1 #include <petsc/private/petscimpl.h> 2 #include <../src/ksp/pc/impls/bddc/bddcprivate.h> 3 #include <../src/ksp/pc/impls/bddc/bddcstructs.h> 4 5 PetscErrorCode PCBDDCGraphGetDirichletDofsB(PCBDDCGraph graph, IS* dirdofs) 6 { 7 PetscErrorCode ierr; 8 9 PetscFunctionBegin; 10 if (graph->dirdofsB) { 11 ierr = PetscObjectReference((PetscObject)graph->dirdofsB);CHKERRQ(ierr); 12 } else if (graph->has_dirichlet) { 13 PetscInt i,size; 14 PetscInt *dirdofs_idxs; 15 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 } 20 21 ierr = PetscMalloc1(size,&dirdofs_idxs);CHKERRQ(ierr); 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 ierr = ISCreateGeneral(PETSC_COMM_SELF,size,dirdofs_idxs,PETSC_OWN_POINTER,&graph->dirdofsB);CHKERRQ(ierr); 27 ierr = PetscObjectReference((PetscObject)graph->dirdofsB);CHKERRQ(ierr); 28 } 29 *dirdofs = graph->dirdofsB; 30 PetscFunctionReturn(0); 31 } 32 33 PetscErrorCode PCBDDCGraphGetDirichletDofs(PCBDDCGraph graph, IS* dirdofs) 34 { 35 PetscErrorCode ierr; 36 37 PetscFunctionBegin; 38 if (graph->dirdofs) { 39 ierr = PetscObjectReference((PetscObject)graph->dirdofs);CHKERRQ(ierr); 40 } else if (graph->has_dirichlet) { 41 PetscInt i,size; 42 PetscInt *dirdofs_idxs; 43 44 size = 0; 45 for (i=0;i<graph->nvtxs;i++) { 46 if (graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) size++; 47 } 48 49 ierr = PetscMalloc1(size,&dirdofs_idxs);CHKERRQ(ierr); 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 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)graph->l2gmap),size,dirdofs_idxs,PETSC_OWN_POINTER,&graph->dirdofs);CHKERRQ(ierr); 55 ierr = PetscObjectReference((PetscObject)graph->dirdofs);CHKERRQ(ierr); 56 } 57 *dirdofs = graph->dirdofs; 58 PetscFunctionReturn(0); 59 } 60 61 PetscErrorCode PCBDDCGraphASCIIView(PCBDDCGraph graph, PetscInt verbosity_level, PetscViewer viewer) 62 { 63 PetscInt i,j,tabs; 64 PetscInt* queue_in_global_numbering; 65 PetscErrorCode ierr; 66 67 PetscFunctionBegin; 68 ierr = PetscViewerASCIIPushSynchronized(viewer);CHKERRQ(ierr); 69 ierr = PetscViewerASCIIGetTab(viewer,&tabs);CHKERRQ(ierr); 70 ierr = PetscViewerASCIIPrintf(viewer,"--------------------------------------------------\n");CHKERRQ(ierr); 71 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 72 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Local BDDC graph for subdomain %04d\n",PetscGlobalRank);CHKERRQ(ierr); 73 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Number of vertices %d\n",graph->nvtxs);CHKERRQ(ierr); 74 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Custom minimal size %d\n",graph->custom_minimal_size);CHKERRQ(ierr); 75 if (graph->maxcount != PETSC_MAX_INT) { 76 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Max count %d\n",graph->maxcount);CHKERRQ(ierr); 77 } 78 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Topological two dim? %d (set %d)\n",graph->twodim,graph->twodimset);CHKERRQ(ierr); 79 if (verbosity_level > 2) { 80 for (i=0;i<graph->nvtxs;i++) { 81 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"%d:\n",i);CHKERRQ(ierr); 82 ierr = PetscViewerASCIISynchronizedPrintf(viewer," which_dof: %d\n",graph->which_dof[i]);CHKERRQ(ierr); 83 ierr = PetscViewerASCIISynchronizedPrintf(viewer," special_dof: %d\n",graph->special_dof[i]);CHKERRQ(ierr); 84 ierr = PetscViewerASCIISynchronizedPrintf(viewer," neighbours: %d\n",graph->count[i]);CHKERRQ(ierr); 85 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 86 if (graph->count[i]) { 87 ierr = PetscViewerASCIISynchronizedPrintf(viewer," set of neighbours:");CHKERRQ(ierr); 88 for (j=0;j<graph->count[i];j++) { 89 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->neighbours_set[i][j]);CHKERRQ(ierr); 90 } 91 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"\n");CHKERRQ(ierr); 92 } 93 ierr = PetscViewerASCIISetTab(viewer,tabs);CHKERRQ(ierr); 94 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 95 if (graph->mirrors) { 96 ierr = PetscViewerASCIISynchronizedPrintf(viewer," mirrors: %d\n",graph->mirrors[i]);CHKERRQ(ierr); 97 if (graph->mirrors[i]) { 98 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 99 ierr = PetscViewerASCIISynchronizedPrintf(viewer," set of mirrors:");CHKERRQ(ierr); 100 for (j=0;j<graph->mirrors[i];j++) { 101 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->mirrors_set[i][j]);CHKERRQ(ierr); 102 } 103 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"\n");CHKERRQ(ierr); 104 ierr = PetscViewerASCIISetTab(viewer,tabs);CHKERRQ(ierr); 105 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 106 } 107 } 108 if (verbosity_level > 3) { 109 if (graph->xadj) { 110 ierr = PetscViewerASCIISynchronizedPrintf(viewer," local adj list:");CHKERRQ(ierr); 111 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 112 for (j=graph->xadj[i];j<graph->xadj[i+1];j++) { 113 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->adjncy[j]);CHKERRQ(ierr); 114 } 115 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"\n");CHKERRQ(ierr); 116 ierr = PetscViewerASCIISetTab(viewer,tabs);CHKERRQ(ierr); 117 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 118 } else { 119 ierr = PetscViewerASCIISynchronizedPrintf(viewer," no adj info\n");CHKERRQ(ierr); 120 } 121 } 122 if (graph->n_local_subs) { 123 ierr = PetscViewerASCIISynchronizedPrintf(viewer," local sub id: %d\n",graph->local_subs[i]);CHKERRQ(ierr); 124 } 125 ierr = PetscViewerASCIISynchronizedPrintf(viewer," interface subset id: %d\n",graph->subset[i]);CHKERRQ(ierr); 126 if (graph->subset[i] && graph->subset_ncc) { 127 ierr = PetscViewerASCIISynchronizedPrintf(viewer," ncc for subset: %d\n",graph->subset_ncc[graph->subset[i]-1]);CHKERRQ(ierr); 128 } 129 } 130 } 131 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Total number of connected components %d\n",graph->ncc);CHKERRQ(ierr); 132 ierr = PetscMalloc1(graph->cptr[graph->ncc],&queue_in_global_numbering);CHKERRQ(ierr); 133 ierr = ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_in_global_numbering);CHKERRQ(ierr); 134 for (i=0;i<graph->ncc;i++) { 135 PetscInt node_num=graph->queue[graph->cptr[i]]; 136 PetscBool printcc = PETSC_FALSE; 137 ierr = PetscViewerASCIISynchronizedPrintf(viewer," cc %d (size %d, fid %d, neighs:",i,graph->cptr[i+1]-graph->cptr[i],graph->which_dof[node_num]);CHKERRQ(ierr); 138 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 139 for (j=0;j<graph->count[node_num];j++) { 140 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->neighbours_set[node_num][j]);CHKERRQ(ierr); 141 } 142 if (verbosity_level > 1) { 143 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"):");CHKERRQ(ierr); 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 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d (%d)",graph->queue[j],queue_in_global_numbering[j]);CHKERRQ(ierr); 150 } 151 } 152 } else { 153 ierr = PetscViewerASCIISynchronizedPrintf(viewer,")");CHKERRQ(ierr); 154 } 155 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"\n");CHKERRQ(ierr); 156 ierr = PetscViewerASCIISetTab(viewer,tabs);CHKERRQ(ierr); 157 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 158 } 159 ierr = PetscFree(queue_in_global_numbering);CHKERRQ(ierr); 160 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 161 PetscFunctionReturn(0); 162 } 163 164 PetscErrorCode PCBDDCGraphRestoreCandidatesIS(PCBDDCGraph graph, PetscInt *n_faces, IS *FacesIS[], PetscInt *n_edges, IS *EdgesIS[], IS *VerticesIS) 165 { 166 PetscInt i; 167 PetscErrorCode ierr; 168 169 PetscFunctionBegin; 170 if (n_faces) { 171 if (FacesIS) { 172 for (i=0;i<*n_faces;i++) { 173 ierr = ISDestroy(&((*FacesIS)[i]));CHKERRQ(ierr); 174 } 175 ierr = PetscFree(*FacesIS);CHKERRQ(ierr); 176 } 177 *n_faces = 0; 178 } 179 if (n_edges) { 180 if (EdgesIS) { 181 for (i=0;i<*n_edges;i++) { 182 ierr = ISDestroy(&((*EdgesIS)[i]));CHKERRQ(ierr); 183 } 184 ierr = PetscFree(*EdgesIS);CHKERRQ(ierr); 185 } 186 *n_edges = 0; 187 } 188 if (VerticesIS) { 189 ierr = ISDestroy(VerticesIS);CHKERRQ(ierr); 190 } 191 PetscFunctionReturn(0); 192 } 193 194 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; 198 PetscErrorCode ierr; 199 200 PetscFunctionBegin; 201 ierr = PetscCalloc1(graph->ncc,&mark);CHKERRQ(ierr); 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 } 220 221 /* allocate IS arrays for faces, edges. Vertices need a single index set. */ 222 if (FacesIS) { 223 ierr = PetscMalloc1(nfc,&ISForFaces);CHKERRQ(ierr); 224 } 225 if (EdgesIS) { 226 ierr = PetscMalloc1(nec,&ISForEdges);CHKERRQ(ierr); 227 } 228 if (VerticesIS) { 229 ierr = PetscMalloc1(nvc,&idx);CHKERRQ(ierr); 230 } 231 232 /* loop on ccs to compute index sets for faces and edges */ 233 if (!graph->queue_sorted) { 234 PetscInt *queue_global; 235 236 ierr = PetscMalloc1(graph->cptr[graph->ncc],&queue_global);CHKERRQ(ierr); 237 ierr = ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_global);CHKERRQ(ierr); 238 for (i=0;i<graph->ncc;i++) { 239 ierr = PetscSortIntWithArray(graph->cptr[i+1]-graph->cptr[i],&queue_global[graph->cptr[i]],&graph->queue[graph->cptr[i]]);CHKERRQ(ierr); 240 } 241 ierr = PetscFree(queue_global);CHKERRQ(ierr); 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 ierr = ISCreateGeneral(PETSC_COMM_SELF,graph->cptr[i+1]-graph->cptr[i],&graph->queue[graph->cptr[i]],PETSC_USE_POINTER,&ISForFaces[nfc]);CHKERRQ(ierr); 250 } 251 nfc++; 252 } else if (mark[i] == 1) { 253 if (EdgesIS) { 254 ierr = ISCreateGeneral(PETSC_COMM_SELF,graph->cptr[i+1]-graph->cptr[i],&graph->queue[graph->cptr[i]],PETSC_USE_POINTER,&ISForEdges[nec]);CHKERRQ(ierr); 255 } 256 nec++; 257 } 258 } 259 260 /* 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; 266 267 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 ierr = PetscSortInt(nvc,idx);CHKERRQ(ierr); 275 ierr = ISCreateGeneral(PETSC_COMM_SELF,nvc,idx,PETSC_OWN_POINTER,&ISForVertices);CHKERRQ(ierr); 276 } 277 ierr = PetscFree(mark);CHKERRQ(ierr); 278 279 /* 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 PetscFunctionReturn(0); 286 } 287 288 PetscErrorCode PCBDDCGraphComputeConnectedComponents(PCBDDCGraph graph) 289 { 290 PetscBool adapt_interface_reduced; 291 MPI_Comm interface_comm; 292 PetscMPIInt size; 293 PetscInt i; 294 PetscBT cornerp; 295 PetscErrorCode ierr; 296 297 PetscFunctionBegin; 298 /* compute connected components locally */ 299 ierr = PetscObjectGetComm((PetscObject)(graph->l2gmap),&interface_comm);CHKERRQ(ierr); 300 ierr = PCBDDCGraphComputeConnectedComponentsLocal(graph);CHKERRQ(ierr); 301 302 cornerp = NULL; 303 if (graph->active_coords) { /* face based corner selection */ 304 PetscReal *wdist; 305 PetscInt n_neigh,*neigh,*n_shared,**shared; 306 PetscInt maxc, ns; 307 308 ierr = PetscBTCreate(graph->nvtxs,&cornerp);CHKERRQ(ierr); 309 ierr = ISLocalToGlobalMappingGetInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);CHKERRQ(ierr); 310 for (ns = 1, maxc = 0; ns < n_neigh; ns++) maxc = PetscMax(maxc,n_shared[ns]); 311 ierr = PetscMalloc1(maxc*graph->cdim,&wdist);CHKERRQ(ierr); 312 313 for (ns = 1; ns < n_neigh; ns++) { /* first proc is self */ 314 PetscReal *anchor,mdist; 315 PetscInt j,k,d,cdim = graph->cdim; 316 PetscInt point1,point2,point3; 317 /* 318 PetscBool isface = PETSC_FALSE; 319 320 for (i=0;i<n_shared[ns];i++) { 321 if (graph->count[shared[ns][i]] == 1) { 322 isface = PETSC_TRUE; 323 break; 324 } 325 } 326 if (!isface) continue; 327 */ 328 /* import coordinates on shared interface */ 329 for (j=0,k=0;j<n_shared[ns];j++) 330 for (d=0;d<cdim;d++) 331 wdist[k++] = graph->coords[shared[ns][j]*cdim+d]; 332 333 /* the dofs are sorted by global numbering, so each rank start from the same id and will detect the same corners */ 334 anchor = wdist; 335 336 /* find the farthest point from the starting one */ 337 mdist = -1.0; 338 for (j=0,point1=0;j<n_shared[ns];j++) { 339 PetscReal dist = 0.0; 340 341 for (d=0;d<cdim;d++) dist += (wdist[j*cdim+d]-anchor[d])*(wdist[j*cdim+d]-anchor[d]); 342 if (dist > mdist) { mdist = dist; point1 = j; } 343 } 344 345 /* find the farthest point from point1 */ 346 anchor = wdist + point1*cdim; 347 mdist = -1.0; 348 for (j=0,point2=0;j<n_shared[ns];j++) { 349 PetscReal dist = 0.0; 350 351 for (d=0;d<cdim;d++) dist += (wdist[j*cdim+d]-anchor[d])*(wdist[j*cdim+d]-anchor[d]); 352 if (dist > mdist) { mdist = dist; point2 = j; } 353 } 354 355 /* find the third point maximizing the triangle area */ 356 point3 = point2; 357 if (cdim > 2) { 358 PetscReal a = 0.0; 359 360 for (d=0;d<cdim;d++) a += (wdist[point1*cdim+d]-wdist[point2*cdim+d])*(wdist[point1*cdim+d]-wdist[point2*cdim+d]); 361 a = PetscSqrtReal(a); 362 mdist = -1.0; 363 for (j=0,point3=0;j<n_shared[ns];j++) { 364 PetscReal area,b = 0.0, c = 0.0,s; 365 366 for (d=0;d<cdim;d++) { 367 b += (wdist[point1*cdim+d]-wdist[j*cdim+d])*(wdist[point1*cdim+d]-wdist[j*cdim+d]); 368 c += (wdist[point2*cdim+d]-wdist[j*cdim+d])*(wdist[point2*cdim+d]-wdist[j*cdim+d]); 369 } 370 b = PetscSqrtReal(b); 371 c = PetscSqrtReal(c); 372 s = 0.5*(a+b+c); 373 area = s*(s-a)*(s-b)*(s-c); /* Heron's formula, area squared */ 374 if (area > mdist) { mdist = area; point3 = j; } 375 } 376 } 377 378 /* all dofs having the same coordinates will be primal */ 379 for (j=0;j<n_shared[ns];j++) { 380 PetscBool same[3] = {PETSC_TRUE,PETSC_TRUE,PETSC_TRUE}; 381 382 for (d=0;d<cdim;d++) { 383 same[0] = (PetscBool)(same[0] && (PetscAbsReal(wdist[j*cdim + d]-wdist[point1*cdim+d]) < PETSC_SMALL)); 384 same[1] = (PetscBool)(same[1] && (PetscAbsReal(wdist[j*cdim + d]-wdist[point2*cdim+d]) < PETSC_SMALL)); 385 same[2] = (PetscBool)(same[2] && (PetscAbsReal(wdist[j*cdim + d]-wdist[point3*cdim+d]) < PETSC_SMALL)); 386 } 387 if (same[0] || same[1] || same[2]) { 388 ierr = PetscBTSet(cornerp,shared[ns][j]);CHKERRQ(ierr); 389 } 390 } 391 } 392 ierr = PetscFree(wdist);CHKERRQ(ierr); 393 ierr = ISLocalToGlobalMappingRestoreInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);CHKERRQ(ierr); 394 } 395 396 /* check consistency of connected components among neighbouring subdomains -> it adapt them in case it is needed */ 397 ierr = MPI_Comm_size(interface_comm,&size);CHKERRQ(ierr); 398 adapt_interface_reduced = PETSC_FALSE; 399 if (size > 1) { 400 PetscInt i; 401 PetscBool adapt_interface = cornerp ? PETSC_TRUE : PETSC_FALSE; 402 for (i=0;i<graph->n_subsets && !adapt_interface;i++) { 403 /* We are not sure that on a given subset of the local interface, 404 with two connected components, the latters be the same among sharing subdomains */ 405 if (graph->subset_ncc[i] > 1) adapt_interface = PETSC_TRUE; 406 } 407 ierr = MPIU_Allreduce(&adapt_interface,&adapt_interface_reduced,1,MPIU_BOOL,MPI_LOR,interface_comm);CHKERRQ(ierr); 408 } 409 410 if (graph->n_subsets && adapt_interface_reduced) { 411 PetscBT subset_cc_adapt; 412 MPI_Request *send_requests,*recv_requests; 413 PetscInt *send_buffer,*recv_buffer; 414 PetscInt sum_requests,start_of_recv,start_of_send; 415 PetscInt *cum_recv_counts; 416 PetscInt *labels; 417 PetscInt ncc,cum_queue,mss,mns,j,k,s; 418 PetscInt **refine_buffer=NULL,*private_labels = NULL; 419 PetscBool *subset_has_corn,*recv_buffer_bool,*send_buffer_bool; 420 421 ierr = PetscCalloc1(graph->n_subsets,&subset_has_corn);CHKERRQ(ierr); 422 if (cornerp) { 423 for (i=0;i<graph->n_subsets;i++) { 424 for (j=0;j<graph->subset_size[i];j++) { 425 if (PetscBTLookup(cornerp,graph->subset_idxs[i][j])) { 426 subset_has_corn[i] = PETSC_TRUE; 427 break; 428 } 429 } 430 } 431 } 432 ierr = PetscMalloc1(graph->nvtxs,&labels);CHKERRQ(ierr); 433 ierr = PetscMemzero(labels,graph->nvtxs*sizeof(*labels));CHKERRQ(ierr); 434 for (i=0,k=0;i<graph->ncc;i++) { 435 PetscInt s = 1; 436 for (j=graph->cptr[i];j<graph->cptr[i+1];j++) { 437 if (cornerp && PetscBTLookup(cornerp,graph->queue[j])) { 438 labels[graph->queue[j]] = k+s; 439 s += 1; 440 } else { 441 labels[graph->queue[j]] = k; 442 } 443 } 444 k += s; 445 } 446 447 /* allocate some space */ 448 ierr = PetscMalloc1(graph->n_subsets+1,&cum_recv_counts);CHKERRQ(ierr); 449 ierr = PetscMemzero(cum_recv_counts,(graph->n_subsets+1)*sizeof(*cum_recv_counts));CHKERRQ(ierr); 450 451 /* first count how many neighbours per connected component I will receive from */ 452 cum_recv_counts[0] = 0; 453 for (i=0;i<graph->n_subsets;i++) cum_recv_counts[i+1] = cum_recv_counts[i]+graph->count[graph->subset_idxs[i][0]]; 454 ierr = PetscMalloc1(graph->n_subsets,&send_buffer_bool);CHKERRQ(ierr); 455 ierr = PetscMalloc1(cum_recv_counts[graph->n_subsets],&recv_buffer_bool);CHKERRQ(ierr); 456 ierr = PetscMalloc2(cum_recv_counts[graph->n_subsets],&send_requests,cum_recv_counts[graph->n_subsets],&recv_requests);CHKERRQ(ierr); 457 for (i=0;i<cum_recv_counts[graph->n_subsets];i++) { 458 send_requests[i] = MPI_REQUEST_NULL; 459 recv_requests[i] = MPI_REQUEST_NULL; 460 } 461 462 /* exchange with my neighbours the number of my connected components on the subset of interface */ 463 sum_requests = 0; 464 for (i=0;i<graph->n_subsets;i++) { 465 send_buffer_bool[i] = (PetscBool)(graph->subset_ncc[i] > 1 || subset_has_corn[i]); 466 } 467 for (i=0;i<graph->n_subsets;i++) { 468 PetscMPIInt neigh,tag; 469 PetscInt count,*neighs; 470 471 count = graph->count[graph->subset_idxs[i][0]]; 472 neighs = graph->neighbours_set[graph->subset_idxs[i][0]]; 473 ierr = PetscMPIIntCast(2*graph->subset_ref_node[i],&tag);CHKERRQ(ierr); 474 for (k=0;k<count;k++) { 475 476 ierr = PetscMPIIntCast(neighs[k],&neigh);CHKERRQ(ierr); 477 ierr = MPI_Isend(send_buffer_bool + i, 1,MPIU_BOOL,neigh,tag,interface_comm,&send_requests[sum_requests]);CHKERRQ(ierr); 478 ierr = MPI_Irecv(recv_buffer_bool + sum_requests,1,MPIU_BOOL,neigh,tag,interface_comm,&recv_requests[sum_requests]);CHKERRQ(ierr); 479 sum_requests++; 480 } 481 } 482 ierr = MPI_Waitall(sum_requests,recv_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 483 ierr = MPI_Waitall(sum_requests,send_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 484 485 /* determine the subsets I have to adapt (those having more than 1 cc) */ 486 ierr = PetscBTCreate(graph->n_subsets,&subset_cc_adapt);CHKERRQ(ierr); 487 ierr = PetscBTMemzero(graph->n_subsets,subset_cc_adapt);CHKERRQ(ierr); 488 for (i=0;i<graph->n_subsets;i++) { 489 if (graph->subset_ncc[i] > 1 || subset_has_corn[i]) { 490 ierr = PetscBTSet(subset_cc_adapt,i);CHKERRQ(ierr); 491 continue; 492 } 493 for (j=cum_recv_counts[i];j<cum_recv_counts[i+1];j++){ 494 if (recv_buffer_bool[j]) { 495 ierr = PetscBTSet(subset_cc_adapt,i);CHKERRQ(ierr); 496 break; 497 } 498 } 499 } 500 ierr = PetscFree(send_buffer_bool);CHKERRQ(ierr); 501 ierr = PetscFree(recv_buffer_bool);CHKERRQ(ierr); 502 ierr = PetscFree(subset_has_corn);CHKERRQ(ierr); 503 504 /* determine send/recv buffers sizes */ 505 j = 0; 506 mss = 0; 507 for (i=0;i<graph->n_subsets;i++) { 508 if (PetscBTLookup(subset_cc_adapt,i)) { 509 j += graph->subset_size[i]; 510 mss = PetscMax(graph->subset_size[i],mss); 511 } 512 } 513 k = 0; 514 mns = 0; 515 for (i=0;i<graph->n_subsets;i++) { 516 if (PetscBTLookup(subset_cc_adapt,i)) { 517 k += (cum_recv_counts[i+1]-cum_recv_counts[i])*graph->subset_size[i]; 518 mns = PetscMax(cum_recv_counts[i+1]-cum_recv_counts[i],mns); 519 } 520 } 521 ierr = PetscMalloc2(j,&send_buffer,k,&recv_buffer);CHKERRQ(ierr); 522 523 /* fill send buffer (order matters: subset_idxs ordered by global ordering) */ 524 j = 0; 525 for (i=0;i<graph->n_subsets;i++) 526 if (PetscBTLookup(subset_cc_adapt,i)) 527 for (k=0;k<graph->subset_size[i];k++) 528 send_buffer[j++] = labels[graph->subset_idxs[i][k]]; 529 530 /* now exchange the data */ 531 start_of_recv = 0; 532 start_of_send = 0; 533 sum_requests = 0; 534 for (i=0;i<graph->n_subsets;i++) { 535 if (PetscBTLookup(subset_cc_adapt,i)) { 536 PetscMPIInt neigh,tag; 537 PetscInt size_of_send = graph->subset_size[i]; 538 539 j = graph->subset_idxs[i][0]; 540 ierr = PetscMPIIntCast(2*graph->subset_ref_node[i]+1,&tag);CHKERRQ(ierr); 541 for (k=0;k<graph->count[j];k++) { 542 ierr = PetscMPIIntCast(graph->neighbours_set[j][k],&neigh);CHKERRQ(ierr); 543 ierr = MPI_Isend(&send_buffer[start_of_send],size_of_send,MPIU_INT,neigh,tag,interface_comm,&send_requests[sum_requests]);CHKERRQ(ierr); 544 ierr = MPI_Irecv(&recv_buffer[start_of_recv],size_of_send,MPIU_INT,neigh,tag,interface_comm,&recv_requests[sum_requests]);CHKERRQ(ierr); 545 start_of_recv += size_of_send; 546 sum_requests++; 547 } 548 start_of_send += size_of_send; 549 } 550 } 551 ierr = MPI_Waitall(sum_requests,recv_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 552 553 /* refine connected components */ 554 start_of_recv = 0; 555 /* allocate some temporary space */ 556 if (mss) { 557 ierr = PetscMalloc1(mss,&refine_buffer);CHKERRQ(ierr); 558 ierr = PetscMalloc2(mss*(mns+1),&refine_buffer[0],mss,&private_labels);CHKERRQ(ierr); 559 } 560 ncc = 0; 561 cum_queue = 0; 562 graph->cptr[0] = 0; 563 for (i=0;i<graph->n_subsets;i++) { 564 if (PetscBTLookup(subset_cc_adapt,i)) { 565 PetscInt subset_counter = 0; 566 PetscInt sharingprocs = cum_recv_counts[i+1]-cum_recv_counts[i]+1; /* count myself */ 567 PetscInt buffer_size = graph->subset_size[i]; 568 569 /* compute pointers */ 570 for (j=1;j<buffer_size;j++) refine_buffer[j] = refine_buffer[j-1] + sharingprocs; 571 /* analyze contributions from subdomains that share the i-th subset 572 The structure of refine_buffer is suitable to find intersections of ccs among sharingprocs. 573 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) 574 sharing procs connected components: 575 neigh 0: [0 1 4], [2 3], labels [4,7] (2 connected components) 576 neigh 1: [0 1], [2 3 4], labels [3 2] (2 connected components) 577 neigh 2: [0 4], [1], [2 3], labels [1 5 6] (3 connected components) 578 refine_buffer will be filled as: 579 [ 4, 3, 1; 580 4, 2, 1; 581 7, 2, 6; 582 4, 3, 5; 583 7, 2, 6; ]; 584 The connected components in local ordering are [0], [1], [2 3], [4] */ 585 /* fill temp_buffer */ 586 for (k=0;k<buffer_size;k++) refine_buffer[k][0] = labels[graph->subset_idxs[i][k]]; 587 for (j=0;j<sharingprocs-1;j++) { 588 for (k=0;k<buffer_size;k++) refine_buffer[k][j+1] = recv_buffer[start_of_recv+k]; 589 start_of_recv += buffer_size; 590 } 591 ierr = PetscMemzero(private_labels,buffer_size*sizeof(PetscInt));CHKERRQ(ierr); 592 for (j=0;j<buffer_size;j++) { 593 if (!private_labels[j]) { /* found a new cc */ 594 PetscBool same_set; 595 596 graph->cptr[ncc] = cum_queue; 597 ncc++; 598 subset_counter++; 599 private_labels[j] = subset_counter; 600 graph->queue[cum_queue++] = graph->subset_idxs[i][j]; 601 for (k=j+1;k<buffer_size;k++) { /* check for other nodes in new cc */ 602 same_set = PETSC_TRUE; 603 for (s=0;s<sharingprocs;s++) { 604 if (refine_buffer[j][s] != refine_buffer[k][s]) { 605 same_set = PETSC_FALSE; 606 break; 607 } 608 } 609 if (same_set) { 610 private_labels[k] = subset_counter; 611 graph->queue[cum_queue++] = graph->subset_idxs[i][k]; 612 } 613 } 614 } 615 } 616 graph->cptr[ncc] = cum_queue; 617 graph->subset_ncc[i] = subset_counter; 618 graph->queue_sorted = PETSC_FALSE; 619 } else { /* this subset does not need to be adapted */ 620 ierr = PetscMemcpy(graph->queue+cum_queue,graph->subset_idxs[i],graph->subset_size[i]*sizeof(PetscInt));CHKERRQ(ierr); 621 ncc++; 622 cum_queue += graph->subset_size[i]; 623 graph->cptr[ncc] = cum_queue; 624 } 625 } 626 graph->cptr[ncc] = cum_queue; 627 graph->ncc = ncc; 628 if (mss) { 629 ierr = PetscFree2(refine_buffer[0],private_labels);CHKERRQ(ierr); 630 ierr = PetscFree(refine_buffer);CHKERRQ(ierr); 631 } 632 ierr = PetscFree(labels);CHKERRQ(ierr); 633 ierr = MPI_Waitall(sum_requests,send_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 634 ierr = PetscFree2(send_requests,recv_requests);CHKERRQ(ierr); 635 ierr = PetscFree2(send_buffer,recv_buffer);CHKERRQ(ierr); 636 ierr = PetscFree(cum_recv_counts);CHKERRQ(ierr); 637 ierr = PetscBTDestroy(&subset_cc_adapt);CHKERRQ(ierr); 638 } 639 ierr = PetscBTDestroy(&cornerp);CHKERRQ(ierr); 640 641 /* Determine if we are in 2D or 3D */ 642 if (!graph->twodimset) { 643 PetscBool twodim = PETSC_TRUE; 644 for (i=0;i<graph->ncc;i++) { 645 PetscInt repdof = graph->queue[graph->cptr[i]]; 646 PetscInt ccsize = graph->cptr[i+1]-graph->cptr[i]; 647 if (graph->count[repdof] > 1 && ccsize > graph->custom_minimal_size) { 648 twodim = PETSC_FALSE; 649 break; 650 } 651 } 652 ierr = MPIU_Allreduce(&twodim,&graph->twodim,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)graph->l2gmap));CHKERRQ(ierr); 653 graph->twodimset = PETSC_TRUE; 654 } 655 PetscFunctionReturn(0); 656 } 657 658 659 PETSC_STATIC_INLINE PetscErrorCode PCBDDCGraphComputeCC_Private(PCBDDCGraph graph,PetscInt pid,PetscInt* queue_tip,PetscInt n_prev,PetscInt* n_added) 660 { 661 PetscInt i,j,n; 662 PetscInt *xadj = graph->xadj,*adjncy = graph->adjncy; 663 PetscBT touched = graph->touched; 664 PetscBool havecsr = (PetscBool)(!!xadj); 665 PetscBool havesubs = (PetscBool)(!!graph->n_local_subs); 666 PetscErrorCode ierr; 667 668 PetscFunctionBegin; 669 n = 0; 670 if (havecsr && !havesubs) { 671 for (i=-n_prev;i<0;i++) { 672 PetscInt start_dof = queue_tip[i]; 673 /* we assume that if a dof has a size 1 adjacency list and the corresponding entry is negative, it is connected to all dofs */ 674 if (xadj[start_dof+1]-xadj[start_dof] == 1 && adjncy[xadj[start_dof]] < 0) { 675 for (j=0;j<graph->subset_size[pid-1];j++) { /* pid \in [1,graph->n_subsets] */ 676 PetscInt dof = graph->subset_idxs[pid-1][j]; 677 if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid) { 678 ierr = PetscBTSet(touched,dof);CHKERRQ(ierr); 679 queue_tip[n] = dof; 680 n++; 681 } 682 } 683 } else { 684 for (j=xadj[start_dof];j<xadj[start_dof+1];j++) { 685 PetscInt dof = adjncy[j]; 686 if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid) { 687 ierr = PetscBTSet(touched,dof);CHKERRQ(ierr); 688 queue_tip[n] = dof; 689 n++; 690 } 691 } 692 } 693 } 694 } else if (havecsr && havesubs) { 695 PetscInt sid = graph->local_subs[queue_tip[-n_prev]]; 696 for (i=-n_prev;i<0;i++) { 697 PetscInt start_dof = queue_tip[i]; 698 /* 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 */ 699 if (xadj[start_dof+1]-xadj[start_dof] == 1 && adjncy[xadj[start_dof]] < 0) { 700 for (j=0;j<graph->subset_size[pid-1];j++) { /* pid \in [1,graph->n_subsets] */ 701 PetscInt dof = graph->subset_idxs[pid-1][j]; 702 if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid && graph->local_subs[dof] == sid) { 703 ierr = PetscBTSet(touched,dof);CHKERRQ(ierr); 704 queue_tip[n] = dof; 705 n++; 706 } 707 } 708 } else { 709 for (j=xadj[start_dof];j<xadj[start_dof+1];j++) { 710 PetscInt dof = adjncy[j]; 711 if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid && graph->local_subs[dof] == sid) { 712 ierr = PetscBTSet(touched,dof);CHKERRQ(ierr); 713 queue_tip[n] = dof; 714 n++; 715 } 716 } 717 } 718 } 719 } else if (havesubs) { /* sub info only */ 720 PetscInt sid = graph->local_subs[queue_tip[-n_prev]]; 721 for (j=0;j<graph->subset_size[pid-1];j++) { /* pid \in [1,graph->n_subsets] */ 722 PetscInt dof = graph->subset_idxs[pid-1][j]; 723 if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid && graph->local_subs[dof] == sid) { 724 ierr = PetscBTSet(touched,dof);CHKERRQ(ierr); 725 queue_tip[n] = dof; 726 n++; 727 } 728 } 729 } else { 730 for (j=0;j<graph->subset_size[pid-1];j++) { /* pid \in [1,graph->n_subsets] */ 731 PetscInt dof = graph->subset_idxs[pid-1][j]; 732 if (!PetscBTLookup(touched,dof) && graph->subset[dof] == pid) { 733 ierr = PetscBTSet(touched,dof);CHKERRQ(ierr); 734 queue_tip[n] = dof; 735 n++; 736 } 737 } 738 } 739 *n_added = n; 740 PetscFunctionReturn(0); 741 } 742 743 PetscErrorCode PCBDDCGraphComputeConnectedComponentsLocal(PCBDDCGraph graph) 744 { 745 PetscInt ncc,cum_queue,n; 746 PetscMPIInt commsize; 747 PetscErrorCode ierr; 748 749 PetscFunctionBegin; 750 if (!graph->setupcalled) SETERRQ(PetscObjectComm((PetscObject)graph->l2gmap),PETSC_ERR_ORDER,"PCBDDCGraphSetUp should be called first"); 751 /* quiet return if there isn't any local info */ 752 if (!graph->xadj && !graph->n_local_subs) { 753 PetscFunctionReturn(0); 754 } 755 756 /* reset any previous search of connected components */ 757 ierr = PetscBTMemzero(graph->nvtxs,graph->touched);CHKERRQ(ierr); 758 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)graph->l2gmap),&commsize);CHKERRQ(ierr); 759 if (commsize > graph->commsizelimit) { 760 PetscInt i; 761 for (i=0;i<graph->nvtxs;i++) { 762 if (graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK || !graph->count[i]) { 763 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 764 } 765 } 766 } 767 768 /* begin search for connected components */ 769 cum_queue = 0; 770 ncc = 0; 771 for (n=0;n<graph->n_subsets;n++) { 772 PetscInt pid = n+1; /* partition labeled by 0 is discarded */ 773 PetscInt found = 0,prev = 0,first = 0,ncc_pid = 0; 774 while (found != graph->subset_size[n]) { 775 PetscInt added = 0; 776 if (!prev) { /* search for new starting dof */ 777 while (PetscBTLookup(graph->touched,graph->subset_idxs[n][first])) first++; 778 ierr = PetscBTSet(graph->touched,graph->subset_idxs[n][first]);CHKERRQ(ierr); 779 graph->queue[cum_queue] = graph->subset_idxs[n][first]; 780 graph->cptr[ncc] = cum_queue; 781 prev = 1; 782 cum_queue++; 783 found++; 784 ncc_pid++; 785 ncc++; 786 } 787 ierr = PCBDDCGraphComputeCC_Private(graph,pid,graph->queue + cum_queue,prev,&added);CHKERRQ(ierr); 788 if (!added) { 789 graph->subset_ncc[n] = ncc_pid; 790 graph->cptr[ncc] = cum_queue; 791 } 792 prev = added; 793 found += added; 794 cum_queue += added; 795 if (added && found == graph->subset_size[n]) { 796 graph->subset_ncc[n] = ncc_pid; 797 graph->cptr[ncc] = cum_queue; 798 } 799 } 800 } 801 graph->ncc = ncc; 802 graph->queue_sorted = PETSC_FALSE; 803 PetscFunctionReturn(0); 804 } 805 806 PetscErrorCode PCBDDCGraphSetUp(PCBDDCGraph graph, PetscInt custom_minimal_size, IS neumann_is, IS dirichlet_is, PetscInt n_ISForDofs, IS ISForDofs[], IS custom_primal_vertices) 807 { 808 IS subset,subset_n; 809 MPI_Comm comm; 810 const PetscInt *is_indices; 811 PetscInt n_neigh,*neigh,*n_shared,**shared,*queue_global; 812 PetscInt i,j,k,s,total_counts,nodes_touched,is_size; 813 PetscMPIInt commsize; 814 PetscBool same_set,mirrors_found; 815 PetscErrorCode ierr; 816 817 PetscFunctionBegin; 818 PetscValidLogicalCollectiveInt(graph->l2gmap,custom_minimal_size,2); 819 if (neumann_is) { 820 PetscValidHeaderSpecific(neumann_is,IS_CLASSID,3); 821 PetscCheckSameComm(graph->l2gmap,1,neumann_is,3); 822 } 823 graph->has_dirichlet = PETSC_FALSE; 824 if (dirichlet_is) { 825 PetscValidHeaderSpecific(dirichlet_is,IS_CLASSID,4); 826 PetscCheckSameComm(graph->l2gmap,1,dirichlet_is,4); 827 graph->has_dirichlet = PETSC_TRUE; 828 } 829 PetscValidLogicalCollectiveInt(graph->l2gmap,n_ISForDofs,5); 830 for (i=0;i<n_ISForDofs;i++) { 831 PetscValidHeaderSpecific(ISForDofs[i],IS_CLASSID,6); 832 PetscCheckSameComm(graph->l2gmap,1,ISForDofs[i],6); 833 } 834 if (custom_primal_vertices) { 835 PetscValidHeaderSpecific(custom_primal_vertices,IS_CLASSID,7); 836 PetscCheckSameComm(graph->l2gmap,1,custom_primal_vertices,7); 837 } 838 ierr = PetscObjectGetComm((PetscObject)(graph->l2gmap),&comm);CHKERRQ(ierr); 839 ierr = MPI_Comm_size(comm,&commsize);CHKERRQ(ierr); 840 841 /* custom_minimal_size */ 842 graph->custom_minimal_size = custom_minimal_size; 843 /* get info l2gmap and allocate work vectors */ 844 ierr = ISLocalToGlobalMappingGetInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);CHKERRQ(ierr); 845 /* check if we have any local periodic nodes (periodic BCs) */ 846 mirrors_found = PETSC_FALSE; 847 if (graph->nvtxs && n_neigh) { 848 for (i=0; i<n_shared[0]; i++) graph->count[shared[0][i]] += 1; 849 for (i=0; i<n_shared[0]; i++) { 850 if (graph->count[shared[0][i]] > 1) { 851 mirrors_found = PETSC_TRUE; 852 break; 853 } 854 } 855 } 856 /* compute local mirrors (if any) */ 857 if (mirrors_found) { 858 IS to,from; 859 PetscInt *local_indices,*global_indices; 860 861 ierr = ISCreateStride(PETSC_COMM_SELF,graph->nvtxs,0,1,&to);CHKERRQ(ierr); 862 ierr = ISLocalToGlobalMappingApplyIS(graph->l2gmap,to,&from);CHKERRQ(ierr); 863 /* get arrays of local and global indices */ 864 ierr = PetscMalloc1(graph->nvtxs,&local_indices);CHKERRQ(ierr); 865 ierr = ISGetIndices(to,(const PetscInt**)&is_indices);CHKERRQ(ierr); 866 ierr = PetscMemcpy(local_indices,is_indices,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 867 ierr = ISRestoreIndices(to,(const PetscInt**)&is_indices);CHKERRQ(ierr); 868 ierr = PetscMalloc1(graph->nvtxs,&global_indices);CHKERRQ(ierr); 869 ierr = ISGetIndices(from,(const PetscInt**)&is_indices);CHKERRQ(ierr); 870 ierr = PetscMemcpy(global_indices,is_indices,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 871 ierr = ISRestoreIndices(from,(const PetscInt**)&is_indices);CHKERRQ(ierr); 872 /* allocate space for mirrors */ 873 ierr = PetscMalloc2(graph->nvtxs,&graph->mirrors,graph->nvtxs,&graph->mirrors_set);CHKERRQ(ierr); 874 ierr = PetscMemzero(graph->mirrors,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 875 graph->mirrors_set[0] = 0; 876 877 k=0; 878 for (i=0;i<n_shared[0];i++) { 879 j=shared[0][i]; 880 if (graph->count[j] > 1) { 881 graph->mirrors[j]++; 882 k++; 883 } 884 } 885 /* allocate space for set of mirrors */ 886 ierr = PetscMalloc1(k,&graph->mirrors_set[0]);CHKERRQ(ierr); 887 for (i=1;i<graph->nvtxs;i++) 888 graph->mirrors_set[i]=graph->mirrors_set[i-1]+graph->mirrors[i-1]; 889 890 /* fill arrays */ 891 ierr = PetscMemzero(graph->mirrors,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 892 for (j=0;j<n_shared[0];j++) { 893 i=shared[0][j]; 894 if (graph->count[i] > 1) 895 graph->mirrors_set[i][graph->mirrors[i]++]=global_indices[i]; 896 } 897 ierr = PetscSortIntWithArray(graph->nvtxs,global_indices,local_indices);CHKERRQ(ierr); 898 for (i=0;i<graph->nvtxs;i++) { 899 if (graph->mirrors[i] > 0) { 900 ierr = PetscFindInt(graph->mirrors_set[i][0],graph->nvtxs,global_indices,&k);CHKERRQ(ierr); 901 j = global_indices[k]; 902 while ( k > 0 && global_indices[k-1] == j) k--; 903 for (j=0;j<graph->mirrors[i];j++) { 904 graph->mirrors_set[i][j]=local_indices[k+j]; 905 } 906 ierr = PetscSortInt(graph->mirrors[i],graph->mirrors_set[i]);CHKERRQ(ierr); 907 } 908 } 909 ierr = PetscFree(local_indices);CHKERRQ(ierr); 910 ierr = PetscFree(global_indices);CHKERRQ(ierr); 911 ierr = ISDestroy(&to);CHKERRQ(ierr); 912 ierr = ISDestroy(&from);CHKERRQ(ierr); 913 } 914 ierr = PetscMemzero(graph->count,graph->nvtxs*sizeof(*graph->count));CHKERRQ(ierr); 915 916 /* Count total number of neigh per node */ 917 k = 0; 918 for (i=1;i<n_neigh;i++) { 919 k += n_shared[i]; 920 for (j=0;j<n_shared[i];j++) { 921 graph->count[shared[i][j]] += 1; 922 } 923 } 924 /* Allocate space for storing the set of neighbours for each node */ 925 if (graph->nvtxs) { 926 ierr = PetscMalloc1(k,&graph->neighbours_set[0]);CHKERRQ(ierr); 927 } 928 for (i=1;i<graph->nvtxs;i++) { /* dont count myself */ 929 graph->neighbours_set[i]=graph->neighbours_set[i-1]+graph->count[i-1]; 930 } 931 /* Get information for sharing subdomains */ 932 ierr = PetscMemzero(graph->count,graph->nvtxs*sizeof(*graph->count));CHKERRQ(ierr); 933 for (i=1;i<n_neigh;i++) { /* dont count myself */ 934 s = n_shared[i]; 935 for (j=0;j<s;j++) { 936 k = shared[i][j]; 937 graph->neighbours_set[k][graph->count[k]] = neigh[i]; 938 graph->count[k] += 1; 939 } 940 } 941 /* sort set of sharing subdomains */ 942 for (i=0;i<graph->nvtxs;i++) { 943 ierr = PetscSortRemoveDupsInt(&graph->count[i],graph->neighbours_set[i]);CHKERRQ(ierr); 944 } 945 /* free memory allocated by ISLocalToGlobalMappingGetInfo */ 946 ierr = ISLocalToGlobalMappingRestoreInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);CHKERRQ(ierr); 947 948 /* 949 Get info for dofs splitting 950 User can specify just a subset; an additional field is considered as a complementary field 951 */ 952 for (i=0,k=0;i<n_ISForDofs;i++) { 953 PetscInt bs; 954 955 ierr = ISGetBlockSize(ISForDofs[i],&bs);CHKERRQ(ierr); 956 k += bs; 957 } 958 for (i=0;i<graph->nvtxs;i++) graph->which_dof[i] = k; /* by default a dof belongs to the complement set */ 959 for (i=0,k=0;i<n_ISForDofs;i++) { 960 PetscInt bs; 961 962 ierr = ISGetLocalSize(ISForDofs[i],&is_size);CHKERRQ(ierr); 963 ierr = ISGetBlockSize(ISForDofs[i],&bs);CHKERRQ(ierr); 964 ierr = ISGetIndices(ISForDofs[i],(const PetscInt**)&is_indices);CHKERRQ(ierr); 965 for (j=0;j<is_size/bs;j++) { 966 PetscInt b; 967 968 for (b=0;b<bs;b++) { 969 PetscInt jj = bs*j + b; 970 971 if (is_indices[jj] > -1 && is_indices[jj] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */ 972 graph->which_dof[is_indices[jj]] = k+b; 973 } 974 } 975 } 976 ierr = ISRestoreIndices(ISForDofs[i],(const PetscInt**)&is_indices);CHKERRQ(ierr); 977 k += bs; 978 } 979 980 /* Take into account Neumann nodes */ 981 if (neumann_is) { 982 ierr = ISGetLocalSize(neumann_is,&is_size);CHKERRQ(ierr); 983 ierr = ISGetIndices(neumann_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); 984 for (i=0;i<is_size;i++) { 985 if (is_indices[i] > -1 && is_indices[i] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */ 986 graph->special_dof[is_indices[i]] = PCBDDCGRAPH_NEUMANN_MARK; 987 } 988 } 989 ierr = ISRestoreIndices(neumann_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); 990 } 991 /* Take into account Dirichlet nodes (they overwrite any neumann boundary mark previously set) */ 992 if (dirichlet_is) { 993 ierr = ISGetLocalSize(dirichlet_is,&is_size);CHKERRQ(ierr); 994 ierr = ISGetIndices(dirichlet_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); 995 for (i=0;i<is_size;i++){ 996 if (is_indices[i] > -1 && is_indices[i] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */ 997 if (commsize > graph->commsizelimit) { /* dirichlet nodes treated as internal */ 998 ierr = PetscBTSet(graph->touched,is_indices[i]);CHKERRQ(ierr); 999 graph->subset[is_indices[i]] = 0; 1000 } 1001 graph->special_dof[is_indices[i]] = PCBDDCGRAPH_DIRICHLET_MARK; 1002 } 1003 } 1004 ierr = ISRestoreIndices(dirichlet_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); 1005 } 1006 /* mark local periodic nodes (if any) and adapt CSR graph (if any) */ 1007 if (graph->mirrors) { 1008 for (i=0;i<graph->nvtxs;i++) 1009 if (graph->mirrors[i]) 1010 graph->special_dof[i] = PCBDDCGRAPH_LOCAL_PERIODIC_MARK; 1011 1012 if (graph->xadj) { 1013 PetscInt *new_xadj,*new_adjncy; 1014 /* sort CSR graph */ 1015 for (i=0;i<graph->nvtxs;i++) 1016 ierr = PetscSortInt(graph->xadj[i+1]-graph->xadj[i],&graph->adjncy[graph->xadj[i]]);CHKERRQ(ierr); 1017 1018 /* adapt local CSR graph in case of local periodicity */ 1019 k = 0; 1020 for (i=0;i<graph->nvtxs;i++) 1021 for (j=graph->xadj[i];j<graph->xadj[i+1];j++) 1022 k += graph->mirrors[graph->adjncy[j]]; 1023 1024 ierr = PetscMalloc1(graph->nvtxs+1,&new_xadj);CHKERRQ(ierr); 1025 ierr = PetscMalloc1(k+graph->xadj[graph->nvtxs],&new_adjncy);CHKERRQ(ierr); 1026 new_xadj[0] = 0; 1027 for (i=0;i<graph->nvtxs;i++) { 1028 k = graph->xadj[i+1]-graph->xadj[i]; 1029 ierr = PetscMemcpy(&new_adjncy[new_xadj[i]],&graph->adjncy[graph->xadj[i]],k*sizeof(PetscInt));CHKERRQ(ierr); 1030 new_xadj[i+1] = new_xadj[i]+k; 1031 for (j=graph->xadj[i];j<graph->xadj[i+1];j++) { 1032 k = graph->mirrors[graph->adjncy[j]]; 1033 ierr = PetscMemcpy(&new_adjncy[new_xadj[i+1]],graph->mirrors_set[graph->adjncy[j]],k*sizeof(PetscInt));CHKERRQ(ierr); 1034 new_xadj[i+1] += k; 1035 } 1036 k = new_xadj[i+1]-new_xadj[i]; 1037 ierr = PetscSortRemoveDupsInt(&k,&new_adjncy[new_xadj[i]]);CHKERRQ(ierr); 1038 new_xadj[i+1] = new_xadj[i]+k; 1039 } 1040 /* set new CSR into graph */ 1041 ierr = PetscFree(graph->xadj);CHKERRQ(ierr); 1042 ierr = PetscFree(graph->adjncy);CHKERRQ(ierr); 1043 graph->xadj = new_xadj; 1044 graph->adjncy = new_adjncy; 1045 } 1046 } 1047 1048 /* mark special nodes (if any) -> each will become a single node equivalence class */ 1049 if (custom_primal_vertices) { 1050 ierr = ISGetLocalSize(custom_primal_vertices,&is_size);CHKERRQ(ierr); 1051 ierr = ISGetIndices(custom_primal_vertices,(const PetscInt**)&is_indices);CHKERRQ(ierr); 1052 for (i=0,j=0;i<is_size;i++){ 1053 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 */ 1054 graph->special_dof[is_indices[i]] = PCBDDCGRAPH_SPECIAL_MARK-j; 1055 j++; 1056 } 1057 } 1058 ierr = ISRestoreIndices(custom_primal_vertices,(const PetscInt**)&is_indices);CHKERRQ(ierr); 1059 } 1060 1061 /* mark interior nodes (if commsize > graph->commsizelimit) as touched and belonging to partition number 0 */ 1062 if (commsize > graph->commsizelimit) { 1063 for (i=0;i<graph->nvtxs;i++) { 1064 if (!graph->count[i]) { 1065 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 1066 graph->subset[i] = 0; 1067 } 1068 } 1069 } 1070 1071 /* init graph structure and compute default subsets */ 1072 nodes_touched = 0; 1073 for (i=0;i<graph->nvtxs;i++) { 1074 if (PetscBTLookup(graph->touched,i)) { 1075 nodes_touched++; 1076 } 1077 } 1078 i = 0; 1079 graph->ncc = 0; 1080 total_counts = 0; 1081 1082 /* allocated space for queues */ 1083 if (commsize == graph->commsizelimit) { 1084 ierr = PetscMalloc2(graph->nvtxs+1,&graph->cptr,graph->nvtxs,&graph->queue);CHKERRQ(ierr); 1085 } else { 1086 PetscInt nused = graph->nvtxs - nodes_touched; 1087 ierr = PetscMalloc2(nused+1,&graph->cptr,nused,&graph->queue);CHKERRQ(ierr); 1088 } 1089 1090 while (nodes_touched<graph->nvtxs) { 1091 /* find first untouched node in local ordering */ 1092 while (PetscBTLookup(graph->touched,i)) i++; 1093 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 1094 graph->subset[i] = graph->ncc+1; 1095 graph->cptr[graph->ncc] = total_counts; 1096 graph->queue[total_counts] = i; 1097 total_counts++; 1098 nodes_touched++; 1099 /* now find all other nodes having the same set of sharing subdomains */ 1100 for (j=i+1;j<graph->nvtxs;j++) { 1101 /* check for same number of sharing subdomains, dof number and same special mark */ 1102 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]) { 1103 /* check for same set of sharing subdomains */ 1104 same_set = PETSC_TRUE; 1105 for (k=0;k<graph->count[j];k++){ 1106 if (graph->neighbours_set[i][k] != graph->neighbours_set[j][k]) { 1107 same_set = PETSC_FALSE; 1108 } 1109 } 1110 /* I have found a friend of mine */ 1111 if (same_set) { 1112 ierr = PetscBTSet(graph->touched,j);CHKERRQ(ierr); 1113 graph->subset[j] = graph->ncc+1; 1114 nodes_touched++; 1115 graph->queue[total_counts] = j; 1116 total_counts++; 1117 } 1118 } 1119 } 1120 graph->ncc++; 1121 } 1122 /* 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 */ 1123 graph->n_subsets = graph->ncc; 1124 ierr = PetscMalloc1(graph->n_subsets,&graph->subset_ncc);CHKERRQ(ierr); 1125 for (i=0;i<graph->n_subsets;i++) { 1126 graph->subset_ncc[i] = 1; 1127 } 1128 /* final pointer */ 1129 graph->cptr[graph->ncc] = total_counts; 1130 1131 /* For consistency reasons (among neighbours), I need to sort (by global ordering) each connected component */ 1132 /* Get a reference node (min index in global ordering) for each subset for tagging messages */ 1133 ierr = PetscMalloc1(graph->ncc,&graph->subset_ref_node);CHKERRQ(ierr); 1134 ierr = PetscMalloc1(graph->cptr[graph->ncc],&queue_global);CHKERRQ(ierr); 1135 ierr = ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_global);CHKERRQ(ierr); 1136 for (j=0;j<graph->ncc;j++) { 1137 ierr = PetscSortIntWithArray(graph->cptr[j+1]-graph->cptr[j],&queue_global[graph->cptr[j]],&graph->queue[graph->cptr[j]]);CHKERRQ(ierr); 1138 graph->subset_ref_node[j] = graph->queue[graph->cptr[j]]; 1139 } 1140 ierr = PetscFree(queue_global);CHKERRQ(ierr); 1141 graph->queue_sorted = PETSC_TRUE; 1142 1143 /* save information on subsets (needed when analyzing the connected components) */ 1144 if (graph->ncc) { 1145 ierr = PetscMalloc2(graph->ncc,&graph->subset_size,graph->ncc,&graph->subset_idxs);CHKERRQ(ierr); 1146 ierr = PetscMalloc1(graph->cptr[graph->ncc],&graph->subset_idxs[0]);CHKERRQ(ierr); 1147 ierr = PetscMemzero(graph->subset_idxs[0],graph->cptr[graph->ncc]*sizeof(PetscInt));CHKERRQ(ierr); 1148 for (j=1;j<graph->ncc;j++) { 1149 graph->subset_size[j-1] = graph->cptr[j] - graph->cptr[j-1]; 1150 graph->subset_idxs[j] = graph->subset_idxs[j-1] + graph->subset_size[j-1]; 1151 } 1152 graph->subset_size[graph->ncc-1] = graph->cptr[graph->ncc] - graph->cptr[graph->ncc-1]; 1153 ierr = PetscMemcpy(graph->subset_idxs[0],graph->queue,graph->cptr[graph->ncc]*sizeof(PetscInt));CHKERRQ(ierr); 1154 } 1155 1156 /* renumber reference nodes */ 1157 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)(graph->l2gmap)),graph->ncc,graph->subset_ref_node,PETSC_COPY_VALUES,&subset_n);CHKERRQ(ierr); 1158 ierr = ISLocalToGlobalMappingApplyIS(graph->l2gmap,subset_n,&subset);CHKERRQ(ierr); 1159 ierr = ISDestroy(&subset_n);CHKERRQ(ierr); 1160 ierr = ISRenumber(subset,NULL,NULL,&subset_n);CHKERRQ(ierr); 1161 ierr = ISDestroy(&subset);CHKERRQ(ierr); 1162 ierr = ISGetLocalSize(subset_n,&k);CHKERRQ(ierr); 1163 if (k != graph->ncc) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Invalid size of new subset! %D != %D",k,graph->ncc); 1164 ierr = ISGetIndices(subset_n,&is_indices);CHKERRQ(ierr); 1165 ierr = PetscMemcpy(graph->subset_ref_node,is_indices,graph->ncc*sizeof(PetscInt));CHKERRQ(ierr); 1166 ierr = ISRestoreIndices(subset_n,&is_indices);CHKERRQ(ierr); 1167 ierr = ISDestroy(&subset_n);CHKERRQ(ierr); 1168 1169 /* free workspace */ 1170 graph->setupcalled = PETSC_TRUE; 1171 PetscFunctionReturn(0); 1172 } 1173 1174 PetscErrorCode PCBDDCGraphResetCoords(PCBDDCGraph graph) 1175 { 1176 PetscErrorCode ierr; 1177 1178 PetscFunctionBegin; 1179 if (!graph) PetscFunctionReturn(0); 1180 ierr = PetscFree(graph->coords);CHKERRQ(ierr); 1181 graph->cdim = 0; 1182 graph->cnloc = 0; 1183 graph->cloc = PETSC_FALSE; 1184 PetscFunctionReturn(0); 1185 } 1186 1187 PetscErrorCode PCBDDCGraphResetCSR(PCBDDCGraph graph) 1188 { 1189 PetscErrorCode ierr; 1190 1191 PetscFunctionBegin; 1192 if (!graph) PetscFunctionReturn(0); 1193 if (graph->freecsr) { 1194 ierr = PetscFree(graph->xadj);CHKERRQ(ierr); 1195 ierr = PetscFree(graph->adjncy);CHKERRQ(ierr); 1196 } else { 1197 graph->xadj = NULL; 1198 graph->adjncy = NULL; 1199 } 1200 graph->freecsr = PETSC_FALSE; 1201 graph->nvtxs_csr = 0; 1202 PetscFunctionReturn(0); 1203 } 1204 1205 PetscErrorCode PCBDDCGraphReset(PCBDDCGraph graph) 1206 { 1207 PetscErrorCode ierr; 1208 1209 PetscFunctionBegin; 1210 if (!graph) PetscFunctionReturn(0); 1211 ierr = ISLocalToGlobalMappingDestroy(&graph->l2gmap);CHKERRQ(ierr); 1212 ierr = PetscFree(graph->subset_ncc);CHKERRQ(ierr); 1213 ierr = PetscFree(graph->subset_ref_node);CHKERRQ(ierr); 1214 if (graph->nvtxs) { 1215 ierr = PetscFree(graph->neighbours_set[0]);CHKERRQ(ierr); 1216 } 1217 ierr = PetscBTDestroy(&graph->touched);CHKERRQ(ierr); 1218 ierr = PetscFree5(graph->count, 1219 graph->neighbours_set, 1220 graph->subset, 1221 graph->which_dof, 1222 graph->special_dof);CHKERRQ(ierr); 1223 ierr = PetscFree2(graph->cptr,graph->queue);CHKERRQ(ierr); 1224 if (graph->mirrors) { 1225 ierr = PetscFree(graph->mirrors_set[0]);CHKERRQ(ierr); 1226 } 1227 ierr = PetscFree2(graph->mirrors,graph->mirrors_set);CHKERRQ(ierr); 1228 if (graph->subset_idxs) { 1229 ierr = PetscFree(graph->subset_idxs[0]);CHKERRQ(ierr); 1230 } 1231 ierr = PetscFree2(graph->subset_size,graph->subset_idxs);CHKERRQ(ierr); 1232 ierr = ISDestroy(&graph->dirdofs);CHKERRQ(ierr); 1233 ierr = ISDestroy(&graph->dirdofsB);CHKERRQ(ierr); 1234 if (graph->n_local_subs) { 1235 ierr = PetscFree(graph->local_subs);CHKERRQ(ierr); 1236 } 1237 graph->has_dirichlet = PETSC_FALSE; 1238 graph->twodimset = PETSC_FALSE; 1239 graph->twodim = PETSC_FALSE; 1240 graph->nvtxs = 0; 1241 graph->nvtxs_global = 0; 1242 graph->n_subsets = 0; 1243 graph->custom_minimal_size = 1; 1244 graph->n_local_subs = 0; 1245 graph->maxcount = PETSC_MAX_INT; 1246 graph->setupcalled = PETSC_FALSE; 1247 PetscFunctionReturn(0); 1248 } 1249 1250 PetscErrorCode PCBDDCGraphInit(PCBDDCGraph graph, ISLocalToGlobalMapping l2gmap, PetscInt N, PetscInt maxcount) 1251 { 1252 PetscInt n; 1253 PetscErrorCode ierr; 1254 1255 PetscFunctionBegin; 1256 PetscValidPointer(graph,1); 1257 PetscValidHeaderSpecific(l2gmap,IS_LTOGM_CLASSID,2); 1258 PetscValidLogicalCollectiveInt(l2gmap,N,3); 1259 PetscValidLogicalCollectiveInt(l2gmap,maxcount,4); 1260 /* raise an error if already allocated */ 1261 if (graph->nvtxs_global) SETERRQ(PetscObjectComm((PetscObject)l2gmap),PETSC_ERR_PLIB,"BDDCGraph already initialized"); 1262 /* set number of vertices */ 1263 ierr = PetscObjectReference((PetscObject)l2gmap);CHKERRQ(ierr); 1264 graph->l2gmap = l2gmap; 1265 ierr = ISLocalToGlobalMappingGetSize(l2gmap,&n);CHKERRQ(ierr); 1266 graph->nvtxs = n; 1267 graph->nvtxs_global = N; 1268 /* allocate used space */ 1269 ierr = PetscBTCreate(graph->nvtxs,&graph->touched);CHKERRQ(ierr); 1270 ierr = PetscMalloc5(graph->nvtxs,&graph->count, 1271 graph->nvtxs,&graph->neighbours_set, 1272 graph->nvtxs,&graph->subset, 1273 graph->nvtxs,&graph->which_dof, 1274 graph->nvtxs,&graph->special_dof);CHKERRQ(ierr); 1275 /* zeroes memory */ 1276 ierr = PetscMemzero(graph->count,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 1277 ierr = PetscMemzero(graph->subset,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 1278 /* use -1 as a default value for which_dof array */ 1279 for (n=0;n<graph->nvtxs;n++) graph->which_dof[n] = -1; 1280 ierr = PetscMemzero(graph->special_dof,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 1281 /* zeroes first pointer to neighbour set */ 1282 if (graph->nvtxs) { 1283 graph->neighbours_set[0] = 0; 1284 } 1285 /* zeroes workspace for values of ncc */ 1286 graph->subset_ncc = 0; 1287 graph->subset_ref_node = 0; 1288 /* maxcount for cc */ 1289 graph->maxcount = maxcount; 1290 PetscFunctionReturn(0); 1291 } 1292 1293 PetscErrorCode PCBDDCGraphDestroy(PCBDDCGraph* graph) 1294 { 1295 PetscErrorCode ierr; 1296 1297 PetscFunctionBegin; 1298 ierr = PCBDDCGraphResetCSR(*graph);CHKERRQ(ierr); 1299 ierr = PCBDDCGraphResetCoords(*graph);CHKERRQ(ierr); 1300 ierr = PCBDDCGraphReset(*graph);CHKERRQ(ierr); 1301 ierr = PetscFree(*graph);CHKERRQ(ierr); 1302 PetscFunctionReturn(0); 1303 } 1304 1305 PetscErrorCode PCBDDCGraphCreate(PCBDDCGraph *graph) 1306 { 1307 PCBDDCGraph new_graph; 1308 PetscErrorCode ierr; 1309 1310 PetscFunctionBegin; 1311 ierr = PetscNew(&new_graph);CHKERRQ(ierr); 1312 new_graph->custom_minimal_size = 1; 1313 new_graph->commsizelimit = 1; 1314 *graph = new_graph; 1315 PetscFunctionReturn(0); 1316 } 1317