine_buffer will be filled as:
    595:              [ 4, 3, 1;
    596:                4, 2, 1;
    597:                7, 2, 6;
    598:                4, 3, 5;
    599:                7, 2, 6; ];
    600:            The connected components in local ordering are [0], [1], [2 3], [4] */
    601:         /* fill temp_buffer */
    602:         for (k=0;k<buffer_size;k++) refine_buffer[k][0] = labels[graph->subset_idxs[i][k]];
    603:         for (j=0;j<sharingprocs-1;j++) {
    604:           for (k=0;k<buffer_size;k++) refine_buffer[k][j+1] = recv_buffer[start_of_recv+k];
    605:           start_of_recv += buffer_size;
    606:         }
    607:         PetscArrayzero(private_labels,buffer_size);
    608:         for (j=0;j<buffer_size;j++) {
    609:           if (!private_labels[j]) { /* found a new cc  */
    610:             PetscBool same_set;

    612:             graph->cptr[ncc] = cum_queue;
    613:             ncc++;
    614:             subset_counter++;
    615:             private_labels[j] = subset_counter;
    616:             graph->queue[cum_queue++] = graph->subset_idxs[i][j];
    617:             for (k=j+1;k<buffer_size;k++) { /* check for other nodes in new cc */
    618:               same_set = PETSC_TRUE;
    619:               for (s=0;s<sharingprocs;s++) {
    620:                 if (refine_buffer[j][s] != refine_buffer[k][s]) {
    621:                   same_set = PETSC_FALSE;
    622:                   break;
    623:                 }
    624:               }
    625:               if (same_set) {
    626:                 private_labels[k] = subset_counter;
    627:                 graph->queue[cum_queue++] = graph->subset_idxs[i][k];
    628:               }
    629:             }
    630:           }
    631:         }
    632:         graph->cptr[ncc]     = cum_queue;
    633:         graph->subset_ncc[i] = subset_counter;
    634:         graph->queue_sorted  = PETSC_FALSE;
    635:       } else { /* this subset does not need to be adapted */
    636:         PetscArraycpy(graph->queue+cum_queue,graph->subset_idxs[i],graph->subset_size[i]);
    637:         ncc++;
    638:         cum_queue += graph->subset_size[i];
    639:         graph->cptr[ncc] = cum_queue;
    640:       }
    641:     }
    642:     graph->cptr[ncc] = cum_queue;
    643:     graph->ncc       = ncc;
    644:     if (mss) {
    645:       PetscFree2(refine_buffer[0],private_labels);
    646:       PetscFree(refine_buffer);
    647:     }
    648:     PetscFree(labels);
    649:     MPI_Waitall(sum_requests,send_requests,MPI_STATUSES_IGNORE);
    650:     PetscFree2(send_requests,recv_requests);
    651:     PetscFree2(send_buffer,recv_buffer);
    652:     PetscFree(cum_recv_counts);
    653:     PetscBTDestroy(&subset_cc_adapt);
    654:   }
    655:   PetscBTDestroy(&cornerp);

    657:   /* Determine if we are in 2D or 3D */
    658:   if (!graph->twodimset) {
    659:     PetscBool twodim = PETSC_TRUE;
    660:     for (i=0;i<graph->ncc;i++) {
    661:       PetscInt repdof = graph->queue[graph->cptr[i]];
    662:       PetscInt ccsize = graph->cptr[i+1]-graph->cptr[i];
    663:       if (graph->count[repdof] > 1 && ccsize > graph->custom_minimal_size) {
    664:         twodim = PETSC_FALSE;
    665:         break;
    666:       }
    667:     }
    668:     MPIU_Allreduce(&twodim,&graph->twodim,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)graph->l2gmap));
    669:     graph->twodimset = PETSC_TRUE;
    670:   }
    671:   return(0);
    672: }

    675: PETSC_STATIC_INLINE PetscErrorCode PCBDDCGraphComputeCC_Private(PCBDDCGraph graph,PetscInt pid,PetscInt* queue_tip,PetscInt n_prev,PetscInt* n_added)
    676: {
    677:   PetscInt       i,j,n;
    678:   PetscInt       *xadj = graph->xadj,*adjncy = graph->adjncy;
    679:   PetscBT        touched = graph->touched;
    680:   PetscBool      havecsr = (PetscBool)(!!xadj);
    681:   PetscBool      havesubs = (PetscBool)(!!graph->n_local_subs);

    685:   n = 0;
    686:   if (havecsr && !havesubs) {
    687:     for (i=-n_prev;i<0;i++) {
    688:       PetscInt start_dof = queue_tip[i];
    689:       /* we assume that if a dof has a size 1 adjacency list and the corresponding entry is negative, it is connected to all dofs */
    690:       if (xadj[start_dof+1]-xadj[start_dof] == 1 && adjncy[xadj[start_dof]] < 0) {
    691:         for (j=0;j<graph->subset_size[pid-1];j++) { /* pid \in [1,graph->n_subsets] */
    692:           PetscInt dof = graph->subset_idxs[pid-1][j];
    693:           if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid) {
    694:             PetscBTSet(touched,dof);
    695:             queue_tip[n] = dof;
    696:             n++;
    697:           }
    698:         }
    699:       } else {
    700:         for (j=xadj[start_dof];j<xadj[start_dof+1];j++) {
    701:           PetscInt dof = adjncy[j];
    702:           if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid) {
    703:             PetscBTSet(touched,dof);
    704:             queue_tip[n] = dof;
    705:             n++;
    706:           }
    707:         }
    708:       }
    709:     }
    710:   } else if (havecsr && havesubs) {
    711:     PetscInt sid = graph->local_subs[queue_tip[-n_prev]];
    712:     for (i=-n_prev;i<0;i++) {
    713:       PetscInt start_dof = queue_tip[i];
    714:       /* we assume that if a dof has a size 1 adjacency list and the corresponding entry is negative, it is connected to all dofs belonging to the local sub */
    715:       if (xadj[start_dof+1]-xadj[start_dof] == 1 && adjncy[xadj[start_dof]] < 0) {
    716:         for (j=0;j<graph->subset_size[pid-1];j++) { /* pid \in [1,graph->n_subsets] */
    717:           PetscInt dof = graph->subset_idxs[pid-1][j];
    718:           if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid && graph->local_subs[dof] == sid) {
    719:             PetscBTSet(touched,dof);
    720:             queue_tip[n] = dof;
    721:             n++;
    722:           }
    723:         }
    724:       } else {
    725:         for (j=xadj[start_dof];j<xadj[start_dof+1];j++) {
    726:           PetscInt dof = adjncy[j];
    727:           if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid && graph->local_subs[dof] == sid) {
    728:             PetscBTSet(touched,dof);
    729:             queue_tip[n] = dof;
    730:             n++;
    731:           }
    732:         }
    733:       }
    734:     }
    735:   } else if (havesubs) { /* sub info only */
    736:     PetscInt sid = graph->local_subs[queue_tip[-n_prev]];
    737:     for (j=0;j<graph->subset_size[pid-1];j++) { /* pid \in [1,graph->n_subsets] */
    738:       PetscInt dof = graph->subset_idxs[pid-1][j];
    739:       if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid && graph->local_subs[dof] == sid) {
    740:         PetscBTSet(touched,dof);
    741:         queue_tip[n] = dof;
    742:         n++;
    743:       }
    744:     }
    745:   } else {
    746:     for (j=0;j<graph->subset_size[pid-1];j++) { /* pid \in [1,graph->n_subsets] */
    747:       PetscInt dof = graph->subset_idxs[pid-1][j];
    748:       if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid) {
    749:         PetscBTSet(touched,dof);
    750:         queue_tip[n] = dof;
    751:         n++;
    752:       }
    753:     }
    754:   }
    755:   *n_added = n;
    756:   return(0);
    757: }

    759: PetscErrorCode PCBDDCGraphComputeConnectedComponentsLocal(PCBDDCGraph graph)
    760: {
    761:   PetscInt       ncc,cum_queue,n;
    762:   PetscMPIInt    commsize;

    766:   if (!graph->setupcalled) SETERRQ(PetscObjectComm((PetscObject)graph->l2gmap),PETSC_ERR_ORDER,"PCBDDCGraphSetUp should be called first");
    767:   /* quiet return if there isn't any local info */
    768:   if (!graph->xadj && !graph->n_local_subs) {
    769:     return(0);
    770:   }

    772:   /* reset any previous search of connected components */
    773:   PetscBTMemzero(graph->nvtxs,graph->touched);
    774:   MPI_Comm_size(PetscObjectComm((PetscObject)graph->l2gmap),&commsize);
    775:   if (commsize > graph->commsizelimit) {
    776:     PetscInt i;
    777:     for (i=0;i<graph->nvtxs;i++) {
    778:       if (graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK || !graph->count[i]) {
    779:         PetscBTSet(graph->touched,i);
    780:       }
    781:     }
    782:   }

    784:   /* begin search for connected components */
    785:   cum_queue = 0;
    786:   ncc = 0;
    787:   for (n=0;n<graph->n_subsets;n++) {
    788:     PetscInt pid = n+1;  /* partition labeled by 0 is discarded */
    789:     PetscInt found = 0,prev = 0,first = 0,ncc_pid = 0;
    790:     while (found != graph->subset_size[n]) {
    791:       PetscInt added = 0;
    792:       if (!prev) { /* search for new starting dof */
    793:         while (PetscBTLookup(graph->touched,graph->subset_idxs[n][first])) first++;
    794:         PetscBTSet(graph->touched,graph->subset_idxs[n][first]);
    795:         graph->queue[cum_queue] = graph->subset_idxs[n][first];
    796:         graph->cptr[ncc] = cum_queue;
    797:         prev = 1;
    798:         cum_queue++;
    799:         found++;
    800:         ncc_pid++;
    801:         ncc++;
    802:       }
    803:       PCBDDCGraphComputeCC_Private(graph,pid,graph->queue + cum_queue,prev,&added);
    804:       if (!added) {
    805:         graph->subset_ncc[n] = ncc_pid;
    806:         graph->cptr[ncc] = cum_queue;
    807:       }
    808:       prev = added;
    809:       found += added;
    810:       cum_queue += added;
    811:       if (added && found == graph->subset_size[n]) {
    812:         graph->subset_ncc[n] = ncc_pid;
    813:         graph->cptr[ncc] = cum_queue;
    814:       }
    815:     }
    816:   }
    817:   graph->ncc = ncc;
    818:   graph->queue_sorted = PETSC_FALSE;
    819:   return(0);
    820: }

    822: PetscErrorCode PCBDDCGraphSetUp(PCBDDCGraph graph, PetscInt custom_minimal_size, IS neumann_is, IS dirichlet_is, PetscInt n_ISForDofs, IS ISForDofs[], IS custom_primal_vertices)
    823: {
    824:   IS             subset,subset_n;
    825:   MPI_Comm       comm;
    826:   const PetscInt *is_indices;
    827:   PetscInt       n_neigh,*neigh,*n_shared,**shared,*queue_global;
    828:   PetscInt       i,j,k,s,total_counts,nodes_touched,is_size;
    829:   PetscMPIInt    commsize;
    830:   PetscBool      same_set,mirrors_found;

    835:   if (neumann_is) {
    838:   }
    839:   graph->has_dirichlet = PETSC_FALSE;
    840:   if (dirichlet_is) {
    843:     graph->has_dirichlet = PETSC_TRUE;
    844:   }
    846:   for (i=0;i<n_ISForDofs;i++) {
    849:   }
    850:   if (custom_primal_vertices) {
    853:   }
    854:   PetscObjectGetComm((PetscObject)(graph->l2gmap),&comm);
    855:   MPI_Comm_size(comm,&commsize);

    857:   /* custom_minimal_size */
    858:   graph->custom_minimal_size = custom_minimal_size;
    859:   /* get info l2gmap and allocate work vectors  */
    860:   ISLocalToGlobalMappingGetInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);
    861:   /* check if we have any local periodic nodes (periodic BCs) */
    862:   mirrors_found = PETSC_FALSE;
    863:   if (graph->nvtxs && n_neigh) {
    864:     for (i=0; i<n_shared[0]; i++) graph->count[shared[0][i]] += 1;
    865:     for (i=0; i<n_shared[0]; i++) {
    866:       if (graph->count[shared[0][i]] > 1) {
    867:         mirrors_found = PETSC_TRUE;
    868:         break;
    869:       }
    870:     }
    871:   }
    872:   /* compute local mirrors (if any) */
    873:   if (mirrors_found) {
    874:     IS       to,from;
    875:     PetscInt *local_indices,*global_indices;

    877:     ISCreateStride(PETSC_COMM_SELF,graph->nvtxs,0,1,&to);
    878:     ISLocalToGlobalMappingApplyIS(graph->l2gmap,to,&from);
    879:     /* get arrays of local and global indices */
    880:     PetscMalloc1(graph->nvtxs,&local_indices);
    881:     ISGetIndices(to,(const PetscInt**)&is_indices);
    882:     PetscArraycpy(local_indices,is_indices,graph->nvtxs);
    883:     ISRestoreIndices(to,(const PetscInt**)&is_indices);
    884:     PetscMalloc1(graph->nvtxs,&global_indices);
    885:     ISGetIndices(from,(const PetscInt**)&is_indices);
    886:     PetscArraycpy(global_indices,is_indices,graph->nvtxs);
    887:     ISRestoreIndices(from,(const PetscInt**)&is_indices);
    888:     /* allocate space for mirrors */
    889:     PetscMalloc2(graph->nvtxs,&graph->mirrors,graph->nvtxs,&graph->mirrors_set);
    890:     PetscArrayzero(graph->mirrors,graph->nvtxs);
    891:     graph->mirrors_set[0] = NULL;

    893:     k=0;
    894:     for (i=0;i<n_shared[0];i++) {
    895:       j=shared[0][i];
    896:       if (graph->count[j] > 1) {
    897:         graph->mirrors[j]++;
    898:         k++;
    899:       }
    900:     }
    901:     /* allocate space for set of mirrors */
    902:     PetscMalloc1(k,&graph->mirrors_set[0]);
    903:     for (i=1;i<graph->nvtxs;i++)
    904:       graph->mirrors_set[i]=graph->mirrors_set[i-1]+graph->mirrors[i-1];

    906:     /* fill arrays */
    907:     PetscArrayzero(graph->mirrors,graph->nvtxs);
    908:     for (j=0;j<n_shared[0];j++) {
    909:       i=shared[0][j];
    910:       if (graph->count[i] > 1)
    911:         graph->mirrors_set[i][graph->mirrors[i]++]=global_indices[i];
    912:     }
    913:     PetscSortIntWithArray(graph->nvtxs,global_indices,local_indices);
    914:     for (i=0;i<graph->nvtxs;i++) {
    915:       if (graph->mirrors[i] > 0) {
    916:         PetscFindInt(graph->mirrors_set[i][0],graph->nvtxs,global_indices,&k);
    917:         j = global_indices[k];
    918:         while (k > 0 && global_indices[k-1] == j) k--;
    919:         for (j=0;j<graph->mirrors[i];j++) {
    920:           graph->mirrors_set[i][j]=local_indices[k+j];
    921:         }
    922:         PetscSortInt(graph->mirrors[i],graph->mirrors_set[i]);
    923:       }
    924:     }
    925:     PetscFree(local_indices);
    926:     PetscFree(global_indices);
    927:     ISDestroy(&to);
    928:     ISDestroy(&from);
    929:   }
    930:   PetscArrayzero(graph->count,graph->nvtxs);

    932:   /* Count total number of neigh per node */
    933:   k = 0;
    934:   for (i=1;i<n_neigh;i++) {
    935:     k += n_shared[i];
    936:     for (j=0;j<n_shared[i];j++) {
    937:       graph->count[shared[i][j]] += 1;
    938:     }
    939:   }
    940:   /* Allocate space for storing the set of neighbours for each node */
    941:   if (graph->nvtxs) {
    942:     PetscMalloc1(k,&graph->neighbours_set[0]);
    943:   }
    944:   for (i=1;i<graph->nvtxs;i++) { /* dont count myself */
    945:     graph->neighbours_set[i]=graph->neighbours_set[i-1]+graph->count[i-1];
    946:   }
    947:   /* Get information for sharing subdomains */
    948:   PetscArrayzero(graph->count,graph->nvtxs);
    949:   for (i=1;i<n_neigh;i++) { /* dont count myself */
    950:     s = n_shared[i];
    951:     for (j=0;j<s;j++) {
    952:       k = shared[i][j];
    953:       graph->neighbours_set[k][graph->count[k]] = neigh[i];
    954:       graph->count[k] += 1;
    955:     }
    956:   }
    957:   /* sort set of sharing subdomains */
    958:   for (i=0;i<graph->nvtxs;i++) {
    959:     PetscSortRemoveDupsInt(&graph->count[i],graph->neighbours_set[i]);
    960:   }
    961:   /* free memory allocated by ISLocalToGlobalMappingGetInfo */
    962:   ISLocalToGlobalMappingRestoreInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);

    964:   /*
    965:      Get info for dofs splitting
    966:      User can specify just a subset; an additional field is considered as a complementary field
    967:   */
    968:   for (i=0,k=0;i<n_ISForDofs;i++) {
    969:     PetscInt bs;

    971:     ISGetBlockSize(ISForDofs[i],&bs);
    972:     k   += bs;
    973:   }
    974:   for (i=0;i<graph->nvtxs;i++) graph->which_dof[i] = k; /* by default a dof belongs to the complement set */
    975:   for (i=0,k=0;i<n_ISForDofs;i++) {
    976:     PetscInt bs;

    978:     ISGetLocalSize(ISForDofs[i],&is_size);
    979:     ISGetBlockSize(ISForDofs[i],&bs);
    980:     ISGetIndices(ISForDofs[i],(const PetscInt**)&is_indices);
    981:     for (j=0;j<is_size/bs;j++) {
    982:       PetscInt b;

    984:       for (b=0;b<bs;b++) {
    985:         PetscInt jj = bs*j + b;

    987:         if (is_indices[jj] > -1 && is_indices[jj] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */
    988:           graph->which_dof[is_indices[jj]] = k+b;
    989:         }
    990:       }
    991:     }
    992:     ISRestoreIndices(ISForDofs[i],(const PetscInt**)&is_indices);
    993:     k   += bs;
    994:   }

    996:   /* Take into account Neumann nodes */
    997:   if (neumann_is) {
    998:     ISGetLocalSize(neumann_is,&is_size);
    999:     ISGetIndices(neumann_is,(const PetscInt**)&is_indices);
    1000:     for (i=0;i<is_size;i++) {
    1001:       if (is_indices[i] > -1 && is_indices[i] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */
    1002:         graph->special_dof[is_indices[i]] = PCBDDCGRAPH_NEUMANN_MARK;
    1003:       }
    1004:     }
    1005:     ISRestoreIndices(neumann_is,(const PetscInt**)&is_indices);
    1006:   }
    1007:   /* Take into account Dirichlet nodes (they overwrite any neumann boundary mark previously set) */
    1008:   if (dirichlet_is) {
    1009:     ISGetLocalSize(dirichlet_is,&is_size);
    1010:     ISGetIndices(dirichlet_is,(const PetscInt**)&is_indices);
    1011:     for (i=0;i<is_size;i++){
    1012:       if (is_indices[i] > -1 && is_indices[i] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */
    1013:         if (commsize > graph->commsizelimit) { /* dirichlet nodes treated as internal */
    1014:           PetscBTSet(graph->touched,is_indices[i]);
    1015:           graph->subset[is_indices[i]] = 0;
    1016:         }
    1017:         graph->special_dof[is_indices[i]] = PCBDDCGRAPH_DIRICHLET_MARK;
    1018:       }
    1019:     }
    1020:     ISRestoreIndices(dirichlet_is,(const PetscInt**)&is_indices);
    1021:   }
    1022:   /* mark local periodic nodes (if any) and adapt CSR graph (if any) */
    1023:   if (graph->mirrors) {
    1024:     for (i=0;i<graph->nvtxs;i++)
    1025:       if (graph->mirrors[i])
    1026:         graph->special_dof[i] = PCBDDCGRAPH_LOCAL_PERIODIC_MARK;

    1028:     if (graph->xadj) {
    1029:       PetscInt *new_xadj,*new_adjncy;
    1030:       /* sort CSR graph */
    1031:       for (i=0;i<graph->nvtxs;i++)
    1032:         PetscSortInt(graph->xadj[i+1]-graph->xadj[i],&graph->adjncy[graph->xadj[i]]);

    1034:       /* adapt local CSR graph in case of local periodicity */
    1035:       k = 0;
    1036:       for (i=0;i<graph->nvtxs;i++)
    1037:         for (j=graph->xadj[i];j<graph->xadj[i+1];j++)
    1038:           k += graph->mirrors[graph->adjncy[j]];

    1040:       PetscMalloc1(graph->nvtxs+1,&new_xadj);
    1041:       PetscMalloc1(k+graph->xadj[graph->nvtxs],&new_adjncy);
    1042:       new_xadj[0] = 0;
    1043:       for (i=0;i<graph->nvtxs;i++) {
    1044:         k = graph->xadj[i+1]-graph->xadj[i];
    1045:         PetscArraycpy(&new_adjncy[new_xadj[i]],&graph->adjncy[graph->xadj[i]],k);
    1046:         new_xadj[i+1] = new_xadj[i]+k;
    1047:         for (j=graph->xadj[i];j<graph->xadj[i+1];j++) {
    1048:           k = graph->mirrors[graph->adjncy[j]];
    1049:           PetscArraycpy(&new_adjncy[new_xadj[i+1]],graph->mirrors_set[graph->adjncy[j]],k);
    1050:           new_xadj[i+1] += k;
    1051:         }
    1052:         k = new_xadj[i+1]-new_xadj[i];
    1053:         PetscSortRemoveDupsInt(&k,&new_adjncy[new_xadj[i]]);
    1054:         new_xadj[i+1] = new_xadj[i]+k;
    1055:       }
    1056:       /* set new CSR into graph */
    1057:       PetscFree(graph->xadj);
    1058:       PetscFree(graph->adjncy);
    1059:       graph->xadj = new_xadj;
    1060:       graph->adjncy = new_adjncy;
    1061:     }
    1062:   }

    1064:   /* mark special nodes (if any) -> each will become a single node equivalence class */
    1065:   if (custom_primal_vertices) {
    1066:     ISGetLocalSize(custom_primal_vertices,&is_size);
    1067:     ISGetIndices(custom_primal_vertices,(const PetscInt**)&is_indices);
    1068:     for (i=0,j=0;i<is_size;i++){
    1069:       if (is_indices[i] > -1 && is_indices[i] < graph->nvtxs  && graph->special_dof[is_indices[i]] != PCBDDCGRAPH_DIRICHLET_MARK) { /* out of bounds indices (if any) are skipped */
    1070:         graph->special_dof[is_indices[i]] = PCBDDCGRAPH_SPECIAL_MARK-j;
    1071:         j++;
    1072:       }
    1073:     }
    1074:     ISRestoreIndices(custom_primal_vertices,(const PetscInt**)&is_indices);
    1075:   }

    1077:   /* mark interior nodes (if commsize > graph->commsizelimit) as touched and belonging to partition number 0 */
    1078:   if (commsize > graph->commsizelimit) {
    1079:     for (i=0;i<graph->nvtxs;i++) {
    1080:       if (!graph->count[i]) {
    1081:         PetscBTSet(graph->touched,i);
    1082:         graph->subset[i] = 0;
    1083:       }
    1084:     }
    1085:   }

    1087:   /* init graph structure and compute default subsets */
    1088:   nodes_touched = 0;
    1089:   for (i=0;i<graph->nvtxs;i++) {
    1090:     if (PetscBTLookup(graph->touched,i)) {
    1091:       nodes_touched++;
    1092:     }
    1093:   }
    1094:   i = 0;
    1095:   graph->ncc = 0;
    1096:   total_counts = 0;

    1098:   /* allocated space for queues */
    1099:   if (commsize == graph->commsizelimit) {
    1100:     PetscMalloc2(graph->nvtxs+1,&graph->cptr,graph->nvtxs,&graph->queue);
    1101:   } else {
    1102:     PetscInt nused = graph->nvtxs - nodes_touched;
    1103:     PetscMalloc2(nused+1,&graph->cptr,nused,&graph->queue);
    1104:   }

    1106:   while (nodes_touched<graph->nvtxs) {
    1107:     /*  find first untouched node in local ordering */
    1108:     while (PetscBTLookup(graph->touched,i)) i++;
    1109:     PetscBTSet(graph->touched,i);
    1110:     graph->subset[i] = graph->ncc+1;
    1111:     graph->cptr[graph->ncc] = total_counts;
    1112:     graph->queue[total_counts] = i;
    1113:     total_counts++;
    1114:     nodes_touched++;
    1115:     /* now find all other nodes having the same set of sharing subdomains */
    1116:     for (j=i+1;j<graph->nvtxs;j++) {
    1117:       /* check for same number of sharing subdomains, dof number and same special mark */
    1118:       if (!PetscBTLookup(graph->touched,j) && graph->count[i] == graph->count[j] && graph->which_dof[i] == graph->which_dof[j] && graph->special_dof[i] == graph->special_dof[j]) {
    1119:         /* check for same set of sharing subdomains */
    1120:         same_set = PETSC_TRUE;
    1121:         for (k=0;k<graph->count[j];k++){
    1122:           if (graph->neighbours_set[i][k] != graph->neighbours_set[j][k]) {
    1123:             same_set = PETSC_FALSE;
    1124:           }
    1125:         }
    1126:         /* I have found a friend of mine */
    1127:         if (same_set) {
    1128:           PetscBTSet(graph->touched,j);
    1129:           graph->subset[j] = graph->ncc+1;
    1130:           nodes_touched++;
    1131:           graph->queue[total_counts] = j;
    1132:           total_counts++;
    1133:         }
    1134:       }
    1135:     }
    1136:     graph->ncc++;
    1137:   }
    1138:   /* set default number of subsets (at this point no info on csr and/or local_subs has been taken into account, so n_subsets = ncc */
    1139:   graph->n_subsets = graph->ncc;
    1140:   PetscMalloc1(graph->n_subsets,&graph->subset_ncc);
    1141:   for (i=0;i<graph->n_subsets;i++) {
    1142:     graph->subset_ncc[i] = 1;
    1143:   }
    1144:   /* final pointer */
    1145:   graph->cptr[graph->ncc] = total_counts;

    1147:   /* For consistency reasons (among neighbours), I need to sort (by global ordering) each connected component */
    1148:   /* Get a reference node (min index in global ordering) for each subset for tagging messages */
    1149:   PetscMalloc1(graph->ncc,&graph->subset_ref_node);
    1150:   PetscMalloc1(graph->cptr[graph->ncc],&queue_global);
    1151:   ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_global);
    1152:   for (j=0;j<graph->ncc;j++) {
    1153:     PetscSortIntWithArray(graph->cptr[j+1]-graph->cptr[j],&queue_global[graph->cptr[j]],&graph->queue[graph->cptr[j]]);
    1154:     graph->subset_ref_node[j] = graph->queue[graph->cptr[j]];
    1155:   }
    1156:   PetscFree(queue_global);
    1157:   graph->queue_sorted = PETSC_TRUE;

    1159:   /* save information on subsets (needed when analyzing the connected components) */
    1160:   if (graph->ncc) {
    1161:     PetscMalloc2(graph->ncc,&graph->subset_size,graph->ncc,&graph->subset_idxs);
    1162:     PetscMalloc1(graph->cptr[graph->ncc],&graph->subset_idxs[0]);
    1163:     PetscArrayzero(graph->subset_idxs[0],graph->cptr[graph->ncc]);
    1164:     for (j=1;j<graph->ncc;j++) {
    1165:       graph->subset_size[j-1] = graph->cptr[j] - graph->cptr[j-1];
    1166:       graph->subset_idxs[j] = graph->subset_idxs[j-1] + graph->subset_size[j-1];
    1167:     }
    1168:     graph->subset_size[graph->ncc-1] = graph->cptr[graph->ncc] - graph->cptr[graph->ncc-1];
    1169:     PetscArraycpy(graph->subset_idxs[0],graph->queue,graph->cptr[graph->ncc]);
    1170:   }

    1172:   /* renumber reference nodes */
    1173:   ISCreateGeneral(PetscObjectComm((PetscObject)(graph->l2gmap)),graph->ncc,graph->subset_ref_node,PETSC_COPY_VALUES,&subset_n);
    1174:   ISLocalToGlobalMappingApplyIS(graph->l2gmap,subset_n,&subset);
    1175:   ISDestroy(&subset_n);
    1176:   ISRenumber(subset,NULL,NULL,&subset_n);
    1177:   ISDestroy(&subset);
    1178:   ISGetLocalSize(subset_n,&k);
    1179:   if (k != graph->ncc) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Invalid size of new subset! %D != %D",k,graph->ncc);
    1180:   ISGetIndices(subset_n,&is_indices);
    1181:   PetscArraycpy(graph->subset_ref_node,is_indices,graph->ncc);
    1182:   ISRestoreIndices(subset_n,&is_indices);
    1183:   ISDestroy(&subset_n);

    1185:   /* free workspace */
    1186:   graph->setupcalled = PETSC_TRUE;
    1187:   return(0);
    1188: }

    1190: PetscErrorCode PCBDDCGraphResetCoords(PCBDDCGraph graph)
    1191: {

    1195:   if (!graph) return(0);
    1196:   PetscFree(graph->coords);
    1197:   graph->cdim  = 0;
    1198:   graph->cnloc = 0;
    1199:   graph->cloc  = PETSC_FALSE;
    1200:   return(0);
    1201: }

    1203: PetscErrorCode PCBDDCGraphResetCSR(PCBDDCGraph graph)
    1204: {

    1208:   if (!graph) return(0);
    1209:   if (graph->freecsr) {
    1210:     PetscFree(graph->xadj);
    1211:     PetscFree(graph->adjncy);
    1212:   } else {
    1213:     graph->xadj = NULL;
    1214:     graph->adjncy = NULL;
    1215:   }
    1216:   graph->freecsr = PETSC_FALSE;
    1217:   graph->nvtxs_csr = 0;
    1218:   return(0);
    1219: }

    1221: PetscErrorCode PCBDDCGraphReset(PCBDDCGraph graph)
    1222: {

    1226:   if (!graph) return(0);
    1227:   ISLocalToGlobalMappingDestroy(&graph->l2gmap);
    1228:   PetscFree(graph->subset_ncc);
    1229:   PetscFree(graph->subset_ref_node);
    1230:   if (graph->nvtxs) {
    1231:     PetscFree(graph->neighbours_set[0]);
    1232:   }
    1233:   PetscBTDestroy(&graph->touched);
    1234:   PetscFree5(graph->count,
    1235:                     graph->neighbours_set,
    1236:                     graph->subset,
    1237:                     graph->which_dof,
    1238:                     graph->special_dof);
    1239:   PetscFree2(graph->cptr,graph->queue);
    1240:   if (graph->mirrors) {
    1241:     PetscFree(graph->mirrors_set[0]);
    1242:   }
    1243:   PetscFree2(graph->mirrors,graph->mirrors_set);
    1244:   if (graph->subset_idxs) {
    1245:     PetscFree(graph->subset_idxs[0]);
    1246:   }
    1247:   PetscFree2(graph->subset_size,graph->subset_idxs);
    1248:   ISDestroy(&graph->dirdofs);
    1249:   ISDestroy(&graph->dirdofsB);
    1250:   if (graph->n_local_subs) {
    1251:     PetscFree(graph->local_subs);
    1252:   }
    1253:   graph->has_dirichlet       = PETSC_FALSE;
    1254:   graph->twodimset           = PETSC_FALSE;
    1255:   graph->twodim              = PETSC_FALSE;
    1256:   graph->nvtxs               = 0;
    1257:   graph->nvtxs_global        = 0;
    1258:   graph->n_subsets           = 0;
    1259:   graph->custom_minimal_size = 1;
    1260:   graph->n_local_subs        = 0;
    1261:   graph->maxcount            = PETSC_MAX_INT;
    1262:   graph->setupcalled         = PETSC_FALSE;
    1263:   return(0);
    1264: }

    1266: PetscErrorCode PCBDDCGraphInit(PCBDDCGraph graph, ISLocalToGlobalMapping l2gmap, PetscInt N, PetscInt maxcount)
    1267: {
    1268:   PetscInt       n;

    1276:   /* raise an error if already allocated */
    1277:   if (graph->nvtxs_global) SETERRQ(PetscObjectComm((PetscObject)l2gmap),PETSC_ERR_PLIB,"BDDCGraph already initialized");
    1278:   /* set number of vertices */
    1279:   PetscObjectReference((PetscObject)l2gmap);
    1280:   graph->l2gmap = l2gmap;
    1281:   ISLocalToGlobalMappingGetSize(l2gmap,&n);
    1282:   graph->nvtxs = n;
    1283:   graph->nvtxs_global = N;
    1284:   /* allocate used space */
    1285:   PetscBTCreate(graph->nvtxs,&graph->touched);
    1286:   PetscMalloc5(graph->nvtxs,&graph->count,graph->nvtxs,&graph->neighbours_set,graph->nvtxs,&graph->subset,graph->nvtxs,&graph->which_dof,graph->nvtxs,&graph->special_dof);
    1287:   /* zeroes memory */
    1288:   PetscArrayzero(graph->count,graph->nvtxs);
    1289:   PetscArrayzero(graph->subset,graph->nvtxs);
    1290:   /* use -1 as a default value for which_dof array */
    1291:   for (n=0;n<graph->nvtxs;n++) graph->which_dof[n] = -1;
    1292:   PetscArrayzero(graph->special_dof,graph->nvtxs);
    1293:   /* zeroes first pointer to neighbour set */
    1294:   if (graph->nvtxs) {
    1295:     graph->neighbours_set[0] = NULL;
    1296:   }
    1297:   /* zeroes workspace for values of ncc */
    1298:   graph->subset_ncc = NULL;
    1299:   graph->subset_ref_node = NULL;
    1300:   /* maxcount for cc */
    1301:   graph->maxcount = maxcount;
    1302:   return(0);
    1303: }

    1305: PetscErrorCode PCBDDCGraphDestroy(PCBDDCGraph* graph)
    1306: {

    1310:   PCBDDCGraphResetCSR(*graph);
    1311:   PCBDDCGraphResetCoords(*graph);
    1312:   PCBDDCGraphReset(*graph);
    1313:   PetscFree(*graph);
    1314:   return(0);
    1315: }

    1317: PetscErrorCode PCBDDCGraphCreate(PCBDDCGraph *graph)
    1318: {
    1319:   PCBDDCGraph    new_graph;

    1323:   PetscNew(&new_graph);
    1324:   new_graph->custom_minimal_size = 1;
    1325:   new_graph->commsizelimit = 1;
    1326:   *graph = new_graph;
    1327:   return(0);
    1328: }