1 #include <petsc-private/petscimpl.h> 2 #include "bddcprivate.h" 3 #include "bddcstructs.h" 4 5 /* special marks: they cannot be enums, since special marks should in principle range from -4 to -max_int */ 6 #define NEUMANN_MARK -1 7 #define DIRICHLET_MARK -2 8 #define LOCAL_PERIODIC_MARK -3 9 #define SPECIAL_MARK -4 10 11 #undef __FUNCT__ 12 #define __FUNCT__ "PCBDDCGraphASCIIView" 13 PetscErrorCode PCBDDCGraphASCIIView(PCBDDCGraph graph, PetscInt verbosity_level, PetscViewer viewer) 14 { 15 PetscInt i,j; 16 PetscInt* queue_in_global_numbering; 17 PetscErrorCode ierr; 18 19 PetscFunctionBegin; 20 ierr = PetscViewerASCIISynchronizedAllow(viewer,PETSC_TRUE);CHKERRQ(ierr); 21 ierr = PetscViewerASCIIPrintf(viewer,"--------------------------------------------------\n");CHKERRQ(ierr); 22 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 23 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Local BDDC graph for subdomain %04d\n",PetscGlobalRank);CHKERRQ(ierr); 24 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Number of vertices %d\n",graph->nvtxs);CHKERRQ(ierr); 25 if (verbosity_level > 1) { 26 for (i=0;i<graph->nvtxs;i++) { 27 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"%d:\n",i);CHKERRQ(ierr); 28 ierr = PetscViewerASCIISynchronizedPrintf(viewer," which_dof: %d\n",graph->which_dof[i]);CHKERRQ(ierr); 29 ierr = PetscViewerASCIISynchronizedPrintf(viewer," special_dof: %d\n",graph->special_dof[i]);CHKERRQ(ierr); 30 ierr = PetscViewerASCIISynchronizedPrintf(viewer," neighbours: %d\n",graph->count[i]);CHKERRQ(ierr); 31 if (graph->count[i]) { 32 ierr = PetscViewerASCIISynchronizedPrintf(viewer," set of neighbours:");CHKERRQ(ierr); 33 for (j=0;j<graph->count[i];j++) { 34 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->neighbours_set[i][j]);CHKERRQ(ierr); 35 } 36 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"\n");CHKERRQ(ierr); 37 } 38 if (graph->mirrors) { 39 ierr = PetscViewerASCIISynchronizedPrintf(viewer," mirrors: %d\n",graph->mirrors[i]);CHKERRQ(ierr); 40 if (graph->mirrors[i]) { 41 ierr = PetscViewerASCIISynchronizedPrintf(viewer," set of mirrors:");CHKERRQ(ierr); 42 for (j=0;j<graph->mirrors[i];j++) { 43 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->mirrors_set[i][j]);CHKERRQ(ierr); 44 } 45 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"\n");CHKERRQ(ierr); 46 } 47 } 48 if (verbosity_level > 2) { 49 if (graph->xadj && graph->adjncy) { 50 ierr = PetscViewerASCIISynchronizedPrintf(viewer," local adj list:");CHKERRQ(ierr); 51 for (j=graph->xadj[i];j<graph->xadj[i+1];j++) { 52 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->adjncy[j]);CHKERRQ(ierr); 53 } 54 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"\n");CHKERRQ(ierr); 55 } 56 } 57 ierr = PetscViewerASCIISynchronizedPrintf(viewer," interface subset id: %d\n",graph->subset[i]);CHKERRQ(ierr); 58 if (graph->subset[i] && graph->subset_ncc) { 59 ierr = PetscViewerASCIISynchronizedPrintf(viewer," ncc for subset: %d\n",graph->subset_ncc[graph->subset[i]-1]);CHKERRQ(ierr); 60 } 61 } 62 } 63 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Total number of connected components %d\n",graph->ncc);CHKERRQ(ierr); 64 ierr = PetscMalloc(graph->cptr[graph->ncc]*sizeof(*queue_in_global_numbering),&queue_in_global_numbering);CHKERRQ(ierr); 65 ierr = ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_in_global_numbering);CHKERRQ(ierr); 66 for (i=0;i<graph->ncc;i++) { 67 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d (neighs:",i);CHKERRQ(ierr); 68 PetscInt node_num=graph->queue[graph->cptr[i]]; 69 for (j=0;j<graph->count[node_num];j++) { 70 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d",graph->neighbours_set[node_num][j]);CHKERRQ(ierr); 71 } 72 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"):");CHKERRQ(ierr); 73 for (j=graph->cptr[i];j<graph->cptr[i+1];j++) { 74 ierr = PetscViewerASCIISynchronizedPrintf(viewer," %d (%d)",graph->queue[j],queue_in_global_numbering[j]);CHKERRQ(ierr); 75 } 76 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"\n");CHKERRQ(ierr); 77 } 78 ierr = PetscFree(queue_in_global_numbering);CHKERRQ(ierr); 79 if (graph->custom_minimal_size > 1 && verbosity_level > 1) { 80 ierr = PetscViewerASCIISynchronizedPrintf(viewer,"Custom minimal size %d\n",graph->custom_minimal_size);CHKERRQ(ierr); 81 } 82 ierr = PetscViewerFlush(viewer);CHKERRQ(ierr); 83 PetscFunctionReturn(0); 84 } 85 86 #undef __FUNCT__ 87 #define __FUNCT__ "PCBDDCGraphGetCandidatesIS" 88 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) 89 { 90 IS *ISForFaces,*ISForEdges,ISForVertices; 91 PetscInt i,j,nfc,nec,nvc,*idx; 92 PetscBool twodim_flag; 93 PetscErrorCode ierr; 94 95 PetscFunctionBegin; 96 /* loop on ccs to evalute number of faces, edges and vertices */ 97 nfc = 0; 98 nec = 0; 99 nvc = 0; 100 twodim_flag = PETSC_FALSE; 101 for (i=0;i<graph->ncc;i++) { 102 if (graph->cptr[i+1]-graph->cptr[i] > graph->custom_minimal_size) { 103 if (graph->count[graph->queue[graph->cptr[i]]] == 1 && graph->special_dof[graph->queue[graph->cptr[i]]] != NEUMANN_MARK) { 104 nfc++; 105 } else { /* note that nec will be zero in 2d */ 106 nec++; 107 } 108 } else { 109 nvc += graph->cptr[i+1]-graph->cptr[i]; 110 } 111 } 112 if (!nec) { /* we are in a 2d case -> no faces, only edges */ 113 nec = nfc; 114 nfc = 0; 115 twodim_flag = PETSC_TRUE; 116 } 117 /* allocate IS arrays for faces, edges. Vertices need a single index set. */ 118 ISForFaces = 0; 119 ISForEdges = 0; 120 ISForVertices = 0; 121 if (use_faces) { 122 ierr = PetscMalloc(nfc*sizeof(IS),&ISForFaces);CHKERRQ(ierr); 123 } 124 if (use_edges) { 125 ierr = PetscMalloc(nec*sizeof(IS),&ISForEdges);CHKERRQ(ierr); 126 } 127 if (use_vertices) { 128 ierr = PetscMalloc(nvc*sizeof(PetscInt),&idx);CHKERRQ(ierr); 129 } 130 /* loop on ccs to compute index sets for faces and edges */ 131 nfc = 0; 132 nec = 0; 133 nvc = 0; 134 for (i=0;i<graph->ncc;i++) { 135 if (graph->cptr[i+1]-graph->cptr[i] > graph->custom_minimal_size) { 136 if (graph->count[graph->queue[graph->cptr[i]]] == 1 && graph->special_dof[graph->queue[graph->cptr[i]]] != NEUMANN_MARK) { 137 if (twodim_flag) { 138 if (use_edges) { 139 ierr = ISCreateGeneral(PETSC_COMM_SELF,graph->cptr[i+1]-graph->cptr[i],&graph->queue[graph->cptr[i]],PETSC_COPY_VALUES,&ISForEdges[nec]);CHKERRQ(ierr); 140 nec++; 141 } 142 } else { 143 if (use_faces) { 144 ierr = ISCreateGeneral(PETSC_COMM_SELF,graph->cptr[i+1]-graph->cptr[i],&graph->queue[graph->cptr[i]],PETSC_COPY_VALUES,&ISForFaces[nfc]);CHKERRQ(ierr); 145 nfc++; 146 } 147 } 148 } else { 149 if (use_edges) { 150 ierr = ISCreateGeneral(PETSC_COMM_SELF,graph->cptr[i+1]-graph->cptr[i],&graph->queue[graph->cptr[i]],PETSC_COPY_VALUES,&ISForEdges[nec]);CHKERRQ(ierr); 151 nec++; 152 } 153 } 154 } 155 } 156 /* index set for vertices */ 157 if (use_vertices) { 158 for (i=0;i<graph->ncc;i++) { 159 if (graph->cptr[i+1]-graph->cptr[i] <= graph->custom_minimal_size) { 160 for (j=graph->cptr[i];j<graph->cptr[i+1];j++) { 161 idx[nvc]=graph->queue[j]; 162 nvc++; 163 } 164 } 165 } 166 /* sort vertex set (by local ordering) */ 167 ierr = PetscSortInt(nvc,idx);CHKERRQ(ierr); 168 ierr = ISCreateGeneral(PETSC_COMM_SELF,nvc,idx,PETSC_OWN_POINTER,&ISForVertices);CHKERRQ(ierr); 169 } 170 /* get back info */ 171 *n_faces = nfc; 172 *FacesIS = ISForFaces; 173 *n_edges = nec; 174 *EdgesIS = ISForEdges; 175 *VerticesIS = ISForVertices; 176 PetscFunctionReturn(0); 177 } 178 179 #undef __FUNCT__ 180 #define __FUNCT__ "PCBDDCGraphComputeConnectedComponents" 181 PetscErrorCode PCBDDCGraphComputeConnectedComponents(PCBDDCGraph graph) 182 { 183 PetscInt adapt_interface,adapt_interface_reduced; 184 MPI_Comm interface_comm; 185 MPI_Request *send_requests; 186 MPI_Request *recv_requests; 187 PetscInt *aux_new_xadj,*new_xadj,*new_adjncy,**temp_buffer; 188 PetscInt i,j,k,s,sum_requests,buffer_size,size_of_recv,temp_buffer_size; 189 PetscMPIInt rank,neigh,tag,mpi_buffer_size; 190 PetscInt *cum_recv_counts,*subset_to_nodes_indices,*recv_buffer_subset,*nodes_to_temp_buffer_indices; 191 PetscInt *send_buffer,*recv_buffer,*queue_in_global_numbering,*sizes_of_sends,*add_to_subset; 192 PetscInt start_of_recv,start_of_send,size_of_send,global_subset_counter,ins_val; 193 PetscBool *subset_cc_adapt,same_set; 194 PetscErrorCode ierr; 195 196 PetscFunctionBegin; 197 /* compute connected components locally */ 198 ierr = PetscObjectGetComm((PetscObject)(graph->l2gmap),&interface_comm);CHKERRQ(ierr); 199 ierr = PCBDDCGraphComputeConnectedComponentsLocal(graph);CHKERRQ(ierr); 200 /* check consistency of connected components among neighbouring subdomains -> it adapt them in case it is needed */ 201 adapt_interface = 0; 202 adapt_interface_reduced = 0; 203 for (i=0;i<graph->n_subsets;i++) { 204 /* We are not sure that on a given subset of the local interface, 205 with two connected components, the latters be the same among sharing subdomains */ 206 if (graph->subset_ncc[i] > 1) { 207 adapt_interface=1; 208 break; 209 } 210 } 211 ierr = MPI_Allreduce(&adapt_interface,&adapt_interface_reduced,1,MPIU_INT,MPI_LOR,interface_comm);CHKERRQ(ierr); 212 213 if (graph->n_subsets && adapt_interface_reduced) { 214 /* Retrict adjacency graph using information from previously computed connected components */ 215 ierr = PetscMalloc(graph->nvtxs*sizeof(PetscInt),&aux_new_xadj);CHKERRQ(ierr); 216 for (i=0;i<graph->nvtxs;i++) { 217 aux_new_xadj[i]=1; 218 } 219 for (i=0;i<graph->ncc;i++) { 220 k = graph->cptr[i+1]-graph->cptr[i]; 221 for (j=0;j<k;j++) { 222 aux_new_xadj[graph->queue[graph->cptr[i]+j]]=k; 223 } 224 } 225 j = 0; 226 for (i=0;i<graph->nvtxs;i++) { 227 j += aux_new_xadj[i]; 228 } 229 ierr = PetscMalloc((graph->nvtxs+1)*sizeof(PetscInt),&new_xadj);CHKERRQ(ierr); 230 ierr = PetscMalloc(j*sizeof(PetscInt),&new_adjncy);CHKERRQ(ierr); 231 new_xadj[0]=0; 232 for (i=0;i<graph->nvtxs;i++) { 233 new_xadj[i+1]=new_xadj[i]+aux_new_xadj[i]; 234 if (aux_new_xadj[i]==1) { 235 new_adjncy[new_xadj[i]]=i; 236 } 237 } 238 ierr = PetscFree(aux_new_xadj);CHKERRQ(ierr); 239 for (i=0;i<graph->ncc;i++) { 240 k = graph->cptr[i+1]-graph->cptr[i]; 241 for (j=0;j<k;j++) { 242 ierr = PetscMemcpy(&new_adjncy[new_xadj[graph->queue[graph->cptr[i]+j]]],&graph->queue[graph->cptr[i]],k*sizeof(PetscInt));CHKERRQ(ierr); 243 } 244 } 245 /* set new CSR into graph */ 246 ierr = PetscFree(graph->xadj);CHKERRQ(ierr); 247 ierr = PetscFree(graph->adjncy);CHKERRQ(ierr); 248 graph->xadj = new_xadj; 249 graph->adjncy = new_adjncy; 250 /* allocate some space */ 251 ierr = MPI_Comm_rank(interface_comm,&rank);CHKERRQ(ierr); 252 ierr = PetscMalloc((graph->n_subsets+1)*sizeof(*cum_recv_counts),&cum_recv_counts);CHKERRQ(ierr); 253 ierr = PetscMemzero(cum_recv_counts,(graph->n_subsets+1)*sizeof(*cum_recv_counts));CHKERRQ(ierr); 254 ierr = PetscMalloc(graph->n_subsets*sizeof(*subset_to_nodes_indices),&subset_to_nodes_indices);CHKERRQ(ierr); 255 /* first count how many neighbours per connected component I will receive from */ 256 cum_recv_counts[0]=0; 257 for (i=1;i<graph->n_subsets+1;i++) { 258 j = 0; 259 while (graph->subset[j] != i) { 260 j++; 261 } 262 subset_to_nodes_indices[i-1]=j; 263 /* We don't want sends/recvs_to/from_self -> here I don't count myself */ 264 cum_recv_counts[i]=cum_recv_counts[i-1]+graph->count[j]; 265 } 266 ierr = PetscMalloc(2*cum_recv_counts[graph->n_subsets]*sizeof(*recv_buffer_subset),&recv_buffer_subset);CHKERRQ(ierr); 267 ierr = PetscMalloc(cum_recv_counts[graph->n_subsets]*sizeof(MPI_Request),&send_requests);CHKERRQ(ierr); 268 ierr = PetscMalloc(cum_recv_counts[graph->n_subsets]*sizeof(MPI_Request),&recv_requests);CHKERRQ(ierr); 269 for (i=0;i<cum_recv_counts[graph->n_subsets];i++) { 270 send_requests[i]=MPI_REQUEST_NULL; 271 recv_requests[i]=MPI_REQUEST_NULL; 272 } 273 /* exchange with my neighbours the number of my connected components on the shared interface */ 274 sum_requests = 0; 275 for (i=0;i<graph->n_subsets;i++) { 276 j = subset_to_nodes_indices[i]; 277 for (k=0;k<graph->count[j];k++) { 278 ierr = PetscMPIIntCast(graph->neighbours_set[j][k],&neigh);CHKERRQ(ierr); 279 ierr = PetscMPIIntCast((PetscInt)(rank+1)*graph->count[j],&tag);CHKERRQ(ierr); 280 ierr = MPI_Isend(&graph->subset_ncc[i],1,MPIU_INT,neigh,tag,interface_comm,&send_requests[sum_requests]);CHKERRQ(ierr); 281 ierr = PetscMPIIntCast((PetscInt)(neigh+1)*graph->count[j],&tag);CHKERRQ(ierr); 282 ierr = MPI_Irecv(&recv_buffer_subset[sum_requests],1,MPIU_INT,neigh,tag,interface_comm,&recv_requests[sum_requests]);CHKERRQ(ierr); 283 sum_requests++; 284 } 285 } 286 ierr = MPI_Waitall(sum_requests,recv_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 287 ierr = MPI_Waitall(sum_requests,send_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 288 /* determine the connected component I need to adapt */ 289 ierr = PetscMalloc(graph->n_subsets*sizeof(*subset_cc_adapt),&subset_cc_adapt);CHKERRQ(ierr); 290 ierr = PetscMemzero(subset_cc_adapt,graph->n_subsets*sizeof(*subset_cc_adapt));CHKERRQ(ierr); 291 for (i=0;i<graph->n_subsets;i++) { 292 for (j=cum_recv_counts[i];j<cum_recv_counts[i+1];j++){ 293 /* The first condition is natural (someone has a different number of ccs than me), the second one is just to be safe */ 294 if ( graph->subset_ncc[i] != recv_buffer_subset[j] || graph->subset_ncc[i] > 1 ) { 295 subset_cc_adapt[i] = PETSC_TRUE; 296 break; 297 } 298 } 299 } 300 buffer_size = 0; 301 for (i=0;i<graph->n_subsets;i++) { 302 if (subset_cc_adapt[i]) { 303 for (j=i;j<graph->ncc;j++) { 304 if (graph->subset[graph->queue[graph->cptr[j]]] == i+1) { /* WARNING -> subset values goes from 1 to graph->n_subsets included */ 305 buffer_size += 1 + graph->cptr[j+1]-graph->cptr[j]; 306 } 307 } 308 } 309 } 310 ierr = PetscMalloc(buffer_size*sizeof(*send_buffer),&send_buffer);CHKERRQ(ierr); 311 /* now get from neighbours their ccs (in global numbering) and adapt them (in case it is needed) */ 312 ierr = PetscMalloc(graph->cptr[graph->ncc]*sizeof(*queue_in_global_numbering),&queue_in_global_numbering);CHKERRQ(ierr); 313 ierr = ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_in_global_numbering);CHKERRQ(ierr); 314 /* determine how much data to send (size of each queue plus the global indices) and communicate it to neighbours */ 315 ierr = PetscMalloc(graph->n_subsets*sizeof(*sizes_of_sends),&sizes_of_sends);CHKERRQ(ierr); 316 ierr = PetscMemzero(sizes_of_sends,graph->n_subsets*sizeof(*sizes_of_sends));CHKERRQ(ierr); 317 sum_requests = 0; 318 start_of_send = 0; 319 start_of_recv = cum_recv_counts[graph->n_subsets]; 320 for (i=0;i<graph->n_subsets;i++) { 321 if (subset_cc_adapt[i]) { 322 size_of_send = 0; 323 for (j=i;j<graph->ncc;j++) { 324 if (graph->subset[graph->queue[graph->cptr[j]]] == i+1) { /* WARNING -> subset values goes from 1 to graph->n_subsets included */ 325 send_buffer[start_of_send+size_of_send]=graph->cptr[j+1]-graph->cptr[j]; 326 size_of_send += 1; 327 ierr = PetscMemcpy(&send_buffer[start_of_send+size_of_send], 328 &queue_in_global_numbering[graph->cptr[j]], 329 (graph->cptr[j+1]-graph->cptr[j])*sizeof(*send_buffer));CHKERRQ(ierr); 330 size_of_send = size_of_send+graph->cptr[j+1]-graph->cptr[j]; 331 } 332 } 333 j = subset_to_nodes_indices[i]; 334 sizes_of_sends[i] = size_of_send; 335 for (k=0;k<graph->count[j];k++) { 336 ierr = PetscMPIIntCast(graph->neighbours_set[j][k],&neigh);CHKERRQ(ierr); 337 ierr = PetscMPIIntCast((PetscInt)(rank+1)*graph->count[j],&tag);CHKERRQ(ierr); 338 ierr = MPI_Isend(&sizes_of_sends[i],1,MPIU_INT,neigh,tag,interface_comm,&send_requests[sum_requests]);CHKERRQ(ierr); 339 ierr = PetscMPIIntCast((PetscInt)(neigh+1)*graph->count[j],&tag);CHKERRQ(ierr); 340 ierr = MPI_Irecv(&recv_buffer_subset[sum_requests+start_of_recv],1,MPIU_INT,neigh,tag,interface_comm,&recv_requests[sum_requests]);CHKERRQ(ierr); 341 sum_requests++; 342 } 343 start_of_send += size_of_send; 344 } 345 } 346 ierr = MPI_Waitall(sum_requests,send_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 347 ierr = MPI_Waitall(sum_requests,recv_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 348 buffer_size = 0; 349 for (k=0;k<sum_requests;k++) { 350 buffer_size += recv_buffer_subset[start_of_recv+k]; 351 } 352 ierr = PetscMalloc(buffer_size*sizeof(*recv_buffer),&recv_buffer);CHKERRQ(ierr); 353 /* now exchange the data */ 354 start_of_recv = 0; 355 start_of_send = 0; 356 sum_requests = 0; 357 for (i=0;i<graph->n_subsets;i++) { 358 if (subset_cc_adapt[i]) { 359 size_of_send = sizes_of_sends[i]; 360 j = subset_to_nodes_indices[i]; 361 for (k=0;k<graph->count[j];k++) { 362 ierr = PetscMPIIntCast(graph->neighbours_set[j][k],&neigh);CHKERRQ(ierr); 363 ierr = PetscMPIIntCast((PetscInt)(rank+1)*graph->count[j],&tag);CHKERRQ(ierr); 364 ierr = PetscMPIIntCast(size_of_send,&mpi_buffer_size);CHKERRQ(ierr); 365 ierr = MPI_Isend(&send_buffer[start_of_send],mpi_buffer_size,MPIU_INT,neigh,tag,interface_comm,&send_requests[sum_requests]);CHKERRQ(ierr); 366 size_of_recv = recv_buffer_subset[cum_recv_counts[graph->n_subsets]+sum_requests]; 367 ierr = PetscMPIIntCast((PetscInt)(neigh+1)*graph->count[j],&tag);CHKERRQ(ierr); 368 ierr = PetscMPIIntCast(size_of_recv,&mpi_buffer_size);CHKERRQ(ierr); 369 ierr = MPI_Irecv(&recv_buffer[start_of_recv],mpi_buffer_size,MPIU_INT,neigh,tag,interface_comm,&recv_requests[sum_requests]);CHKERRQ(ierr); 370 start_of_recv += size_of_recv; 371 sum_requests++; 372 } 373 start_of_send += size_of_send; 374 } 375 } 376 ierr = MPI_Waitall(sum_requests,recv_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 377 ierr = MPI_Waitall(sum_requests,send_requests,MPI_STATUSES_IGNORE);CHKERRQ(ierr); 378 for (j=0;j<buffer_size;) { 379 ierr = ISGlobalToLocalMappingApply(graph->l2gmap,IS_GTOLM_MASK,recv_buffer[j],&recv_buffer[j+1],&recv_buffer[j],&recv_buffer[j+1]);CHKERRQ(ierr); 380 /* we need to adapt the output of GlobalToLocal mapping if there are mirrored nodes */ 381 if (graph->mirrors) { 382 PetscBool mirrored_found=PETSC_FALSE; 383 for (k=0;k<recv_buffer[j];k++) { 384 if (graph->mirrors[recv_buffer[j+k+1]]) { 385 mirrored_found=PETSC_TRUE; 386 recv_buffer[j+k+1]=graph->mirrors_set[recv_buffer[j+k+1]][0]; 387 } 388 } 389 if (mirrored_found) { 390 ierr = PetscSortInt(recv_buffer[j],&recv_buffer[j+1]);CHKERRQ(ierr); 391 k=0; 392 while (k<recv_buffer[j]) { 393 for (s=1;s<graph->mirrors[recv_buffer[j+1+k]];s++) { 394 recv_buffer[j+1+k+s] = graph->mirrors_set[recv_buffer[j+1+k]][s]; 395 } 396 k+=graph->mirrors[recv_buffer[j+1+k]]+s; 397 } 398 } 399 } 400 k = recv_buffer[j]+1; 401 j += k; 402 } 403 sum_requests = cum_recv_counts[graph->n_subsets]; 404 start_of_recv = 0; 405 ierr = PetscMalloc(graph->nvtxs*sizeof(*nodes_to_temp_buffer_indices),&nodes_to_temp_buffer_indices);CHKERRQ(ierr); 406 global_subset_counter = 0; 407 for (i=0;i<graph->n_subsets;i++) { 408 if (subset_cc_adapt[i]) { 409 temp_buffer_size = 0; 410 /* find nodes on the shared interface we need to adapt */ 411 for (j=0;j<graph->nvtxs;j++) { 412 if (graph->subset[j]==i+1) { 413 nodes_to_temp_buffer_indices[j] = temp_buffer_size; 414 temp_buffer_size++; 415 } else { 416 nodes_to_temp_buffer_indices[j] = -1; 417 } 418 } 419 /* allocate some temporary space */ 420 ierr = PetscMalloc(temp_buffer_size*sizeof(PetscInt*),&temp_buffer);CHKERRQ(ierr); 421 ierr = PetscMalloc(temp_buffer_size*(cum_recv_counts[i+1]-cum_recv_counts[i])*sizeof(PetscInt),&temp_buffer[0]);CHKERRQ(ierr); 422 ierr = PetscMemzero(temp_buffer[0],temp_buffer_size*(cum_recv_counts[i+1]-cum_recv_counts[i])*sizeof(PetscInt));CHKERRQ(ierr); 423 for (j=1;j<temp_buffer_size;j++) { 424 temp_buffer[j] = temp_buffer[j-1]+cum_recv_counts[i+1]-cum_recv_counts[i]; 425 } 426 /* analyze contributions from neighbouring subdomains for i-th conn comp 427 temp buffer structure: 428 supposing part of the interface has dimension 5 (for example with global dofs 0,1,2,3,4) 429 3 neighs procs with structured connected components: 430 neigh 0: [0 1 4], [2 3]; (2 connected components) 431 neigh 1: [0 1], [2 3 4]; (2 connected components) 432 neigh 2: [0 4], [1], [2 3]; (3 connected components) 433 tempbuffer (row-oriented) will be filled as: 434 [ 0, 0, 0; 435 0, 0, 1; 436 1, 1, 2; 437 1, 1, 2; 438 0, 1, 0; ]; 439 This way we can simply find intersections of ccs among neighs. 440 For the example above, the graph->subset array will be modified to reproduce the following 4 connected components [0], [1], [2 3], [4]; 441 */ 442 for (j=0;j<cum_recv_counts[i+1]-cum_recv_counts[i];j++) { 443 ins_val = 0; 444 size_of_recv = recv_buffer_subset[sum_requests]; /* total size of recv from neighs */ 445 for (buffer_size=0;buffer_size<size_of_recv;) { /* loop until all data from neighs has been taken into account */ 446 for (k=1;k<recv_buffer[buffer_size+start_of_recv]+1;k++) { /* filling properly temp_buffer using data from a single recv */ 447 temp_buffer[nodes_to_temp_buffer_indices[recv_buffer[start_of_recv+buffer_size+k]]][j] = ins_val; 448 } 449 buffer_size += k; 450 ins_val++; 451 } 452 start_of_recv += size_of_recv; 453 sum_requests++; 454 } 455 ierr = PetscMalloc(temp_buffer_size*sizeof(*add_to_subset),&add_to_subset);CHKERRQ(ierr); 456 ierr = PetscMemzero(add_to_subset,temp_buffer_size*sizeof(*add_to_subset));CHKERRQ(ierr); 457 for (j=0;j<temp_buffer_size;j++) { 458 if (!add_to_subset[j]) { /* found a new cc */ 459 global_subset_counter++; 460 add_to_subset[j] = global_subset_counter; 461 for (k=j+1;k<temp_buffer_size;k++) { /* check for other nodes in new cc */ 462 same_set = PETSC_TRUE; 463 for (s=0;s<cum_recv_counts[i+1]-cum_recv_counts[i];s++) { 464 if (temp_buffer[j][s]!=temp_buffer[k][s]) { 465 same_set = PETSC_FALSE; 466 break; 467 } 468 } 469 if (same_set) { 470 add_to_subset[k] = global_subset_counter; 471 } 472 } 473 } 474 } 475 /* insert new data in subset array */ 476 temp_buffer_size = 0; 477 for (j=0;j<graph->nvtxs;j++) { 478 if (graph->subset[j]==i+1) { 479 graph->subset[j] = graph->n_subsets+add_to_subset[temp_buffer_size]; 480 temp_buffer_size++; 481 } 482 } 483 ierr = PetscFree(temp_buffer[0]);CHKERRQ(ierr); 484 ierr = PetscFree(temp_buffer);CHKERRQ(ierr); 485 ierr = PetscFree(add_to_subset);CHKERRQ(ierr); 486 } 487 } 488 ierr = PetscFree(nodes_to_temp_buffer_indices);CHKERRQ(ierr); 489 ierr = PetscFree(sizes_of_sends);CHKERRQ(ierr); 490 ierr = PetscFree(send_requests);CHKERRQ(ierr); 491 ierr = PetscFree(recv_requests);CHKERRQ(ierr); 492 ierr = PetscFree(recv_buffer);CHKERRQ(ierr); 493 ierr = PetscFree(recv_buffer_subset);CHKERRQ(ierr); 494 ierr = PetscFree(send_buffer);CHKERRQ(ierr); 495 ierr = PetscFree(cum_recv_counts);CHKERRQ(ierr); 496 ierr = PetscFree(subset_to_nodes_indices);CHKERRQ(ierr); 497 ierr = PetscFree(subset_cc_adapt);CHKERRQ(ierr); 498 /* We are ready to find for connected components consistent among neighbouring subdomains */ 499 if (global_subset_counter) { 500 ierr = PetscBTMemzero(graph->nvtxs,graph->touched);CHKERRQ(ierr); 501 global_subset_counter = 0; 502 for (i=0;i<graph->nvtxs;i++) { 503 if (graph->subset[i] && !PetscBTLookup(graph->touched,i)) { 504 global_subset_counter++; 505 for (j=i+1;j<graph->nvtxs;j++) { 506 if (!PetscBTLookup(graph->touched,j) && graph->subset[j]==graph->subset[i]) { 507 graph->subset[j] = global_subset_counter; 508 ierr = PetscBTSet(graph->touched,j);CHKERRQ(ierr); 509 } 510 } 511 graph->subset[i] = global_subset_counter; 512 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 513 } 514 } 515 /* refine connected components locally */ 516 ierr = PCBDDCGraphComputeConnectedComponentsLocal(graph);CHKERRQ(ierr); 517 } 518 ierr = PetscFree(queue_in_global_numbering);CHKERRQ(ierr); 519 } 520 PetscFunctionReturn(0); 521 } 522 523 /* The following code has been adapted from function IsConnectedSubdomain contained 524 in source file contig.c of METIS library (version 5.0.1) 525 It finds connected components for each subset */ 526 #undef __FUNCT__ 527 #define __FUNCT__ "PCBDDCGraphComputeConnectedComponentsLocal" 528 PetscErrorCode PCBDDCGraphComputeConnectedComponentsLocal(PCBDDCGraph graph) 529 { 530 PetscInt i,j,k,first,last,nleft,ncc,pid,cum_queue,n,ncc_pid; 531 PetscInt *queue_global; 532 PetscErrorCode ierr; 533 534 PetscFunctionBegin; 535 /* quiet return if no csr info is available */ 536 if (!graph->xadj || !graph->adjncy) { 537 PetscFunctionReturn(0); 538 } 539 540 /* reset any previous search of connected components */ 541 ierr = PetscBTMemzero(graph->nvtxs,graph->touched);CHKERRQ(ierr); 542 graph->n_subsets = 0; 543 for (i=0;i<graph->nvtxs;i++) { 544 if (graph->special_dof[i] == DIRICHLET_MARK || !graph->count[i]) { 545 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 546 graph->subset[i] = 0; 547 } 548 graph->n_subsets = PetscMax(graph->n_subsets,graph->subset[i]); 549 } 550 ierr = PetscFree(graph->subset_ncc);CHKERRQ(ierr); 551 ierr = PetscMalloc(graph->n_subsets*sizeof(*graph->subset_ncc),&graph->subset_ncc);CHKERRQ(ierr); 552 ierr = PetscMemzero(graph->subset_ncc,graph->n_subsets*sizeof(*graph->subset_ncc));CHKERRQ(ierr); 553 ierr = PetscMemzero(graph->cptr,(graph->nvtxs+1)*sizeof(*graph->cptr));CHKERRQ(ierr); 554 ierr = PetscMemzero(graph->queue,graph->nvtxs*sizeof(*graph->queue));CHKERRQ(ierr); 555 556 /* begin search for connected components */ 557 cum_queue = 0; 558 ncc = 0; 559 for (n=0;n<graph->n_subsets;n++) { 560 pid = n+1; /* partition labeled by 0 is discarded */ 561 nleft = 0; 562 for (i=0;i<graph->nvtxs;i++) { 563 if (graph->subset[i] == pid) { 564 nleft++; 565 } 566 } 567 for (i=0; i<graph->nvtxs; i++) { 568 if (graph->subset[i] == pid) { 569 break; 570 } 571 } 572 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 573 graph->queue[cum_queue] = i; 574 first = 0; 575 last = 1; 576 graph->cptr[ncc] = cum_queue; 577 ncc_pid = 0; 578 while (first != nleft) { 579 if (first == last) { 580 graph->cptr[++ncc] = first+cum_queue; 581 ncc_pid++; 582 for (i=0; i<graph->nvtxs; i++) { /* TODO-> use a while! */ 583 if (graph->subset[i] == pid && !PetscBTLookup(graph->touched,i)) { 584 break; 585 } 586 } 587 graph->queue[cum_queue+last] = i; 588 last++; 589 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 590 } 591 i = graph->queue[cum_queue+first]; 592 first++; 593 for (j=graph->xadj[i];j<graph->xadj[i+1];j++) { 594 k = graph->adjncy[j]; 595 if (graph->subset[k] == pid && !PetscBTLookup(graph->touched,k)) { 596 graph->queue[cum_queue+last] = k; 597 last++; 598 ierr = PetscBTSet(graph->touched,k);CHKERRQ(ierr); 599 } 600 } 601 } 602 graph->cptr[++ncc] = first+cum_queue; 603 ncc_pid++; 604 cum_queue = graph->cptr[ncc]; 605 graph->subset_ncc[n] = ncc_pid; 606 } 607 graph->ncc = ncc; 608 /* For consistency among neighbours, I need to sort (by global ordering) each connected component */ 609 ierr = PetscMalloc(graph->cptr[graph->ncc]*sizeof(*queue_global),&queue_global);CHKERRQ(ierr); 610 ierr = ISLocalToGlobalMappingApply(graph->l2gmap,graph->cptr[graph->ncc],graph->queue,queue_global);CHKERRQ(ierr); 611 for (i=0;i<graph->ncc;i++) { 612 ierr = PetscSortIntWithArray(graph->cptr[i+1]-graph->cptr[i],&queue_global[graph->cptr[i]],&graph->queue[graph->cptr[i]]);CHKERRQ(ierr); 613 } 614 ierr = PetscFree(queue_global);CHKERRQ(ierr); 615 PetscFunctionReturn(0); 616 } 617 618 #undef __FUNCT__ 619 #define __FUNCT__ "PCBDDCGraphSetUp" 620 PetscErrorCode PCBDDCGraphSetUp(PCBDDCGraph graph, PetscInt custom_minimal_size, IS neumann_is, IS dirichlet_is, PetscInt n_ISForDofs, IS ISForDofs[], IS custom_primal_vertices) 621 { 622 VecScatter scatter_ctx; 623 Vec local_vec,local_vec2,global_vec; 624 IS to,from; 625 MPI_Comm comm; 626 PetscScalar *array,*array2; 627 const PetscInt *is_indices; 628 PetscInt n_neigh,*neigh,*n_shared,**shared; 629 PetscInt i,j,k,s,total_counts,nodes_touched,is_size; 630 PetscErrorCode ierr; 631 PetscBool same_set,mirrors_found; 632 633 PetscFunctionBegin; 634 ierr = PetscObjectGetComm((PetscObject)(graph->l2gmap),&comm);CHKERRQ(ierr); 635 /* custom_minimal_size */ 636 graph->custom_minimal_size = PetscMax(graph->custom_minimal_size,custom_minimal_size); 637 /* get info l2gmap and allocate work vectors */ 638 ierr = ISLocalToGlobalMappingGetInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);CHKERRQ(ierr); 639 ierr = ISLocalToGlobalMappingGetIndices(graph->l2gmap,&is_indices);CHKERRQ(ierr); 640 j = 0; 641 for (i=0;i<graph->nvtxs;i++) { 642 j = PetscMax(j,is_indices[i]); 643 } 644 ierr = MPI_Allreduce(&j,&i,1,MPIU_INT,MPI_MAX,comm);CHKERRQ(ierr); 645 i++; 646 ierr = VecCreate(PETSC_COMM_SELF,&local_vec);CHKERRQ(ierr); 647 ierr = VecSetSizes(local_vec,PETSC_DECIDE,graph->nvtxs);CHKERRQ(ierr); 648 ierr = VecSetType(local_vec,VECSTANDARD);CHKERRQ(ierr); 649 ierr = VecDuplicate(local_vec,&local_vec2);CHKERRQ(ierr); 650 ierr = VecCreate(comm,&global_vec);CHKERRQ(ierr); 651 ierr = VecSetSizes(global_vec,PETSC_DECIDE,i);CHKERRQ(ierr); 652 ierr = VecSetType(global_vec,VECSTANDARD);CHKERRQ(ierr); 653 ierr = ISCreateStride(PETSC_COMM_SELF,graph->nvtxs,0,1,&to);CHKERRQ(ierr); 654 ierr = ISLocalToGlobalMappingApplyIS(graph->l2gmap,to,&from);CHKERRQ(ierr); 655 ierr = VecScatterCreate(global_vec,from,local_vec,to,&scatter_ctx);CHKERRQ(ierr); 656 657 /* get local periodic nodes */ 658 mirrors_found=PETSC_FALSE; 659 if (graph->nvtxs) { 660 for (i=0;i<n_shared[0];i++) 661 graph->count[shared[0][i]] += 1; 662 for (i=0;i<n_shared[0];i++) { 663 if (graph->count[shared[0][i]] > 1) { 664 mirrors_found=PETSC_TRUE; 665 break; 666 } 667 } 668 } 669 /* compute local mirrors (if any) */ 670 if (mirrors_found) { 671 PetscInt *local_indices,*global_indices; 672 /* get arrays of local and global indices */ 673 ierr = PetscMalloc(graph->nvtxs*sizeof(PetscInt),&local_indices);CHKERRQ(ierr); 674 ierr = ISGetIndices(to,(const PetscInt**)&is_indices);CHKERRQ(ierr); 675 ierr = PetscMemcpy(local_indices,is_indices,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 676 ierr = ISRestoreIndices(to,(const PetscInt**)&is_indices);CHKERRQ(ierr); 677 ierr = PetscMalloc(graph->nvtxs*sizeof(PetscInt),&global_indices);CHKERRQ(ierr); 678 ierr = ISGetIndices(from,(const PetscInt**)&is_indices);CHKERRQ(ierr); 679 ierr = PetscMemcpy(global_indices,is_indices,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 680 ierr = ISRestoreIndices(from,(const PetscInt**)&is_indices);CHKERRQ(ierr); 681 /* allocate space for mirrors */ 682 ierr = PetscMalloc2(graph->nvtxs,PetscInt,&graph->mirrors, 683 graph->nvtxs,PetscInt*,&graph->mirrors_set);CHKERRQ(ierr); 684 ierr = PetscMemzero(graph->mirrors,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 685 graph->mirrors_set[0] = 0; 686 687 k=0; 688 for (i=0;i<n_shared[0];i++) { 689 j=shared[0][i]; 690 if (graph->count[j] > 1) { 691 graph->mirrors[j]++; 692 k++; 693 } 694 } 695 /* allocate space for set of mirrors */ 696 ierr = PetscMalloc(k*sizeof(PetscInt*),&graph->mirrors_set[0]);CHKERRQ(ierr); 697 for (i=1;i<graph->nvtxs;i++) 698 graph->mirrors_set[i]=graph->mirrors_set[i-1]+graph->mirrors[i-1]; 699 700 /* fill arrays */ 701 ierr = PetscMemzero(graph->mirrors,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 702 for (j=0;j<n_shared[0];j++) { 703 i=shared[0][j]; 704 if (graph->count[i] > 1) 705 graph->mirrors_set[i][graph->mirrors[i]++]=global_indices[i]; 706 } 707 ierr = PetscSortIntWithArray(graph->nvtxs,global_indices,local_indices);CHKERRQ(ierr); 708 for (i=0;i<graph->nvtxs;i++) { 709 if (graph->mirrors[i] > 0) { 710 ierr = PetscFindInt(graph->mirrors_set[i][0],graph->nvtxs,global_indices,&k);CHKERRQ(ierr); 711 j = global_indices[k]; 712 while ( k > 0 && global_indices[k-1] == j) k--; 713 for (j=0;j<graph->mirrors[i];j++) { 714 graph->mirrors_set[i][j]=local_indices[k+j]; 715 } 716 ierr = PetscSortInt(graph->mirrors[i],graph->mirrors_set[i]);CHKERRQ(ierr); 717 } 718 } 719 ierr = PetscFree(local_indices);CHKERRQ(ierr); 720 ierr = PetscFree(global_indices);CHKERRQ(ierr); 721 } 722 ierr = PetscMemzero(graph->count,graph->nvtxs*sizeof(*graph->count));CHKERRQ(ierr); 723 ierr = ISDestroy(&to);CHKERRQ(ierr); 724 ierr = ISDestroy(&from);CHKERRQ(ierr); 725 726 /* Count total number of neigh per node */ 727 k=0; 728 for (i=1;i<n_neigh;i++) { 729 k += n_shared[i]; 730 for (j=0;j<n_shared[i];j++) { 731 graph->count[shared[i][j]] += 1; 732 } 733 } 734 /* Allocate space for storing the set of neighbours for each node */ 735 if (graph->nvtxs) { 736 ierr = PetscMalloc(k*sizeof(PetscInt),&graph->neighbours_set[0]);CHKERRQ(ierr); 737 } 738 for (i=1;i<graph->nvtxs;i++) { /* dont count myself */ 739 graph->neighbours_set[i]=graph->neighbours_set[i-1]+graph->count[i-1]; 740 } 741 /* Get information for sharing subdomains */ 742 ierr = PetscMemzero(graph->count,graph->nvtxs*sizeof(*graph->count));CHKERRQ(ierr); 743 for (i=1;i<n_neigh;i++) { /* dont count myself */ 744 s = n_shared[i]; 745 for (j=0;j<s;j++) { 746 k = shared[i][j]; 747 graph->neighbours_set[k][graph->count[k]] = neigh[i]; 748 graph->count[k] += 1; 749 } 750 } 751 /* sort set of sharing subdomains */ 752 for (i=0;i<graph->nvtxs;i++) { 753 ierr = PetscSortRemoveDupsInt(&graph->count[i],graph->neighbours_set[i]);CHKERRQ(ierr); 754 } 755 /* Get info for dofs splitting */ 756 for (i=0;i<n_ISForDofs;i++) { 757 ierr = ISGetSize(ISForDofs[i],&is_size);CHKERRQ(ierr); 758 ierr = ISGetIndices(ISForDofs[i],(const PetscInt**)&is_indices);CHKERRQ(ierr); 759 for (j=0;j<is_size;j++) { 760 graph->which_dof[is_indices[j]]=i; 761 } 762 ierr = ISRestoreIndices(ISForDofs[i],(const PetscInt**)&is_indices);CHKERRQ(ierr); 763 } 764 /* Take into account Neumann nodes */ 765 ierr = VecSet(local_vec,0.0);CHKERRQ(ierr); 766 ierr = VecSet(local_vec2,0.0);CHKERRQ(ierr); 767 if (neumann_is) { 768 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 769 ierr = ISGetSize(neumann_is,&is_size);CHKERRQ(ierr); 770 ierr = ISGetIndices(neumann_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); 771 for (i=0;i<is_size;i++) { 772 array[is_indices[i]] = 1.0; 773 } 774 ierr = ISRestoreIndices(neumann_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); 775 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 776 } 777 /* Neumann nodes: impose consistency among neighbours */ 778 ierr = VecSet(global_vec,0.0);CHKERRQ(ierr); 779 ierr = VecScatterBegin(scatter_ctx,local_vec,global_vec,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 780 ierr = VecScatterEnd(scatter_ctx,local_vec,global_vec,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 781 ierr = VecScatterBegin(scatter_ctx,global_vec,local_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 782 ierr = VecScatterEnd(scatter_ctx,global_vec,local_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 783 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 784 for (i=0;i<graph->nvtxs;i++) { 785 if (PetscRealPart(array[i]) > 0.0) { 786 graph->special_dof[i] = NEUMANN_MARK; 787 } 788 } 789 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 790 /* Take into account Dirichlet nodes */ 791 ierr = VecSet(local_vec2,0.0);CHKERRQ(ierr); 792 if (dirichlet_is) { 793 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 794 ierr = VecGetArray(local_vec2,&array2);CHKERRQ(ierr); 795 ierr = ISGetSize(dirichlet_is,&is_size);CHKERRQ(ierr); 796 ierr = ISGetIndices(dirichlet_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); 797 for (i=0;i<is_size;i++){ 798 k = is_indices[i]; 799 if (graph->count[k] && !PetscBTLookup(graph->touched,k)) { 800 if (PetscRealPart(array[k]) > 0.0) { 801 SETERRQ1(PETSC_COMM_SELF,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); 802 } 803 array2[k] = 1.0; 804 } 805 } 806 ierr = ISRestoreIndices(dirichlet_is,(const PetscInt**)&is_indices);CHKERRQ(ierr); 807 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 808 ierr = VecRestoreArray(local_vec2,&array2);CHKERRQ(ierr); 809 } 810 /* Dirichlet nodes: impose consistency among neighbours */ 811 ierr = VecSet(global_vec,0.0);CHKERRQ(ierr); 812 ierr = VecScatterBegin(scatter_ctx,local_vec2,global_vec,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 813 ierr = VecScatterEnd(scatter_ctx,local_vec2,global_vec,ADD_VALUES,SCATTER_REVERSE);CHKERRQ(ierr); 814 ierr = VecScatterBegin(scatter_ctx,global_vec,local_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 815 ierr = VecScatterEnd(scatter_ctx,global_vec,local_vec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 816 ierr = VecGetArray(local_vec,&array);CHKERRQ(ierr); 817 for (i=0;i<graph->nvtxs;i++) { 818 if (PetscRealPart(array[i]) > 0.0) { 819 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 820 graph->subset[i] = 0; /* dirichlet nodes treated as internal -> is it ok? */ 821 graph->special_dof[i] = DIRICHLET_MARK; 822 } 823 } 824 ierr = VecRestoreArray(local_vec,&array);CHKERRQ(ierr); 825 826 /* mark local periodic nodes (if any) and adapt CSR graph */ 827 if (graph->mirrors) { 828 PetscInt *new_xadj,*new_adjncy; 829 830 for (i=0;i<graph->nvtxs;i++) 831 if (graph->mirrors[i]) 832 graph->special_dof[i] = LOCAL_PERIODIC_MARK; 833 834 /* sort CSR graph */ 835 for (i=0;i<graph->nvtxs;i++) 836 ierr = PetscSortInt(graph->xadj[i+1]-graph->xadj[i],&graph->adjncy[graph->xadj[i]]);CHKERRQ(ierr); 837 838 /* adapt local CSR graph in case of local periodicity */ 839 k=0; 840 for (i=0;i<graph->nvtxs;i++) 841 for (j=graph->xadj[i];j<graph->xadj[i+1];j++) 842 k += graph->mirrors[graph->adjncy[j]]; 843 844 ierr = PetscMalloc((graph->nvtxs+1)*sizeof(PetscInt),&new_xadj);CHKERRQ(ierr); 845 ierr = PetscMalloc((k+graph->xadj[graph->nvtxs])*sizeof(PetscInt),&new_adjncy);CHKERRQ(ierr); 846 new_xadj[0]=0; 847 for (i=0;i<graph->nvtxs;i++) { 848 k = graph->xadj[i+1]-graph->xadj[i]; 849 ierr = PetscMemcpy(&new_adjncy[new_xadj[i]],&graph->adjncy[graph->xadj[i]],k*sizeof(PetscInt));CHKERRQ(ierr); 850 new_xadj[i+1]=new_xadj[i]+k; 851 for (j=graph->xadj[i];j<graph->xadj[i+1];j++) { 852 k = graph->mirrors[graph->adjncy[j]]; 853 ierr = PetscMemcpy(&new_adjncy[new_xadj[i+1]],graph->mirrors_set[graph->adjncy[j]],k*sizeof(PetscInt));CHKERRQ(ierr); 854 new_xadj[i+1]+=k; 855 } 856 k = new_xadj[i+1]-new_xadj[i]; 857 ierr = PetscSortRemoveDupsInt(&k,&new_adjncy[new_xadj[i]]);CHKERRQ(ierr); 858 new_xadj[i+1]=new_xadj[i]+k; 859 } 860 /* set new CSR into graph */ 861 ierr = PetscFree(graph->xadj);CHKERRQ(ierr); 862 ierr = PetscFree(graph->adjncy);CHKERRQ(ierr); 863 graph->xadj = new_xadj; 864 graph->adjncy = new_adjncy; 865 } 866 867 /* mark special nodes -> each will become a single node equivalence class */ 868 if (custom_primal_vertices) { 869 ierr = ISGetSize(custom_primal_vertices,&is_size);CHKERRQ(ierr); 870 ierr = ISGetIndices(custom_primal_vertices,(const PetscInt**)&is_indices);CHKERRQ(ierr); 871 for (i=0;i<is_size;i++) { 872 graph->special_dof[is_indices[i]] = SPECIAL_MARK-i; 873 } 874 ierr = ISRestoreIndices(custom_primal_vertices,(const PetscInt**)&is_indices);CHKERRQ(ierr); 875 } 876 /* mark interior nodes as touched and belonging to partition number 0 */ 877 for (i=0;i<graph->nvtxs;i++) { 878 if (!graph->count[i]) { 879 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 880 graph->subset[i] = 0; 881 } 882 } 883 /* init graph structure and compute default subsets */ 884 nodes_touched=0; 885 for (i=0;i<graph->nvtxs;i++) { 886 if (PetscBTLookup(graph->touched,i)) { 887 nodes_touched++; 888 } 889 } 890 i = 0; 891 graph->ncc = 0; 892 total_counts = 0; 893 while (nodes_touched<graph->nvtxs) { 894 /* find first untouched node in local ordering */ 895 while (PetscBTLookup(graph->touched,i)) { 896 i++; 897 } 898 ierr = PetscBTSet(graph->touched,i);CHKERRQ(ierr); 899 graph->subset[i] = graph->ncc+1; 900 graph->cptr[graph->ncc] = total_counts; 901 graph->queue[total_counts] = i; 902 total_counts++; 903 nodes_touched++; 904 /* now find all other nodes having the same set of sharing subdomains */ 905 for (j=i+1;j<graph->nvtxs;j++) { 906 /* check for same number of sharing subdomains, dof number and same special mark */ 907 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]) { 908 /* check for same set of sharing subdomains */ 909 same_set=PETSC_TRUE; 910 for (k=0;k<graph->count[j];k++){ 911 if (graph->neighbours_set[i][k]!=graph->neighbours_set[j][k]) { 912 same_set=PETSC_FALSE; 913 } 914 } 915 /* I found a friend of mine */ 916 if (same_set) { 917 graph->subset[j]=graph->ncc+1; 918 ierr = PetscBTSet(graph->touched,j);CHKERRQ(ierr); 919 nodes_touched++; 920 graph->queue[total_counts] = j; 921 total_counts++; 922 } 923 } 924 } 925 graph->ncc++; 926 } 927 /* set default number of subsets (at this point no info on csr graph has been taken into account, so n_subsets = ncc */ 928 graph->n_subsets = graph->ncc; 929 ierr = PetscMalloc(graph->n_subsets*sizeof(*graph->subset_ncc),&graph->subset_ncc);CHKERRQ(ierr); 930 for (i=0;i<graph->n_subsets;i++) { 931 graph->subset_ncc[i] = 1; 932 } 933 /* final pointer */ 934 graph->cptr[graph->ncc] = total_counts; 935 /* free memory allocated by ISLocalToGlobalMappingGetInfo */ 936 ierr = ISLocalToGlobalMappingRestoreInfo(graph->l2gmap,&n_neigh,&neigh,&n_shared,&shared);CHKERRQ(ierr); 937 /* free objects */ 938 ierr = VecDestroy(&local_vec);CHKERRQ(ierr); 939 ierr = VecDestroy(&local_vec2);CHKERRQ(ierr); 940 ierr = VecDestroy(&global_vec);CHKERRQ(ierr); 941 ierr = VecScatterDestroy(&scatter_ctx);CHKERRQ(ierr); 942 PetscFunctionReturn(0); 943 } 944 945 #undef __FUNCT__ 946 #define __FUNCT__ "PCBDDCGraphResetCSR" 947 PetscErrorCode PCBDDCGraphResetCSR(PCBDDCGraph graph) 948 { 949 PetscErrorCode ierr; 950 951 PetscFunctionBegin; 952 ierr = PetscFree(graph->xadj);CHKERRQ(ierr); 953 ierr = PetscFree(graph->adjncy);CHKERRQ(ierr); 954 graph->nvtxs_csr = 0; 955 PetscFunctionReturn(0); 956 } 957 958 #undef __FUNCT__ 959 #define __FUNCT__ "PCBDDCGraphReset" 960 PetscErrorCode PCBDDCGraphReset(PCBDDCGraph graph) 961 { 962 PetscErrorCode ierr; 963 964 PetscFunctionBegin; 965 ierr = ISLocalToGlobalMappingDestroy(&graph->l2gmap);CHKERRQ(ierr); 966 ierr = PetscFree(graph->subset_ncc);CHKERRQ(ierr); 967 if (graph->nvtxs) { 968 ierr = PetscFree(graph->neighbours_set[0]);CHKERRQ(ierr); 969 } 970 ierr = PetscBTDestroy(&graph->touched);CHKERRQ(ierr); 971 ierr = PetscFree7(graph->count, 972 graph->neighbours_set, 973 graph->subset, 974 graph->which_dof, 975 graph->cptr, 976 graph->queue, 977 graph->special_dof);CHKERRQ(ierr); 978 if (graph->mirrors) { 979 ierr = PetscFree(graph->mirrors_set[0]);CHKERRQ(ierr); 980 } 981 ierr = PetscFree2(graph->mirrors,graph->mirrors_set);CHKERRQ(ierr); 982 graph->nvtxs = 0; 983 graph->n_subsets = 0; 984 graph->custom_minimal_size = 1; 985 PetscFunctionReturn(0); 986 } 987 988 #undef __FUNCT__ 989 #define __FUNCT__ "PCBDDCGraphInit" 990 PetscErrorCode PCBDDCGraphInit(PCBDDCGraph graph, ISLocalToGlobalMapping l2gmap) 991 { 992 PetscInt n; 993 PetscErrorCode ierr; 994 995 PetscFunctionBegin; 996 PetscValidPointer(graph,1); 997 PetscValidHeaderSpecific(l2gmap,IS_LTOGM_CLASSID,2); 998 /* reset graph if already allocated */ 999 if (graph->nvtxs) { 1000 ierr = PCBDDCGraphReset(graph);CHKERRQ(ierr); 1001 } 1002 /* set number of vertices */ 1003 ierr = PetscObjectReference((PetscObject)l2gmap);CHKERRQ(ierr); 1004 graph->l2gmap = l2gmap; 1005 ierr = ISLocalToGlobalMappingGetSize(l2gmap,&n);CHKERRQ(ierr); 1006 graph->nvtxs = n; 1007 /* allocate used space */ 1008 ierr = PetscBTCreate(graph->nvtxs,&graph->touched);CHKERRQ(ierr); 1009 ierr = PetscMalloc7(graph->nvtxs,PetscInt,&graph->count, 1010 graph->nvtxs,PetscInt*,&graph->neighbours_set, 1011 graph->nvtxs,PetscInt,&graph->subset, 1012 graph->nvtxs,PetscInt,&graph->which_dof, 1013 graph->nvtxs+1,PetscInt,&graph->cptr, 1014 graph->nvtxs,PetscInt,&graph->queue, 1015 graph->nvtxs,PetscInt,&graph->special_dof);CHKERRQ(ierr); 1016 /* zeroes memory */ 1017 ierr = PetscMemzero(graph->count,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 1018 ierr = PetscMemzero(graph->subset,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 1019 ierr = PetscMemzero(graph->which_dof,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 1020 ierr = PetscMemzero(graph->cptr,(graph->nvtxs+1)*sizeof(PetscInt));CHKERRQ(ierr); 1021 ierr = PetscMemzero(graph->queue,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 1022 ierr = PetscMemzero(graph->special_dof,graph->nvtxs*sizeof(PetscInt));CHKERRQ(ierr); 1023 /* zeroes first pointer to neighbour set */ 1024 if (graph->nvtxs) { 1025 graph->neighbours_set[0] = 0; 1026 } 1027 /* zeroes workspace for values of ncc */ 1028 graph->subset_ncc = 0; 1029 PetscFunctionReturn(0); 1030 } 1031 1032 #undef __FUNCT__ 1033 #define __FUNCT__ "PCBDDCGraphDestroy" 1034 PetscErrorCode PCBDDCGraphDestroy(PCBDDCGraph* graph) 1035 { 1036 PetscErrorCode ierr; 1037 1038 PetscFunctionBegin; 1039 ierr = PCBDDCGraphReset(*graph);CHKERRQ(ierr); 1040 ierr = PetscFree(*graph);CHKERRQ(ierr); 1041 PetscFunctionReturn(0); 1042 } 1043 1044 #undef __FUNCT__ 1045 #define __FUNCT__ "PCBDDCGraphCreate" 1046 PetscErrorCode PCBDDCGraphCreate(PCBDDCGraph *graph) 1047 { 1048 PCBDDCGraph new_graph; 1049 PetscErrorCode ierr; 1050 1051 PetscFunctionBegin; 1052 ierr = PetscMalloc(sizeof(*new_graph),&new_graph);CHKERRQ(ierr); 1053 /* local to global mapping of dofs */ 1054 new_graph->l2gmap = 0; 1055 /* vertex size */ 1056 new_graph->nvtxs = 0; 1057 new_graph->n_subsets = 0; 1058 new_graph->custom_minimal_size = 1; 1059 /* zeroes ponters */ 1060 new_graph->mirrors = 0; 1061 new_graph->mirrors_set = 0; 1062 new_graph->neighbours_set = 0; 1063 new_graph->subset = 0; 1064 new_graph->which_dof = 0; 1065 new_graph->special_dof = 0; 1066 new_graph->cptr = 0; 1067 new_graph->queue = 0; 1068 new_graph->count = 0; 1069 new_graph->subset_ncc = 0; 1070 new_graph->touched = 0; 1071 /* zeroes pointers to csr graph of local nodes connectivity (optional data) */ 1072 new_graph->nvtxs_csr = 0; 1073 new_graph->xadj = 0; 1074 new_graph->adjncy = 0; 1075 *graph = new_graph; 1076 PetscFunctionReturn(0); 1077 } 1078