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__ "PCBDDCGraphASCIIView" 7 PetscErrorCode PCBDDCGraphASCIIView(PCBDDCGraph graph, PetscInt verbosity_level, PetscViewer viewer) 8 { 9 PetscInt i,j,tabs; 10 PetscInt* queue_in_global_numbering; 11 PetscErrorCode ierr; 12 13 PetscFunctionBegin; 14 ierr = PetscViewerASCIISynchronizedAllow(viewer,PETSC_TRUE);CHKERRQ(ierr); 15 ierr = PetscViewerASCIIGetTab(viewer,&tabs);CHKERRQ(ierr); 16 ierr = PetscViewerASCIIPrintf(viewer,"--------------------------------------------------\n");CHKERRQ(ierr); 17 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 18 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Local BDDC graph for subdomain %04d\n",PetscGlobalRank);CHKERRQ(ierr); 19 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Number of vertices %d\n",graph->nvtxs);CHKERRQ(ierr); 20 if (verbosity_level > 1) { 21 for (i=0;i<graph->nvtxs;i++) { 22 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"%d:\n",i);CHKERRQ(ierr); 23 ierr = PetscViewerASCIISynchronizedPrintf(viewer," which_dof: %d\n",graph->which_dof[i]);CHKERRQ(ierr); 24 ierr = PetscViewerASCIISynchronizedPrintf(viewer," special_dof: %d\n",graph->special_dof[i]);CHKERRQ(ierr); 25 ierr = PetscViewerASCIISynchronizedPrintf(viewer," neighbours: %d\n",graph->count[i]);CHKERRQ(ierr); 26 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 27 if (graph->count[i]) { 28 ierr = PetscViewerASCIISynchronizedPrintf(viewer," set of neighbours:");CHKERRQ(ierr); 29 for (j=0;j<graph->count[i];j++) { 30 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->neighbours_set[i][j]);CHKERRQ(ierr); 31 } 32 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"\n");CHKERRQ(ierr); 33 } 34 ierr = PetscViewerASCIISetTab(viewer,tabs);CHKERRQ(ierr); 35 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 36 if (graph->mirrors) { 37 ierr = PetscViewerASCIISynchronizedPrintf(viewer," mirrors: %d\n",graph->mirrors[i]);CHKERRQ(ierr); 38 if (graph->mirrors[i]) { 39 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 40 ierr = PetscViewerASCIISynchronizedPrintf(viewer," set of mirrors:");CHKERRQ(ierr); 41 for (j=0;j<graph->mirrors[i];j++) { 42 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->mirrors_set[i][j]);CHKERRQ(ierr); 43 } 44 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"\n");CHKERRQ(ierr); 45 ierr = PetscViewerASCIISetTab(viewer,tabs);CHKERRQ(ierr); 46 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 47 } 48 } 49 if (verbosity_level > 2) { 50 if (graph->xadj && graph->adjncy) { 51 ierr = PetscViewerASCIISynchronizedPrintf(viewer," local adj list:");CHKERRQ(ierr); 52 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 53 for (j=graph->xadj[i];j<graph->xadj[i+1];j++) { 54 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->adjncy[j]);CHKERRQ(ierr); 55 } 56 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"\n");CHKERRQ(ierr); 57 ierr = PetscViewerASCIISetTab(viewer,tabs);CHKERRQ(ierr); 58 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 59 } 60 } 61 ierr = PetscViewerASCIISynchronizedPrintf(viewer," interface subset id: %d\n",graph->subset[i]);CHKERRQ(ierr); 62 if (graph->subset[i] && graph->subset_ncc) { 63 ierr = PetscViewerASCIISynchronizedPrintf(viewer," ncc for subset: %d\n",graph->subset_ncc[graph->subset[i]-1]);CHKERRQ(ierr); 64 } 65 } 66 } 67 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Total number of connected components %d\n",graph->ncc);CHKERRQ(ierr); 68 ierr = PetscMalloc1(graph->cptr[graph->ncc],&queue_in_global_numbering);CHKERRQ(ierr); 69 ierr = ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_in_global_numbering);CHKERRQ(ierr); 70 for (i=0;i<graph->ncc;i++) { 71 PetscInt node_num=graph->queue[graph->cptr[i]]; 72 PetscBool printcc = PETSC_FALSE; 73 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d (neighs:",i);CHKERRQ(ierr); 74 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_FALSE);CHKERRQ(ierr); 75 for (j=0;j<graph->count[node_num];j++) { 76 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->neighbours_set[node_num][j]);CHKERRQ(ierr); 77 } 78 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"):");CHKERRQ(ierr); 79 if (verbosity_level > 1) { 80 printcc = PETSC_TRUE; 81 } else if (graph->count[node_num] > 1 || (graph->count[node_num] == 1 && graph->special_dof[node_num] == PCBDDCGRAPH_NEUMANN_MARK)) { 82 printcc = PETSC_TRUE; 83 } 84 if (printcc) { 85 for (j=graph->cptr[i];j<graph->cptr[i+1];j++) { 86 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d (%d)",graph->queue[j],queue_in_global_numbering[j]);CHKERRQ(ierr); 87 } 88 } 89 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"\n");CHKERRQ(ierr); 90 ierr = PetscViewerASCIISetTab(viewer,tabs);CHKERRQ(ierr); 91 ierr = PetscViewerASCIIUseTabs(viewer,PETSC_TRUE);CHKERRQ(ierr); 92 } 93 ierr = PetscFree(queue_in_global_numbering);CHKERRQ(ierr); 94 if (graph->custom_minimal_size > 1 && verbosity_level > 1) { 95 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Custom minimal size %d\n",graph->custom_minimal_size);CHKERRQ(ierr); 96 } 97 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 98 PetscFunctionReturn(0); 99 } 100 101 #undef __FUNCT__ 102 #define __FUNCT__ "PCBDDCGraphGetCandidatesIS" 103 PetscErrorCode PCBDDCGraphGetCandidatesIS(PCBDDCGraph graph, PetscBool use_faces, PetscBool use_edges, PetscBool use_vertices, PetscInt *n_faces, IS *FacesIS[], PetscInt *n_edges, IS *EdgesIS[], IS *VerticesIS) 104 { 105 IS *ISForFaces,*ISForEdges,ISForVertices; 106 PetscInt i,j,nfc,nec,nvc,*idx; 107 PetscBool twodim_flag; 108 PetscErrorCode ierr; 109 110 PetscFunctionBegin; 111 /* loop on ccs to evalute number of faces, edges and vertices */ 112 nfc = 0; 113 nec = 0; 114 nvc = 0; 115 twodim_flag = PETSC_FALSE; 116 for (i=0;i<graph->ncc;i++) { 117 PetscInt repdof = graph->queue[graph->cptr[i]]; 118 if (graph->cptr[i+1]-graph->cptr[i] > graph->custom_minimal_size) { 119 if (graph->count[repdof] == 1 && graph->special_dof[repdof] != PCBDDCGRAPH_NEUMANN_MARK) { 120 nfc++; 121 } else { /* note that nec will be zero in 2d */ 122 nec++; 123 } 124 } else { 125 if (graph->count[repdof] > 1 || (graph->count[repdof] == 1 && graph->special_dof[repdof] == PCBDDCGRAPH_NEUMANN_MARK)) { 126 nvc += graph->cptr[i+1]-graph->cptr[i]; 127 } 128 } 129 } 130 j=0; 131 ierr = MPI_Allreduce(&nec,&j,1,MPIU_INT,MPI_SUM,PetscObjectComm((PetscObject)graph->l2gmap));CHKERRQ(ierr); 132 if (!j) { /* we are in a 2D case -> no faces, only edges */ 133 nec = nfc; 134 nfc = 0; 135 twodim_flag = PETSC_TRUE; 136 } 137 /* allocate IS arrays for faces, edges. Vertices need a single index set. */ 138 ISForFaces = 0; 139 ISForEdges = 0; 140 ISForVertices = 0; 141 if (use_faces && nfc) { 142 ierr = PetscMalloc1(nfc,&ISForFaces);CHKERRQ(ierr); 143 } 144 if (use_edges && nec) { 145 ierr = PetscMalloc1(nec,&ISForEdges);CHKERRQ(ierr); 146 } 147 if (use_vertices && nvc) { 148 ierr = PetscMalloc1(nvc,&idx);CHKERRQ(ierr); 149 } 150 /* loop on ccs to compute index sets for faces and edges */ 151 nfc = 0; 152 nec = 0; 153 for (i=0;i<graph->ncc;i++) { 154 PetscInt repdof = graph->queue[graph->cptr[i]]; 155 if (graph->cptr[i+1]-graph->cptr[i] > graph->custom_minimal_size) { 156 if (graph->count[repdof] == 1 && graph->special_dof[repdof] != PCBDDCGRAPH_NEUMANN_MARK) { 157 if (twodim_flag) { 158 if (use_edges) { 159 ierr = ISCreateGeneral(PETSC_COMM_SELF,graph->cptr[i+1]-graph->cptr[i],&graph->queue[graph->cptr[i]],PETSC_COPY_VALUES,&ISForEdges[nec]);CHKERRQ(ierr); 160 nec++; 161 } 162 } else { 163 if (use_faces) { 164 ierr = ISCreateGeneral(PETSC_COMM_SELF,graph->cptr[i+1]-graph->cptr[i],&graph->queue[graph->cptr[i]],PETSC_COPY_VALUES,&ISForFaces[nfc]);CHKERRQ(ierr); 165 nfc++; 166 } 167 } 168 } else { 169 if (use_edges) { 170 ierr = ISCreateGeneral(PETSC_COMM_SELF,graph->cptr[i+1]-graph->cptr[i],&graph->queue[graph->cptr[i]],PETSC_COPY_VALUES,&ISForEdges[nec]);CHKERRQ(ierr); 171 nec++; 172 } 173 } 174 } 175 } 176 /* index set for vertices */ 177 if (use_vertices && nvc) { 178 nvc = 0; 179 for (i=0;i<graph->ncc;i++) { 180 if (graph->cptr[i+1]-graph->cptr[i] <= graph->custom_minimal_size) { 181 PetscInt repdof = graph->queue[graph->cptr[i]]; 182 if (graph->count[repdof] > 1 || (graph->count[repdof] == 1 && graph->special_dof[repdof] == PCBDDCGRAPH_NEUMANN_MARK)) { 183 for (j=graph->cptr[i];j<graph->cptr[i+1];j++) { 184 idx[nvc]=graph->queue[j]; 185 nvc++; 186 } 187 } 188 } 189 } 190 /* sort vertex set (by local ordering) */ 191 ierr = PetscSortInt(nvc,idx);CHKERRQ(ierr); 192 ierr = ISCreateGeneral(PETSC_COMM_SELF,nvc,idx,PETSC_OWN_POINTER,&ISForVertices);CHKERRQ(ierr); 193 } 194 /* get back info */ 195 *n_faces = nfc; 196 *FacesIS = ISForFaces; 197 *n_edges = nec; 198 *EdgesIS = ISForEdges; 199 *VerticesIS = ISForVertices; 200 PetscFunctionReturn(0); 201 } 202 203 #undef __FUNCT__ 204 #define __FUNCT__ "PCBDDCGraphComputeConnectedComponents" 205 PetscErrorCode PCBDDCGraphComputeConnectedComponents(PCBDDCGraph graph) 206 { 207 PetscInt i,adapt_interface,adapt_interface_reduced; 208 MPI_Comm interface_comm; 209 PetscErrorCode ierr; 210 211 PetscFunctionBegin; 212 /* compute connected components locally */ 213 ierr = PetscObjectGetComm((PetscObject)(graph->l2gmap),&interface_comm);CHKERRQ(ierr); 214 ierr = PCBDDCGraphComputeConnectedComponentsLocal(graph);CHKERRQ(ierr); 215 /* check consistency of connected components among neighbouring subdomains -> it adapt them in case it is needed */ 216 adapt_interface = 0; 217 adapt_interface_reduced = 0; 218 for (i=0;i<graph->n_subsets;i++) { 219 /* We are not sure that on a given subset of the local interface, 220 with two connected components, the latters be the same among sharing subdomains */ 221 if (graph->subset_ncc[i] > 1) { 222 adapt_interface=1; 223 break; 224 } 225 } 226 ierr = MPI_Allreduce(&adapt_interface,&adapt_interface_reduced,1,MPIU_INT,MPI_LOR,interface_comm);CHKERRQ(ierr); 227 228 if (graph->n_subsets && adapt_interface_reduced) { 229 MPI_Request *send_requests; 230 MPI_Request *recv_requests; 231 PetscInt *aux_new_xadj,*new_xadj,*new_adjncy,**temp_buffer; 232 PetscInt *old_xadj,*old_adjncy; 233 PetscInt j,k,s,sum_requests,buffer_size,size_of_recv,temp_buffer_size; 234 PetscMPIInt rank,neigh,tag,mpi_buffer_size; 235 PetscInt *cum_recv_counts,*subset_to_nodes_indices,*recv_buffer_subset,*nodes_to_temp_buffer_indices; 236 PetscInt *send_buffer,*recv_buffer,*queue_in_global_numbering,*sizes_of_sends,*add_to_subset; 237 PetscInt start_of_recv,start_of_send,size_of_send,global_subset_counter,ins_val; 238 PetscBool *subset_cc_adapt,same_set; 239 240 /* Retrict adjacency graph using information from previously computed connected components */ 241 ierr = PetscMalloc1(graph->nvtxs,&aux_new_xadj);CHKERRQ(ierr); 242 for (i=0;i<graph->nvtxs;i++) { 243 aux_new_xadj[i]=1; 244 } 245 for (i=0;i<graph->ncc;i++) { 246 k = graph->cptr[i+1]-graph->cptr[i]; 247 for (j=0;j<k;j++) { 248 aux_new_xadj[graph->queue[graph->cptr[i]+j]]=k; 249 } 250 } 251 j = 0; 252 for (i=0;i<graph->nvtxs;i++) { 253 j += aux_new_xadj[i]; 254 } 255 ierr = PetscMalloc1((graph->nvtxs+1),&new_xadj);CHKERRQ(ierr); 256 ierr = PetscMalloc1(j,&new_adjncy);CHKERRQ(ierr); 257 new_xadj[0]=0; 258 for (i=0;i<graph->nvtxs;i++) { 259 new_xadj[i+1]=new_xadj[i]+aux_new_xadj[i]; 260 if (aux_new_xadj[i]==1) { 261 new_adjncy[new_xadj[i]]=i; 262 } 263 } 264 ierr = PetscFree(aux_new_xadj);CHKERRQ(ierr); 265 for (i=0;i<graph->ncc;i++) { 266 k = graph->cptr[i+1]-graph->cptr[i]; 267 for (j=0;j<k;j++) { 268 ierr = PetscMemcpy(&new_adjncy[new_xadj[graph->queue[graph->cptr[i]+j]]],&graph->queue[graph->cptr[i]],k*sizeof(PetscInt));CHKERRQ(ierr); 269 } 270 } 271 /* set temporarly new CSR into graph */ 272 old_xadj = graph->xadj; 273 old_adjncy = graph->adjncy; 274 graph->xadj = new_xadj; 275 graph->adjncy = new_adjncy; 276 /* allocate some space */ 277 ierr = MPI_Comm_rank(interface_comm,&rank);CHKERRQ(ierr); 278 ierr = PetscMalloc1((graph->n_subsets+1),&cum_recv_counts);CHKERRQ(ierr); 279 ierr = PetscMemzero(cum_recv_counts,(graph->n_subsets+1)*sizeof(*cum_recv_counts));CHKERRQ(ierr); 280 ierr = PetscMalloc1(graph->n_subsets,&subset_to_nodes_indices);CHKERRQ(ierr); 281 /* first count how many neighbours per connected component I will receive from */ 282 cum_recv_counts[0]=0; 283 for (i=1;i<graph->n_subsets+1;i++) { 284 j = 0; 285 while (graph->subset[j] != i) { 286 j++; 287 } 288 subset_to_nodes_indices[i-1]=j; 289 /* We don't want sends/recvs_to/from_self -> here I don't count myself */ 290 cum_recv_counts[i]=cum_recv_counts[i-1]+graph->count[j]; 291 } 292 ierr = PetscMalloc1(2*cum_recv_counts[graph->n_subsets],&recv_buffer_subset);CHKERRQ(ierr); 293 ierr = PetscMalloc1(cum_recv_counts[graph->n_subsets],&send_requests);CHKERRQ(ierr); 294 ierr = PetscMalloc1(cum_recv_counts[graph->n_subsets],&recv_requests);CHKERRQ(ierr); 295 for (i=0;i<cum_recv_counts[graph->n_subsets];i++) { 296 send_requests[i]=MPI_REQUEST_NULL; 297 recv_requests[i]=MPI_REQUEST_NULL; 298 } 299 /* exchange with my neighbours the number of my connected components on the shared interface */ 300 sum_requests = 0; 301 for (i=0;i<graph->n_subsets;i++) { 302 j = subset_to_nodes_indices[i]; 303 ierr = PetscMPIIntCast(graph->subset_ref_node[i],&tag);CHKERRQ(ierr); 304 for (k=0;k<graph->count[j];k++) { 305 ierr = PetscMPIIntCast(graph->neighbours_set[j][k],&neigh);CHKERRQ(ierr); 306 ierr = MPI_Isend(&graph->subset_ncc[i],1,MPIU_INT,neigh,tag,interface_comm,&send_requests[sum_requests]);CHKERRQ(ierr); 307 ierr = MPI_Irecv(&recv_buffer_subset[sum_requests],1,MPIU_INT,neigh,tag,interface_comm,&recv_requests[sum_requests]);CHKERRQ(ierr); 308 sum_requests++; 309 } 310 } 311 ierr = MPI_Waitall(sum_requests,recv_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 312 ierr = MPI_Waitall(sum_requests,send_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 313 /* determine the connected component I need to adapt */ 314 ierr = PetscMalloc1(graph->n_subsets,&subset_cc_adapt);CHKERRQ(ierr); 315 ierr = PetscMemzero(subset_cc_adapt,graph->n_subsets*sizeof(*subset_cc_adapt));CHKERRQ(ierr); 316 for (i=0;i<graph->n_subsets;i++) { 317 for (j=cum_recv_counts[i];j<cum_recv_counts[i+1];j++){ 318 /* The first condition is natural (someone has a different number of ccs than me), the second one is just to be safe */ 319 if (graph->subset_ncc[i] != recv_buffer_subset[j] || graph->subset_ncc[i] > 1) { 320 subset_cc_adapt[i] = PETSC_TRUE; 321 break; 322 } 323 } 324 } 325 buffer_size = 0; 326 for (i=0;i<graph->n_subsets;i++) { 327 if (subset_cc_adapt[i]) { 328 for (j=i;j<graph->ncc;j++) { 329 if (graph->subset[graph->queue[graph->cptr[j]]] == i+1) { /* WARNING -> subset values goes from 1 to graph->n_subsets included */ 330 buffer_size += 1 + graph->cptr[j+1]-graph->cptr[j]; 331 } 332 } 333 } 334 } 335 ierr = PetscMalloc1(buffer_size,&send_buffer);CHKERRQ(ierr); 336 /* now get from neighbours their ccs (in global numbering) and adapt them (in case it is needed) */ 337 ierr = PetscMalloc1(graph->cptr[graph->ncc],&queue_in_global_numbering);CHKERRQ(ierr); 338 ierr = ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_in_global_numbering);CHKERRQ(ierr); 339 /* determine how much data to send (size of each queue plus the global indices) and communicate it to neighbours */ 340 ierr = PetscMalloc1(graph->n_subsets,&sizes_of_sends);CHKERRQ(ierr); 341 ierr = PetscMemzero(sizes_of_sends,graph->n_subsets*sizeof(*sizes_of_sends));CHKERRQ(ierr); 342 sum_requests = 0; 343 start_of_send = 0; 344 start_of_recv = cum_recv_counts[graph->n_subsets]; 345 for (i=0;i<graph->n_subsets;i++) { 346 if (subset_cc_adapt[i]) { 347 size_of_send = 0; 348 for (j=i;j<graph->ncc;j++) { 349 if (graph->subset[graph->queue[graph->cptr[j]]] == i+1) { /* WARNING -> subset values goes from 1 to graph->n_subsets included */ 350 send_buffer[start_of_send+size_of_send]=graph->cptr[j+1]-graph->cptr[j]; 351 size_of_send += 1; 352 ierr = PetscMemcpy(&send_buffer[start_of_send+size_of_send], 353 &queue_in_global_numbering[graph->cptr[j]], 354 (graph->cptr[j+1]-graph->cptr[j])*sizeof(*send_buffer));CHKERRQ(ierr); 355 size_of_send = size_of_send+graph->cptr[j+1]-graph->cptr[j]; 356 } 357 } 358 j = subset_to_nodes_indices[i]; 359 sizes_of_sends[i] = size_of_send; 360 ierr = PetscMPIIntCast(graph->subset_ref_node[i]+1,&tag);CHKERRQ(ierr); 361 for (k=0;k<graph->count[j];k++) { 362 ierr = PetscMPIIntCast(graph->neighbours_set[j][k],&neigh);CHKERRQ(ierr); 363 ierr = MPI_Isend(&sizes_of_sends[i],1,MPIU_INT,neigh,tag,interface_comm,&send_requests[sum_requests]);CHKERRQ(ierr); 364 ierr = MPI_Irecv(&recv_buffer_subset[sum_requests+start_of_recv],1,MPIU_INT,neigh,tag,interface_comm,&recv_requests[sum_requests]);CHKERRQ(ierr); 365 sum_requests++; 366 } 367 start_of_send += size_of_send; 368 } 369 } 370 ierr = MPI_Waitall(sum_requests,send_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 371 ierr = MPI_Waitall(sum_requests,recv_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 372 buffer_size = 0; 373 for (k=0;k<sum_requests;k++) { 374 buffer_size += recv_buffer_subset[start_of_recv+k]; 375 } 376 ierr = PetscMalloc1(buffer_size,&recv_buffer);CHKERRQ(ierr); 377 /* now exchange the data */ 378 start_of_recv = 0; 379 start_of_send = 0; 380 sum_requests = 0; 381 for (i=0;i<graph->n_subsets;i++) { 382 if (subset_cc_adapt[i]) { 383 size_of_send = sizes_of_sends[i]; 384 j = subset_to_nodes_indices[i]; 385 ierr = PetscMPIIntCast(graph->subset_ref_node[i]+2,&tag);CHKERRQ(ierr); 386 for (k=0;k<graph->count[j];k++) { 387 ierr = PetscMPIIntCast(graph->neighbours_set[j][k],&neigh);CHKERRQ(ierr); 388 ierr = PetscMPIIntCast(size_of_send,&mpi_buffer_size);CHKERRQ(ierr); 389 ierr = MPI_Isend(&send_buffer[start_of_send],mpi_buffer_size,MPIU_INT,neigh,tag,interface_comm,&send_requests[sum_requests]);CHKERRQ(ierr); 390 size_of_recv = recv_buffer_subset[cum_recv_counts[graph->n_subsets]+sum_requests]; 391 ierr = PetscMPIIntCast(size_of_recv,&mpi_buffer_size);CHKERRQ(ierr); 392 ierr = MPI_Irecv(&recv_buffer[start_of_recv],mpi_buffer_size,MPIU_INT,neigh,tag,interface_comm,&recv_requests[sum_requests]);CHKERRQ(ierr); 393 start_of_recv += size_of_recv; 394 sum_requests++; 395 } 396 start_of_send += size_of_send; 397 } 398 } 399 ierr = MPI_Waitall(sum_requests,recv_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 400 ierr = MPI_Waitall(sum_requests,send_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 401 for (j=0;j<buffer_size;) { 402 ierr = ISGlobalToLocalMappingApply(graph->l2gmap,IS_GTOLM_MASK,recv_buffer[j],&recv_buffer[j+1],&recv_buffer[j],&recv_buffer[j+1]);CHKERRQ(ierr); 403 /* we need to adapt the output of GlobalToLocal mapping if there are mirrored nodes */ 404 if (graph->mirrors) { 405 PetscBool mirrored_found=PETSC_FALSE; 406 for (k=0;k<recv_buffer[j];k++) { 407 if (graph->mirrors[recv_buffer[j+k+1]]) { 408 mirrored_found=PETSC_TRUE; 409 recv_buffer[j+k+1]=graph->mirrors_set[recv_buffer[j+k+1]][0]; 410 } 411 } 412 if (mirrored_found) { 413 ierr = PetscSortInt(recv_buffer[j],&recv_buffer[j+1]);CHKERRQ(ierr); 414 k=0; 415 while (k<recv_buffer[j]) { 416 for (s=1;s<graph->mirrors[recv_buffer[j+1+k]];s++) { 417 recv_buffer[j+1+k+s] = graph->mirrors_set[recv_buffer[j+1+k]][s]; 418 } 419 k+=graph->mirrors[recv_buffer[j+1+k]]+s; 420 } 421 } 422 } 423 k = recv_buffer[j]+1; 424 j += k; 425 } 426 sum_requests = cum_recv_counts[graph->n_subsets]; 427 start_of_recv = 0; 428 ierr = PetscMalloc1(graph->nvtxs,&nodes_to_temp_buffer_indices);CHKERRQ(ierr); 429 global_subset_counter = 0; 430 for (i=0;i<graph->n_subsets;i++) { 431 if (subset_cc_adapt[i]) { 432 temp_buffer_size = 0; 433 /* find nodes on the shared interface we need to adapt */ 434 for (j=0;j<graph->nvtxs;j++) { 435 if (graph->subset[j]==i+1) { 436 nodes_to_temp_buffer_indices[j] = temp_buffer_size; 437 temp_buffer_size++; 438 } else { 439 nodes_to_temp_buffer_indices[j] = -1; 440 } 441 } 442 /* allocate some temporary space */ 443 ierr = PetscMalloc1(temp_buffer_size,&temp_buffer);CHKERRQ(ierr); 444 ierr = PetscMalloc1(temp_buffer_size*(cum_recv_counts[i+1]-cum_recv_counts[i]),&temp_buffer[0]);CHKERRQ(ierr); 445 ierr = PetscMemzero(temp_buffer[0],temp_buffer_size*(cum_recv_counts[i+1]-cum_recv_counts[i])*sizeof(PetscInt));CHKERRQ(ierr); 446 for (j=1;j<temp_buffer_size;j++) { 447 temp_buffer[j] = temp_buffer[j-1]+cum_recv_counts[i+1]-cum_recv_counts[i]; 448 } 449 /* analyze contributions from neighbouring subdomains for i-th conn comp 450 temp buffer structure: 451 supposing part of the interface has dimension 5 (for example with global dofs 0,1,2,3,4) 452 3 neighs procs with structured connected components: 453 neigh 0: [0 1 4], [2 3]; (2 connected components) 454 neigh 1: [0 1], [2 3 4]; (2 connected components) 455 neigh 2: [0 4], [1], [2 3]; (3 connected components) 456 tempbuffer (row-oriented) will be filled as: 457 [ 0, 0, 0; 458 0, 0, 1; 459 1, 1, 2; 460 1, 1, 2; 461 0, 1, 0; ]; 462 This way we can simply find intersections of ccs among neighs. 463 For the example above, the graph->subset array will be modified to reproduce the following 4 connected components [0], [1], [2 3], [4]; 464 */ 465 for (j=0;j<cum_recv_counts[i+1]-cum_recv_counts[i];j++) { 466 ins_val = 0; 467 size_of_recv = recv_buffer_subset[sum_requests]; /* total size of recv from neighs */ 468 for (buffer_size=0;buffer_size<size_of_recv;) { /* loop until all data from neighs has been taken into account */ 469 for (k=1;k<recv_buffer[buffer_size+start_of_recv]+1;k++) { /* filling properly temp_buffer using data from a single recv */ 470 temp_buffer[nodes_to_temp_buffer_indices[recv_buffer[start_of_recv+buffer_size+k]]][j] = ins_val; 471 } 472 buffer_size += k; 473 ins_val++; 474 } 475 start_of_recv += size_of_recv; 476 sum_requests++; 477 } 478 ierr = PetscMalloc1(temp_buffer_size,&add_to_subset);CHKERRQ(ierr); 479 ierr = PetscMemzero(add_to_subset,temp_buffer_size*sizeof(*add_to_subset));CHKERRQ(ierr); 480 for (j=0;j<temp_buffer_size;j++) { 481 if (!add_to_subset[j]) { /* found a new cc */ 482 global_subset_counter++; 483 add_to_subset[j] = global_subset_counter; 484 for (k=j+1;k<temp_buffer_size;k++) { /* check for other nodes in new cc */ 485 same_set = PETSC_TRUE; 486 for (s=0;s<cum_recv_counts[i+1]-cum_recv_counts[i];s++) { 487 if (temp_buffer[j][s]!=temp_buffer[k][s]) { 488 same_set = PETSC_FALSE; 489 break; 490 } 491 } 492 if (same_set) { 493 add_to_subset[k] = global_subset_counter; 494 } 495 } 496 } 497 } 498 /* insert new data in subset array */ 499 temp_buffer_size = 0; 500 for (j=0;j<graph->nvtxs;j++) { 501 if (graph->subset[j]==i+1) { 502 graph->subset[j] = graph->n_subsets+add_to_subset[temp_buffer_size]; 503 temp_buffer_size++; 504 } 505 } 506 ierr = PetscFree(temp_buffer[0]);CHKERRQ(ierr); 507 ierr = PetscFree(temp_buffer);CHKERRQ(ierr); 508 ierr = PetscFree(add_to_subset);CHKERRQ(ierr); 509 } 510 } 511 ierr = PetscFree(nodes_to_temp_buffer_indices);CHKERRQ(ierr); 512 ierr = PetscFree(sizes_of_sends);CHKERRQ(ierr); 513 ierr = PetscFree(send_requests);CHKERRQ(ierr); 514 ierr = PetscFree(recv_requests);CHKERRQ(ierr); 515 ierr = PetscFree(recv_buffer);CHKERRQ(ierr); 516 ierr = PetscFree(recv_buffer_subset);CHKERRQ(ierr); 517 ierr = PetscFree(send_buffer);CHKERRQ(ierr); 518 ierr = PetscFree(cum_recv_counts);CHKERRQ(ierr); 519 ierr = PetscFree(subset_to_nodes_indices);CHKERRQ(ierr); 520 ierr = PetscFree(subset_cc_adapt);CHKERRQ(ierr); 521 /* We are ready to find for connected components consistent among neighbouring subdomains */ 522 if (global_subset_counter) { 523 ierr = PetscBTMemzero(graph->nvtxs,graph->touched);CHKERRQ(ierr); 524 global_subset_counter = 0; 525 for (i=0;i<graph->nvtxs;i++) { 526 if (graph->subset[i] && !PetscBTLookup(graph->touched,i)) { 527 global_subset_counter++; 528 for (j=i+1;j<graph->nvtxs;j++) { 529 if (!PetscBTLookup(graph->touched,j) && graph->subset[j]==graph->subset[i]) { 530 graph->subset[j] = global_subset_counter; 531 ierr = PetscBTSet(graph->touched,j);CHKERRQ(ierr); 532 } 533 } 534 graph->subset[i] = global_subset_counter; 535 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 536 } 537 } 538 /* refine connected components locally */ 539 ierr = PCBDDCGraphComputeConnectedComponentsLocal(graph);CHKERRQ(ierr); 540 } 541 /* restore original CSR graph of dofs */ 542 ierr = PetscFree(new_xadj);CHKERRQ(ierr); 543 ierr = PetscFree(new_adjncy);CHKERRQ(ierr); 544 graph->xadj = old_xadj; 545 graph->adjncy = old_adjncy; 546 ierr = PetscFree(queue_in_global_numbering);CHKERRQ(ierr); 547 } 548 PetscFunctionReturn(0); 549 } 550 551 /* The following code has been adapted from function IsConnectedSubdomain contained 552 in source file contig.c of METIS library (version 5.0.1) 553 It finds connected components for each subset */ 554 #undef __FUNCT__ 555 #define __FUNCT__ "PCBDDCGraphComputeConnectedComponentsLocal" 556 PetscErrorCode PCBDDCGraphComputeConnectedComponentsLocal(PCBDDCGraph graph) 557 { 558 PetscInt i,j,k,first,last,nleft,ncc,pid,cum_queue,n,ncc_pid; 559 PetscInt *queue_global; 560 PetscErrorCode ierr; 561 562 PetscFunctionBegin; 563 /* quiet return if no csr info is available */ 564 if (!graph->xadj || !graph->adjncy) { 565 PetscFunctionReturn(0); 566 } 567 568 /* reset any previous search of connected components */ 569 ierr = PetscBTMemzero(graph->nvtxs,graph->touched);CHKERRQ(ierr); 570 graph->n_subsets = 0; 571 for (i=0;i<graph->nvtxs;i++) { 572 if (graph->special_dof[i] == PCBDDCGRAPH_DIRICHLET_MARK || !graph->count[i]) { 573 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 574 graph->subset[i] = 0; 575 } 576 graph->n_subsets = PetscMax(graph->n_subsets,graph->subset[i]); 577 } 578 ierr = PetscFree(graph->subset_ncc);CHKERRQ(ierr); 579 ierr = PetscMalloc1(graph->n_subsets,&graph->subset_ncc);CHKERRQ(ierr); 580 ierr = PetscMemzero(graph->subset_ncc,graph->n_subsets*sizeof(*graph->subset_ncc));CHKERRQ(ierr); 581 ierr = PetscMemzero(graph->cptr,(graph->nvtxs+1)*sizeof(*graph->cptr));CHKERRQ(ierr); 582 ierr = PetscMemzero(graph->queue,graph->nvtxs*sizeof(*graph->queue));CHKERRQ(ierr); 583 584 /* begin search for connected components */ 585 cum_queue = 0; 586 ncc = 0; 587 for (n=0;n<graph->n_subsets;n++) { 588 pid = n+1; /* partition labeled by 0 is discarded */ 589 nleft = 0; 590 for (i=0;i<graph->nvtxs;i++) { 591 if (graph->subset[i] == pid) { 592 nleft++; 593 } 594 } 595 for (i=0; i<graph->nvtxs; i++) { 596 if (graph->subset[i] == pid) { 597 break; 598 } 599 } 600 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 601 graph->queue[cum_queue] = i; 602 first = 0; 603 last = 1; 604 graph->cptr[ncc] = cum_queue; 605 ncc_pid = 0; 606 while (first != nleft) { 607 if (first == last) { 608 graph->cptr[++ncc] = first+cum_queue; 609 ncc_pid++; 610 for (i=0; i<graph->nvtxs; i++) { /* TODO-> use a while! */ 611 if (graph->subset[i] == pid && !PetscBTLookup(graph->touched,i)) { 612 break; 613 } 614 } 615 graph->queue[cum_queue+last] = i; 616 last++; 617 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 618 } 619 i = graph->queue[cum_queue+first]; 620 first++; 621 for (j=graph->xadj[i];j<graph->xadj[i+1];j++) { 622 k = graph->adjncy[j]; 623 if (graph->subset[k] == pid && !PetscBTLookup(graph->touched,k)) { 624 graph->queue[cum_queue+last] = k; 625 last++; 626 ierr = PetscBTSet(graph->touched,k);CHKERRQ(ierr); 627 } 628 } 629 } 630 graph->cptr[++ncc] = first+cum_queue; 631 ncc_pid++; 632 cum_queue = graph->cptr[ncc]; 633 graph->subset_ncc[n] = ncc_pid; 634 } 635 graph->ncc = ncc; 636 /* For consistency among neighbours, I need to sort (by global ordering) each connected component */ 637 ierr = PetscMalloc1(graph->cptr[graph->ncc],&queue_global);CHKERRQ(ierr); 638 ierr = ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_global);CHKERRQ(ierr); 639 for (i=0;i<graph->ncc;i++) { 640 ierr = PetscSortIntWithArray(graph->cptr[i+1]-graph->cptr[i],&queue_global[graph->cptr[i]],&graph->queue[graph->cptr[i]]);CHKERRQ(ierr); 641 } 642 ierr = PetscFree(queue_global);CHKERRQ(ierr); 643 PetscFunctionReturn(0); 644 } 645 646 #undef __FUNCT__ 647 #define __FUNCT__ "PCBDDCGraphSetUp" 648 PetscErrorCode PCBDDCGraphSetUp(PCBDDCGraph graph, PetscInt custom_minimal_size, IS neumann_is, IS dirichlet_is, PetscInt n_ISForDofs, IS ISForDofs[], IS custom_primal_vertices) 649 { 650 VecScatter scatter_ctx; 651 Vec local_vec,local_vec2,global_vec; 652 IS to,from; 653 MPI_Comm comm; 654 PetscScalar *array,*array2; 655 const PetscInt *is_indices; 656 PetscInt n_neigh,*neigh,*n_shared,**shared,*queue_global; 657 PetscInt i,j,k,s,total_counts,nodes_touched,is_size; 658 PetscErrorCode ierr; 659 PetscBool same_set,mirrors_found; 660 661 PetscFunctionBegin; 662 ierr = PetscObjectGetComm((PetscObject)(graph->l2gmap),&comm);CHKERRQ(ierr); 663 /* custom_minimal_size */ 664 graph->custom_minimal_size = PetscMax(graph->custom_minimal_size,custom_minimal_size); 665 /* get info l2gmap and allocate work vectors */ 666 ierr = ISLocalToGlobalMappingGetInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);CHKERRQ(ierr); 667 ierr = ISLocalToGlobalMappingGetIndices(graph->l2gmap,&is_indices);CHKERRQ(ierr); 668 j = 0; 669 for (i=0;i<graph->nvtxs;i++) { 670 j = PetscMax(j,is_indices[i]); 671 } 672 ierr = MPI_Allreduce(&j,&i,1,MPIU_INT,MPI_MAX,comm);CHKERRQ(ierr); 673 i++; 674 ierr = VecCreate(PETSC_COMM_SELF,&local_vec);CHKERRQ(ierr); 675 ierr = VecSetSizes(local_vec,PETSC_DECIDE,graph->nvtxs);CHKERRQ(ierr); 676 ierr = VecSetType(local_vec,VECSTANDARD);CHKERRQ(ierr); 677 ierr = VecDuplicate(local_vec,&local_vec2);CHKERRQ(ierr); 678 ierr = VecCreate(comm,&global_vec);CHKERRQ(ierr); 679 ierr = VecSetSizes(global_vec,PETSC_DECIDE,i);CHKERRQ(ierr); 680 ierr = VecSetType(global_vec,VECSTANDARD);CHKERRQ(ierr); 681 ierr = ISCreateStride(PETSC_COMM_SELF,graph->nvtxs,0,1,&to);CHKERRQ(ierr); 682 ierr = ISLocalToGlobalMappingApplyIS(graph->l2gmap,to,&from);CHKERRQ(ierr); 683 ierr = VecScatterCreate(global_vec,from,local_vec,to,&scatter_ctx);CHKERRQ(ierr); 684 685 /* get local periodic nodes */ 686 mirrors_found = PETSC_FALSE; 687 if (graph->nvtxs && n_neigh) { 688 for (i=0; i<n_shared[0]; i++) graph->count[shared[0][i]] += 1; 689 for (i=0; i<n_shared[0]; i++) { 690 if (graph->count[shared[0][i]] > 1) { 691 mirrors_found = PETSC_TRUE; 692 break; 693 } 694 } 695 } 696 /* compute local mirrors (if any) */ 697 if (mirrors_found) { 698 PetscInt *local_indices,*global_indices; 699 /* get arrays of local and global indices */ 700 ierr = PetscMalloc1(graph->nvtxs,&local_indices);CHKERRQ(ierr); 701 ierr = ISGetIndices(to,(const PetscInt**)&is_indices);CHKERRQ(ierr); 702 ierr = PetscMemcpy(local_indices,is_indices,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 703 ierr = ISRestoreIndices(to,(const PetscInt**)&is_indices);CHKERRQ(ierr); 704 ierr = PetscMalloc1(graph->nvtxs,&global_indices);CHKERRQ(ierr); 705 ierr = ISGetIndices(from,(const PetscInt**)&is_indices);CHKERRQ(ierr); 706 ierr = PetscMemcpy(global_indices,is_indices,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 707 ierr = ISRestoreIndices(from,(const PetscInt**)&is_indices);CHKERRQ(ierr); 708 /* allocate space for mirrors */ 709 ierr = PetscMalloc2(graph->nvtxs,&graph->mirrors,graph->nvtxs,&graph->mirrors_set);CHKERRQ(ierr); 710 ierr = PetscMemzero(graph->mirrors,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 711 graph->mirrors_set[0] = 0; 712 713 k=0; 714 for (i=0;i<n_shared[0];i++) { 715 j=shared[0][i]; 716 if (graph->count[j] > 1) { 717 graph->mirrors[j]++; 718 k++; 719 } 720 } 721 /* allocate space for set of mirrors */ 722 ierr = PetscMalloc1(k,&graph->mirrors_set[0]);CHKERRQ(ierr); 723 for (i=1;i<graph->nvtxs;i++) 724 graph->mirrors_set[i]=graph->mirrors_set[i-1]+graph->mirrors[i-1]; 725 726 /* fill arrays */ 727 ierr = PetscMemzero(graph->mirrors,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 728 for (j=0;j<n_shared[0];j++) { 729 i=shared[0][j]; 730 if (graph->count[i] > 1) 731 graph->mirrors_set[i][graph->mirrors[i]++]=global_indices[i]; 732 } 733 ierr = PetscSortIntWithArray(graph->nvtxs,global_indices,local_indices);CHKERRQ(ierr); 734 for (i=0;i<graph->nvtxs;i++) { 735 if (graph->mirrors[i] > 0) { 736 ierr = PetscFindInt(graph->mirrors_set[i][0],graph->nvtxs,global_indices,&k);CHKERRQ(ierr); 737 j = global_indices[k]; 738 while ( k > 0 && global_indices[k-1] == j) k--; 739 for (j=0;j<graph->mirrors[i];j++) { 740 graph->mirrors_set[i][j]=local_indices[k+j]; 741 } 742 ierr = PetscSortInt(graph->mirrors[i],graph->mirrors_set[i]);CHKERRQ(ierr); 743 } 744 } 745 ierr = PetscFree(local_indices);CHKERRQ(ierr); 746 ierr = PetscFree(global_indices);CHKERRQ(ierr); 747 } 748 ierr = PetscMemzero(graph->count,graph->nvtxs*sizeof(*graph->count));CHKERRQ(ierr); 749 ierr = ISDestroy(&to);CHKERRQ(ierr); 750 ierr = ISDestroy(&from);CHKERRQ(ierr); 751 752 /* Count total number of neigh per node */ 753 k=0; 754 for (i=1;i<n_neigh;i++) { 755 k += n_shared[i]; 756 for (j=0;j<n_shared[i];j++) { 757 graph->count[shared[i][j]] += 1; 758 } 759 } 760 /* Allocate space for storing the set of neighbours for each node */ 761 if (graph->nvtxs) { 762 ierr = PetscMalloc1(k,&graph->neighbours_set[0]);CHKERRQ(ierr); 763 } 764 for (i=1;i<graph->nvtxs;i++) { /* dont count myself */ 765 graph->neighbours_set[i]=graph->neighbours_set[i-1]+graph->count[i-1]; 766 } 767 /* Get information for sharing subdomains */ 768 ierr = PetscMemzero(graph->count,graph->nvtxs*sizeof(*graph->count));CHKERRQ(ierr); 769 for (i=1;i<n_neigh;i++) { /* dont count myself */ 770 s = n_shared[i]; 771 for (j=0;j<s;j++) { 772 k = shared[i][j]; 773 graph->neighbours_set[k][graph->count[k]] = neigh[i]; 774 graph->count[k] += 1; 775 } 776 } 777 /* sort set of sharing subdomains */ 778 for (i=0;i<graph->nvtxs;i++) { 779 ierr = PetscSortRemoveDupsInt(&graph->count[i],graph->neighbours_set[i]);CHKERRQ(ierr); 780 } 781 /* 782 Get info for dofs splitting 783 User can specify only a subset; an additional field is considered as a complementary set 784 */ 785 for (i=0;i<graph->nvtxs;i++) { 786 graph->which_dof[i] = n_ISForDofs; /* by default a dof belongs to the complement set */ 787 } 788 for (i=0;i<n_ISForDofs;i++) { 789 ierr = ISGetLocalSize(ISForDofs[i],&is_size);CHKERRQ(ierr); 790 ierr = ISGetIndices(ISForDofs[i],(const PetscInt**)&is_indices);CHKERRQ(ierr); 791 for (j=0;j<is_size;j++) { 792 if (is_indices[j] > -1 && is_indices[j] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */ 793 graph->which_dof[is_indices[j]] = i; 794 } 795 } 796 ierr = ISRestoreIndices(ISForDofs[i],(const PetscInt**)&is_indices);CHKERRQ(ierr); 797 } 798 /* Take into account Neumann nodes */ 799 ierr = VecSet(local_vec,0.0);CHKERRQ(ierr); 800 ierr = VecSet(local_vec2,0.0);CHKERRQ(ierr); 801 if (neumann_is) { 802 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 803 ierr = ISGetLocalSize(neumann_is,&is_size);CHKERRQ(ierr); 804 ierr = ISGetIndices(neumann_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); 805 for (i=0;i<is_size;i++) { 806 if (is_indices[i] > -1 && is_indices[i] < graph->nvtxs) { /* out of bounds indices (if any) are skipped */ 807 array[is_indices[i]] = 1.0; 808 } 809 } 810 ierr = ISRestoreIndices(neumann_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); 811 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 812 } 813 /* Neumann nodes: impose consistency among neighbours */ 814 ierr = VecSet(global_vec,0.0);CHKERRQ(ierr); 815 ierr = VecScatterBegin(scatter_ctx,local_vec,global_vec,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 816 ierr = VecScatterEnd(scatter_ctx,local_vec,global_vec,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 817 ierr = VecScatterBegin(scatter_ctx,global_vec,local_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 818 ierr = VecScatterEnd(scatter_ctx,global_vec,local_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 819 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 820 for (i=0;i<graph->nvtxs;i++) { 821 if (PetscRealPart(array[i]) > 0.1) { 822 graph->special_dof[i] = PCBDDCGRAPH_NEUMANN_MARK; 823 } 824 } 825 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 826 /* Take into account Dirichlet nodes */ 827 ierr = VecSet(local_vec2,0.0);CHKERRQ(ierr); 828 if (dirichlet_is) { 829 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 830 ierr = VecGetArray(local_vec2,&array2);CHKERRQ(ierr); 831 ierr = ISGetLocalSize(dirichlet_is,&is_size);CHKERRQ(ierr); 832 ierr = ISGetIndices(dirichlet_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 k = is_indices[i]; 836 if (graph->count[k] && !PetscBTLookup(graph->touched,k)) { 837 if (PetscRealPart(array[k]) > 0.1) { 838 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); 839 } 840 array2[k] = 1.0; 841 } 842 } 843 } 844 ierr = ISRestoreIndices(dirichlet_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); 845 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 846 ierr = VecRestoreArray(local_vec2,&array2);CHKERRQ(ierr); 847 } 848 /* Dirichlet nodes: impose consistency among neighbours */ 849 ierr = VecSet(global_vec,0.0);CHKERRQ(ierr); 850 ierr = VecScatterBegin(scatter_ctx,local_vec2,global_vec,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 851 ierr = VecScatterEnd(scatter_ctx,local_vec2,global_vec,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 852 ierr = VecScatterBegin(scatter_ctx,global_vec,local_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 853 ierr = VecScatterEnd(scatter_ctx,global_vec,local_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 854 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 855 for (i=0;i<graph->nvtxs;i++) { 856 if (PetscRealPart(array[i]) > 0.1) { 857 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 858 graph->subset[i] = 0; /* dirichlet nodes treated as internal -> is it ok? */ 859 graph->special_dof[i] = PCBDDCGRAPH_DIRICHLET_MARK; 860 } 861 } 862 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 863 864 /* mark local periodic nodes (if any) and adapt CSR graph (if any) */ 865 if (graph->mirrors) { 866 for (i=0;i<graph->nvtxs;i++) 867 if (graph->mirrors[i]) 868 graph->special_dof[i] = PCBDDCGRAPH_LOCAL_PERIODIC_MARK; 869 870 if (graph->xadj && graph->adjncy) { 871 PetscInt *new_xadj,*new_adjncy; 872 /* sort CSR graph */ 873 for (i=0;i<graph->nvtxs;i++) 874 ierr = PetscSortInt(graph->xadj[i+1]-graph->xadj[i],&graph->adjncy[graph->xadj[i]]);CHKERRQ(ierr); 875 876 /* adapt local CSR graph in case of local periodicity */ 877 k=0; 878 for (i=0;i<graph->nvtxs;i++) 879 for (j=graph->xadj[i];j<graph->xadj[i+1];j++) 880 k += graph->mirrors[graph->adjncy[j]]; 881 882 ierr = PetscMalloc1((graph->nvtxs+1),&new_xadj);CHKERRQ(ierr); 883 ierr = PetscMalloc1((k+graph->xadj[graph->nvtxs]),&new_adjncy);CHKERRQ(ierr); 884 new_xadj[0]=0; 885 for (i=0;i<graph->nvtxs;i++) { 886 k = graph->xadj[i+1]-graph->xadj[i]; 887 ierr = PetscMemcpy(&new_adjncy[new_xadj[i]],&graph->adjncy[graph->xadj[i]],k*sizeof(PetscInt));CHKERRQ(ierr); 888 new_xadj[i+1]=new_xadj[i]+k; 889 for (j=graph->xadj[i];j<graph->xadj[i+1];j++) { 890 k = graph->mirrors[graph->adjncy[j]]; 891 ierr = PetscMemcpy(&new_adjncy[new_xadj[i+1]],graph->mirrors_set[graph->adjncy[j]],k*sizeof(PetscInt));CHKERRQ(ierr); 892 new_xadj[i+1]+=k; 893 } 894 k = new_xadj[i+1]-new_xadj[i]; 895 ierr = PetscSortRemoveDupsInt(&k,&new_adjncy[new_xadj[i]]);CHKERRQ(ierr); 896 new_xadj[i+1]=new_xadj[i]+k; 897 } 898 /* set new CSR into graph */ 899 ierr = PetscFree(graph->xadj);CHKERRQ(ierr); 900 ierr = PetscFree(graph->adjncy);CHKERRQ(ierr); 901 graph->xadj = new_xadj; 902 graph->adjncy = new_adjncy; 903 } 904 } 905 906 /* mark special nodes -> each will become a single node equivalence class */ 907 if (custom_primal_vertices) { 908 ierr = ISGetLocalSize(custom_primal_vertices,&is_size);CHKERRQ(ierr); 909 ierr = ISGetIndices(custom_primal_vertices,(const PetscInt**)&is_indices);CHKERRQ(ierr); 910 for (i=0;i<is_size;i++) { 911 graph->special_dof[is_indices[i]] = PCBDDCGRAPH_SPECIAL_MARK-i; 912 } 913 ierr = ISRestoreIndices(custom_primal_vertices,(const PetscInt**)&is_indices);CHKERRQ(ierr); 914 } 915 /* mark interior nodes as touched and belonging to partition number 0 */ 916 for (i=0;i<graph->nvtxs;i++) { 917 if (!graph->count[i]) { 918 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 919 graph->subset[i] = 0; 920 } 921 } 922 /* init graph structure and compute default subsets */ 923 nodes_touched=0; 924 for (i=0;i<graph->nvtxs;i++) { 925 if (PetscBTLookup(graph->touched,i)) { 926 nodes_touched++; 927 } 928 } 929 i = 0; 930 graph->ncc = 0; 931 total_counts = 0; 932 while (nodes_touched<graph->nvtxs) { 933 /* find first untouched node in local ordering */ 934 while (PetscBTLookup(graph->touched,i)) { 935 i++; 936 } 937 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 938 graph->subset[i] = graph->ncc+1; 939 graph->cptr[graph->ncc] = total_counts; 940 graph->queue[total_counts] = i; 941 total_counts++; 942 nodes_touched++; 943 /* now find all other nodes having the same set of sharing subdomains */ 944 for (j=i+1;j<graph->nvtxs;j++) { 945 /* check for same number of sharing subdomains, dof number and same special mark */ 946 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]) { 947 /* check for same set of sharing subdomains */ 948 same_set=PETSC_TRUE; 949 for (k=0;k<graph->count[j];k++){ 950 if (graph->neighbours_set[i][k]!=graph->neighbours_set[j][k]) { 951 same_set=PETSC_FALSE; 952 } 953 } 954 /* I found a friend of mine */ 955 if (same_set) { 956 graph->subset[j]=graph->ncc+1; 957 ierr = PetscBTSet(graph->touched,j);CHKERRQ(ierr); 958 nodes_touched++; 959 graph->queue[total_counts] = j; 960 total_counts++; 961 } 962 } 963 } 964 graph->ncc++; 965 } 966 /* set default number of subsets (at this point no info on csr graph has been taken into account, so n_subsets = ncc */ 967 graph->n_subsets = graph->ncc; 968 ierr = PetscMalloc1(graph->n_subsets,&graph->subset_ncc);CHKERRQ(ierr); 969 for (i=0;i<graph->n_subsets;i++) { 970 graph->subset_ncc[i] = 1; 971 } 972 /* final pointer */ 973 graph->cptr[graph->ncc] = total_counts; 974 /* free memory allocated by ISLocalToGlobalMappingGetInfo */ 975 ierr = ISLocalToGlobalMappingRestoreInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);CHKERRQ(ierr); 976 /* get a reference node (min index in global ordering) for each subset */ 977 ierr = PetscMalloc1(graph->ncc,&graph->subset_ref_node);CHKERRQ(ierr); 978 ierr = PetscMalloc1(graph->cptr[graph->ncc],&queue_global);CHKERRQ(ierr); 979 ierr = ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_global);CHKERRQ(ierr); 980 for (i=0;i<graph->ncc;i++) { 981 PetscInt minval = queue_global[graph->cptr[i]]; 982 for (j=graph->cptr[i]+1;j<graph->cptr[i+1];j++) { 983 minval = PetscMin(minval,queue_global[j]); 984 } 985 graph->subset_ref_node[i] = minval; 986 } 987 ierr = PetscFree(queue_global);CHKERRQ(ierr); 988 /* free objects */ 989 ierr = VecDestroy(&local_vec);CHKERRQ(ierr); 990 ierr = VecDestroy(&local_vec2);CHKERRQ(ierr); 991 ierr = VecDestroy(&global_vec);CHKERRQ(ierr); 992 ierr = VecScatterDestroy(&scatter_ctx);CHKERRQ(ierr); 993 PetscFunctionReturn(0); 994 } 995 996 #undef __FUNCT__ 997 #define __FUNCT__ "PCBDDCGraphResetCSR" 998 PetscErrorCode PCBDDCGraphResetCSR(PCBDDCGraph graph) 999 { 1000 PetscErrorCode ierr; 1001 1002 PetscFunctionBegin; 1003 ierr = PetscFree(graph->xadj);CHKERRQ(ierr); 1004 ierr = PetscFree(graph->adjncy);CHKERRQ(ierr); 1005 graph->nvtxs_csr = 0; 1006 PetscFunctionReturn(0); 1007 } 1008 1009 #undef __FUNCT__ 1010 #define __FUNCT__ "PCBDDCGraphReset" 1011 PetscErrorCode PCBDDCGraphReset(PCBDDCGraph graph) 1012 { 1013 PetscErrorCode ierr; 1014 1015 PetscFunctionBegin; 1016 ierr = ISLocalToGlobalMappingDestroy(&graph->l2gmap);CHKERRQ(ierr); 1017 ierr = PetscFree(graph->subset_ncc);CHKERRQ(ierr); 1018 ierr = PetscFree(graph->subset_ref_node);CHKERRQ(ierr); 1019 if (graph->nvtxs) { 1020 ierr = PetscFree(graph->neighbours_set[0]);CHKERRQ(ierr); 1021 } 1022 ierr = PetscBTDestroy(&graph->touched);CHKERRQ(ierr); 1023 ierr = PetscFree7(graph->count, 1024 graph->neighbours_set, 1025 graph->subset, 1026 graph->which_dof, 1027 graph->cptr, 1028 graph->queue, 1029 graph->special_dof);CHKERRQ(ierr); 1030 if (graph->mirrors) { 1031 ierr = PetscFree(graph->mirrors_set[0]);CHKERRQ(ierr); 1032 } 1033 ierr = PetscFree2(graph->mirrors,graph->mirrors_set);CHKERRQ(ierr); 1034 graph->nvtxs = 0; 1035 graph->n_subsets = 0; 1036 graph->custom_minimal_size = 1; 1037 PetscFunctionReturn(0); 1038 } 1039 1040 #undef __FUNCT__ 1041 #define __FUNCT__ "PCBDDCGraphInit" 1042 PetscErrorCode PCBDDCGraphInit(PCBDDCGraph graph, ISLocalToGlobalMapping l2gmap) 1043 { 1044 PetscInt n; 1045 PetscErrorCode ierr; 1046 1047 PetscFunctionBegin; 1048 PetscValidPointer(graph,1); 1049 PetscValidHeaderSpecific(l2gmap,IS_LTOGM_CLASSID,2); 1050 /* raise an error if already allocated */ 1051 if (graph->nvtxs) { 1052 SETERRQ(PetscObjectComm((PetscObject)l2gmap),PETSC_ERR_PLIB,"BDDCGraph already initialized"); 1053 } 1054 /* set number of vertices */ 1055 ierr = PetscObjectReference((PetscObject)l2gmap);CHKERRQ(ierr); 1056 graph->l2gmap = l2gmap; 1057 ierr = ISLocalToGlobalMappingGetSize(l2gmap,&n);CHKERRQ(ierr); 1058 graph->nvtxs = n; 1059 /* allocate used space */ 1060 ierr = PetscBTCreate(graph->nvtxs,&graph->touched);CHKERRQ(ierr); 1061 ierr = PetscMalloc7(graph->nvtxs,&graph->count, 1062 graph->nvtxs,&graph->neighbours_set, 1063 graph->nvtxs,&graph->subset, 1064 graph->nvtxs,&graph->which_dof, 1065 graph->nvtxs+1,&graph->cptr, 1066 graph->nvtxs,&graph->queue, 1067 graph->nvtxs,&graph->special_dof);CHKERRQ(ierr); 1068 /* zeroes memory */ 1069 ierr = PetscMemzero(graph->count,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 1070 ierr = PetscMemzero(graph->subset,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 1071 /* use -1 as a default value for which_dof array */ 1072 for (n=0;n<graph->nvtxs;n++) graph->which_dof[n] = -1; 1073 ierr = PetscMemzero(graph->cptr,(graph->nvtxs+1)*sizeof(PetscInt));CHKERRQ(ierr); 1074 ierr = PetscMemzero(graph->queue,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 1075 ierr = PetscMemzero(graph->special_dof,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 1076 /* zeroes first pointer to neighbour set */ 1077 if (graph->nvtxs) { 1078 graph->neighbours_set[0] = 0; 1079 } 1080 /* zeroes workspace for values of ncc */ 1081 graph->subset_ncc = 0; 1082 graph->subset_ref_node = 0; 1083 PetscFunctionReturn(0); 1084 } 1085 1086 #undef __FUNCT__ 1087 #define __FUNCT__ "PCBDDCGraphDestroy" 1088 PetscErrorCode PCBDDCGraphDestroy(PCBDDCGraph* graph) 1089 { 1090 PetscErrorCode ierr; 1091 1092 PetscFunctionBegin; 1093 ierr = PCBDDCGraphReset(*graph);CHKERRQ(ierr); 1094 ierr = PetscFree(*graph);CHKERRQ(ierr); 1095 PetscFunctionReturn(0); 1096 } 1097 1098 #undef __FUNCT__ 1099 #define __FUNCT__ "PCBDDCGraphCreate" 1100 PetscErrorCode PCBDDCGraphCreate(PCBDDCGraph *graph) 1101 { 1102 PCBDDCGraph new_graph; 1103 PetscErrorCode ierr; 1104 1105 PetscFunctionBegin; 1106 ierr = PetscMalloc(sizeof(*new_graph),&new_graph);CHKERRQ(ierr); 1107 /* local to global mapping of dofs */ 1108 new_graph->l2gmap = 0; 1109 /* vertex size */ 1110 new_graph->nvtxs = 0; 1111 new_graph->n_subsets = 0; 1112 new_graph->custom_minimal_size = 1; 1113 /* zeroes ponters */ 1114 new_graph->mirrors = 0; 1115 new_graph->mirrors_set = 0; 1116 new_graph->neighbours_set = 0; 1117 new_graph->subset = 0; 1118 new_graph->which_dof = 0; 1119 new_graph->special_dof = 0; 1120 new_graph->cptr = 0; 1121 new_graph->queue = 0; 1122 new_graph->count = 0; 1123 new_graph->subset_ncc = 0; 1124 new_graph->subset_ref_node = 0; 1125 new_graph->touched = 0; 1126 /* zeroes pointers to csr graph of local nodes connectivity (optional data) */ 1127 new_graph->nvtxs_csr = 0; 1128 new_graph->xadj = 0; 1129 new_graph->adjncy = 0; 1130 *graph = new_graph; 1131 PetscFunctionReturn(0); 1132 } 1133