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__ "PCBDDCGraphGetDirichletDofs" 7 PetscErrorCode PCBDDCGraphGetDirichletDofs(PCBDDCGraph graph, IS* dirdofs) 8 { 9 PetscErrorCode ierr; 10 11 PetscFunctionBegin; 12 if (graph->dirdofs) { 13 ierr = PetscObjectReference((PetscObject)graph->dirdofs);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->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->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK) dirdofs_idxs[size++] = i; 27 } 28 ierr = ISCreateGeneral(PetscObjectComm((PetscObject)graph->l2gmap),size,dirdofs_idxs,PETSC_OWN_POINTER,&graph->dirdofs);CHKERRQ(ierr); 29 ierr = PetscObjectReference((PetscObject)graph->dirdofs);CHKERRQ(ierr); 30 } 31 *dirdofs = graph->dirdofs; 32 PetscFunctionReturn(0); 33 } 34 35 #undef __FUNCT__ 36 #define __FUNCT__ "PCBDDCGraphASCIIView" 37 PetscErrorCode PCBDDCGraphASCIIView(PCBDDCGraph graph, PetscInt verbosity_level, PetscViewer viewer) 38 { 39 PetscInt i,j,tabs; 40 PetscInt* queue_in_global_numbering; 41 PetscErrorCode ierr; 42 43 PetscFunctionBegin; 44 ierr = PetscViewerASCIISynchronizedAllow(viewer,PETSC_TRUE);CHKERRQ(ierr); 45 ierr = PetscViewerASCIIGetTab(viewer,&tabs);CHKERRQ(ierr); 46 ierr = PetscViewerASCIIPrintf(viewer,"--------------------------------------------------\n");CHKERRQ(ierr); 47 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 48 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Local BDDC graph for subdomain %04d\n",PetscGlobalRank);CHKERRQ(ierr); 49 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Number of vertices %d\n",graph->nvtxs);CHKERRQ(ierr); 50 if (verbosity_level > 1) { 51 for (i=0;i<graph->nvtxs;i++) { 52 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"%d:\n",i);CHKERRQ(ierr); 53 ierr = PetscViewerASCIISynchronizedPrintf(viewer," which_dof: %d\n",graph->which_dof[i]);CHKERRQ(ierr); 54 ierr = PetscViewerASCIISynchronizedPrintf(viewer," special_dof: %d\n",graph->special_dof[i]);CHKERRQ(ierr); 55 ierr = PetscViewerASCIISynchronizedPrintf(viewer," neighbours: %d\n",graph->count[i]);CHKERRQ(ierr); 56 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 57 if (graph->count[i]) { 58 ierr = PetscViewerASCIISynchronizedPrintf(viewer," set of neighbours:");CHKERRQ(ierr); 59 for (j=0;j<graph->count[i];j++) { 60 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->neighbours_set[i][j]);CHKERRQ(ierr); 61 } 62 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"\n");CHKERRQ(ierr); 63 } 64 ierr = PetscViewerASCIISetTab(viewer,tabs);CHKERRQ(ierr); 65 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 66 if (graph->mirrors) { 67 ierr = PetscViewerASCIISynchronizedPrintf(viewer," mirrors: %d\n",graph->mirrors[i]);CHKERRQ(ierr); 68 if (graph->mirrors[i]) { 69 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 70 ierr = PetscViewerASCIISynchronizedPrintf(viewer," set of mirrors:");CHKERRQ(ierr); 71 for (j=0;j<graph->mirrors[i];j++) { 72 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->mirrors_set[i][j]);CHKERRQ(ierr); 73 } 74 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"\n");CHKERRQ(ierr); 75 ierr = PetscViewerASCIISetTab(viewer,tabs);CHKERRQ(ierr); 76 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 77 } 78 } 79 if (verbosity_level > 2) { 80 if (graph->xadj && graph->adjncy) { 81 ierr = PetscViewerASCIISynchronizedPrintf(viewer," local adj list:");CHKERRQ(ierr); 82 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 83 for (j=graph->xadj[i];j<graph->xadj[i+1];j++) { 84 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->adjncy[j]);CHKERRQ(ierr); 85 } 86 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"\n");CHKERRQ(ierr); 87 ierr = PetscViewerASCIISetTab(viewer,tabs);CHKERRQ(ierr); 88 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 89 } else { 90 ierr = PetscViewerASCIISynchronizedPrintf(viewer," no adj info\n");CHKERRQ(ierr); 91 } 92 } 93 ierr = PetscViewerASCIISynchronizedPrintf(viewer," interface subset id: %d\n",graph->subset[i]);CHKERRQ(ierr); 94 if (graph->subset[i] && graph->subset_ncc) { 95 ierr = PetscViewerASCIISynchronizedPrintf(viewer," ncc for subset: %d\n",graph->subset_ncc[graph->subset[i]-1]);CHKERRQ(ierr); 96 } 97 } 98 } 99 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Total number of connected components %d\n",graph->ncc);CHKERRQ(ierr); 100 ierr = PetscMalloc1(graph->cptr[graph->ncc],&queue_in_global_numbering);CHKERRQ(ierr); 101 ierr = ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_in_global_numbering);CHKERRQ(ierr); 102 for (i=0;i<graph->ncc;i++) { 103 PetscInt node_num=graph->queue[graph->cptr[i]]; 104 PetscBool printcc = PETSC_FALSE; 105 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d (neighs:",i);CHKERRQ(ierr); 106 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 107 for (j=0;j<graph->count[node_num];j++) { 108 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->neighbours_set[node_num][j]);CHKERRQ(ierr); 109 } 110 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"):");CHKERRQ(ierr); 111 if (verbosity_level > 1) { 112 printcc = PETSC_TRUE; 113 } else if (graph->count[node_num] > 1 || (graph->count[node_num] == 1 && graph->special_dof[node_num] == PCBDDCGRAPH_NEUMANN_MARK)) { 114 printcc = PETSC_TRUE; 115 } 116 if (printcc) { 117 for (j=graph->cptr[i];j<graph->cptr[i+1];j++) { 118 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d (%d)",graph->queue[j],queue_in_global_numbering[j]);CHKERRQ(ierr); 119 } 120 } 121 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"\n");CHKERRQ(ierr); 122 ierr = PetscViewerASCIISetTab(viewer,tabs);CHKERRQ(ierr); 123 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 124 } 125 ierr = PetscFree(queue_in_global_numbering);CHKERRQ(ierr); 126 if (graph->custom_minimal_size > 1 && verbosity_level > 1) { 127 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Custom minimal size %d\n",graph->custom_minimal_size);CHKERRQ(ierr); 128 } 129 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 130 PetscFunctionReturn(0); 131 } 132 133 #undef __FUNCT__ 134 #define __FUNCT__ "PCBDDCGraphGetCandidatesIS" 135 PetscErrorCode PCBDDCGraphGetCandidatesIS(PCBDDCGraph graph, PetscInt *n_faces, IS *FacesIS[], PetscInt *n_edges, IS *EdgesIS[], IS *VerticesIS) 136 { 137 IS *ISForFaces,*ISForEdges,ISForVertices; 138 PetscInt i,nfc,nec,nvc,*idx; 139 PetscErrorCode ierr; 140 141 PetscFunctionBegin; 142 /* loop on ccs to evalute number of faces, edges and vertices */ 143 nfc = 0; 144 nec = 0; 145 nvc = 0; 146 for (i=0;i<graph->ncc;i++) { 147 PetscInt repdof = graph->queue[graph->cptr[i]]; 148 if (graph->cptr[i+1]-graph->cptr[i] > graph->custom_minimal_size) { 149 if (graph->count[repdof] == 1 && graph->special_dof[repdof] != PCBDDCGRAPH_NEUMANN_MARK) { 150 nfc++; 151 } else { /* note that nec will be zero in 2d */ 152 nec++; 153 } 154 } else { 155 nvc += graph->cptr[i+1]-graph->cptr[i]; 156 } 157 } 158 159 /* check if we are in 2D or 3D */ 160 if (graph->twodim) { /* we are in a 2D case -> edges are shared by 2 subregions and faces don't exist */ 161 nec = nfc; 162 nfc = 0; 163 } 164 165 /* allocate IS arrays for faces, edges. Vertices need a single index set. */ 166 if (FacesIS) { 167 ierr = PetscMalloc1(nfc,&ISForFaces);CHKERRQ(ierr); 168 } 169 if (EdgesIS) { 170 ierr = PetscMalloc1(nec,&ISForEdges);CHKERRQ(ierr); 171 } 172 if (VerticesIS) { 173 ierr = PetscMalloc1(nvc,&idx);CHKERRQ(ierr); 174 } 175 176 /* loop on ccs to compute index sets for faces and edges */ 177 if (!graph->queue_sorted) { 178 PetscInt *queue_global; 179 180 ierr = PetscMalloc1(graph->cptr[graph->ncc],&queue_global);CHKERRQ(ierr); 181 ierr = ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_global);CHKERRQ(ierr); 182 for (i=0;i<graph->ncc;i++) { 183 ierr = PetscSortIntWithArray(graph->cptr[i+1]-graph->cptr[i],&queue_global[graph->cptr[i]],&graph->queue[graph->cptr[i]]);CHKERRQ(ierr); 184 } 185 ierr = PetscFree(queue_global);CHKERRQ(ierr); 186 graph->queue_sorted = PETSC_TRUE; 187 } 188 nfc = 0; 189 nec = 0; 190 for (i=0;i<graph->ncc;i++) { 191 PetscInt repdof = graph->queue[graph->cptr[i]]; 192 if (graph->cptr[i+1]-graph->cptr[i] > graph->custom_minimal_size) { 193 if (graph->count[repdof] == 1 && graph->special_dof[repdof] != PCBDDCGRAPH_NEUMANN_MARK) { 194 if (graph->twodim) { 195 if (EdgesIS) { 196 ierr = ISCreateGeneral(PETSC_COMM_SELF,graph->cptr[i+1]-graph->cptr[i],&graph->queue[graph->cptr[i]],PETSC_COPY_VALUES,&ISForEdges[nec]);CHKERRQ(ierr); 197 } 198 nec++; 199 } else { 200 if (FacesIS) { 201 ierr = ISCreateGeneral(PETSC_COMM_SELF,graph->cptr[i+1]-graph->cptr[i],&graph->queue[graph->cptr[i]],PETSC_COPY_VALUES,&ISForFaces[nfc]);CHKERRQ(ierr); 202 } 203 nfc++; 204 } 205 } else { 206 if (EdgesIS) { 207 ierr = ISCreateGeneral(PETSC_COMM_SELF,graph->cptr[i+1]-graph->cptr[i],&graph->queue[graph->cptr[i]],PETSC_COPY_VALUES,&ISForEdges[nec]);CHKERRQ(ierr); 208 } 209 nec++; 210 } 211 } 212 } 213 /* index set for vertices */ 214 if (VerticesIS) { 215 nvc = 0; 216 for (i=0;i<graph->ncc;i++) { 217 if (graph->cptr[i+1]-graph->cptr[i] <= graph->custom_minimal_size) { 218 PetscInt j; 219 220 for (j=graph->cptr[i];j<graph->cptr[i+1];j++) { 221 idx[nvc]=graph->queue[j]; 222 nvc++; 223 } 224 } 225 } 226 /* sort vertex set (by local ordering) */ 227 ierr = PetscSortInt(nvc,idx);CHKERRQ(ierr); 228 ierr = ISCreateGeneral(PETSC_COMM_SELF,nvc,idx,PETSC_OWN_POINTER,&ISForVertices);CHKERRQ(ierr); 229 } 230 /* get back info */ 231 if (n_faces) *n_faces = nfc; 232 if (FacesIS) { 233 *FacesIS = ISForFaces; 234 } 235 if (n_edges) *n_edges = nec; 236 if (EdgesIS) { 237 *EdgesIS = ISForEdges; 238 } 239 if (VerticesIS) { 240 *VerticesIS = ISForVertices; 241 } 242 PetscFunctionReturn(0); 243 } 244 245 #undef __FUNCT__ 246 #define __FUNCT__ "PCBDDCGraphComputeConnectedComponents" 247 PetscErrorCode PCBDDCGraphComputeConnectedComponents(PCBDDCGraph graph) 248 { 249 PetscBool adapt_interface_reduced; 250 MPI_Comm interface_comm; 251 PetscMPIInt size; 252 PetscInt i; 253 PetscBool twodim; 254 PetscErrorCode ierr; 255 256 PetscFunctionBegin; 257 /* compute connected components locally */ 258 ierr = PetscObjectGetComm((PetscObject)(graph->l2gmap),&interface_comm);CHKERRQ(ierr); 259 ierr = PCBDDCGraphComputeConnectedComponentsLocal(graph);CHKERRQ(ierr); 260 /* check consistency of connected components among neighbouring subdomains -> it adapt them in case it is needed */ 261 ierr = MPI_Comm_size(interface_comm,&size);CHKERRQ(ierr); 262 adapt_interface_reduced = PETSC_FALSE; 263 if (size > 1) { 264 PetscInt i; 265 PetscBool adapt_interface = PETSC_FALSE; 266 for (i=0;i<graph->n_subsets;i++) { 267 /* We are not sure that on a given subset of the local interface, 268 with two connected components, the latters be the same among sharing subdomains */ 269 if (graph->subset_ncc[i] > 1) { 270 adapt_interface = PETSC_TRUE; 271 break; 272 } 273 } 274 ierr = MPI_Allreduce(&adapt_interface,&adapt_interface_reduced,1,MPIU_BOOL,MPI_LOR,interface_comm);CHKERRQ(ierr); 275 } 276 277 if (graph->n_subsets && adapt_interface_reduced) { 278 /* old csr stuff */ 279 PetscInt *aux_new_xadj,*new_xadj,*new_adjncy; 280 PetscInt *old_xadj,*old_adjncy; 281 PetscBT subset_cc_adapt; 282 /* MPI */ 283 MPI_Request *send_requests,*recv_requests; 284 PetscInt *send_buffer,*recv_buffer; 285 PetscInt sum_requests,start_of_recv,start_of_send; 286 PetscInt *cum_recv_counts; 287 /* others */ 288 PetscInt *labels; 289 PetscInt global_subset_counter; 290 PetscInt j,k,s; 291 292 /* Retrict adjacency graph using information from previously computed connected components */ 293 ierr = PetscMalloc1(graph->nvtxs,&aux_new_xadj);CHKERRQ(ierr); 294 for (i=0;i<graph->nvtxs;i++) { 295 aux_new_xadj[i]=1; 296 } 297 for (i=0;i<graph->ncc;i++) { 298 k = graph->cptr[i+1]-graph->cptr[i]; 299 for (j=0;j<k;j++) { 300 aux_new_xadj[graph->queue[graph->cptr[i]+j]]=k; 301 } 302 } 303 j = 0; 304 for (i=0;i<graph->nvtxs;i++) { 305 j += aux_new_xadj[i]; 306 } 307 ierr = PetscMalloc1(graph->nvtxs+1,&new_xadj);CHKERRQ(ierr); 308 ierr = PetscMalloc1(j,&new_adjncy);CHKERRQ(ierr); 309 new_xadj[0]=0; 310 for (i=0;i<graph->nvtxs;i++) { 311 new_xadj[i+1]=new_xadj[i]+aux_new_xadj[i]; 312 if (aux_new_xadj[i]==1) { 313 new_adjncy[new_xadj[i]]=i; 314 } 315 } 316 ierr = PetscFree(aux_new_xadj);CHKERRQ(ierr); 317 ierr = PetscMalloc1(graph->nvtxs,&labels);CHKERRQ(ierr); 318 ierr = PetscMemzero(labels,graph->nvtxs*sizeof(*labels));CHKERRQ(ierr); 319 for (i=0;i<graph->ncc;i++) { 320 k = graph->cptr[i+1]-graph->cptr[i]; 321 for (j=0;j<k;j++) { 322 ierr = PetscMemcpy(&new_adjncy[new_xadj[graph->queue[graph->cptr[i]+j]]],&graph->queue[graph->cptr[i]],k*sizeof(PetscInt));CHKERRQ(ierr); 323 labels[graph->queue[graph->cptr[i]+j]] = i; 324 } 325 } 326 /* set temporarly new CSR into graph */ 327 old_xadj = graph->xadj; 328 old_adjncy = graph->adjncy; 329 graph->xadj = new_xadj; 330 graph->adjncy = new_adjncy; 331 /* allocate some space */ 332 ierr = PetscMalloc1(graph->n_subsets+1,&cum_recv_counts);CHKERRQ(ierr); 333 ierr = PetscMemzero(cum_recv_counts,(graph->n_subsets+1)*sizeof(*cum_recv_counts));CHKERRQ(ierr); 334 /* first count how many neighbours per connected component I will receive from */ 335 cum_recv_counts[0]=0; 336 for (i=0;i<graph->n_subsets;i++) { 337 cum_recv_counts[i+1]=cum_recv_counts[i]+graph->count[graph->subsets[i][0]]; 338 } 339 ierr = PetscMalloc1(cum_recv_counts[graph->n_subsets],&recv_buffer);CHKERRQ(ierr); 340 ierr = PetscMalloc2(cum_recv_counts[graph->n_subsets],&send_requests,cum_recv_counts[graph->n_subsets],&recv_requests);CHKERRQ(ierr); 341 for (i=0;i<cum_recv_counts[graph->n_subsets];i++) { 342 send_requests[i]=MPI_REQUEST_NULL; 343 recv_requests[i]=MPI_REQUEST_NULL; 344 } 345 /* exchange with my neighbours the number of my connected components on the subset of interface */ 346 sum_requests = 0; 347 for (i=0;i<graph->n_subsets;i++) { 348 PetscMPIInt neigh,tag; 349 350 j = graph->subsets[i][0]; 351 ierr = PetscMPIIntCast(2*graph->subset_ref_node[i],&tag);CHKERRQ(ierr); 352 for (k=0;k<graph->count[j];k++) { 353 ierr = PetscMPIIntCast(graph->neighbours_set[j][k],&neigh);CHKERRQ(ierr); 354 ierr = MPI_Isend(&graph->subset_ncc[i],1,MPIU_INT,neigh,tag,interface_comm,&send_requests[sum_requests]);CHKERRQ(ierr); 355 ierr = MPI_Irecv(&recv_buffer[sum_requests],1,MPIU_INT,neigh,tag,interface_comm,&recv_requests[sum_requests]);CHKERRQ(ierr); 356 sum_requests++; 357 } 358 } 359 ierr = MPI_Waitall(sum_requests,recv_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 360 ierr = MPI_Waitall(sum_requests,send_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 361 /* determine the subsets I have to adapt */ 362 ierr = PetscBTCreate(graph->n_subsets,&subset_cc_adapt);CHKERRQ(ierr); 363 ierr = PetscBTMemzero(graph->n_subsets,subset_cc_adapt);CHKERRQ(ierr); 364 for (i=0;i<graph->n_subsets;i++) { 365 for (j=cum_recv_counts[i];j<cum_recv_counts[i+1];j++){ 366 /* adapt if more than one cc is present */ 367 if (graph->subset_ncc[i] > 1 || recv_buffer[j] > 1) { 368 ierr = PetscBTSet(subset_cc_adapt,i); 369 break; 370 } 371 } 372 } 373 ierr = PetscFree(recv_buffer);CHKERRQ(ierr); 374 /* determine send/recv buffers sizes */ 375 j = 0; 376 for (i=0;i<graph->n_subsets;i++) { 377 if (PetscBTLookup(subset_cc_adapt,i)) { 378 j += graph->subsets_size[i]; 379 } 380 } 381 k = 0; 382 for (i=0;i<graph->n_subsets;i++) { 383 if (PetscBTLookup(subset_cc_adapt,i)) { 384 k += (cum_recv_counts[i+1]-cum_recv_counts[i])*graph->subsets_size[i]; 385 } 386 } 387 ierr = PetscMalloc2(j,&send_buffer,k,&recv_buffer);CHKERRQ(ierr); 388 389 /* fill send buffer */ 390 j = 0; 391 for (i=0;i<graph->n_subsets;i++) { 392 if (PetscBTLookup(subset_cc_adapt,i)) { 393 for (k=0;k<graph->subsets_size[i];k++) { 394 send_buffer[j++] = labels[graph->subsets[i][k]]; 395 } 396 } 397 } 398 ierr = PetscFree(labels);CHKERRQ(ierr); 399 400 /* now exchange the data */ 401 start_of_recv = 0; 402 start_of_send = 0; 403 sum_requests = 0; 404 for (i=0;i<graph->n_subsets;i++) { 405 if (PetscBTLookup(subset_cc_adapt,i)) { 406 PetscMPIInt neigh,tag; 407 PetscInt size_of_send = graph->subsets_size[i]; 408 409 j = graph->subsets[i][0]; 410 ierr = PetscMPIIntCast(2*graph->subset_ref_node[i]+1,&tag);CHKERRQ(ierr); 411 for (k=0;k<graph->count[j];k++) { 412 ierr = PetscMPIIntCast(graph->neighbours_set[j][k],&neigh);CHKERRQ(ierr); 413 ierr = MPI_Isend(&send_buffer[start_of_send],size_of_send,MPIU_INT,neigh,tag,interface_comm,&send_requests[sum_requests]);CHKERRQ(ierr); 414 ierr = MPI_Irecv(&recv_buffer[start_of_recv],size_of_send,MPIU_INT,neigh,tag,interface_comm,&recv_requests[sum_requests]);CHKERRQ(ierr); 415 start_of_recv += size_of_send; 416 sum_requests++; 417 } 418 start_of_send += size_of_send; 419 } 420 } 421 ierr = MPI_Waitall(sum_requests,recv_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 422 ierr = MPI_Waitall(sum_requests,send_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 423 ierr = PetscFree2(send_requests,recv_requests);CHKERRQ(ierr); 424 425 start_of_recv = 0; 426 global_subset_counter = 0; 427 for (i=0;i<graph->n_subsets;i++) { 428 if (PetscBTLookup(subset_cc_adapt,i)) { 429 PetscInt **temp_buffer,temp_buffer_size,*private_label; 430 431 /* allocate some temporary space */ 432 temp_buffer_size = graph->subsets_size[i]; 433 ierr = PetscMalloc1(temp_buffer_size,&temp_buffer);CHKERRQ(ierr); 434 ierr = PetscMalloc1(temp_buffer_size*(cum_recv_counts[i+1]-cum_recv_counts[i]),&temp_buffer[0]);CHKERRQ(ierr); 435 ierr = PetscMemzero(temp_buffer[0],temp_buffer_size*(cum_recv_counts[i+1]-cum_recv_counts[i])*sizeof(PetscInt));CHKERRQ(ierr); 436 for (j=1;j<temp_buffer_size;j++) { 437 temp_buffer[j] = temp_buffer[j-1]+cum_recv_counts[i+1]-cum_recv_counts[i]; 438 } 439 /* analyze contributions from neighbouring subdomains for i-th subset 440 temp buffer structure: 441 supposing part of the interface has dimension 5 442 e.g with global dofs 0,1,2,3,4, locally ordered on the current process as 0,4,3,1,2 443 3 neighs procs having connected components: 444 neigh 0: [0 1 4], [2 3], labels [4,7] (2 connected components) 445 neigh 1: [0 1], [2 3 4], labels [3 2] (2 connected components) 446 neigh 2: [0 4], [1], [2 3], labels [1 5 6] (3 connected components) 447 tempbuffer (row-oriented) will be filled as: 448 [ 4, 3, 1; 449 4, 2, 1; 450 7, 2, 6; 451 4, 3, 5; 452 7, 2, 6; ]; 453 This way we can simply find intersections of ccs among neighs. 454 The graph->subset array will need to be modified. The output for the example is [0], [1], [2 3], [4]; 455 */ 456 for (j=0;j<cum_recv_counts[i+1]-cum_recv_counts[i];j++) { 457 for (k=0;k<temp_buffer_size;k++) { 458 temp_buffer[k][j] = recv_buffer[start_of_recv+k]; 459 } 460 start_of_recv += temp_buffer_size; 461 } 462 ierr = PetscMalloc1(temp_buffer_size,&private_label);CHKERRQ(ierr); 463 ierr = PetscMemzero(private_label,temp_buffer_size*sizeof(*private_label));CHKERRQ(ierr); 464 for (j=0;j<temp_buffer_size;j++) { 465 if (!private_label[j]) { /* found a new cc */ 466 PetscBool same_set; 467 468 global_subset_counter++; 469 private_label[j] = global_subset_counter; 470 for (k=j+1;k<temp_buffer_size;k++) { /* check for other nodes in new cc */ 471 same_set = PETSC_TRUE; 472 for (s=0;s<cum_recv_counts[i+1]-cum_recv_counts[i];s++) { 473 if (temp_buffer[j][s] != temp_buffer[k][s]) { 474 same_set = PETSC_FALSE; 475 break; 476 } 477 } 478 if (same_set) { 479 private_label[k] = global_subset_counter; 480 } 481 } 482 } 483 } 484 /* insert private labels in graph structure */ 485 for (j=0;j<graph->subsets_size[i];j++) { 486 graph->subset[graph->subsets[i][j]] = graph->n_subsets+private_label[j]; 487 } 488 ierr = PetscFree(private_label);CHKERRQ(ierr); 489 ierr = PetscFree(temp_buffer[0]);CHKERRQ(ierr); 490 ierr = PetscFree(temp_buffer);CHKERRQ(ierr); 491 } 492 } 493 ierr = PetscFree2(send_buffer,recv_buffer);CHKERRQ(ierr); 494 ierr = PetscFree(cum_recv_counts);CHKERRQ(ierr); 495 ierr = PetscBTDestroy(&subset_cc_adapt);CHKERRQ(ierr); 496 /* We are ready to find for connected components which are consistent among neighbouring subdomains */ 497 if (global_subset_counter) { 498 ierr = PetscBTMemzero(graph->nvtxs,graph->touched);CHKERRQ(ierr); 499 global_subset_counter = 0; 500 for (i=0;i<graph->nvtxs;i++) { 501 if (graph->subset[i] && !PetscBTLookup(graph->touched,i)) { 502 global_subset_counter++; 503 for (j=i+1;j<graph->nvtxs;j++) { 504 if (!PetscBTLookup(graph->touched,j) && graph->subset[j]==graph->subset[i]) { 505 graph->subset[j] = global_subset_counter; 506 ierr = PetscBTSet(graph->touched,j);CHKERRQ(ierr); 507 } 508 } 509 graph->subset[i] = global_subset_counter; 510 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 511 } 512 } 513 /* refine connected components locally */ 514 ierr = PCBDDCGraphComputeConnectedComponentsLocal(graph);CHKERRQ(ierr); 515 } 516 /* restore original CSR graph of dofs */ 517 ierr = PetscFree(new_xadj);CHKERRQ(ierr); 518 ierr = PetscFree(new_adjncy);CHKERRQ(ierr); 519 graph->xadj = old_xadj; 520 graph->adjncy = old_adjncy; 521 } 522 523 /* Determine if we are in 2D or 3D */ 524 twodim = PETSC_TRUE; 525 for (i=0;i<graph->ncc;i++) { 526 PetscInt repdof = graph->queue[graph->cptr[i]]; 527 if (graph->cptr[i+1]-graph->cptr[i] > graph->custom_minimal_size) { 528 if (graph->count[repdof] > 1 || graph->special_dof[repdof] == PCBDDCGRAPH_NEUMANN_MARK) { 529 twodim = PETSC_FALSE; 530 break; 531 } 532 } 533 } 534 ierr = MPI_Allreduce(&twodim,&graph->twodim,1,MPIU_BOOL,MPI_LAND,PetscObjectComm((PetscObject)graph->l2gmap));CHKERRQ(ierr); 535 PetscFunctionReturn(0); 536 } 537 538 /* The following code has been adapted from function IsConnectedSubdomain contained 539 in source file contig.c of METIS library (version 5.0.1) 540 It finds connected components for each subset */ 541 #undef __FUNCT__ 542 #define __FUNCT__ "PCBDDCGraphComputeConnectedComponentsLocal" 543 PetscErrorCode PCBDDCGraphComputeConnectedComponentsLocal(PCBDDCGraph graph) 544 { 545 PetscInt i,j,k,first,last,nleft,ncc,pid,cum_queue,n,ncc_pid; 546 PetscMPIInt size; 547 PetscErrorCode ierr; 548 549 PetscFunctionBegin; 550 /* quiet return if no csr info is available */ 551 if (!graph->xadj || !graph->adjncy) { 552 PetscFunctionReturn(0); 553 } 554 555 /* reset any previous search of connected components */ 556 ierr = PetscBTMemzero(graph->nvtxs,graph->touched);CHKERRQ(ierr); 557 graph->n_subsets = 0; 558 ierr = MPI_Comm_size(PetscObjectComm((PetscObject)graph->l2gmap),&size);CHKERRQ(ierr); 559 if (size == 1) { 560 if (graph->nvtxs) { 561 graph->n_subsets = 1; 562 for (i=0;i<graph->nvtxs;i++) { 563 graph->subset[i] = 1; 564 } 565 } 566 } else { 567 for (i=0;i<graph->nvtxs;i++) { 568 if (graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK || !graph->count[i]) { 569 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 570 graph->subset[i] = 0; 571 } 572 graph->n_subsets = PetscMax(graph->n_subsets,graph->subset[i]); 573 } 574 } 575 ierr = PetscFree(graph->subset_ncc);CHKERRQ(ierr); 576 ierr = PetscMalloc1(graph->n_subsets,&graph->subset_ncc);CHKERRQ(ierr); 577 578 /* begin search for connected components */ 579 cum_queue = 0; 580 ncc = 0; 581 for (n=0;n<graph->n_subsets;n++) { 582 pid = n+1; /* partition labeled by 0 is discarded */ 583 nleft = 0; 584 for (i=0;i<graph->nvtxs;i++) { 585 if (graph->subset[i] == pid) { 586 nleft++; 587 } 588 } 589 for (i=0; i<graph->nvtxs; i++) { 590 if (graph->subset[i] == pid) { 591 break; 592 } 593 } 594 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 595 graph->queue[cum_queue] = i; 596 first = 0; 597 last = 1; 598 graph->cptr[ncc] = cum_queue; 599 ncc_pid = 0; 600 while (first != nleft) { 601 if (first == last) { 602 graph->cptr[++ncc] = first+cum_queue; 603 ncc_pid++; 604 for (i=0; i<graph->nvtxs; i++) { /* TODO-> use a while! */ 605 if (graph->subset[i] == pid && !PetscBTLookup(graph->touched,i)) { 606 break; 607 } 608 } 609 graph->queue[cum_queue+last] = i; 610 last++; 611 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 612 } 613 i = graph->queue[cum_queue+first]; 614 first++; 615 for (j=graph->xadj[i];j<graph->xadj[i+1];j++) { 616 k = graph->adjncy[j]; 617 if (graph->subset[k] == pid && !PetscBTLookup(graph->touched,k)) { 618 graph->queue[cum_queue+last] = k; 619 last++; 620 ierr = PetscBTSet(graph->touched,k);CHKERRQ(ierr); 621 } 622 } 623 } 624 graph->cptr[++ncc] = first+cum_queue; 625 ncc_pid++; 626 cum_queue = graph->cptr[ncc]; 627 graph->subset_ncc[n] = ncc_pid; 628 } 629 graph->ncc = ncc; 630 graph->queue_sorted = PETSC_FALSE; 631 PetscFunctionReturn(0); 632 } 633 634 #undef __FUNCT__ 635 #define __FUNCT__ "PCBDDCGraphSetUp" 636 PetscErrorCode PCBDDCGraphSetUp(PCBDDCGraph graph, PetscInt custom_minimal_size, IS neumann_is, IS dirichlet_is, PetscInt n_ISForDofs, IS ISForDofs[], IS custom_primal_vertices) 637 { 638 VecScatter scatter_ctx; 639 Vec local_vec,local_vec2,global_vec; 640 IS to,from; 641 MPI_Comm comm; 642 PetscScalar *array,*array2; 643 const PetscInt *is_indices; 644 PetscInt n_neigh,*neigh,*n_shared,**shared,*queue_global,*subset_ref_node_global; 645 PetscInt i,j,k,s,total_counts,nodes_touched,is_size; 646 PetscMPIInt size; 647 PetscBool same_set,mirrors_found; 648 PetscErrorCode ierr; 649 650 PetscFunctionBegin; 651 graph->has_dirichlet = PETSC_FALSE; 652 if (dirichlet_is) { 653 PetscCheckSameComm(graph->l2gmap,1,dirichlet_is,4); 654 graph->has_dirichlet = PETSC_TRUE; 655 } 656 ierr = PetscObjectGetComm((PetscObject)(graph->l2gmap),&comm);CHKERRQ(ierr); 657 /* custom_minimal_size */ 658 graph->custom_minimal_size = PetscMax(graph->custom_minimal_size,custom_minimal_size); 659 /* get info l2gmap and allocate work vectors */ 660 ierr = ISLocalToGlobalMappingGetInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);CHKERRQ(ierr); 661 /* check if we have any local periodic nodes (periodic BCs) */ 662 mirrors_found = PETSC_FALSE; 663 if (graph->nvtxs && n_neigh) { 664 for (i=0; i<n_shared[0]; i++) graph->count[shared[0][i]] += 1; 665 for (i=0; i<n_shared[0]; i++) { 666 if (graph->count[shared[0][i]] > 1) { 667 mirrors_found = PETSC_TRUE; 668 break; 669 } 670 } 671 } 672 /* create some workspace objects */ 673 local_vec = NULL; 674 local_vec2 = NULL; 675 global_vec = NULL; 676 to = NULL; 677 from = NULL; 678 scatter_ctx = NULL; 679 if (n_ISForDofs || dirichlet_is || neumann_is || custom_primal_vertices) { 680 ierr = VecCreate(PETSC_COMM_SELF,&local_vec);CHKERRQ(ierr); 681 ierr = VecSetSizes(local_vec,PETSC_DECIDE,graph->nvtxs);CHKERRQ(ierr); 682 ierr = VecSetType(local_vec,VECSTANDARD);CHKERRQ(ierr); 683 ierr = VecDuplicate(local_vec,&local_vec2);CHKERRQ(ierr); 684 ierr = VecCreate(comm,&global_vec);CHKERRQ(ierr); 685 ierr = VecSetSizes(global_vec,PETSC_DECIDE,graph->nvtxs_global);CHKERRQ(ierr); 686 ierr = VecSetType(global_vec,VECSTANDARD);CHKERRQ(ierr); 687 ierr = ISCreateStride(PETSC_COMM_SELF,graph->nvtxs,0,1,&to);CHKERRQ(ierr); 688 ierr = ISLocalToGlobalMappingApplyIS(graph->l2gmap,to,&from);CHKERRQ(ierr); 689 ierr = VecScatterCreate(global_vec,from,local_vec,to,&scatter_ctx);CHKERRQ(ierr); 690 } else if (mirrors_found) { 691 ierr = ISCreateStride(PETSC_COMM_SELF,graph->nvtxs,0,1,&to);CHKERRQ(ierr); 692 ierr = ISLocalToGlobalMappingApplyIS(graph->l2gmap,to,&from);CHKERRQ(ierr); 693 } 694 /* compute local mirrors (if any) */ 695 if (mirrors_found) { 696 PetscInt *local_indices,*global_indices; 697 /* get arrays of local and global indices */ 698 ierr = PetscMalloc1(graph->nvtxs,&local_indices);CHKERRQ(ierr); 699 ierr = ISGetIndices(to,(const PetscInt**)&is_indices);CHKERRQ(ierr); 700 ierr = PetscMemcpy(local_indices,is_indices,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 701 ierr = ISRestoreIndices(to,(const PetscInt**)&is_indices);CHKERRQ(ierr); 702 ierr = PetscMalloc1(graph->nvtxs,&global_indices);CHKERRQ(ierr); 703 ierr = ISGetIndices(from,(const PetscInt**)&is_indices);CHKERRQ(ierr); 704 ierr = PetscMemcpy(global_indices,is_indices,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 705 ierr = ISRestoreIndices(from,(const PetscInt**)&is_indices);CHKERRQ(ierr); 706 /* allocate space for mirrors */ 707 ierr = PetscMalloc2(graph->nvtxs,&graph->mirrors,graph->nvtxs,&graph->mirrors_set);CHKERRQ(ierr); 708 ierr = PetscMemzero(graph->mirrors,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 709 graph->mirrors_set[0] = 0; 710 711 k=0; 712 for (i=0;i<n_shared[0];i++) { 713 j=shared[0][i]; 714 if (graph->count[j] > 1) { 715 graph->mirrors[j]++; 716 k++; 717 } 718 } 719 /* allocate space for set of mirrors */ 720 ierr = PetscMalloc1(k,&graph->mirrors_set[0]);CHKERRQ(ierr); 721 for (i=1;i<graph->nvtxs;i++) 722 graph->mirrors_set[i]=graph->mirrors_set[i-1]+graph->mirrors[i-1]; 723 724 /* fill arrays */ 725 ierr = PetscMemzero(graph->mirrors,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 726 for (j=0;j<n_shared[0];j++) { 727 i=shared[0][j]; 728 if (graph->count[i] > 1) 729 graph->mirrors_set[i][graph->mirrors[i]++]=global_indices[i]; 730 } 731 ierr = PetscSortIntWithArray(graph->nvtxs,global_indices,local_indices);CHKERRQ(ierr); 732 for (i=0;i<graph->nvtxs;i++) { 733 if (graph->mirrors[i] > 0) { 734 ierr = PetscFindInt(graph->mirrors_set[i][0],graph->nvtxs,global_indices,&k);CHKERRQ(ierr); 735 j = global_indices[k]; 736 while ( k > 0 && global_indices[k-1] == j) k--; 737 for (j=0;j<graph->mirrors[i];j++) { 738 graph->mirrors_set[i][j]=local_indices[k+j]; 739 } 740 ierr = PetscSortInt(graph->mirrors[i],graph->mirrors_set[i]);CHKERRQ(ierr); 741 } 742 } 743 ierr = PetscFree(local_indices);CHKERRQ(ierr); 744 ierr = PetscFree(global_indices);CHKERRQ(ierr); 745 } 746 ierr = PetscMemzero(graph->count,graph->nvtxs*sizeof(*graph->count));CHKERRQ(ierr); 747 ierr = ISDestroy(&to);CHKERRQ(ierr); 748 ierr = ISDestroy(&from);CHKERRQ(ierr); 749 750 /* Count total number of neigh per node */ 751 k=0; 752 for (i=1;i<n_neigh;i++) { 753 k += n_shared[i]; 754 for (j=0;j<n_shared[i];j++) { 755 graph->count[shared[i][j]] += 1; 756 } 757 } 758 /* Allocate space for storing the set of neighbours for each node */ 759 if (graph->nvtxs) { 760 ierr = PetscMalloc1(k,&graph->neighbours_set[0]);CHKERRQ(ierr); 761 } 762 for (i=1;i<graph->nvtxs;i++) { /* dont count myself */ 763 graph->neighbours_set[i]=graph->neighbours_set[i-1]+graph->count[i-1]; 764 } 765 /* Get information for sharing subdomains */ 766 ierr = PetscMemzero(graph->count,graph->nvtxs*sizeof(*graph->count));CHKERRQ(ierr); 767 for (i=1;i<n_neigh;i++) { /* dont count myself */ 768 s = n_shared[i]; 769 for (j=0;j<s;j++) { 770 k = shared[i][j]; 771 graph->neighbours_set[k][graph->count[k]] = neigh[i]; 772 graph->count[k] += 1; 773 } 774 } 775 /* sort set of sharing subdomains */ 776 for (i=0;i<graph->nvtxs;i++) { 777 ierr = PetscSortRemoveDupsInt(&graph->count[i],graph->neighbours_set[i]);CHKERRQ(ierr); 778 } 779 /* free memory allocated by ISLocalToGlobalMappingGetInfo */ 780 ierr = ISLocalToGlobalMappingRestoreInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);CHKERRQ(ierr); 781 782 /* 783 Get info for dofs splitting 784 User can specify just a subset; an additional field is considered as a complementary field 785 */ 786 for (i=0;i<graph->nvtxs;i++) { 787 graph->which_dof[i] = n_ISForDofs; /* by default a dof belongs to the complement set */ 788 } 789 if (n_ISForDofs) { 790 ierr = VecSet(local_vec,-1.0);CHKERRQ(ierr); 791 } 792 for (i=0;i<n_ISForDofs;i++) { 793 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 794 ierr = ISGetLocalSize(ISForDofs[i],&is_size);CHKERRQ(ierr); 795 ierr = ISGetIndices(ISForDofs[i],(const PetscInt**)&is_indices);CHKERRQ(ierr); 796 for (j=0;j<is_size;j++) { 797 if (is_indices[j] > -1 && is_indices[j] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */ 798 graph->which_dof[is_indices[j]] = i; 799 array[is_indices[j]] = 1.*i; 800 } 801 } 802 ierr = ISRestoreIndices(ISForDofs[i],(const PetscInt**)&is_indices);CHKERRQ(ierr); 803 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 804 } 805 /* Check consistency among neighbours */ 806 if (n_ISForDofs) { 807 ierr = VecScatterBegin(scatter_ctx,local_vec,global_vec,INSERT_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 808 ierr = VecScatterEnd(scatter_ctx,local_vec,global_vec,INSERT_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 809 ierr = VecScatterBegin(scatter_ctx,global_vec,local_vec2,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 810 ierr = VecScatterEnd(scatter_ctx,global_vec,local_vec2,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 811 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 812 ierr = VecGetArray(local_vec2,&array2);CHKERRQ(ierr); 813 for (i=0;i<graph->nvtxs;i++){ 814 PetscInt field1,field2; 815 816 field1 = (PetscInt)PetscRealPart(array[i]); 817 field2 = (PetscInt)PetscRealPart(array2[i]); 818 if (field1 != field2) { 819 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); 820 } 821 } 822 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 823 ierr = VecRestoreArray(local_vec2,&array2);CHKERRQ(ierr); 824 } 825 if (neumann_is || dirichlet_is) { 826 /* Take into account Neumann nodes */ 827 ierr = VecSet(local_vec,0.0);CHKERRQ(ierr); 828 ierr = VecSet(local_vec2,0.0);CHKERRQ(ierr); 829 if (neumann_is) { 830 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 831 ierr = ISGetLocalSize(neumann_is,&is_size);CHKERRQ(ierr); 832 ierr = ISGetIndices(neumann_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); 833 for (i=0;i<is_size;i++) { 834 if (is_indices[i] > -1 && is_indices[i] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */ 835 array[is_indices[i]] = 1.0; 836 } 837 } 838 ierr = ISRestoreIndices(neumann_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); 839 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 840 } 841 /* Neumann nodes: impose consistency among neighbours */ 842 ierr = VecSet(global_vec,0.0);CHKERRQ(ierr); 843 ierr = VecScatterBegin(scatter_ctx,local_vec,global_vec,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 844 ierr = VecScatterEnd(scatter_ctx,local_vec,global_vec,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 845 ierr = VecScatterBegin(scatter_ctx,global_vec,local_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 846 ierr = VecScatterEnd(scatter_ctx,global_vec,local_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 847 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 848 for (i=0;i<graph->nvtxs;i++) { 849 if (PetscRealPart(array[i]) > 0.1) { 850 graph->special_dof[i] = PCBDDCGRAPH_NEUMANN_MARK; 851 } 852 } 853 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 854 /* Take into account Dirichlet nodes */ 855 ierr = VecSet(local_vec2,0.0);CHKERRQ(ierr); 856 if (dirichlet_is) { 857 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 858 ierr = VecGetArray(local_vec2,&array2);CHKERRQ(ierr); 859 ierr = ISGetLocalSize(dirichlet_is,&is_size);CHKERRQ(ierr); 860 ierr = ISGetIndices(dirichlet_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); 861 for (i=0;i<is_size;i++){ 862 if (is_indices[i] > -1 && is_indices[i] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */ 863 k = is_indices[i]; 864 if (graph->count[k] && !PetscBTLookup(graph->touched,k)) { 865 if (PetscRealPart(array[k]) > 0.1) { 866 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); 867 } 868 array2[k] = 1.0; 869 } 870 } 871 } 872 ierr = ISRestoreIndices(dirichlet_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); 873 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 874 ierr = VecRestoreArray(local_vec2,&array2);CHKERRQ(ierr); 875 } 876 /* Dirichlet nodes: impose consistency among neighbours */ 877 ierr = VecSet(global_vec,0.0);CHKERRQ(ierr); 878 ierr = VecScatterBegin(scatter_ctx,local_vec2,global_vec,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 879 ierr = VecScatterEnd(scatter_ctx,local_vec2,global_vec,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 880 ierr = VecScatterBegin(scatter_ctx,global_vec,local_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 881 ierr = VecScatterEnd(scatter_ctx,global_vec,local_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 882 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 883 for (i=0;i<graph->nvtxs;i++) { 884 if (PetscRealPart(array[i]) > 0.1) { 885 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 886 graph->subset[i] = 0; /* dirichlet nodes treated as internal -> is it ok? */ 887 graph->special_dof[i] = PCBDDCGRAPH_DIRICHLET_MARK; 888 } 889 } 890 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 891 } 892 /* mark local periodic nodes (if any) and adapt CSR graph (if any) */ 893 if (graph->mirrors) { 894 for (i=0;i<graph->nvtxs;i++) 895 if (graph->mirrors[i]) 896 graph->special_dof[i] = PCBDDCGRAPH_LOCAL_PERIODIC_MARK; 897 898 if (graph->xadj && graph->adjncy) { 899 PetscInt *new_xadj,*new_adjncy; 900 /* sort CSR graph */ 901 for (i=0;i<graph->nvtxs;i++) 902 ierr = PetscSortInt(graph->xadj[i+1]-graph->xadj[i],&graph->adjncy[graph->xadj[i]]);CHKERRQ(ierr); 903 904 /* adapt local CSR graph in case of local periodicity */ 905 k=0; 906 for (i=0;i<graph->nvtxs;i++) 907 for (j=graph->xadj[i];j<graph->xadj[i+1];j++) 908 k += graph->mirrors[graph->adjncy[j]]; 909 910 ierr = PetscMalloc1(graph->nvtxs+1,&new_xadj);CHKERRQ(ierr); 911 ierr = PetscMalloc1(k+graph->xadj[graph->nvtxs],&new_adjncy);CHKERRQ(ierr); 912 new_xadj[0]=0; 913 for (i=0;i<graph->nvtxs;i++) { 914 k = graph->xadj[i+1]-graph->xadj[i]; 915 ierr = PetscMemcpy(&new_adjncy[new_xadj[i]],&graph->adjncy[graph->xadj[i]],k*sizeof(PetscInt));CHKERRQ(ierr); 916 new_xadj[i+1]=new_xadj[i]+k; 917 for (j=graph->xadj[i];j<graph->xadj[i+1];j++) { 918 k = graph->mirrors[graph->adjncy[j]]; 919 ierr = PetscMemcpy(&new_adjncy[new_xadj[i+1]],graph->mirrors_set[graph->adjncy[j]],k*sizeof(PetscInt));CHKERRQ(ierr); 920 new_xadj[i+1]+=k; 921 } 922 k = new_xadj[i+1]-new_xadj[i]; 923 ierr = PetscSortRemoveDupsInt(&k,&new_adjncy[new_xadj[i]]);CHKERRQ(ierr); 924 new_xadj[i+1]=new_xadj[i]+k; 925 } 926 /* set new CSR into graph */ 927 ierr = PetscFree(graph->xadj);CHKERRQ(ierr); 928 ierr = PetscFree(graph->adjncy);CHKERRQ(ierr); 929 graph->xadj = new_xadj; 930 graph->adjncy = new_adjncy; 931 } 932 } 933 934 /* mark special nodes (if any) -> each will become a single node equivalence class */ 935 if (custom_primal_vertices) { 936 ierr = VecSet(local_vec,0.0);CHKERRQ(ierr); 937 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 938 ierr = ISGetLocalSize(custom_primal_vertices,&is_size);CHKERRQ(ierr); 939 ierr = ISGetIndices(custom_primal_vertices,(const PetscInt**)&is_indices);CHKERRQ(ierr); 940 for (i=0;i<is_size;i++){ 941 if (is_indices[i] > -1 && is_indices[i] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */ 942 array[is_indices[i]] = 1.0; 943 } 944 } 945 ierr = ISRestoreIndices(custom_primal_vertices,(const PetscInt**)&is_indices);CHKERRQ(ierr); 946 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 947 /* special nodes: impose consistency among neighbours */ 948 ierr = VecSet(global_vec,0.0);CHKERRQ(ierr); 949 ierr = VecScatterBegin(scatter_ctx,local_vec,global_vec,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 950 ierr = VecScatterEnd(scatter_ctx,local_vec,global_vec,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 951 ierr = VecScatterBegin(scatter_ctx,global_vec,local_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 952 ierr = VecScatterEnd(scatter_ctx,global_vec,local_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 953 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 954 j = 0; 955 for (i=0;i<graph->nvtxs;i++) { 956 if (PetscRealPart(array[i]) > 0.1 && graph->special_dof[i] != PCBDDCGRAPH_DIRICHLET_MARK) { 957 graph->special_dof[i] = PCBDDCGRAPH_SPECIAL_MARK-j; 958 j++; 959 } 960 } 961 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 962 } 963 964 /* mark interior nodes as touched and belonging to partition number 0 */ 965 for (i=0;i<graph->nvtxs;i++) { 966 if (!graph->count[i]) { 967 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 968 graph->subset[i] = 0; 969 } 970 } 971 /* init graph structure and compute default subsets */ 972 nodes_touched=0; 973 for (i=0;i<graph->nvtxs;i++) { 974 if (PetscBTLookup(graph->touched,i)) { 975 nodes_touched++; 976 } 977 } 978 i = 0; 979 graph->ncc = 0; 980 total_counts = 0; 981 982 /* allocated space for queues */ 983 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 984 if (size == 1) { 985 ierr = PetscMalloc2(graph->nvtxs+1,&graph->cptr,graph->nvtxs,&graph->queue);CHKERRQ(ierr); 986 } else { 987 PetscInt nused = graph->nvtxs - nodes_touched; 988 ierr = PetscMalloc2(nused+1,&graph->cptr,nused,&graph->queue);CHKERRQ(ierr); 989 } 990 991 while (nodes_touched<graph->nvtxs) { 992 /* find first untouched node in local ordering */ 993 while (PetscBTLookup(graph->touched,i)) { 994 i++; 995 } 996 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 997 graph->subset[i] = graph->ncc+1; 998 graph->cptr[graph->ncc] = total_counts; 999 graph->queue[total_counts] = i; 1000 total_counts++; 1001 nodes_touched++; 1002 /* now find all other nodes having the same set of sharing subdomains */ 1003 for (j=i+1;j<graph->nvtxs;j++) { 1004 /* check for same number of sharing subdomains, dof number and same special mark */ 1005 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]) { 1006 /* check for same set of sharing subdomains */ 1007 same_set=PETSC_TRUE; 1008 for (k=0;k<graph->count[j];k++){ 1009 if (graph->neighbours_set[i][k]!=graph->neighbours_set[j][k]) { 1010 same_set=PETSC_FALSE; 1011 } 1012 } 1013 /* I found a friend of mine */ 1014 if (same_set) { 1015 graph->subset[j]=graph->ncc+1; 1016 ierr = PetscBTSet(graph->touched,j);CHKERRQ(ierr); 1017 nodes_touched++; 1018 graph->queue[total_counts] = j; 1019 total_counts++; 1020 } 1021 } 1022 } 1023 graph->ncc++; 1024 } 1025 /* set default number of subsets (at this point no info on csr graph has been taken into account, so n_subsets = ncc */ 1026 graph->n_subsets = graph->ncc; 1027 ierr = PetscMalloc1(graph->n_subsets,&graph->subset_ncc);CHKERRQ(ierr); 1028 for (i=0;i<graph->n_subsets;i++) { 1029 graph->subset_ncc[i] = 1; 1030 } 1031 /* final pointer */ 1032 graph->cptr[graph->ncc] = total_counts; 1033 1034 /* save information on subsets (needed if we have to adapt the connected components later) */ 1035 /* For consistency reasons (among neighbours), I need to sort (by global ordering) each subset */ 1036 /* Get a reference node (min index in global ordering) for each subset for tagging messages */ 1037 ierr = PetscMalloc2(graph->ncc,&subset_ref_node_global,graph->cptr[graph->ncc],&queue_global);CHKERRQ(ierr); 1038 ierr = ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_global);CHKERRQ(ierr); 1039 for (j=0;j<graph->ncc;j++) { 1040 ierr = PetscSortIntWithArray(graph->cptr[j+1]-graph->cptr[j],&queue_global[graph->cptr[j]],&graph->queue[graph->cptr[j]]);CHKERRQ(ierr); 1041 subset_ref_node_global[j] = graph->queue[graph->cptr[j]]; 1042 } 1043 graph->queue_sorted = PETSC_TRUE; 1044 if (graph->ncc) { 1045 ierr = PetscMalloc2(graph->ncc,&graph->subsets_size,graph->ncc,&graph->subsets);CHKERRQ(ierr); 1046 ierr = PetscMalloc1(graph->cptr[graph->ncc],&graph->subsets[0]);CHKERRQ(ierr); 1047 ierr = PetscMemzero(graph->subsets[0],graph->cptr[graph->ncc]*sizeof(PetscInt));CHKERRQ(ierr); 1048 for (j=1;j<graph->ncc;j++) { 1049 graph->subsets_size[j-1] = graph->cptr[j] - graph->cptr[j-1]; 1050 graph->subsets[j] = graph->subsets[j-1] + graph->subsets_size[j-1]; 1051 } 1052 graph->subsets_size[graph->ncc-1] = graph->cptr[graph->ncc] - graph->cptr[graph->ncc-1]; 1053 for (j=0;j<graph->ncc;j++) { 1054 ierr = PetscMemcpy(graph->subsets[j],&graph->queue[graph->cptr[j]],graph->subsets_size[j]*sizeof(PetscInt));CHKERRQ(ierr); 1055 } 1056 } 1057 /* renumber reference nodes */ 1058 ierr = PCBDDCSubsetNumbering(PetscObjectComm((PetscObject)(graph->l2gmap)),graph->l2gmap,graph->ncc,subset_ref_node_global,NULL,&k,&graph->subset_ref_node);CHKERRQ(ierr); 1059 1060 /* free workspace */ 1061 ierr = PetscFree2(subset_ref_node_global,queue_global);CHKERRQ(ierr); 1062 ierr = VecDestroy(&local_vec);CHKERRQ(ierr); 1063 ierr = VecDestroy(&local_vec2);CHKERRQ(ierr); 1064 ierr = VecDestroy(&global_vec);CHKERRQ(ierr); 1065 ierr = VecScatterDestroy(&scatter_ctx);CHKERRQ(ierr); 1066 PetscFunctionReturn(0); 1067 } 1068 1069 #undef __FUNCT__ 1070 #define __FUNCT__ "PCBDDCGraphResetCSR" 1071 PetscErrorCode PCBDDCGraphResetCSR(PCBDDCGraph graph) 1072 { 1073 PetscErrorCode ierr; 1074 1075 PetscFunctionBegin; 1076 ierr = PetscFree(graph->xadj);CHKERRQ(ierr); 1077 ierr = PetscFree(graph->adjncy);CHKERRQ(ierr); 1078 graph->nvtxs_csr = 0; 1079 PetscFunctionReturn(0); 1080 } 1081 1082 #undef __FUNCT__ 1083 #define __FUNCT__ "PCBDDCGraphReset" 1084 PetscErrorCode PCBDDCGraphReset(PCBDDCGraph graph) 1085 { 1086 PetscErrorCode ierr; 1087 1088 PetscFunctionBegin; 1089 ierr = ISLocalToGlobalMappingDestroy(&graph->l2gmap);CHKERRQ(ierr); 1090 ierr = PetscFree(graph->subset_ncc);CHKERRQ(ierr); 1091 ierr = PetscFree(graph->subset_ref_node);CHKERRQ(ierr); 1092 if (graph->nvtxs) { 1093 ierr = PetscFree(graph->neighbours_set[0]);CHKERRQ(ierr); 1094 } 1095 ierr = PetscBTDestroy(&graph->touched);CHKERRQ(ierr); 1096 ierr = PetscFree5(graph->count, 1097 graph->neighbours_set, 1098 graph->subset, 1099 graph->which_dof, 1100 graph->special_dof);CHKERRQ(ierr); 1101 ierr = PetscFree2(graph->cptr,graph->queue);CHKERRQ(ierr); 1102 if (graph->mirrors) { 1103 ierr = PetscFree(graph->mirrors_set[0]);CHKERRQ(ierr); 1104 } 1105 ierr = PetscFree2(graph->mirrors,graph->mirrors_set);CHKERRQ(ierr); 1106 if (graph->subsets) { 1107 ierr = PetscFree(graph->subsets[0]);CHKERRQ(ierr); 1108 } 1109 ierr = PetscFree2(graph->subsets_size,graph->subsets);CHKERRQ(ierr); 1110 ierr = ISDestroy(&graph->dirdofs);CHKERRQ(ierr); 1111 graph->has_dirichlet = PETSC_FALSE; 1112 graph->nvtxs = 0; 1113 graph->nvtxs_global = 0; 1114 graph->n_subsets = 0; 1115 graph->custom_minimal_size = 1; 1116 PetscFunctionReturn(0); 1117 } 1118 1119 #undef __FUNCT__ 1120 #define __FUNCT__ "PCBDDCGraphInit" 1121 PetscErrorCode PCBDDCGraphInit(PCBDDCGraph graph, ISLocalToGlobalMapping l2gmap, PetscInt N) 1122 { 1123 PetscInt n; 1124 PetscErrorCode ierr; 1125 1126 PetscFunctionBegin; 1127 PetscValidPointer(graph,1); 1128 PetscValidHeaderSpecific(l2gmap,IS_LTOGM_CLASSID,2); 1129 PetscValidLogicalCollectiveInt(l2gmap,N,3); 1130 /* raise an error if already allocated */ 1131 if (graph->nvtxs_global) { 1132 SETERRQ(PetscObjectComm((PetscObject)l2gmap),PETSC_ERR_PLIB,"BDDCGraph already initialized"); 1133 } 1134 /* set number of vertices */ 1135 ierr = PetscObjectReference((PetscObject)l2gmap);CHKERRQ(ierr); 1136 graph->l2gmap = l2gmap; 1137 ierr = ISLocalToGlobalMappingGetSize(l2gmap,&n);CHKERRQ(ierr); 1138 graph->nvtxs = n; 1139 graph->nvtxs_global = N; 1140 /* allocate used space */ 1141 ierr = PetscBTCreate(graph->nvtxs,&graph->touched);CHKERRQ(ierr); 1142 ierr = PetscMalloc5(graph->nvtxs,&graph->count, 1143 graph->nvtxs,&graph->neighbours_set, 1144 graph->nvtxs,&graph->subset, 1145 graph->nvtxs,&graph->which_dof, 1146 graph->nvtxs,&graph->special_dof);CHKERRQ(ierr); 1147 /* zeroes memory */ 1148 ierr = PetscMemzero(graph->count,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 1149 ierr = PetscMemzero(graph->subset,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 1150 /* use -1 as a default value for which_dof array */ 1151 for (n=0;n<graph->nvtxs;n++) graph->which_dof[n] = -1; 1152 ierr = PetscMemzero(graph->special_dof,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 1153 /* zeroes first pointer to neighbour set */ 1154 if (graph->nvtxs) { 1155 graph->neighbours_set[0] = 0; 1156 } 1157 /* zeroes workspace for values of ncc */ 1158 graph->subset_ncc = 0; 1159 graph->subset_ref_node = 0; 1160 PetscFunctionReturn(0); 1161 } 1162 1163 #undef __FUNCT__ 1164 #define __FUNCT__ "PCBDDCGraphDestroy" 1165 PetscErrorCode PCBDDCGraphDestroy(PCBDDCGraph* graph) 1166 { 1167 PetscErrorCode ierr; 1168 1169 PetscFunctionBegin; 1170 ierr = PCBDDCGraphReset(*graph);CHKERRQ(ierr); 1171 ierr = PetscFree(*graph);CHKERRQ(ierr); 1172 PetscFunctionReturn(0); 1173 } 1174 1175 #undef __FUNCT__ 1176 #define __FUNCT__ "PCBDDCGraphCreate" 1177 PetscErrorCode PCBDDCGraphCreate(PCBDDCGraph *graph) 1178 { 1179 PCBDDCGraph new_graph; 1180 PetscErrorCode ierr; 1181 1182 PetscFunctionBegin; 1183 ierr = PetscNew(&new_graph);CHKERRQ(ierr); 1184 new_graph->custom_minimal_size = 1; 1185 *graph = new_graph; 1186 PetscFunctionReturn(0); 1187 } 1188