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 #undef __FUNCT__ 6 #define __FUNCT__ "PCBDDCGraphGetDirichletDofsB" 7 PetscErrorCode PCBDDCGraphGetDirichletDofsB(PCBDDCGraph graph, IS* dirdofs) 8 { 9 PetscErrorCode ierr; 10 11 PetscFunctionBegin; 12 if (graph->dirdofsB) { 13 ierr = PetscObjectReference((PetscObject)graph->dirdofsB);CHKERRQ(ierr); 14 } else if (graph->has_dirichlet) { 15 PetscInt i,size; 16 PetscInt *dirdofs_idxs; 17 18 size = 0; 19 for (i=0;i<graph->nvtxs;i++) { 20 if (graph->count[i] && graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) size++; 21 } 22 23 ierr = PetscMalloc1(size,&dirdofs_idxs);CHKERRQ(ierr); 24 size = 0; 25 for (i=0;i<graph->nvtxs;i++) { 26 if (graph->count[i] && graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) dirdofs_idxs[size++] = i; 27 } 28 ierr = ISCreateGeneral(PETSC_COMM_SELF,size,dirdofs_idxs,PETSC_OWN_POINTER,&graph->dirdofsB);CHKERRQ(ierr); 29 ierr = PetscObjectReference((PetscObject)graph->dirdofsB);CHKERRQ(ierr); 30 } 31 *dirdofs = graph->dirdofsB; 32 PetscFunctionReturn(0); 33 } 34 35 #undef __FUNCT__ 36 #define __FUNCT__ "PCBDDCGraphGetDirichletDofs" 37 PetscErrorCode PCBDDCGraphGetDirichletDofs(PCBDDCGraph graph, IS* dirdofs) 38 { 39 PetscErrorCode ierr; 40 41 PetscFunctionBegin; 42 if (graph->dirdofs) { 43 ierr = PetscObjectReference((PetscObject)graph->dirdofs);CHKERRQ(ierr); 44 } else if (graph->has_dirichlet) { 45 PetscInt i,size; 46 PetscInt *dirdofs_idxs; 47 48 size = 0; 49 for (i=0;i<graph->nvtxs;i++) { 50 if (graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) size++; 51 } 52 53 ierr = PetscMalloc1(size,&dirdofs_idxs);CHKERRQ(ierr); 54 size = 0; 55 for (i=0;i<graph->nvtxs;i++) { 56 if (graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) dirdofs_idxs[size++] = i; 57 } 58 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)graph->l2gmap),size,dirdofs_idxs,PETSC_OWN_POINTER,&graph->dirdofs);CHKERRQ(ierr); 59 ierr = PetscObjectReference((PetscObject)graph->dirdofs);CHKERRQ(ierr); 60 } 61 *dirdofs = graph->dirdofs; 62 PetscFunctionReturn(0); 63 } 64 65 #undef __FUNCT__ 66 #define __FUNCT__ "PCBDDCGraphASCIIView" 67 PetscErrorCode PCBDDCGraphASCIIView(PCBDDCGraph graph, PetscInt verbosity_level, PetscViewer viewer) 68 { 69 PetscInt i,j,tabs; 70 PetscInt* queue_in_global_numbering; 71 PetscErrorCode ierr; 72 73 PetscFunctionBegin; 74 ierr = PetscViewerASCIIPushSynchronized(viewer);CHKERRQ(ierr); 75 ierr = PetscViewerASCIIGetTab(viewer,&tabs);CHKERRQ(ierr); 76 ierr = PetscViewerASCIIPrintf(viewer,"--------------------------------------------------\n");CHKERRQ(ierr); 77 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 78 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Local BDDC graph for subdomain %04d\n",PetscGlobalRank);CHKERRQ(ierr); 79 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Number of vertices %d\n",graph->nvtxs);CHKERRQ(ierr); 80 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Custom minimal size %d\n",graph->custom_minimal_size);CHKERRQ(ierr); 81 if (verbosity_level > 1) { 82 for (i=0;i<graph->nvtxs;i++) { 83 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"%d:\n",i);CHKERRQ(ierr); 84 ierr = PetscViewerASCIISynchronizedPrintf(viewer," which_dof: %d\n",graph->which_dof[i]);CHKERRQ(ierr); 85 ierr = PetscViewerASCIISynchronizedPrintf(viewer," special_dof: %d\n",graph->special_dof[i]);CHKERRQ(ierr); 86 ierr = PetscViewerASCIISynchronizedPrintf(viewer," neighbours: %d\n",graph->count[i]);CHKERRQ(ierr); 87 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 88 if (graph->count[i]) { 89 ierr = PetscViewerASCIISynchronizedPrintf(viewer," set of neighbours:");CHKERRQ(ierr); 90 for (j=0;j<graph->count[i];j++) { 91 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->neighbours_set[i][j]);CHKERRQ(ierr); 92 } 93 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"\n");CHKERRQ(ierr); 94 } 95 ierr = PetscViewerASCIISetTab(viewer,tabs);CHKERRQ(ierr); 96 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 97 if (graph->mirrors) { 98 ierr = PetscViewerASCIISynchronizedPrintf(viewer," mirrors: %d\n",graph->mirrors[i]);CHKERRQ(ierr); 99 if (graph->mirrors[i]) { 100 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 101 ierr = PetscViewerASCIISynchronizedPrintf(viewer," set of mirrors:");CHKERRQ(ierr); 102 for (j=0;j<graph->mirrors[i];j++) { 103 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->mirrors_set[i][j]);CHKERRQ(ierr); 104 } 105 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"\n");CHKERRQ(ierr); 106 ierr = PetscViewerASCIISetTab(viewer,tabs);CHKERRQ(ierr); 107 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 108 } 109 } 110 if (verbosity_level > 2) { 111 if (graph->xadj && graph->adjncy) { 112 ierr = PetscViewerASCIISynchronizedPrintf(viewer," local adj list:");CHKERRQ(ierr); 113 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 114 for (j=graph->xadj[i];j<graph->xadj[i+1];j++) { 115 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->adjncy[j]);CHKERRQ(ierr); 116 } 117 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"\n");CHKERRQ(ierr); 118 ierr = PetscViewerASCIISetTab(viewer,tabs);CHKERRQ(ierr); 119 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 120 } else { 121 ierr = PetscViewerASCIISynchronizedPrintf(viewer," no adj info\n");CHKERRQ(ierr); 122 } 123 } 124 if (graph->n_local_subs) { 125 ierr = PetscViewerASCIISynchronizedPrintf(viewer," local sub id: %d\n",graph->local_subs[i]);CHKERRQ(ierr); 126 } 127 ierr = PetscViewerASCIISynchronizedPrintf(viewer," interface subset id: %d\n",graph->subset[i]);CHKERRQ(ierr); 128 if (graph->subset[i] && graph->subset_ncc) { 129 ierr = PetscViewerASCIISynchronizedPrintf(viewer," ncc for subset: %d\n",graph->subset_ncc[graph->subset[i]-1]);CHKERRQ(ierr); 130 } 131 } 132 } 133 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Total number of connected components %d\n",graph->ncc);CHKERRQ(ierr); 134 ierr = PetscMalloc1(graph->cptr[graph->ncc],&queue_in_global_numbering);CHKERRQ(ierr); 135 ierr = ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_in_global_numbering);CHKERRQ(ierr); 136 for (i=0;i<graph->ncc;i++) { 137 PetscInt node_num=graph->queue[graph->cptr[i]]; 138 PetscBool printcc = PETSC_FALSE; 139 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d (neighs:",i);CHKERRQ(ierr); 140 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 141 for (j=0;j<graph->count[node_num];j++) { 142 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->neighbours_set[node_num][j]);CHKERRQ(ierr); 143 } 144 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"):");CHKERRQ(ierr); 145 if (verbosity_level > 1 || graph->twodim) { 146 printcc = PETSC_TRUE; 147 } else if (graph->count[node_num] > 1 || (graph->count[node_num] == 1 && graph->special_dof[node_num] == PCBDDCGRAPH_NEUMANN_MARK)) { 148 printcc = PETSC_TRUE; 149 } 150 if (printcc) { 151 for (j=graph->cptr[i];j<graph->cptr[i+1];j++) { 152 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d (%d)",graph->queue[j],queue_in_global_numbering[j]);CHKERRQ(ierr); 153 } 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 #undef __FUNCT__ 165 #define __FUNCT__ "PCBDDCGraphGetCandidatesIS" 166 PetscErrorCode PCBDDCGraphGetCandidatesIS(PCBDDCGraph graph, PetscInt *n_faces, IS *FacesIS[], PetscInt *n_edges, IS *EdgesIS[], IS *VerticesIS) 167 { 168 IS *ISForFaces,*ISForEdges,ISForVertices; 169 PetscInt i,nfc,nec,nvc,*idx; 170 PetscErrorCode ierr; 171 172 PetscFunctionBegin; 173 /* loop on ccs to evalute number of faces, edges and vertices */ 174 nfc = 0; 175 nec = 0; 176 nvc = 0; 177 for (i=0;i<graph->ncc;i++) { 178 PetscInt repdof = graph->queue[graph->cptr[i]]; 179 if (graph->cptr[i+1]-graph->cptr[i] > graph->custom_minimal_size) { 180 if (graph->count[repdof] == 1 && graph->special_dof[repdof] != PCBDDCGRAPH_NEUMANN_MARK) { 181 nfc++; 182 } else { /* note that nec will be zero in 2d */ 183 nec++; 184 } 185 } else { 186 nvc += graph->cptr[i+1]-graph->cptr[i]; 187 } 188 } 189 190 /* check if we are in 2D or 3D */ 191 if (graph->twodim) { /* we are in a 2D case -> edges are shared by 2 subregions and faces don't exist */ 192 nec = nfc; 193 nfc = 0; 194 } 195 196 /* allocate IS arrays for faces, edges. Vertices need a single index set. */ 197 if (FacesIS) { 198 ierr = PetscMalloc1(nfc,&ISForFaces);CHKERRQ(ierr); 199 } 200 if (EdgesIS) { 201 ierr = PetscMalloc1(nec,&ISForEdges);CHKERRQ(ierr); 202 } 203 if (VerticesIS) { 204 ierr = PetscMalloc1(nvc,&idx);CHKERRQ(ierr); 205 } 206 207 /* loop on ccs to compute index sets for faces and edges */ 208 if (!graph->queue_sorted) { 209 PetscInt *queue_global; 210 211 ierr = PetscMalloc1(graph->cptr[graph->ncc],&queue_global);CHKERRQ(ierr); 212 ierr = ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_global);CHKERRQ(ierr); 213 for (i=0;i<graph->ncc;i++) { 214 ierr = PetscSortIntWithArray(graph->cptr[i+1]-graph->cptr[i],&queue_global[graph->cptr[i]],&graph->queue[graph->cptr[i]]);CHKERRQ(ierr); 215 } 216 ierr = PetscFree(queue_global);CHKERRQ(ierr); 217 graph->queue_sorted = PETSC_TRUE; 218 } 219 nfc = 0; 220 nec = 0; 221 for (i=0;i<graph->ncc;i++) { 222 PetscInt repdof = graph->queue[graph->cptr[i]]; 223 if (graph->cptr[i+1]-graph->cptr[i] > graph->custom_minimal_size) { 224 if (graph->count[repdof] == 1 && graph->special_dof[repdof] != PCBDDCGRAPH_NEUMANN_MARK) { 225 if (graph->twodim) { 226 if (EdgesIS) { 227 ierr = ISCreateGeneral(PETSC_COMM_SELF,graph->cptr[i+1]-graph->cptr[i],&graph->queue[graph->cptr[i]],PETSC_COPY_VALUES,&ISForEdges[nec]);CHKERRQ(ierr); 228 } 229 nec++; 230 } else { 231 if (FacesIS) { 232 ierr = ISCreateGeneral(PETSC_COMM_SELF,graph->cptr[i+1]-graph->cptr[i],&graph->queue[graph->cptr[i]],PETSC_COPY_VALUES,&ISForFaces[nfc]);CHKERRQ(ierr); 233 } 234 nfc++; 235 } 236 } else { 237 if (EdgesIS) { 238 ierr = ISCreateGeneral(PETSC_COMM_SELF,graph->cptr[i+1]-graph->cptr[i],&graph->queue[graph->cptr[i]],PETSC_COPY_VALUES,&ISForEdges[nec]);CHKERRQ(ierr); 239 } 240 nec++; 241 } 242 } 243 } 244 /* index set for vertices */ 245 if (VerticesIS) { 246 nvc = 0; 247 for (i=0;i<graph->ncc;i++) { 248 if (graph->cptr[i+1]-graph->cptr[i] <= graph->custom_minimal_size) { 249 PetscInt j; 250 251 for (j=graph->cptr[i];j<graph->cptr[i+1];j++) { 252 idx[nvc]=graph->queue[j]; 253 nvc++; 254 } 255 } 256 } 257 /* sort vertex set (by local ordering) */ 258 ierr = PetscSortInt(nvc,idx);CHKERRQ(ierr); 259 ierr = ISCreateGeneral(PETSC_COMM_SELF,nvc,idx,PETSC_OWN_POINTER,&ISForVertices);CHKERRQ(ierr); 260 } 261 /* get back info */ 262 if (n_faces) *n_faces = nfc; 263 if (FacesIS) { 264 *FacesIS = ISForFaces; 265 } 266 if (n_edges) *n_edges = nec; 267 if (EdgesIS) { 268 *EdgesIS = ISForEdges; 269 } 270 if (VerticesIS) { 271 *VerticesIS = ISForVertices; 272 } 273 PetscFunctionReturn(0); 274 } 275 276 #undef __FUNCT__ 277 #define __FUNCT__ "PCBDDCGraphComputeConnectedComponents" 278 PetscErrorCode PCBDDCGraphComputeConnectedComponents(PCBDDCGraph graph) 279 { 280 PetscBool adapt_interface_reduced; 281 MPI_Comm interface_comm; 282 PetscMPIInt size; 283 PetscInt i; 284 PetscBool twodim; 285 PetscErrorCode ierr; 286 287 PetscFunctionBegin; 288 /* compute connected components locally */ 289 ierr = PetscObjectGetComm((PetscObject)(graph->l2gmap),&interface_comm);CHKERRQ(ierr); 290 ierr = PCBDDCGraphComputeConnectedComponentsLocal(graph);CHKERRQ(ierr); 291 /* check consistency of connected components among neighbouring subdomains -> it adapt them in case it is needed */ 292 ierr = MPI_Comm_size(interface_comm,&size);CHKERRQ(ierr); 293 adapt_interface_reduced = PETSC_FALSE; 294 if (size > 1) { 295 PetscInt i; 296 PetscBool adapt_interface = PETSC_FALSE; 297 for (i=0;i<graph->n_subsets;i++) { 298 /* We are not sure that on a given subset of the local interface, 299 with two connected components, the latters be the same among sharing subdomains */ 300 if (graph->subset_ncc[i] > 1) { 301 adapt_interface = PETSC_TRUE; 302 break; 303 } 304 } 305 ierr = MPIU_Allreduce(&adapt_interface,&adapt_interface_reduced,1,MPIU_BOOL,MPI_LOR,interface_comm);CHKERRQ(ierr); 306 } 307 308 if (graph->n_subsets && adapt_interface_reduced) { 309 /* old csr stuff */ 310 PetscInt *aux_new_xadj,*new_xadj,*new_adjncy; 311 PetscInt *old_xadj,*old_adjncy; 312 PetscBT subset_cc_adapt; 313 /* MPI */ 314 MPI_Request *send_requests,*recv_requests; 315 PetscInt *send_buffer,*recv_buffer; 316 PetscInt sum_requests,start_of_recv,start_of_send; 317 PetscInt *cum_recv_counts; 318 /* others */ 319 PetscInt *labels; 320 PetscInt global_subset_counter; 321 PetscInt j,k,s; 322 323 /* Retrict adjacency graph using information from previously computed connected components */ 324 ierr = PetscMalloc1(graph->nvtxs,&aux_new_xadj);CHKERRQ(ierr); 325 for (i=0;i<graph->nvtxs;i++) { 326 aux_new_xadj[i]=1; 327 } 328 for (i=0;i<graph->ncc;i++) { 329 k = graph->cptr[i+1]-graph->cptr[i]; 330 for (j=0;j<k;j++) { 331 aux_new_xadj[graph->queue[graph->cptr[i]+j]]=k; 332 } 333 } 334 j = 0; 335 for (i=0;i<graph->nvtxs;i++) { 336 j += aux_new_xadj[i]; 337 } 338 ierr = PetscMalloc1(graph->nvtxs+1,&new_xadj);CHKERRQ(ierr); 339 ierr = PetscMalloc1(j,&new_adjncy);CHKERRQ(ierr); 340 new_xadj[0]=0; 341 for (i=0;i<graph->nvtxs;i++) { 342 new_xadj[i+1]=new_xadj[i]+aux_new_xadj[i]; 343 if (aux_new_xadj[i]==1) { 344 new_adjncy[new_xadj[i]]=i; 345 } 346 } 347 ierr = PetscFree(aux_new_xadj);CHKERRQ(ierr); 348 ierr = PetscMalloc1(graph->nvtxs,&labels);CHKERRQ(ierr); 349 ierr = PetscMemzero(labels,graph->nvtxs*sizeof(*labels));CHKERRQ(ierr); 350 for (i=0;i<graph->ncc;i++) { 351 k = graph->cptr[i+1]-graph->cptr[i]; 352 for (j=0;j<k;j++) { 353 ierr = PetscMemcpy(&new_adjncy[new_xadj[graph->queue[graph->cptr[i]+j]]],&graph->queue[graph->cptr[i]],k*sizeof(PetscInt));CHKERRQ(ierr); 354 labels[graph->queue[graph->cptr[i]+j]] = i; 355 } 356 } 357 /* set temporarly new CSR into graph */ 358 old_xadj = graph->xadj; 359 old_adjncy = graph->adjncy; 360 graph->xadj = new_xadj; 361 graph->adjncy = new_adjncy; 362 /* allocate some space */ 363 ierr = PetscMalloc1(graph->n_subsets+1,&cum_recv_counts);CHKERRQ(ierr); 364 ierr = PetscMemzero(cum_recv_counts,(graph->n_subsets+1)*sizeof(*cum_recv_counts));CHKERRQ(ierr); 365 /* first count how many neighbours per connected component I will receive from */ 366 cum_recv_counts[0]=0; 367 for (i=0;i<graph->n_subsets;i++) { 368 cum_recv_counts[i+1]=cum_recv_counts[i]+graph->count[graph->subsets[i][0]]; 369 } 370 ierr = PetscMalloc1(cum_recv_counts[graph->n_subsets],&recv_buffer);CHKERRQ(ierr); 371 ierr = PetscMalloc2(cum_recv_counts[graph->n_subsets],&send_requests,cum_recv_counts[graph->n_subsets],&recv_requests);CHKERRQ(ierr); 372 for (i=0;i<cum_recv_counts[graph->n_subsets];i++) { 373 send_requests[i]=MPI_REQUEST_NULL; 374 recv_requests[i]=MPI_REQUEST_NULL; 375 } 376 /* exchange with my neighbours the number of my connected components on the subset of interface */ 377 sum_requests = 0; 378 for (i=0;i<graph->n_subsets;i++) { 379 PetscMPIInt neigh,tag; 380 381 j = graph->subsets[i][0]; 382 ierr = PetscMPIIntCast(2*graph->subset_ref_node[i],&tag);CHKERRQ(ierr); 383 for (k=0;k<graph->count[j];k++) { 384 ierr = PetscMPIIntCast(graph->neighbours_set[j][k],&neigh);CHKERRQ(ierr); 385 ierr = MPI_Isend(&graph->subset_ncc[i],1,MPIU_INT,neigh,tag,interface_comm,&send_requests[sum_requests]);CHKERRQ(ierr); 386 ierr = MPI_Irecv(&recv_buffer[sum_requests],1,MPIU_INT,neigh,tag,interface_comm,&recv_requests[sum_requests]);CHKERRQ(ierr); 387 sum_requests++; 388 } 389 } 390 ierr = MPI_Waitall(sum_requests,recv_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 391 ierr = MPI_Waitall(sum_requests,send_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 392 /* determine the subsets I have to adapt */ 393 ierr = PetscBTCreate(graph->n_subsets,&subset_cc_adapt);CHKERRQ(ierr); 394 ierr = PetscBTMemzero(graph->n_subsets,subset_cc_adapt);CHKERRQ(ierr); 395 for (i=0;i<graph->n_subsets;i++) { 396 for (j=cum_recv_counts[i];j<cum_recv_counts[i+1];j++){ 397 /* adapt if more than one cc is present */ 398 if (graph->subset_ncc[i] > 1 || recv_buffer[j] > 1) { 399 ierr = PetscBTSet(subset_cc_adapt,i); 400 break; 401 } 402 } 403 } 404 ierr = PetscFree(recv_buffer);CHKERRQ(ierr); 405 /* determine send/recv buffers sizes */ 406 j = 0; 407 for (i=0;i<graph->n_subsets;i++) { 408 if (PetscBTLookup(subset_cc_adapt,i)) { 409 j += graph->subsets_size[i]; 410 } 411 } 412 k = 0; 413 for (i=0;i<graph->n_subsets;i++) { 414 if (PetscBTLookup(subset_cc_adapt,i)) { 415 k += (cum_recv_counts[i+1]-cum_recv_counts[i])*graph->subsets_size[i]; 416 } 417 } 418 ierr = PetscMalloc2(j,&send_buffer,k,&recv_buffer);CHKERRQ(ierr); 419 420 /* fill send buffer */ 421 j = 0; 422 for (i=0;i<graph->n_subsets;i++) { 423 if (PetscBTLookup(subset_cc_adapt,i)) { 424 for (k=0;k<graph->subsets_size[i];k++) { 425 send_buffer[j++] = labels[graph->subsets[i][k]]; 426 } 427 } 428 } 429 ierr = PetscFree(labels);CHKERRQ(ierr); 430 431 /* now exchange the data */ 432 start_of_recv = 0; 433 start_of_send = 0; 434 sum_requests = 0; 435 for (i=0;i<graph->n_subsets;i++) { 436 if (PetscBTLookup(subset_cc_adapt,i)) { 437 PetscMPIInt neigh,tag; 438 PetscInt size_of_send = graph->subsets_size[i]; 439 440 j = graph->subsets[i][0]; 441 ierr = PetscMPIIntCast(2*graph->subset_ref_node[i]+1,&tag);CHKERRQ(ierr); 442 for (k=0;k<graph->count[j];k++) { 443 ierr = PetscMPIIntCast(graph->neighbours_set[j][k],&neigh);CHKERRQ(ierr); 444 ierr = MPI_Isend(&send_buffer[start_of_send],size_of_send,MPIU_INT,neigh,tag,interface_comm,&send_requests[sum_requests]);CHKERRQ(ierr); 445 ierr = MPI_Irecv(&recv_buffer[start_of_recv],size_of_send,MPIU_INT,neigh,tag,interface_comm,&recv_requests[sum_requests]);CHKERRQ(ierr); 446 start_of_recv += size_of_send; 447 sum_requests++; 448 } 449 start_of_send += size_of_send; 450 } 451 } 452 ierr = MPI_Waitall(sum_requests,recv_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 453 ierr = MPI_Waitall(sum_requests,send_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 454 ierr = PetscFree2(send_requests,recv_requests);CHKERRQ(ierr); 455 456 start_of_recv = 0; 457 global_subset_counter = 0; 458 for (i=0;i<graph->n_subsets;i++) { 459 if (PetscBTLookup(subset_cc_adapt,i)) { 460 PetscInt **temp_buffer,temp_buffer_size,*private_label; 461 462 /* allocate some temporary space */ 463 temp_buffer_size = graph->subsets_size[i]; 464 ierr = PetscMalloc1(temp_buffer_size,&temp_buffer);CHKERRQ(ierr); 465 ierr = PetscMalloc1(temp_buffer_size*(cum_recv_counts[i+1]-cum_recv_counts[i]),&temp_buffer[0]);CHKERRQ(ierr); 466 ierr = PetscMemzero(temp_buffer[0],temp_buffer_size*(cum_recv_counts[i+1]-cum_recv_counts[i])*sizeof(PetscInt));CHKERRQ(ierr); 467 for (j=1;j<temp_buffer_size;j++) { 468 temp_buffer[j] = temp_buffer[j-1]+cum_recv_counts[i+1]-cum_recv_counts[i]; 469 } 470 /* analyze contributions from neighbouring subdomains for i-th subset 471 temp buffer structure: 472 supposing part of the interface has dimension 5 473 e.g with global dofs 0,1,2,3,4, locally ordered on the current process as 0,4,3,1,2 474 3 neighs procs having connected components: 475 neigh 0: [0 1 4], [2 3], labels [4,7] (2 connected components) 476 neigh 1: [0 1], [2 3 4], labels [3 2] (2 connected components) 477 neigh 2: [0 4], [1], [2 3], labels [1 5 6] (3 connected components) 478 tempbuffer (row-oriented) will be filled as: 479 [ 4, 3, 1; 480 4, 2, 1; 481 7, 2, 6; 482 4, 3, 5; 483 7, 2, 6; ]; 484 This way we can simply find intersections of ccs among neighs. 485 The graph->subset array will need to be modified. The output for the example is [0], [1], [2 3], [4]; 486 */ 487 for (j=0;j<cum_recv_counts[i+1]-cum_recv_counts[i];j++) { 488 for (k=0;k<temp_buffer_size;k++) { 489 temp_buffer[k][j] = recv_buffer[start_of_recv+k]; 490 } 491 start_of_recv += temp_buffer_size; 492 } 493 ierr = PetscMalloc1(temp_buffer_size,&private_label);CHKERRQ(ierr); 494 ierr = PetscMemzero(private_label,temp_buffer_size*sizeof(*private_label));CHKERRQ(ierr); 495 for (j=0;j<temp_buffer_size;j++) { 496 if (!private_label[j]) { /* found a new cc */ 497 PetscBool same_set; 498 499 global_subset_counter++; 500 private_label[j] = global_subset_counter; 501 for (k=j+1;k<temp_buffer_size;k++) { /* check for other nodes in new cc */ 502 same_set = PETSC_TRUE; 503 for (s=0;s<cum_recv_counts[i+1]-cum_recv_counts[i];s++) { 504 if (temp_buffer[j][s] != temp_buffer[k][s]) { 505 same_set = PETSC_FALSE; 506 break; 507 } 508 } 509 if (same_set) { 510 private_label[k] = global_subset_counter; 511 } 512 } 513 } 514 } 515 /* insert private labels in graph structure */ 516 for (j=0;j<graph->subsets_size[i];j++) { 517 graph->subset[graph->subsets[i][j]] = graph->n_subsets+private_label[j]; 518 } 519 ierr = PetscFree(private_label);CHKERRQ(ierr); 520 ierr = PetscFree(temp_buffer[0]);CHKERRQ(ierr); 521 ierr = PetscFree(temp_buffer);CHKERRQ(ierr); 522 } 523 } 524 ierr = PetscFree2(send_buffer,recv_buffer);CHKERRQ(ierr); 525 ierr = PetscFree(cum_recv_counts);CHKERRQ(ierr); 526 ierr = PetscBTDestroy(&subset_cc_adapt);CHKERRQ(ierr); 527 /* We are ready to find for connected components which are consistent among neighbouring subdomains */ 528 if (global_subset_counter) { 529 PetscInt o_nsubs; 530 531 ierr = PetscBTMemzero(graph->nvtxs,graph->touched);CHKERRQ(ierr); 532 global_subset_counter = 0; 533 for (i=0;i<graph->nvtxs;i++) { 534 if (graph->subset[i] && !PetscBTLookup(graph->touched,i)) { 535 global_subset_counter++; 536 for (j=i+1;j<graph->nvtxs;j++) { 537 if (!PetscBTLookup(graph->touched,j) && graph->subset[j]==graph->subset[i]) { 538 graph->subset[j] = global_subset_counter; 539 ierr = PetscBTSet(graph->touched,j);CHKERRQ(ierr); 540 } 541 } 542 graph->subset[i] = global_subset_counter; 543 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 544 } 545 } 546 /* disable subdomains info since it is local (info contained in CSR) */ 547 o_nsubs = graph->n_local_subs; 548 graph->n_local_subs = 0; 549 /* refine connected components locally */ 550 ierr = PCBDDCGraphComputeConnectedComponentsLocal(graph);CHKERRQ(ierr); 551 /* restore subdomains info */ 552 graph->n_local_subs = o_nsubs; 553 } 554 /* restore original CSR graph of dofs */ 555 ierr = PetscFree(new_xadj);CHKERRQ(ierr); 556 ierr = PetscFree(new_adjncy);CHKERRQ(ierr); 557 graph->xadj = old_xadj; 558 graph->adjncy = old_adjncy; 559 } 560 561 /* Determine if we are in 2D or 3D */ 562 twodim = PETSC_TRUE; 563 for (i=0;i<graph->ncc;i++) { 564 PetscInt repdof = graph->queue[graph->cptr[i]]; 565 if (graph->cptr[i+1]-graph->cptr[i] > graph->custom_minimal_size) { 566 if (graph->count[repdof] > 1 || graph->special_dof[repdof] == PCBDDCGRAPH_NEUMANN_MARK) { 567 twodim = PETSC_FALSE; 568 break; 569 } 570 } 571 } 572 ierr = MPIU_Allreduce(&twodim,&graph->twodim,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)graph->l2gmap));CHKERRQ(ierr); 573 PetscFunctionReturn(0); 574 } 575 576 /* The following code has been adapted from function IsConnectedSubdomain contained 577 in source file contig.c of METIS library (version 5.0.1) 578 It finds connected components for each subset */ 579 #undef __FUNCT__ 580 #define __FUNCT__ "PCBDDCGraphComputeConnectedComponentsLocal" 581 PetscErrorCode PCBDDCGraphComputeConnectedComponentsLocal(PCBDDCGraph graph) 582 { 583 PetscInt i,j,k,first,last,nleft,ncc,pid,cum_queue,n,ncc_pid; 584 PetscMPIInt size; 585 PetscErrorCode ierr; 586 587 PetscFunctionBegin; 588 /* quiet return if no csr info is available */ 589 if ((!graph->xadj || !graph->adjncy) && !graph->n_local_subs) { 590 PetscFunctionReturn(0); 591 } 592 593 /* reset any previous search of connected components */ 594 ierr = PetscBTMemzero(graph->nvtxs,graph->touched);CHKERRQ(ierr); 595 graph->n_subsets = 0; 596 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)graph->l2gmap),&size);CHKERRQ(ierr); 597 if (size == 1) { 598 if (graph->nvtxs) { 599 graph->n_subsets = 1; 600 for (i=0;i<graph->nvtxs;i++) { 601 graph->subset[i] = 1; 602 } 603 } 604 } else { 605 for (i=0;i<graph->nvtxs;i++) { 606 if (graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK || !graph->count[i]) { 607 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 608 graph->subset[i] = 0; 609 } 610 graph->n_subsets = PetscMax(graph->n_subsets,graph->subset[i]); 611 } 612 } 613 ierr = PetscFree(graph->subset_ncc);CHKERRQ(ierr); 614 ierr = PetscMalloc1(graph->n_subsets,&graph->subset_ncc);CHKERRQ(ierr); 615 616 /* begin search for connected components */ 617 cum_queue = 0; 618 ncc = 0; 619 for (n=0;n<graph->n_subsets;n++) { 620 pid = n+1; /* partition labeled by 0 is discarded */ 621 nleft = 0; 622 for (i=0;i<graph->nvtxs;i++) { 623 if (graph->subset[i] == pid) { 624 nleft++; 625 } 626 } 627 for (i=0; i<graph->nvtxs; i++) { 628 if (graph->subset[i] == pid) { 629 break; 630 } 631 } 632 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 633 graph->queue[cum_queue] = i; 634 first = 0; 635 last = 1; 636 graph->cptr[ncc] = cum_queue; 637 ncc_pid = 0; 638 while (first != nleft) { 639 if (first == last) { 640 graph->cptr[++ncc] = first+cum_queue; 641 ncc_pid++; 642 for (i=0; i<graph->nvtxs; i++) { 643 if (graph->subset[i] == pid && !PetscBTLookup(graph->touched,i)) { 644 break; 645 } 646 } 647 graph->queue[cum_queue+last] = i; 648 last++; 649 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 650 } 651 i = graph->queue[cum_queue+first]; 652 first++; 653 if (!graph->xadj || !graph->adjncy) { /* sub info only, loop over all remaining vertices */ 654 for (k=i+1;k<graph->nvtxs;k++) { 655 if (!PetscBTLookup(graph->touched,k) && graph->subset[k] == pid && graph->local_subs[i] == graph->local_subs[k]) { 656 graph->queue[cum_queue+last] = k; 657 last++; 658 ierr = PetscBTSet(graph->touched,k);CHKERRQ(ierr); 659 } 660 } 661 } else { 662 for (j=graph->xadj[i];j<graph->xadj[i+1];j++) { 663 PetscBool same_sub; 664 665 k = graph->adjncy[j]; 666 /* get local subdomain id if needed */ 667 if (graph->n_local_subs) { 668 same_sub = (PetscBool)(graph->local_subs[i] == graph->local_subs[k]); 669 } else { 670 same_sub = PETSC_TRUE; 671 } 672 if (!PetscBTLookup(graph->touched,k) && graph->subset[k] == pid && same_sub) { 673 graph->queue[cum_queue+last] = k; 674 last++; 675 ierr = PetscBTSet(graph->touched,k);CHKERRQ(ierr); 676 } 677 } 678 } 679 } 680 graph->cptr[++ncc] = first+cum_queue; 681 ncc_pid++; 682 cum_queue = graph->cptr[ncc]; 683 graph->subset_ncc[n] = ncc_pid; 684 } 685 graph->ncc = ncc; 686 graph->queue_sorted = PETSC_FALSE; 687 PetscFunctionReturn(0); 688 } 689 690 #undef __FUNCT__ 691 #define __FUNCT__ "PCBDDCGraphSetUp" 692 PetscErrorCode PCBDDCGraphSetUp(PCBDDCGraph graph, PetscInt custom_minimal_size, IS neumann_is, IS dirichlet_is, PetscInt n_ISForDofs, IS ISForDofs[], IS custom_primal_vertices) 693 { 694 VecScatter scatter_ctx; 695 Vec local_vec,local_vec2,global_vec; 696 IS to,from,subset,subset_n; 697 MPI_Comm comm; 698 PetscScalar *array,*array2; 699 const PetscInt *is_indices; 700 PetscInt n_neigh,*neigh,*n_shared,**shared,*queue_global; 701 PetscInt i,j,k,s,total_counts,nodes_touched,is_size; 702 PetscMPIInt size; 703 PetscBool same_set,mirrors_found; 704 PetscErrorCode ierr; 705 706 PetscFunctionBegin; 707 graph->has_dirichlet = PETSC_FALSE; 708 if (dirichlet_is) { 709 PetscCheckSameComm(graph->l2gmap,1,dirichlet_is,4); 710 graph->has_dirichlet = PETSC_TRUE; 711 } 712 ierr = PetscObjectGetComm((PetscObject)(graph->l2gmap),&comm);CHKERRQ(ierr); 713 /* custom_minimal_size */ 714 graph->custom_minimal_size = custom_minimal_size; 715 /* get info l2gmap and allocate work vectors */ 716 ierr = ISLocalToGlobalMappingGetInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);CHKERRQ(ierr); 717 /* check if we have any local periodic nodes (periodic BCs) */ 718 mirrors_found = PETSC_FALSE; 719 if (graph->nvtxs && n_neigh) { 720 for (i=0; i<n_shared[0]; i++) graph->count[shared[0][i]] += 1; 721 for (i=0; i<n_shared[0]; i++) { 722 if (graph->count[shared[0][i]] > 1) { 723 mirrors_found = PETSC_TRUE; 724 break; 725 } 726 } 727 } 728 /* create some workspace objects */ 729 local_vec = NULL; 730 local_vec2 = NULL; 731 global_vec = NULL; 732 to = NULL; 733 from = NULL; 734 scatter_ctx = NULL; 735 if (n_ISForDofs || dirichlet_is || neumann_is || custom_primal_vertices) { 736 ierr = VecCreate(PETSC_COMM_SELF,&local_vec);CHKERRQ(ierr); 737 ierr = VecSetSizes(local_vec,PETSC_DECIDE,graph->nvtxs);CHKERRQ(ierr); 738 ierr = VecSetType(local_vec,VECSTANDARD);CHKERRQ(ierr); 739 ierr = VecDuplicate(local_vec,&local_vec2);CHKERRQ(ierr); 740 ierr = VecCreate(comm,&global_vec);CHKERRQ(ierr); 741 ierr = VecSetSizes(global_vec,PETSC_DECIDE,graph->nvtxs_global);CHKERRQ(ierr); 742 ierr = VecSetType(global_vec,VECSTANDARD);CHKERRQ(ierr); 743 ierr = ISCreateStride(PETSC_COMM_SELF,graph->nvtxs,0,1,&to);CHKERRQ(ierr); 744 ierr = ISLocalToGlobalMappingApplyIS(graph->l2gmap,to,&from);CHKERRQ(ierr); 745 ierr = VecScatterCreate(global_vec,from,local_vec,to,&scatter_ctx);CHKERRQ(ierr); 746 } else if (mirrors_found) { 747 ierr = ISCreateStride(PETSC_COMM_SELF,graph->nvtxs,0,1,&to);CHKERRQ(ierr); 748 ierr = ISLocalToGlobalMappingApplyIS(graph->l2gmap,to,&from);CHKERRQ(ierr); 749 } 750 /* compute local mirrors (if any) */ 751 if (mirrors_found) { 752 PetscInt *local_indices,*global_indices; 753 /* get arrays of local and global indices */ 754 ierr = PetscMalloc1(graph->nvtxs,&local_indices);CHKERRQ(ierr); 755 ierr = ISGetIndices(to,(const PetscInt**)&is_indices);CHKERRQ(ierr); 756 ierr = PetscMemcpy(local_indices,is_indices,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 757 ierr = ISRestoreIndices(to,(const PetscInt**)&is_indices);CHKERRQ(ierr); 758 ierr = PetscMalloc1(graph->nvtxs,&global_indices);CHKERRQ(ierr); 759 ierr = ISGetIndices(from,(const PetscInt**)&is_indices);CHKERRQ(ierr); 760 ierr = PetscMemcpy(global_indices,is_indices,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 761 ierr = ISRestoreIndices(from,(const PetscInt**)&is_indices);CHKERRQ(ierr); 762 /* allocate space for mirrors */ 763 ierr = PetscMalloc2(graph->nvtxs,&graph->mirrors,graph->nvtxs,&graph->mirrors_set);CHKERRQ(ierr); 764 ierr = PetscMemzero(graph->mirrors,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 765 graph->mirrors_set[0] = 0; 766 767 k=0; 768 for (i=0;i<n_shared[0];i++) { 769 j=shared[0][i]; 770 if (graph->count[j] > 1) { 771 graph->mirrors[j]++; 772 k++; 773 } 774 } 775 /* allocate space for set of mirrors */ 776 ierr = PetscMalloc1(k,&graph->mirrors_set[0]);CHKERRQ(ierr); 777 for (i=1;i<graph->nvtxs;i++) 778 graph->mirrors_set[i]=graph->mirrors_set[i-1]+graph->mirrors[i-1]; 779 780 /* fill arrays */ 781 ierr = PetscMemzero(graph->mirrors,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 782 for (j=0;j<n_shared[0];j++) { 783 i=shared[0][j]; 784 if (graph->count[i] > 1) 785 graph->mirrors_set[i][graph->mirrors[i]++]=global_indices[i]; 786 } 787 ierr = PetscSortIntWithArray(graph->nvtxs,global_indices,local_indices);CHKERRQ(ierr); 788 for (i=0;i<graph->nvtxs;i++) { 789 if (graph->mirrors[i] > 0) { 790 ierr = PetscFindInt(graph->mirrors_set[i][0],graph->nvtxs,global_indices,&k);CHKERRQ(ierr); 791 j = global_indices[k]; 792 while ( k > 0 && global_indices[k-1] == j) k--; 793 for (j=0;j<graph->mirrors[i];j++) { 794 graph->mirrors_set[i][j]=local_indices[k+j]; 795 } 796 ierr = PetscSortInt(graph->mirrors[i],graph->mirrors_set[i]);CHKERRQ(ierr); 797 } 798 } 799 ierr = PetscFree(local_indices);CHKERRQ(ierr); 800 ierr = PetscFree(global_indices);CHKERRQ(ierr); 801 } 802 ierr = PetscMemzero(graph->count,graph->nvtxs*sizeof(*graph->count));CHKERRQ(ierr); 803 ierr = ISDestroy(&to);CHKERRQ(ierr); 804 ierr = ISDestroy(&from);CHKERRQ(ierr); 805 806 /* Count total number of neigh per node */ 807 k=0; 808 for (i=1;i<n_neigh;i++) { 809 k += n_shared[i]; 810 for (j=0;j<n_shared[i];j++) { 811 graph->count[shared[i][j]] += 1; 812 } 813 } 814 /* Allocate space for storing the set of neighbours for each node */ 815 if (graph->nvtxs) { 816 ierr = PetscMalloc1(k,&graph->neighbours_set[0]);CHKERRQ(ierr); 817 } 818 for (i=1;i<graph->nvtxs;i++) { /* dont count myself */ 819 graph->neighbours_set[i]=graph->neighbours_set[i-1]+graph->count[i-1]; 820 } 821 /* Get information for sharing subdomains */ 822 ierr = PetscMemzero(graph->count,graph->nvtxs*sizeof(*graph->count));CHKERRQ(ierr); 823 for (i=1;i<n_neigh;i++) { /* dont count myself */ 824 s = n_shared[i]; 825 for (j=0;j<s;j++) { 826 k = shared[i][j]; 827 graph->neighbours_set[k][graph->count[k]] = neigh[i]; 828 graph->count[k] += 1; 829 } 830 } 831 /* sort set of sharing subdomains */ 832 for (i=0;i<graph->nvtxs;i++) { 833 ierr = PetscSortRemoveDupsInt(&graph->count[i],graph->neighbours_set[i]);CHKERRQ(ierr); 834 } 835 /* free memory allocated by ISLocalToGlobalMappingGetInfo */ 836 ierr = ISLocalToGlobalMappingRestoreInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);CHKERRQ(ierr); 837 838 /* 839 Get info for dofs splitting 840 User can specify just a subset; an additional field is considered as a complementary field 841 */ 842 for (i=0;i<graph->nvtxs;i++) { 843 graph->which_dof[i] = n_ISForDofs; /* by default a dof belongs to the complement set */ 844 } 845 if (n_ISForDofs) { 846 ierr = VecSet(local_vec,-1.0);CHKERRQ(ierr); 847 } 848 for (i=0;i<n_ISForDofs;i++) { 849 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 850 ierr = ISGetLocalSize(ISForDofs[i],&is_size);CHKERRQ(ierr); 851 ierr = ISGetIndices(ISForDofs[i],(const PetscInt**)&is_indices);CHKERRQ(ierr); 852 for (j=0;j<is_size;j++) { 853 if (is_indices[j] > -1 && is_indices[j] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */ 854 graph->which_dof[is_indices[j]] = i; 855 array[is_indices[j]] = 1.*i; 856 } 857 } 858 ierr = ISRestoreIndices(ISForDofs[i],(const PetscInt**)&is_indices);CHKERRQ(ierr); 859 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 860 } 861 /* Check consistency among neighbours */ 862 if (n_ISForDofs) { 863 ierr = VecScatterBegin(scatter_ctx,local_vec,global_vec,INSERT_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 864 ierr = VecScatterEnd(scatter_ctx,local_vec,global_vec,INSERT_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 865 ierr = VecScatterBegin(scatter_ctx,global_vec,local_vec2,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 866 ierr = VecScatterEnd(scatter_ctx,global_vec,local_vec2,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 867 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 868 ierr = VecGetArray(local_vec2,&array2);CHKERRQ(ierr); 869 for (i=0;i<graph->nvtxs;i++){ 870 PetscInt field1,field2; 871 872 field1 = (PetscInt)PetscRealPart(array[i]); 873 field2 = (PetscInt)PetscRealPart(array2[i]); 874 if (field1 != field2) SETERRQ3(comm,PETSC_ERR_USER,"Local node %D have been assigned two different field ids %D and %D at the same time\n",i,field1,field2); 875 } 876 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 877 ierr = VecRestoreArray(local_vec2,&array2);CHKERRQ(ierr); 878 } 879 if (neumann_is || dirichlet_is) { 880 /* Take into account Neumann nodes */ 881 ierr = VecSet(local_vec,0.0);CHKERRQ(ierr); 882 ierr = VecSet(local_vec2,0.0);CHKERRQ(ierr); 883 if (neumann_is) { 884 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 885 ierr = ISGetLocalSize(neumann_is,&is_size);CHKERRQ(ierr); 886 ierr = ISGetIndices(neumann_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); 887 for (i=0;i<is_size;i++) { 888 if (is_indices[i] > -1 && is_indices[i] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */ 889 array[is_indices[i]] = 1.0; 890 } 891 } 892 ierr = ISRestoreIndices(neumann_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); 893 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 894 } 895 /* Neumann nodes: impose consistency among neighbours */ 896 ierr = VecSet(global_vec,0.0);CHKERRQ(ierr); 897 ierr = VecScatterBegin(scatter_ctx,local_vec,global_vec,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 898 ierr = VecScatterEnd(scatter_ctx,local_vec,global_vec,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 899 ierr = VecScatterBegin(scatter_ctx,global_vec,local_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 900 ierr = VecScatterEnd(scatter_ctx,global_vec,local_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 901 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 902 for (i=0;i<graph->nvtxs;i++) { 903 if (PetscRealPart(array[i]) > 0.1) { 904 graph->special_dof[i] = PCBDDCGRAPH_NEUMANN_MARK; 905 } 906 } 907 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 908 /* Take into account Dirichlet nodes */ 909 ierr = VecSet(local_vec2,0.0);CHKERRQ(ierr); 910 if (dirichlet_is) { 911 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 912 ierr = VecGetArray(local_vec2,&array2);CHKERRQ(ierr); 913 ierr = ISGetLocalSize(dirichlet_is,&is_size);CHKERRQ(ierr); 914 ierr = ISGetIndices(dirichlet_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); 915 for (i=0;i<is_size;i++){ 916 if (is_indices[i] > -1 && is_indices[i] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */ 917 k = is_indices[i]; 918 if (!PetscBTLookup(graph->touched,k)) { 919 if (PetscRealPart(array[k]) > 0.1) SETERRQ1(comm,PETSC_ERR_USER,"BDDC cannot have boundary nodes which are marked Neumann and Dirichlet at the same time! Local node %d is wrong\n",k); 920 array2[k] = 1.0; 921 } 922 } 923 } 924 ierr = ISRestoreIndices(dirichlet_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); 925 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 926 ierr = VecRestoreArray(local_vec2,&array2);CHKERRQ(ierr); 927 } 928 /* Dirichlet nodes: impose consistency among neighbours */ 929 ierr = VecSet(global_vec,0.0);CHKERRQ(ierr); 930 ierr = VecScatterBegin(scatter_ctx,local_vec2,global_vec,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 931 ierr = VecScatterEnd(scatter_ctx,local_vec2,global_vec,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 932 ierr = VecScatterBegin(scatter_ctx,global_vec,local_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 933 ierr = VecScatterEnd(scatter_ctx,global_vec,local_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 934 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 935 for (i=0;i<graph->nvtxs;i++) { 936 if (PetscRealPart(array[i]) > 0.1) { 937 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 938 graph->subset[i] = 0; /* dirichlet nodes treated as internal -> is it ok? */ 939 graph->special_dof[i] = PCBDDCGRAPH_DIRICHLET_MARK; 940 } 941 } 942 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 943 } 944 /* mark local periodic nodes (if any) and adapt CSR graph (if any) */ 945 if (graph->mirrors) { 946 for (i=0;i<graph->nvtxs;i++) 947 if (graph->mirrors[i]) 948 graph->special_dof[i] = PCBDDCGRAPH_LOCAL_PERIODIC_MARK; 949 950 if (graph->xadj && graph->adjncy) { 951 PetscInt *new_xadj,*new_adjncy; 952 /* sort CSR graph */ 953 for (i=0;i<graph->nvtxs;i++) 954 ierr = PetscSortInt(graph->xadj[i+1]-graph->xadj[i],&graph->adjncy[graph->xadj[i]]);CHKERRQ(ierr); 955 956 /* adapt local CSR graph in case of local periodicity */ 957 k=0; 958 for (i=0;i<graph->nvtxs;i++) 959 for (j=graph->xadj[i];j<graph->xadj[i+1];j++) 960 k += graph->mirrors[graph->adjncy[j]]; 961 962 ierr = PetscMalloc1(graph->nvtxs+1,&new_xadj);CHKERRQ(ierr); 963 ierr = PetscMalloc1(k+graph->xadj[graph->nvtxs],&new_adjncy);CHKERRQ(ierr); 964 new_xadj[0]=0; 965 for (i=0;i<graph->nvtxs;i++) { 966 k = graph->xadj[i+1]-graph->xadj[i]; 967 ierr = PetscMemcpy(&new_adjncy[new_xadj[i]],&graph->adjncy[graph->xadj[i]],k*sizeof(PetscInt));CHKERRQ(ierr); 968 new_xadj[i+1]=new_xadj[i]+k; 969 for (j=graph->xadj[i];j<graph->xadj[i+1];j++) { 970 k = graph->mirrors[graph->adjncy[j]]; 971 ierr = PetscMemcpy(&new_adjncy[new_xadj[i+1]],graph->mirrors_set[graph->adjncy[j]],k*sizeof(PetscInt));CHKERRQ(ierr); 972 new_xadj[i+1]+=k; 973 } 974 k = new_xadj[i+1]-new_xadj[i]; 975 ierr = PetscSortRemoveDupsInt(&k,&new_adjncy[new_xadj[i]]);CHKERRQ(ierr); 976 new_xadj[i+1]=new_xadj[i]+k; 977 } 978 /* set new CSR into graph */ 979 ierr = PetscFree(graph->xadj);CHKERRQ(ierr); 980 ierr = PetscFree(graph->adjncy);CHKERRQ(ierr); 981 graph->xadj = new_xadj; 982 graph->adjncy = new_adjncy; 983 } 984 } 985 986 /* mark special nodes (if any) -> each will become a single node equivalence class */ 987 if (custom_primal_vertices) { 988 ierr = VecSet(local_vec,0.0);CHKERRQ(ierr); 989 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 990 ierr = ISGetLocalSize(custom_primal_vertices,&is_size);CHKERRQ(ierr); 991 ierr = ISGetIndices(custom_primal_vertices,(const PetscInt**)&is_indices);CHKERRQ(ierr); 992 for (i=0;i<is_size;i++){ 993 if (is_indices[i] > -1 && is_indices[i] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */ 994 array[is_indices[i]] = 1.0; 995 } 996 } 997 ierr = ISRestoreIndices(custom_primal_vertices,(const PetscInt**)&is_indices);CHKERRQ(ierr); 998 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 999 /* special nodes: impose consistency among neighbours */ 1000 ierr = VecSet(global_vec,0.0);CHKERRQ(ierr); 1001 ierr = VecScatterBegin(scatter_ctx,local_vec,global_vec,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1002 ierr = VecScatterEnd(scatter_ctx,local_vec,global_vec,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 1003 ierr = VecScatterBegin(scatter_ctx,global_vec,local_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1004 ierr = VecScatterEnd(scatter_ctx,global_vec,local_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 1005 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 1006 j = 0; 1007 for (i=0;i<graph->nvtxs;i++) { 1008 if (PetscRealPart(array[i]) > 0.1 && graph->special_dof[i] != PCBDDCGRAPH_DIRICHLET_MARK) { 1009 graph->special_dof[i] = PCBDDCGRAPH_SPECIAL_MARK-j; 1010 j++; 1011 } 1012 } 1013 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 1014 } 1015 1016 /* mark interior nodes as touched and belonging to partition number 0 */ 1017 for (i=0;i<graph->nvtxs;i++) { 1018 if (!graph->count[i]) { 1019 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 1020 graph->subset[i] = 0; 1021 } 1022 } 1023 /* init graph structure and compute default subsets */ 1024 nodes_touched=0; 1025 for (i=0;i<graph->nvtxs;i++) { 1026 if (PetscBTLookup(graph->touched,i)) { 1027 nodes_touched++; 1028 } 1029 } 1030 i = 0; 1031 graph->ncc = 0; 1032 total_counts = 0; 1033 1034 /* allocated space for queues */ 1035 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1036 if (size == 1) { 1037 ierr = PetscMalloc2(graph->nvtxs+1,&graph->cptr,graph->nvtxs,&graph->queue);CHKERRQ(ierr); 1038 } else { 1039 PetscInt nused = graph->nvtxs - nodes_touched; 1040 ierr = PetscMalloc2(nused+1,&graph->cptr,nused,&graph->queue);CHKERRQ(ierr); 1041 } 1042 1043 while (nodes_touched<graph->nvtxs) { 1044 /* find first untouched node in local ordering */ 1045 while (PetscBTLookup(graph->touched,i)) { 1046 i++; 1047 } 1048 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 1049 graph->subset[i] = graph->ncc+1; 1050 graph->cptr[graph->ncc] = total_counts; 1051 graph->queue[total_counts] = i; 1052 total_counts++; 1053 nodes_touched++; 1054 /* now find all other nodes having the same set of sharing subdomains */ 1055 for (j=i+1;j<graph->nvtxs;j++) { 1056 /* check for same number of sharing subdomains, dof number and same special mark */ 1057 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]) { 1058 /* check for same set of sharing subdomains */ 1059 same_set=PETSC_TRUE; 1060 for (k=0;k<graph->count[j];k++){ 1061 if (graph->neighbours_set[i][k]!=graph->neighbours_set[j][k]) { 1062 same_set=PETSC_FALSE; 1063 } 1064 } 1065 /* I found a friend of mine */ 1066 if (same_set) { 1067 graph->subset[j]=graph->ncc+1; 1068 ierr = PetscBTSet(graph->touched,j);CHKERRQ(ierr); 1069 nodes_touched++; 1070 graph->queue[total_counts] = j; 1071 total_counts++; 1072 } 1073 } 1074 } 1075 graph->ncc++; 1076 } 1077 /* set default number of subsets (at this point no info on csr graph has been taken into account, so n_subsets = ncc */ 1078 graph->n_subsets = graph->ncc; 1079 ierr = PetscMalloc1(graph->n_subsets,&graph->subset_ncc);CHKERRQ(ierr); 1080 for (i=0;i<graph->n_subsets;i++) { 1081 graph->subset_ncc[i] = 1; 1082 } 1083 /* final pointer */ 1084 graph->cptr[graph->ncc] = total_counts; 1085 1086 /* save information on subsets (needed if we have to adapt the connected components later) */ 1087 /* For consistency reasons (among neighbours), I need to sort (by global ordering) each subset */ 1088 /* Get a reference node (min index in global ordering) for each subset for tagging messages */ 1089 ierr = PetscMalloc1(graph->ncc,&graph->subset_ref_node);CHKERRQ(ierr); 1090 ierr = PetscMalloc1(graph->cptr[graph->ncc],&queue_global);CHKERRQ(ierr); 1091 ierr = ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_global);CHKERRQ(ierr); 1092 for (j=0;j<graph->ncc;j++) { 1093 ierr = PetscSortIntWithArray(graph->cptr[j+1]-graph->cptr[j],&queue_global[graph->cptr[j]],&graph->queue[graph->cptr[j]]);CHKERRQ(ierr); 1094 graph->subset_ref_node[j] = graph->queue[graph->cptr[j]]; 1095 } 1096 ierr = PetscFree(queue_global);CHKERRQ(ierr); 1097 graph->queue_sorted = PETSC_TRUE; 1098 if (graph->ncc) { 1099 ierr = PetscMalloc2(graph->ncc,&graph->subsets_size,graph->ncc,&graph->subsets);CHKERRQ(ierr); 1100 ierr = PetscMalloc1(graph->cptr[graph->ncc],&graph->subsets[0]);CHKERRQ(ierr); 1101 ierr = PetscMemzero(graph->subsets[0],graph->cptr[graph->ncc]*sizeof(PetscInt));CHKERRQ(ierr); 1102 for (j=1;j<graph->ncc;j++) { 1103 graph->subsets_size[j-1] = graph->cptr[j] - graph->cptr[j-1]; 1104 graph->subsets[j] = graph->subsets[j-1] + graph->subsets_size[j-1]; 1105 } 1106 graph->subsets_size[graph->ncc-1] = graph->cptr[graph->ncc] - graph->cptr[graph->ncc-1]; 1107 for (j=0;j<graph->ncc;j++) { 1108 ierr = PetscMemcpy(graph->subsets[j],&graph->queue[graph->cptr[j]],graph->subsets_size[j]*sizeof(PetscInt));CHKERRQ(ierr); 1109 } 1110 } 1111 /* renumber reference nodes */ 1112 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)(graph->l2gmap)),graph->ncc,graph->subset_ref_node,PETSC_COPY_VALUES,&subset_n);CHKERRQ(ierr); 1113 ierr = ISLocalToGlobalMappingApplyIS(graph->l2gmap,subset_n,&subset);CHKERRQ(ierr); 1114 ierr = ISDestroy(&subset_n);CHKERRQ(ierr); 1115 ierr = PCBDDCSubsetNumbering(subset,NULL,NULL,&subset_n);CHKERRQ(ierr); 1116 ierr = ISDestroy(&subset);CHKERRQ(ierr); 1117 ierr = ISGetLocalSize(subset_n,&k);CHKERRQ(ierr); 1118 if (k != graph->ncc) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Invalid size of new subset! %D != %D",k,graph->ncc); 1119 ierr = ISGetIndices(subset_n,&is_indices);CHKERRQ(ierr); 1120 ierr = PetscMemcpy(graph->subset_ref_node,is_indices,graph->ncc*sizeof(PetscInt));CHKERRQ(ierr); 1121 ierr = ISRestoreIndices(subset_n,&is_indices);CHKERRQ(ierr); 1122 ierr = ISDestroy(&subset_n);CHKERRQ(ierr); 1123 1124 /* free workspace */ 1125 ierr = VecDestroy(&local_vec);CHKERRQ(ierr); 1126 ierr = VecDestroy(&local_vec2);CHKERRQ(ierr); 1127 ierr = VecDestroy(&global_vec);CHKERRQ(ierr); 1128 ierr = VecScatterDestroy(&scatter_ctx);CHKERRQ(ierr); 1129 PetscFunctionReturn(0); 1130 } 1131 1132 #undef __FUNCT__ 1133 #define __FUNCT__ "PCBDDCGraphResetCSR" 1134 PetscErrorCode PCBDDCGraphResetCSR(PCBDDCGraph graph) 1135 { 1136 PetscErrorCode ierr; 1137 1138 PetscFunctionBegin; 1139 ierr = PetscFree(graph->xadj);CHKERRQ(ierr); 1140 ierr = PetscFree(graph->adjncy);CHKERRQ(ierr); 1141 graph->nvtxs_csr = 0; 1142 PetscFunctionReturn(0); 1143 } 1144 1145 #undef __FUNCT__ 1146 #define __FUNCT__ "PCBDDCGraphReset" 1147 PetscErrorCode PCBDDCGraphReset(PCBDDCGraph graph) 1148 { 1149 PetscErrorCode ierr; 1150 1151 PetscFunctionBegin; 1152 ierr = ISLocalToGlobalMappingDestroy(&graph->l2gmap);CHKERRQ(ierr); 1153 ierr = PetscFree(graph->subset_ncc);CHKERRQ(ierr); 1154 ierr = PetscFree(graph->subset_ref_node);CHKERRQ(ierr); 1155 if (graph->nvtxs) { 1156 ierr = PetscFree(graph->neighbours_set[0]);CHKERRQ(ierr); 1157 } 1158 ierr = PetscBTDestroy(&graph->touched);CHKERRQ(ierr); 1159 ierr = PetscFree5(graph->count, 1160 graph->neighbours_set, 1161 graph->subset, 1162 graph->which_dof, 1163 graph->special_dof);CHKERRQ(ierr); 1164 ierr = PetscFree2(graph->cptr,graph->queue);CHKERRQ(ierr); 1165 if (graph->mirrors) { 1166 ierr = PetscFree(graph->mirrors_set[0]);CHKERRQ(ierr); 1167 } 1168 ierr = PetscFree2(graph->mirrors,graph->mirrors_set);CHKERRQ(ierr); 1169 if (graph->subsets) { 1170 ierr = PetscFree(graph->subsets[0]);CHKERRQ(ierr); 1171 } 1172 ierr = PetscFree2(graph->subsets_size,graph->subsets);CHKERRQ(ierr); 1173 ierr = ISDestroy(&graph->dirdofs);CHKERRQ(ierr); 1174 ierr = ISDestroy(&graph->dirdofsB);CHKERRQ(ierr); 1175 if (graph->n_local_subs) { 1176 ierr = PetscFree(graph->local_subs);CHKERRQ(ierr); 1177 } 1178 graph->has_dirichlet = PETSC_FALSE; 1179 graph->nvtxs = 0; 1180 graph->nvtxs_global = 0; 1181 graph->n_subsets = 0; 1182 graph->custom_minimal_size = 1; 1183 graph->n_local_subs = 0; 1184 PetscFunctionReturn(0); 1185 } 1186 1187 #undef __FUNCT__ 1188 #define __FUNCT__ "PCBDDCGraphInit" 1189 PetscErrorCode PCBDDCGraphInit(PCBDDCGraph graph, ISLocalToGlobalMapping l2gmap, PetscInt N) 1190 { 1191 PetscInt n; 1192 PetscErrorCode ierr; 1193 1194 PetscFunctionBegin; 1195 PetscValidPointer(graph,1); 1196 PetscValidHeaderSpecific(l2gmap,IS_LTOGM_CLASSID,2); 1197 PetscValidLogicalCollectiveInt(l2gmap,N,3); 1198 /* raise an error if already allocated */ 1199 if (graph->nvtxs_global) SETERRQ(PetscObjectComm((PetscObject)l2gmap),PETSC_ERR_PLIB,"BDDCGraph already initialized"); 1200 /* set number of vertices */ 1201 ierr = PetscObjectReference((PetscObject)l2gmap);CHKERRQ(ierr); 1202 graph->l2gmap = l2gmap; 1203 ierr = ISLocalToGlobalMappingGetSize(l2gmap,&n);CHKERRQ(ierr); 1204 graph->nvtxs = n; 1205 graph->nvtxs_global = N; 1206 /* allocate used space */ 1207 ierr = PetscBTCreate(graph->nvtxs,&graph->touched);CHKERRQ(ierr); 1208 ierr = PetscMalloc5(graph->nvtxs,&graph->count, 1209 graph->nvtxs,&graph->neighbours_set, 1210 graph->nvtxs,&graph->subset, 1211 graph->nvtxs,&graph->which_dof, 1212 graph->nvtxs,&graph->special_dof);CHKERRQ(ierr); 1213 /* zeroes memory */ 1214 ierr = PetscMemzero(graph->count,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 1215 ierr = PetscMemzero(graph->subset,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 1216 /* use -1 as a default value for which_dof array */ 1217 for (n=0;n<graph->nvtxs;n++) graph->which_dof[n] = -1; 1218 ierr = PetscMemzero(graph->special_dof,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 1219 /* zeroes first pointer to neighbour set */ 1220 if (graph->nvtxs) { 1221 graph->neighbours_set[0] = 0; 1222 } 1223 /* zeroes workspace for values of ncc */ 1224 graph->subset_ncc = 0; 1225 graph->subset_ref_node = 0; 1226 PetscFunctionReturn(0); 1227 } 1228 1229 #undef __FUNCT__ 1230 #define __FUNCT__ "PCBDDCGraphDestroy" 1231 PetscErrorCode PCBDDCGraphDestroy(PCBDDCGraph* graph) 1232 { 1233 PetscErrorCode ierr; 1234 1235 PetscFunctionBegin; 1236 ierr = PCBDDCGraphReset(*graph);CHKERRQ(ierr); 1237 ierr = PetscFree(*graph);CHKERRQ(ierr); 1238 PetscFunctionReturn(0); 1239 } 1240 1241 #undef __FUNCT__ 1242 #define __FUNCT__ "PCBDDCGraphCreate" 1243 PetscErrorCode PCBDDCGraphCreate(PCBDDCGraph *graph) 1244 { 1245 PCBDDCGraph new_graph; 1246 PetscErrorCode ierr; 1247 1248 PetscFunctionBegin; 1249 ierr = PetscNew(&new_graph);CHKERRQ(ierr); 1250 new_graph->custom_minimal_size = 1; 1251 *graph = new_graph; 1252 PetscFunctionReturn(0); 1253 } 1254