1 /* 2 GAMG geometric-algebric multigrid PC - Mark Adams 2011 3 */ 4 5 #include <../src/ksp/pc/impls/gamg/gamg.h> /*I "petscpc.h" I*/ 6 /* Next line needed to deactivate KSP_Solve logging */ 7 #include <petsc/private/kspimpl.h> 8 #include <petscblaslapack.h> 9 #include <petscdm.h> 10 11 typedef struct { 12 PetscInt nsmooths; 13 PetscBool sym_graph; 14 PetscInt square_graph; 15 } PC_GAMG_AGG; 16 17 /*@ 18 PCGAMGSetNSmooths - Set number of smoothing steps (1 is typical) 19 20 Not Collective on PC 21 22 Input Parameters: 23 . pc - the preconditioner context 24 25 Options Database Key: 26 . -pc_gamg_agg_nsmooths <nsmooth, default=1> - number of smoothing steps to use with smooth aggregation 27 28 Level: intermediate 29 30 Concepts: Aggregation AMG preconditioner 31 32 .seealso: () 33 @*/ 34 PetscErrorCode PCGAMGSetNSmooths(PC pc, PetscInt n) 35 { 36 PetscErrorCode ierr; 37 38 PetscFunctionBegin; 39 PetscValidHeaderSpecific(pc,PC_CLASSID,1); 40 ierr = PetscTryMethod(pc,"PCGAMGSetNSmooths_C",(PC,PetscInt),(pc,n));CHKERRQ(ierr); 41 PetscFunctionReturn(0); 42 } 43 44 static PetscErrorCode PCGAMGSetNSmooths_AGG(PC pc, PetscInt n) 45 { 46 PC_MG *mg = (PC_MG*)pc->data; 47 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 48 PC_GAMG_AGG *pc_gamg_agg = (PC_GAMG_AGG*)pc_gamg->subctx; 49 50 PetscFunctionBegin; 51 pc_gamg_agg->nsmooths = n; 52 PetscFunctionReturn(0); 53 } 54 55 /*@ 56 PCGAMGSetSymGraph - Symmetrize the graph before computing the aggregation. Some algorithms require the graph be symmetric 57 58 Not Collective on PC 59 60 Input Parameters: 61 + pc - the preconditioner context 62 . n - PETSC_TRUE or PETSC_FALSE 63 64 Options Database Key: 65 . -pc_gamg_sym_graph <true,default=false> - symmetrize the graph before computing the aggregation 66 67 Level: intermediate 68 69 Concepts: Aggregation AMG preconditioner 70 71 .seealso: PCGAMGSetSquareGraph() 72 @*/ 73 PetscErrorCode PCGAMGSetSymGraph(PC pc, PetscBool n) 74 { 75 PetscErrorCode ierr; 76 77 PetscFunctionBegin; 78 PetscValidHeaderSpecific(pc,PC_CLASSID,1); 79 ierr = PetscTryMethod(pc,"PCGAMGSetSymGraph_C",(PC,PetscBool),(pc,n));CHKERRQ(ierr); 80 PetscFunctionReturn(0); 81 } 82 83 static PetscErrorCode PCGAMGSetSymGraph_AGG(PC pc, PetscBool n) 84 { 85 PC_MG *mg = (PC_MG*)pc->data; 86 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 87 PC_GAMG_AGG *pc_gamg_agg = (PC_GAMG_AGG*)pc_gamg->subctx; 88 89 PetscFunctionBegin; 90 pc_gamg_agg->sym_graph = n; 91 PetscFunctionReturn(0); 92 } 93 94 /*@ 95 PCGAMGSetSquareGraph - Square the graph, ie. compute A'*A before aggregating it 96 97 Not Collective on PC 98 99 Input Parameters: 100 + pc - the preconditioner context 101 - n - PETSC_TRUE or PETSC_FALSE 102 103 Options Database Key: 104 . -pc_gamg_square_graph <n,default = 1> - number of levels to square the graph on before aggregating it 105 106 Level: intermediate 107 108 Concepts: Aggregation AMG preconditioner 109 110 .seealso: PCGAMGSetSymGraph() 111 @*/ 112 PetscErrorCode PCGAMGSetSquareGraph(PC pc, PetscInt n) 113 { 114 PetscErrorCode ierr; 115 116 PetscFunctionBegin; 117 PetscValidHeaderSpecific(pc,PC_CLASSID,1); 118 ierr = PetscTryMethod(pc,"PCGAMGSetSquareGraph_C",(PC,PetscInt),(pc,n));CHKERRQ(ierr); 119 PetscFunctionReturn(0); 120 } 121 122 static PetscErrorCode PCGAMGSetSquareGraph_AGG(PC pc, PetscInt n) 123 { 124 PC_MG *mg = (PC_MG*)pc->data; 125 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 126 PC_GAMG_AGG *pc_gamg_agg = (PC_GAMG_AGG*)pc_gamg->subctx; 127 128 PetscFunctionBegin; 129 pc_gamg_agg->square_graph = n; 130 PetscFunctionReturn(0); 131 } 132 133 static PetscErrorCode PCSetFromOptions_GAMG_AGG(PetscOptionItems *PetscOptionsObject,PC pc) 134 { 135 PetscErrorCode ierr; 136 PC_MG *mg = (PC_MG*)pc->data; 137 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 138 PC_GAMG_AGG *pc_gamg_agg = (PC_GAMG_AGG*)pc_gamg->subctx; 139 140 PetscFunctionBegin; 141 ierr = PetscOptionsHead(PetscOptionsObject,"GAMG-AGG options");CHKERRQ(ierr); 142 { 143 ierr = PetscOptionsInt("-pc_gamg_agg_nsmooths","smoothing steps for smoothed aggregation, usually 1","PCGAMGSetNSmooths",pc_gamg_agg->nsmooths,&pc_gamg_agg->nsmooths,NULL);CHKERRQ(ierr); 144 ierr = PetscOptionsBool("-pc_gamg_sym_graph","Set for asymmetric matrices","PCGAMGSetSymGraph",pc_gamg_agg->sym_graph,&pc_gamg_agg->sym_graph,NULL);CHKERRQ(ierr); 145 ierr = PetscOptionsInt("-pc_gamg_square_graph","Number of levels to square graph for faster coarsening and lower coarse grid complexity","PCGAMGSetSquareGraph",pc_gamg_agg->square_graph,&pc_gamg_agg->square_graph,NULL);CHKERRQ(ierr); 146 } 147 ierr = PetscOptionsTail();CHKERRQ(ierr); 148 PetscFunctionReturn(0); 149 } 150 151 /* -------------------------------------------------------------------------- */ 152 static PetscErrorCode PCDestroy_GAMG_AGG(PC pc) 153 { 154 PetscErrorCode ierr; 155 PC_MG *mg = (PC_MG*)pc->data; 156 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 157 158 PetscFunctionBegin; 159 ierr = PetscFree(pc_gamg->subctx);CHKERRQ(ierr); 160 ierr = PetscObjectComposeFunction((PetscObject)pc,"PCSetCoordinates_C",NULL);CHKERRQ(ierr); 161 PetscFunctionReturn(0); 162 } 163 164 /* -------------------------------------------------------------------------- */ 165 /* 166 PCSetCoordinates_AGG 167 - collective 168 169 Input Parameter: 170 . pc - the preconditioner context 171 . ndm - dimesion of data (used for dof/vertex for Stokes) 172 . a_nloc - number of vertices local 173 . coords - [a_nloc][ndm] - interleaved coordinate data: {x_0, y_0, z_0, x_1, y_1, ...} 174 */ 175 176 static PetscErrorCode PCSetCoordinates_AGG(PC pc, PetscInt ndm, PetscInt a_nloc, PetscReal *coords) 177 { 178 PC_MG *mg = (PC_MG*)pc->data; 179 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 180 PetscErrorCode ierr; 181 PetscInt arrsz,kk,ii,jj,nloc,ndatarows,ndf; 182 Mat mat = pc->pmat; 183 184 PetscFunctionBegin; 185 PetscValidHeaderSpecific(pc,PC_CLASSID,1); 186 PetscValidHeaderSpecific(mat,MAT_CLASSID,1); 187 nloc = a_nloc; 188 189 /* SA: null space vectors */ 190 ierr = MatGetBlockSize(mat, &ndf);CHKERRQ(ierr); /* this does not work for Stokes */ 191 if (coords && ndf==1) pc_gamg->data_cell_cols = 1; /* scalar w/ coords and SA (not needed) */ 192 else if (coords) { 193 if (ndm > ndf) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"degrees of motion %D > block size %D",ndm,ndf); 194 pc_gamg->data_cell_cols = (ndm==2 ? 3 : 6); /* displacement elasticity */ 195 if (ndm != ndf) { 196 if (pc_gamg->data_cell_cols != ndf) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Don't know how to create null space for ndm=%D, ndf=%D. Use MatSetNearNullSpace.",ndm,ndf); 197 } 198 } else pc_gamg->data_cell_cols = ndf; /* no data, force SA with constant null space vectors */ 199 pc_gamg->data_cell_rows = ndatarows = ndf; 200 if (pc_gamg->data_cell_cols <= 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"pc_gamg->data_cell_cols %D <= 0",pc_gamg->data_cell_cols); 201 arrsz = nloc*pc_gamg->data_cell_rows*pc_gamg->data_cell_cols; 202 203 /* create data - syntactic sugar that should be refactored at some point */ 204 if (!pc_gamg->data || (pc_gamg->data_sz != arrsz)) { 205 ierr = PetscFree(pc_gamg->data);CHKERRQ(ierr); 206 ierr = PetscMalloc1(arrsz+1, &pc_gamg->data);CHKERRQ(ierr); 207 } 208 /* copy data in - column oriented */ 209 for (kk=0; kk<nloc; kk++) { 210 const PetscInt M = nloc*pc_gamg->data_cell_rows; /* stride into data */ 211 PetscReal *data = &pc_gamg->data[kk*ndatarows]; /* start of cell */ 212 if (pc_gamg->data_cell_cols==1) *data = 1.0; 213 else { 214 /* translational modes */ 215 for (ii=0;ii<ndatarows;ii++) { 216 for (jj=0;jj<ndatarows;jj++) { 217 if (ii==jj)data[ii*M + jj] = 1.0; 218 else data[ii*M + jj] = 0.0; 219 } 220 } 221 222 /* rotational modes */ 223 if (coords) { 224 if (ndm == 2) { 225 data += 2*M; 226 data[0] = -coords[2*kk+1]; 227 data[1] = coords[2*kk]; 228 } else { 229 data += 3*M; 230 data[0] = 0.0; data[M+0] = coords[3*kk+2]; data[2*M+0] = -coords[3*kk+1]; 231 data[1] = -coords[3*kk+2]; data[M+1] = 0.0; data[2*M+1] = coords[3*kk]; 232 data[2] = coords[3*kk+1]; data[M+2] = -coords[3*kk]; data[2*M+2] = 0.0; 233 } 234 } 235 } 236 } 237 238 pc_gamg->data_sz = arrsz; 239 PetscFunctionReturn(0); 240 } 241 242 typedef PetscInt NState; 243 static const NState NOT_DONE=-2; 244 static const NState DELETED =-1; 245 static const NState REMOVED =-3; 246 #define IS_SELECTED(s) (s!=DELETED && s!=NOT_DONE && s!=REMOVED) 247 248 /* -------------------------------------------------------------------------- */ 249 /* 250 smoothAggs - greedy grab of with G1 (unsquared graph) -- AIJ specific 251 - AGG-MG specific: clears singletons out of 'selected_2' 252 253 Input Parameter: 254 . Gmat_2 - glabal matrix of graph (data not defined) base (squared) graph 255 . Gmat_1 - base graph to grab with base graph 256 Input/Output Parameter: 257 . aggs_2 - linked list of aggs with gids) 258 */ 259 static PetscErrorCode smoothAggs(PC pc,Mat Gmat_2, Mat Gmat_1,PetscCoarsenData *aggs_2) 260 { 261 PetscErrorCode ierr; 262 PetscBool isMPI; 263 Mat_SeqAIJ *matA_1, *matB_1=0; 264 MPI_Comm comm; 265 PetscInt lid,*ii,*idx,ix,Iend,my0,kk,n,j; 266 Mat_MPIAIJ *mpimat_2 = 0, *mpimat_1=0; 267 const PetscInt nloc = Gmat_2->rmap->n; 268 PetscScalar *cpcol_1_state,*cpcol_2_state,*cpcol_2_par_orig,*lid_parent_gid; 269 PetscInt *lid_cprowID_1; 270 NState *lid_state; 271 Vec ghost_par_orig2; 272 273 PetscFunctionBegin; 274 ierr = PetscObjectGetComm((PetscObject)Gmat_2,&comm);CHKERRQ(ierr); 275 ierr = MatGetOwnershipRange(Gmat_1,&my0,&Iend);CHKERRQ(ierr); 276 277 /* get submatrices */ 278 ierr = PetscObjectTypeCompare((PetscObject)Gmat_1, MATMPIAIJ, &isMPI);CHKERRQ(ierr); 279 if (isMPI) { 280 /* grab matrix objects */ 281 mpimat_2 = (Mat_MPIAIJ*)Gmat_2->data; 282 mpimat_1 = (Mat_MPIAIJ*)Gmat_1->data; 283 matA_1 = (Mat_SeqAIJ*)mpimat_1->A->data; 284 matB_1 = (Mat_SeqAIJ*)mpimat_1->B->data; 285 286 /* force compressed row storage for B matrix in AuxMat */ 287 ierr = MatCheckCompressedRow(mpimat_1->B,matB_1->nonzerorowcnt,&matB_1->compressedrow,matB_1->i,Gmat_1->rmap->n,-1.0);CHKERRQ(ierr); 288 289 ierr = PetscMalloc1(nloc, &lid_cprowID_1);CHKERRQ(ierr); 290 for (lid = 0; lid < nloc; lid++) lid_cprowID_1[lid] = -1; 291 for (ix=0; ix<matB_1->compressedrow.nrows; ix++) { 292 PetscInt lid = matB_1->compressedrow.rindex[ix]; 293 lid_cprowID_1[lid] = ix; 294 } 295 } else { 296 PetscBool isAIJ; 297 ierr = PetscObjectBaseTypeCompare((PetscObject)Gmat_1,MATSEQAIJ,&isAIJ);CHKERRQ(ierr); 298 if (!isAIJ) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"Require AIJ matrix."); 299 matA_1 = (Mat_SeqAIJ*)Gmat_1->data; 300 lid_cprowID_1 = NULL; 301 } 302 if (nloc>0) { 303 if (matB_1 && !matB_1->compressedrow.use) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"matB_1 && !matB_1->compressedrow.use: PETSc bug???"); 304 } 305 /* get state of locals and selected gid for deleted */ 306 ierr = PetscMalloc2(nloc, &lid_state,nloc, &lid_parent_gid);CHKERRQ(ierr); 307 for (lid = 0; lid < nloc; lid++) { 308 lid_parent_gid[lid] = -1.0; 309 lid_state[lid] = DELETED; 310 } 311 312 /* set lid_state */ 313 for (lid = 0; lid < nloc; lid++) { 314 PetscCDIntNd *pos; 315 ierr = PetscCDGetHeadPos(aggs_2,lid,&pos);CHKERRQ(ierr); 316 if (pos) { 317 PetscInt gid1; 318 319 ierr = PetscCDIntNdGetID(pos, &gid1);CHKERRQ(ierr); 320 if (gid1 != lid+my0) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"gid1 %D != lid %D + my0 %D",gid1,lid,my0); 321 lid_state[lid] = gid1; 322 } 323 } 324 325 /* map local to selected local, DELETED means a ghost owns it */ 326 for (lid=kk=0; lid<nloc; lid++) { 327 NState state = lid_state[lid]; 328 if (IS_SELECTED(state)) { 329 PetscCDIntNd *pos; 330 ierr = PetscCDGetHeadPos(aggs_2,lid,&pos);CHKERRQ(ierr); 331 while (pos) { 332 PetscInt gid1; 333 ierr = PetscCDIntNdGetID(pos, &gid1);CHKERRQ(ierr); 334 ierr = PetscCDGetNextPos(aggs_2,lid,&pos);CHKERRQ(ierr); 335 336 if (gid1 >= my0 && gid1 < Iend) lid_parent_gid[gid1-my0] = (PetscScalar)(lid + my0); 337 } 338 } 339 } 340 /* get 'cpcol_1/2_state' & cpcol_2_par_orig - uses mpimat_1/2->lvec for temp space */ 341 if (isMPI) { 342 Vec tempVec; 343 /* get 'cpcol_1_state' */ 344 ierr = MatCreateVecs(Gmat_1, &tempVec, 0);CHKERRQ(ierr); 345 for (kk=0,j=my0; kk<nloc; kk++,j++) { 346 PetscScalar v = (PetscScalar)lid_state[kk]; 347 ierr = VecSetValues(tempVec, 1, &j, &v, INSERT_VALUES);CHKERRQ(ierr); 348 } 349 ierr = VecAssemblyBegin(tempVec);CHKERRQ(ierr); 350 ierr = VecAssemblyEnd(tempVec);CHKERRQ(ierr); 351 ierr = VecScatterBegin(mpimat_1->Mvctx,tempVec, mpimat_1->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 352 ierr = VecScatterEnd(mpimat_1->Mvctx,tempVec, mpimat_1->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 353 ierr = VecGetArray(mpimat_1->lvec, &cpcol_1_state);CHKERRQ(ierr); 354 /* get 'cpcol_2_state' */ 355 ierr = VecScatterBegin(mpimat_2->Mvctx,tempVec, mpimat_2->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 356 ierr = VecScatterEnd(mpimat_2->Mvctx,tempVec, mpimat_2->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 357 ierr = VecGetArray(mpimat_2->lvec, &cpcol_2_state);CHKERRQ(ierr); 358 /* get 'cpcol_2_par_orig' */ 359 for (kk=0,j=my0; kk<nloc; kk++,j++) { 360 PetscScalar v = (PetscScalar)lid_parent_gid[kk]; 361 ierr = VecSetValues(tempVec, 1, &j, &v, INSERT_VALUES);CHKERRQ(ierr); 362 } 363 ierr = VecAssemblyBegin(tempVec);CHKERRQ(ierr); 364 ierr = VecAssemblyEnd(tempVec);CHKERRQ(ierr); 365 ierr = VecDuplicate(mpimat_2->lvec, &ghost_par_orig2);CHKERRQ(ierr); 366 ierr = VecScatterBegin(mpimat_2->Mvctx,tempVec, ghost_par_orig2,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 367 ierr = VecScatterEnd(mpimat_2->Mvctx,tempVec, ghost_par_orig2,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 368 ierr = VecGetArray(ghost_par_orig2, &cpcol_2_par_orig);CHKERRQ(ierr); 369 370 ierr = VecDestroy(&tempVec);CHKERRQ(ierr); 371 } /* ismpi */ 372 373 /* doit */ 374 for (lid=0; lid<nloc; lid++) { 375 NState state = lid_state[lid]; 376 if (IS_SELECTED(state)) { 377 /* steal locals */ 378 ii = matA_1->i; n = ii[lid+1] - ii[lid]; 379 idx = matA_1->j + ii[lid]; 380 for (j=0; j<n; j++) { 381 PetscInt lidj = idx[j], sgid; 382 NState statej = lid_state[lidj]; 383 if (statej==DELETED && (sgid=(PetscInt)PetscRealPart(lid_parent_gid[lidj])) != lid+my0) { /* steal local */ 384 lid_parent_gid[lidj] = (PetscScalar)(lid+my0); /* send this if sgid is not local */ 385 if (sgid >= my0 && sgid < Iend) { /* I'm stealing this local from a local sgid */ 386 PetscInt hav=0,slid=sgid-my0,gidj=lidj+my0; 387 PetscCDIntNd *pos,*last=NULL; 388 /* looking for local from local so id_llist_2 works */ 389 ierr = PetscCDGetHeadPos(aggs_2,slid,&pos);CHKERRQ(ierr); 390 while (pos) { 391 PetscInt gid; 392 ierr = PetscCDIntNdGetID(pos, &gid);CHKERRQ(ierr); 393 if (gid == gidj) { 394 if (!last) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"last cannot be null"); 395 ierr = PetscCDRemoveNextNode(aggs_2, slid, last);CHKERRQ(ierr); 396 ierr = PetscCDAppendNode(aggs_2, lid, pos);CHKERRQ(ierr); 397 hav = 1; 398 break; 399 } else last = pos; 400 401 ierr = PetscCDGetNextPos(aggs_2,slid,&pos);CHKERRQ(ierr); 402 } 403 if (hav!=1) { 404 if (!hav) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"failed to find adj in 'selected' lists - structurally unsymmetric matrix"); 405 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"found node %D times???",hav); 406 } 407 } else { /* I'm stealing this local, owned by a ghost */ 408 if (sgid != -1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Have un-symmetric graph (apparently). Use '-%spc_gamg_sym_graph true' to symetrize the graph or '-%spc_gamg_threshold -1' if the matrix is structurally symmetric.",((PetscObject)pc)->prefix,((PetscObject)pc)->prefix); 409 ierr = PetscCDAppendID(aggs_2, lid, lidj+my0);CHKERRQ(ierr); 410 } 411 } 412 } /* local neighbors */ 413 } else if (state == DELETED && lid_cprowID_1) { 414 PetscInt sgidold = (PetscInt)PetscRealPart(lid_parent_gid[lid]); 415 /* see if I have a selected ghost neighbor that will steal me */ 416 if ((ix=lid_cprowID_1[lid]) != -1) { 417 ii = matB_1->compressedrow.i; n = ii[ix+1] - ii[ix]; 418 idx = matB_1->j + ii[ix]; 419 for (j=0; j<n; j++) { 420 PetscInt cpid = idx[j]; 421 NState statej = (NState)PetscRealPart(cpcol_1_state[cpid]); 422 if (IS_SELECTED(statej) && sgidold != (PetscInt)statej) { /* ghost will steal this, remove from my list */ 423 lid_parent_gid[lid] = (PetscScalar)statej; /* send who selected */ 424 if (sgidold>=my0 && sgidold<Iend) { /* this was mine */ 425 PetscInt hav=0,oldslidj=sgidold-my0; 426 PetscCDIntNd *pos,*last=NULL; 427 /* remove from 'oldslidj' list */ 428 ierr = PetscCDGetHeadPos(aggs_2,oldslidj,&pos);CHKERRQ(ierr); 429 while (pos) { 430 PetscInt gid; 431 ierr = PetscCDIntNdGetID(pos, &gid);CHKERRQ(ierr); 432 if (lid+my0 == gid) { 433 /* id_llist_2[lastid] = id_llist_2[flid]; /\* remove lid from oldslidj list *\/ */ 434 if (!last) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"last cannot be null"); 435 ierr = PetscCDRemoveNextNode(aggs_2, oldslidj, last);CHKERRQ(ierr); 436 /* ghost (PetscScalar)statej will add this later */ 437 hav = 1; 438 break; 439 } else last = pos; 440 441 ierr = PetscCDGetNextPos(aggs_2,oldslidj,&pos);CHKERRQ(ierr); 442 } 443 if (hav!=1) { 444 if (!hav) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"failed to find adj in 'selected' lists - structurally unsymmetric matrix"); 445 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"found node %D times???",hav); 446 } 447 } else { 448 /* ghosts remove this later */ 449 } 450 } 451 } 452 } 453 } /* selected/deleted */ 454 } /* node loop */ 455 456 if (isMPI) { 457 PetscScalar *cpcol_2_parent,*cpcol_2_gid; 458 Vec tempVec,ghostgids2,ghostparents2; 459 PetscInt cpid,nghost_2; 460 PCGAMGHashTable gid_cpid; 461 462 ierr = VecGetSize(mpimat_2->lvec, &nghost_2);CHKERRQ(ierr); 463 ierr = MatCreateVecs(Gmat_2, &tempVec, 0);CHKERRQ(ierr); 464 465 /* get 'cpcol_2_parent' */ 466 for (kk=0,j=my0; kk<nloc; kk++,j++) { 467 ierr = VecSetValues(tempVec, 1, &j, &lid_parent_gid[kk], INSERT_VALUES);CHKERRQ(ierr); 468 } 469 ierr = VecAssemblyBegin(tempVec);CHKERRQ(ierr); 470 ierr = VecAssemblyEnd(tempVec);CHKERRQ(ierr); 471 ierr = VecDuplicate(mpimat_2->lvec, &ghostparents2);CHKERRQ(ierr); 472 ierr = VecScatterBegin(mpimat_2->Mvctx,tempVec, ghostparents2,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 473 ierr = VecScatterEnd(mpimat_2->Mvctx,tempVec, ghostparents2,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 474 ierr = VecGetArray(ghostparents2, &cpcol_2_parent);CHKERRQ(ierr); 475 476 /* get 'cpcol_2_gid' */ 477 for (kk=0,j=my0; kk<nloc; kk++,j++) { 478 PetscScalar v = (PetscScalar)j; 479 ierr = VecSetValues(tempVec, 1, &j, &v, INSERT_VALUES);CHKERRQ(ierr); 480 } 481 ierr = VecAssemblyBegin(tempVec);CHKERRQ(ierr); 482 ierr = VecAssemblyEnd(tempVec);CHKERRQ(ierr); 483 ierr = VecDuplicate(mpimat_2->lvec, &ghostgids2);CHKERRQ(ierr); 484 ierr = VecScatterBegin(mpimat_2->Mvctx,tempVec, ghostgids2,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 485 ierr = VecScatterEnd(mpimat_2->Mvctx,tempVec, ghostgids2,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 486 ierr = VecGetArray(ghostgids2, &cpcol_2_gid);CHKERRQ(ierr); 487 ierr = VecDestroy(&tempVec);CHKERRQ(ierr); 488 489 /* look for deleted ghosts and add to table */ 490 ierr = PCGAMGHashTableCreate(2*nghost_2+1, &gid_cpid);CHKERRQ(ierr); 491 for (cpid = 0; cpid < nghost_2; cpid++) { 492 NState state = (NState)PetscRealPart(cpcol_2_state[cpid]); 493 if (state==DELETED) { 494 PetscInt sgid_new = (PetscInt)PetscRealPart(cpcol_2_parent[cpid]); 495 PetscInt sgid_old = (PetscInt)PetscRealPart(cpcol_2_par_orig[cpid]); 496 if (sgid_old == -1 && sgid_new != -1) { 497 PetscInt gid = (PetscInt)PetscRealPart(cpcol_2_gid[cpid]); 498 ierr = PCGAMGHashTableAdd(&gid_cpid, gid, cpid);CHKERRQ(ierr); 499 } 500 } 501 } 502 503 /* look for deleted ghosts and see if they moved - remove it */ 504 for (lid=0; lid<nloc; lid++) { 505 NState state = lid_state[lid]; 506 if (IS_SELECTED(state)) { 507 PetscCDIntNd *pos,*last=NULL; 508 /* look for deleted ghosts and see if they moved */ 509 ierr = PetscCDGetHeadPos(aggs_2,lid,&pos);CHKERRQ(ierr); 510 while (pos) { 511 PetscInt gid; 512 ierr = PetscCDIntNdGetID(pos, &gid);CHKERRQ(ierr); 513 514 if (gid < my0 || gid >= Iend) { 515 ierr = PCGAMGHashTableFind(&gid_cpid, gid, &cpid);CHKERRQ(ierr); 516 if (cpid != -1) { 517 /* a moved ghost - */ 518 /* id_llist_2[lastid] = id_llist_2[flid]; /\* remove 'flid' from list *\/ */ 519 ierr = PetscCDRemoveNextNode(aggs_2, lid, last);CHKERRQ(ierr); 520 } else last = pos; 521 } else last = pos; 522 523 ierr = PetscCDGetNextPos(aggs_2,lid,&pos);CHKERRQ(ierr); 524 } /* loop over list of deleted */ 525 } /* selected */ 526 } 527 ierr = PCGAMGHashTableDestroy(&gid_cpid);CHKERRQ(ierr); 528 529 /* look at ghosts, see if they changed - and it */ 530 for (cpid = 0; cpid < nghost_2; cpid++) { 531 PetscInt sgid_new = (PetscInt)PetscRealPart(cpcol_2_parent[cpid]); 532 if (sgid_new >= my0 && sgid_new < Iend) { /* this is mine */ 533 PetscInt gid = (PetscInt)PetscRealPart(cpcol_2_gid[cpid]); 534 PetscInt slid_new=sgid_new-my0,hav=0; 535 PetscCDIntNd *pos; 536 537 /* search for this gid to see if I have it */ 538 ierr = PetscCDGetHeadPos(aggs_2,slid_new,&pos);CHKERRQ(ierr); 539 while (pos) { 540 PetscInt gidj; 541 ierr = PetscCDIntNdGetID(pos, &gidj);CHKERRQ(ierr); 542 ierr = PetscCDGetNextPos(aggs_2,slid_new,&pos);CHKERRQ(ierr); 543 544 if (gidj == gid) { hav = 1; break; } 545 } 546 if (hav != 1) { 547 /* insert 'flidj' into head of llist */ 548 ierr = PetscCDAppendID(aggs_2, slid_new, gid);CHKERRQ(ierr); 549 } 550 } 551 } 552 553 ierr = VecRestoreArray(mpimat_1->lvec, &cpcol_1_state);CHKERRQ(ierr); 554 ierr = VecRestoreArray(mpimat_2->lvec, &cpcol_2_state);CHKERRQ(ierr); 555 ierr = VecRestoreArray(ghostparents2, &cpcol_2_parent);CHKERRQ(ierr); 556 ierr = VecRestoreArray(ghostgids2, &cpcol_2_gid);CHKERRQ(ierr); 557 ierr = PetscFree(lid_cprowID_1);CHKERRQ(ierr); 558 ierr = VecDestroy(&ghostgids2);CHKERRQ(ierr); 559 ierr = VecDestroy(&ghostparents2);CHKERRQ(ierr); 560 ierr = VecDestroy(&ghost_par_orig2);CHKERRQ(ierr); 561 } 562 563 ierr = PetscFree2(lid_state,lid_parent_gid);CHKERRQ(ierr); 564 PetscFunctionReturn(0); 565 } 566 567 /* -------------------------------------------------------------------------- */ 568 /* 569 PCSetData_AGG - called if data is not set with PCSetCoordinates. 570 Looks in Mat for near null space. 571 Does not work for Stokes 572 573 Input Parameter: 574 . pc - 575 . a_A - matrix to get (near) null space out of. 576 */ 577 static PetscErrorCode PCSetData_AGG(PC pc, Mat a_A) 578 { 579 PetscErrorCode ierr; 580 PC_MG *mg = (PC_MG*)pc->data; 581 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 582 MatNullSpace mnull; 583 584 PetscFunctionBegin; 585 ierr = MatGetNearNullSpace(a_A, &mnull);CHKERRQ(ierr); 586 if (!mnull) { 587 DM dm; 588 ierr = PCGetDM(pc, &dm);CHKERRQ(ierr); 589 if (!dm) { 590 ierr = MatGetDM(a_A, &dm);CHKERRQ(ierr); 591 } 592 if (dm) { 593 PetscObject deformation; 594 PetscInt Nf; 595 596 ierr = DMGetNumFields(dm, &Nf);CHKERRQ(ierr); 597 if (Nf) { 598 ierr = DMGetField(dm, 0, &deformation);CHKERRQ(ierr); 599 ierr = PetscObjectQuery((PetscObject)deformation,"nearnullspace",(PetscObject*)&mnull);CHKERRQ(ierr); 600 if (!mnull) { 601 ierr = PetscObjectQuery((PetscObject)deformation,"nullspace",(PetscObject*)&mnull);CHKERRQ(ierr); 602 } 603 } 604 } 605 } 606 607 if (!mnull) { 608 PetscInt bs,NN,MM; 609 ierr = MatGetBlockSize(a_A, &bs);CHKERRQ(ierr); 610 ierr = MatGetLocalSize(a_A, &MM, &NN);CHKERRQ(ierr); 611 if (MM % bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"MM %D must be divisible by bs %D",MM,bs); 612 ierr = PCSetCoordinates_AGG(pc, bs, MM/bs, NULL);CHKERRQ(ierr); 613 } else { 614 PetscReal *nullvec; 615 PetscBool has_const; 616 PetscInt i,j,mlocal,nvec,bs; 617 const Vec *vecs; const PetscScalar *v; 618 619 ierr = MatGetLocalSize(a_A,&mlocal,NULL);CHKERRQ(ierr); 620 ierr = MatNullSpaceGetVecs(mnull, &has_const, &nvec, &vecs);CHKERRQ(ierr); 621 pc_gamg->data_sz = (nvec+!!has_const)*mlocal; 622 ierr = PetscMalloc1((nvec+!!has_const)*mlocal,&nullvec);CHKERRQ(ierr); 623 if (has_const) for (i=0; i<mlocal; i++) nullvec[i] = 1.0; 624 for (i=0; i<nvec; i++) { 625 ierr = VecGetArrayRead(vecs[i],&v);CHKERRQ(ierr); 626 for (j=0; j<mlocal; j++) nullvec[(i+!!has_const)*mlocal + j] = PetscRealPart(v[j]); 627 ierr = VecRestoreArrayRead(vecs[i],&v);CHKERRQ(ierr); 628 } 629 pc_gamg->data = nullvec; 630 pc_gamg->data_cell_cols = (nvec+!!has_const); 631 ierr = MatGetBlockSize(a_A, &bs);CHKERRQ(ierr); 632 pc_gamg->data_cell_rows = bs; 633 } 634 PetscFunctionReturn(0); 635 } 636 637 /* -------------------------------------------------------------------------- */ 638 /* 639 formProl0 640 641 Input Parameter: 642 . agg_llists - list of arrays with aggregates -- list from selected vertices of aggregate unselected vertices 643 . bs - row block size 644 . nSAvec - column bs of new P 645 . my0crs - global index of start of locals 646 . data_stride - bs*(nloc nodes + ghost nodes) [data_stride][nSAvec] 647 . data_in[data_stride*nSAvec] - local data on fine grid 648 . flid_fgid[data_stride/bs] - make local to global IDs, includes ghosts in 'locals_llist' 649 Output Parameter: 650 . a_data_out - in with fine grid data (w/ghosts), out with coarse grid data 651 . a_Prol - prolongation operator 652 */ 653 static PetscErrorCode formProl0(PetscCoarsenData *agg_llists,PetscInt bs,PetscInt nSAvec,PetscInt my0crs,PetscInt data_stride,PetscReal data_in[],const PetscInt flid_fgid[],PetscReal **a_data_out,Mat a_Prol) 654 { 655 PetscErrorCode ierr; 656 PetscInt Istart,my0,Iend,nloc,clid,flid = 0,aggID,kk,jj,ii,mm,ndone,nSelected,minsz,nghosts,out_data_stride; 657 MPI_Comm comm; 658 PetscMPIInt rank; 659 PetscReal *out_data; 660 PetscCDIntNd *pos; 661 PCGAMGHashTable fgid_flid; 662 663 PetscFunctionBegin; 664 ierr = PetscObjectGetComm((PetscObject)a_Prol,&comm);CHKERRQ(ierr); 665 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 666 ierr = MatGetOwnershipRange(a_Prol, &Istart, &Iend);CHKERRQ(ierr); 667 nloc = (Iend-Istart)/bs; my0 = Istart/bs; 668 if ((Iend-Istart) % bs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Iend %D - Istart %D must be divisible by bs %D",Iend,Istart,bs); 669 Iend /= bs; 670 nghosts = data_stride/bs - nloc; 671 672 ierr = PCGAMGHashTableCreate(2*nghosts+1, &fgid_flid);CHKERRQ(ierr); 673 for (kk=0; kk<nghosts; kk++) { 674 ierr = PCGAMGHashTableAdd(&fgid_flid, flid_fgid[nloc+kk], nloc+kk);CHKERRQ(ierr); 675 } 676 677 /* count selected -- same as number of cols of P */ 678 for (nSelected=mm=0; mm<nloc; mm++) { 679 PetscBool ise; 680 ierr = PetscCDEmptyAt(agg_llists, mm, &ise);CHKERRQ(ierr); 681 if (!ise) nSelected++; 682 } 683 ierr = MatGetOwnershipRangeColumn(a_Prol, &ii, &jj);CHKERRQ(ierr); 684 if ((ii/nSAvec) != my0crs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"ii %D /nSAvec %D != my0crs %D",ii,nSAvec,my0crs); 685 if (nSelected != (jj-ii)/nSAvec) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_PLIB,"nSelected %D != (jj %D - ii %D)/nSAvec %D",nSelected,jj,ii,nSAvec); 686 687 /* aloc space for coarse point data (output) */ 688 out_data_stride = nSelected*nSAvec; 689 690 ierr = PetscMalloc1(out_data_stride*nSAvec, &out_data);CHKERRQ(ierr); 691 for (ii=0;ii<out_data_stride*nSAvec;ii++) out_data[ii]=PETSC_MAX_REAL; 692 *a_data_out = out_data; /* output - stride nSelected*nSAvec */ 693 694 /* find points and set prolongation */ 695 minsz = 100; 696 ndone = 0; 697 for (mm = clid = 0; mm < nloc; mm++) { 698 ierr = PetscCDSizeAt(agg_llists, mm, &jj);CHKERRQ(ierr); 699 if (jj > 0) { 700 const PetscInt lid = mm, cgid = my0crs + clid; 701 PetscInt cids[100]; /* max bs */ 702 PetscBLASInt asz =jj,M=asz*bs,N=nSAvec,INFO; 703 PetscBLASInt Mdata=M+((N-M>0) ? N-M : 0),LDA=Mdata,LWORK=N*bs; 704 PetscScalar *qqc,*qqr,*TAU,*WORK; 705 PetscInt *fids; 706 PetscReal *data; 707 708 /* count agg */ 709 if (asz<minsz) minsz = asz; 710 711 /* get block */ 712 ierr = PetscMalloc5(Mdata*N, &qqc,M*N, &qqr,N, &TAU,LWORK, &WORK,M, &fids);CHKERRQ(ierr); 713 714 aggID = 0; 715 ierr = PetscCDGetHeadPos(agg_llists,lid,&pos);CHKERRQ(ierr); 716 while (pos) { 717 PetscInt gid1; 718 ierr = PetscCDIntNdGetID(pos, &gid1);CHKERRQ(ierr); 719 ierr = PetscCDGetNextPos(agg_llists,lid,&pos);CHKERRQ(ierr); 720 721 if (gid1 >= my0 && gid1 < Iend) flid = gid1 - my0; 722 else { 723 ierr = PCGAMGHashTableFind(&fgid_flid, gid1, &flid);CHKERRQ(ierr); 724 if (flid < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Cannot find gid1 in table"); 725 } 726 /* copy in B_i matrix - column oriented */ 727 data = &data_in[flid*bs]; 728 for (ii = 0; ii < bs; ii++) { 729 for (jj = 0; jj < N; jj++) { 730 PetscReal d = data[jj*data_stride + ii]; 731 qqc[jj*Mdata + aggID*bs + ii] = d; 732 } 733 } 734 /* set fine IDs */ 735 for (kk=0; kk<bs; kk++) fids[aggID*bs + kk] = flid_fgid[flid]*bs + kk; 736 aggID++; 737 } 738 739 /* pad with zeros */ 740 for (ii = asz*bs; ii < Mdata; ii++) { 741 for (jj = 0; jj < N; jj++, kk++) { 742 qqc[jj*Mdata + ii] = .0; 743 } 744 } 745 746 ndone += aggID; 747 /* QR */ 748 ierr = PetscFPTrapPush(PETSC_FP_TRAP_OFF);CHKERRQ(ierr); 749 PetscStackCallBLAS("LAPACKgeqrf",LAPACKgeqrf_(&Mdata, &N, qqc, &LDA, TAU, WORK, &LWORK, &INFO)); 750 ierr = PetscFPTrapPop();CHKERRQ(ierr); 751 if (INFO != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"xGEQRF error"); 752 /* get R - column oriented - output B_{i+1} */ 753 { 754 PetscReal *data = &out_data[clid*nSAvec]; 755 for (jj = 0; jj < nSAvec; jj++) { 756 for (ii = 0; ii < nSAvec; ii++) { 757 if (data[jj*out_data_stride + ii] != PETSC_MAX_REAL) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"data[jj*out_data_stride + ii] != %e",PETSC_MAX_REAL); 758 if (ii <= jj) data[jj*out_data_stride + ii] = PetscRealPart(qqc[jj*Mdata + ii]); 759 else data[jj*out_data_stride + ii] = 0.; 760 } 761 } 762 } 763 764 /* get Q - row oriented */ 765 PetscStackCallBLAS("LAPACKorgqr",LAPACKorgqr_(&Mdata, &N, &N, qqc, &LDA, TAU, WORK, &LWORK, &INFO)); 766 if (INFO != 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"xORGQR error arg %d",-INFO); 767 768 for (ii = 0; ii < M; ii++) { 769 for (jj = 0; jj < N; jj++) { 770 qqr[N*ii + jj] = qqc[jj*Mdata + ii]; 771 } 772 } 773 774 /* add diagonal block of P0 */ 775 for (kk=0; kk<N; kk++) { 776 cids[kk] = N*cgid + kk; /* global col IDs in P0 */ 777 } 778 ierr = MatSetValues(a_Prol,M,fids,N,cids,qqr,INSERT_VALUES);CHKERRQ(ierr); 779 ierr = PetscFree5(qqc,qqr,TAU,WORK,fids);CHKERRQ(ierr); 780 clid++; 781 } /* coarse agg */ 782 } /* for all fine nodes */ 783 ierr = MatAssemblyBegin(a_Prol,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 784 ierr = MatAssemblyEnd(a_Prol,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 785 ierr = PCGAMGHashTableDestroy(&fgid_flid);CHKERRQ(ierr); 786 PetscFunctionReturn(0); 787 } 788 789 static PetscErrorCode PCView_GAMG_AGG(PC pc,PetscViewer viewer) 790 { 791 PetscErrorCode ierr; 792 PC_MG *mg = (PC_MG*)pc->data; 793 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 794 PC_GAMG_AGG *pc_gamg_agg = (PC_GAMG_AGG*)pc_gamg->subctx; 795 796 PetscFunctionBegin; 797 ierr = PetscViewerASCIIPrintf(viewer," AGG specific options\n");CHKERRQ(ierr); 798 ierr = PetscViewerASCIIPrintf(viewer," Symmetric graph %s\n",pc_gamg_agg->sym_graph ? "true" : "false");CHKERRQ(ierr); 799 ierr = PetscViewerASCIIPrintf(viewer," Number of levels to square graph %D\n",pc_gamg_agg->square_graph);CHKERRQ(ierr); 800 ierr = PetscViewerASCIIPrintf(viewer," Number smoothing steps %D\n",pc_gamg_agg->nsmooths);CHKERRQ(ierr); 801 PetscFunctionReturn(0); 802 } 803 804 /* -------------------------------------------------------------------------- */ 805 /* 806 PCGAMGGraph_AGG 807 808 Input Parameter: 809 . pc - this 810 . Amat - matrix on this fine level 811 Output Parameter: 812 . a_Gmat - 813 */ 814 static PetscErrorCode PCGAMGGraph_AGG(PC pc,Mat Amat,Mat *a_Gmat) 815 { 816 PetscErrorCode ierr; 817 PC_MG *mg = (PC_MG*)pc->data; 818 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 819 const PetscReal vfilter = pc_gamg->threshold[pc_gamg->current_level]; 820 PC_GAMG_AGG *pc_gamg_agg = (PC_GAMG_AGG*)pc_gamg->subctx; 821 Mat Gmat; 822 MPI_Comm comm; 823 PetscBool /* set,flg , */ symm; 824 825 PetscFunctionBegin; 826 ierr = PetscObjectGetComm((PetscObject)Amat,&comm);CHKERRQ(ierr); 827 ierr = PetscLogEventBegin(PC_GAMGGraph_AGG,0,0,0,0);CHKERRQ(ierr); 828 829 /* ierr = MatIsSymmetricKnown(Amat, &set, &flg);CHKERRQ(ierr); || !(set && flg) -- this causes lot of symm calls */ 830 symm = (PetscBool)(pc_gamg_agg->sym_graph); /* && !pc_gamg_agg->square_graph; */ 831 832 ierr = PCGAMGCreateGraph(Amat, &Gmat);CHKERRQ(ierr); 833 ierr = PCGAMGFilterGraph(&Gmat, vfilter, symm);CHKERRQ(ierr); 834 *a_Gmat = Gmat; 835 ierr = PetscLogEventEnd(PC_GAMGGraph_AGG,0,0,0,0);CHKERRQ(ierr); 836 PetscFunctionReturn(0); 837 } 838 839 /* -------------------------------------------------------------------------- */ 840 /* 841 PCGAMGCoarsen_AGG 842 843 Input Parameter: 844 . a_pc - this 845 Input/Output Parameter: 846 . a_Gmat1 - graph on this fine level - coarsening can change this (squares it) 847 Output Parameter: 848 . agg_lists - list of aggregates 849 */ 850 static PetscErrorCode PCGAMGCoarsen_AGG(PC a_pc,Mat *a_Gmat1,PetscCoarsenData **agg_lists) 851 { 852 PetscErrorCode ierr; 853 PC_MG *mg = (PC_MG*)a_pc->data; 854 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 855 PC_GAMG_AGG *pc_gamg_agg = (PC_GAMG_AGG*)pc_gamg->subctx; 856 Mat mat,Gmat2, Gmat1 = *a_Gmat1; /* squared graph */ 857 IS perm; 858 PetscInt Istart,Iend,Ii,nloc,bs,n,m; 859 PetscInt *permute; 860 PetscBool *bIndexSet; 861 MatCoarsen crs; 862 MPI_Comm comm; 863 PetscMPIInt rank; 864 PetscReal hashfact; 865 PetscInt iSwapIndex; 866 PetscRandom random; 867 868 PetscFunctionBegin; 869 ierr = PetscLogEventBegin(PC_GAMGCoarsen_AGG,0,0,0,0);CHKERRQ(ierr); 870 ierr = PetscObjectGetComm((PetscObject)Gmat1,&comm);CHKERRQ(ierr); 871 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 872 ierr = MatGetLocalSize(Gmat1, &n, &m);CHKERRQ(ierr); 873 ierr = MatGetBlockSize(Gmat1, &bs);CHKERRQ(ierr); 874 if (bs != 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"bs %D must be 1",bs); 875 nloc = n/bs; 876 877 if (pc_gamg->current_level < pc_gamg_agg->square_graph) { 878 ierr = PetscInfo2(a_pc,"Square Graph on level %D of %D to square\n",pc_gamg->current_level+1,pc_gamg_agg->square_graph);CHKERRQ(ierr); 879 ierr = MatTransposeMatMult(Gmat1, Gmat1, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &Gmat2);CHKERRQ(ierr); 880 } else Gmat2 = Gmat1; 881 882 /* get MIS aggs - randomize */ 883 ierr = PetscMalloc1(nloc, &permute);CHKERRQ(ierr); 884 ierr = PetscCalloc1(nloc, &bIndexSet);CHKERRQ(ierr); 885 for (Ii = 0; Ii < nloc; Ii++) { 886 permute[Ii] = Ii; 887 } 888 ierr = PetscRandomCreate(PETSC_COMM_SELF,&random);CHKERRQ(ierr); 889 ierr = MatGetOwnershipRange(Gmat1, &Istart, &Iend);CHKERRQ(ierr); 890 for (Ii = 0; Ii < nloc; Ii++) { 891 ierr = PetscRandomGetValueReal(random,&hashfact);CHKERRQ(ierr); 892 iSwapIndex = (PetscInt) (hashfact*nloc)%nloc; 893 if (!bIndexSet[iSwapIndex] && iSwapIndex != Ii) { 894 PetscInt iTemp = permute[iSwapIndex]; 895 permute[iSwapIndex] = permute[Ii]; 896 permute[Ii] = iTemp; 897 bIndexSet[iSwapIndex] = PETSC_TRUE; 898 } 899 } 900 ierr = PetscFree(bIndexSet);CHKERRQ(ierr); 901 ierr = PetscRandomDestroy(&random);CHKERRQ(ierr); 902 ierr = ISCreateGeneral(PETSC_COMM_SELF, nloc, permute, PETSC_USE_POINTER, &perm);CHKERRQ(ierr); 903 #if defined PETSC_GAMG_USE_LOG 904 ierr = PetscLogEventBegin(petsc_gamg_setup_events[SET4],0,0,0,0);CHKERRQ(ierr); 905 #endif 906 ierr = MatCoarsenCreate(comm, &crs);CHKERRQ(ierr); 907 ierr = MatCoarsenSetFromOptions(crs);CHKERRQ(ierr); 908 ierr = MatCoarsenSetGreedyOrdering(crs, perm);CHKERRQ(ierr); 909 ierr = MatCoarsenSetAdjacency(crs, Gmat2);CHKERRQ(ierr); 910 ierr = MatCoarsenSetStrictAggs(crs, PETSC_TRUE);CHKERRQ(ierr); 911 ierr = MatCoarsenApply(crs);CHKERRQ(ierr); 912 ierr = MatCoarsenGetData(crs, agg_lists);CHKERRQ(ierr); /* output */ 913 ierr = MatCoarsenDestroy(&crs);CHKERRQ(ierr); 914 915 ierr = ISDestroy(&perm);CHKERRQ(ierr); 916 ierr = PetscFree(permute);CHKERRQ(ierr); 917 #if defined PETSC_GAMG_USE_LOG 918 ierr = PetscLogEventEnd(petsc_gamg_setup_events[SET4],0,0,0,0);CHKERRQ(ierr); 919 #endif 920 921 /* smooth aggs */ 922 if (Gmat2 != Gmat1) { 923 const PetscCoarsenData *llist = *agg_lists; 924 ierr = smoothAggs(a_pc,Gmat2, Gmat1, *agg_lists);CHKERRQ(ierr); 925 ierr = MatDestroy(&Gmat1);CHKERRQ(ierr); 926 *a_Gmat1 = Gmat2; /* output */ 927 ierr = PetscCDGetMat(llist, &mat);CHKERRQ(ierr); 928 if (mat) SETERRQ(comm,PETSC_ERR_ARG_WRONG, "Auxilary matrix with squared graph????"); 929 } else { 930 const PetscCoarsenData *llist = *agg_lists; 931 /* see if we have a matrix that takes precedence (returned from MatCoarsenApply) */ 932 ierr = PetscCDGetMat(llist, &mat);CHKERRQ(ierr); 933 if (mat) { 934 ierr = MatDestroy(&Gmat1);CHKERRQ(ierr); 935 *a_Gmat1 = mat; /* output */ 936 } 937 } 938 ierr = PetscLogEventEnd(PC_GAMGCoarsen_AGG,0,0,0,0);CHKERRQ(ierr); 939 PetscFunctionReturn(0); 940 } 941 942 /* -------------------------------------------------------------------------- */ 943 /* 944 PCGAMGProlongator_AGG 945 946 Input Parameter: 947 . pc - this 948 . Amat - matrix on this fine level 949 . Graph - used to get ghost data for nodes in 950 . agg_lists - list of aggregates 951 Output Parameter: 952 . a_P_out - prolongation operator to the next level 953 */ 954 static PetscErrorCode PCGAMGProlongator_AGG(PC pc,Mat Amat,Mat Gmat,PetscCoarsenData *agg_lists,Mat *a_P_out) 955 { 956 PC_MG *mg = (PC_MG*)pc->data; 957 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 958 const PetscInt col_bs = pc_gamg->data_cell_cols; 959 PetscErrorCode ierr; 960 PetscInt Istart,Iend,nloc,ii,jj,kk,my0,nLocalSelected,bs; 961 Mat Prol; 962 PetscMPIInt rank, size; 963 MPI_Comm comm; 964 PetscReal *data_w_ghost; 965 PetscInt myCrs0, nbnodes=0, *flid_fgid; 966 MatType mtype; 967 968 PetscFunctionBegin; 969 ierr = PetscObjectGetComm((PetscObject)Amat,&comm);CHKERRQ(ierr); 970 if (col_bs < 1) SETERRQ(comm,PETSC_ERR_PLIB,"Column bs cannot be less than 1"); 971 ierr = PetscLogEventBegin(PC_GAMGProlongator_AGG,0,0,0,0);CHKERRQ(ierr); 972 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 973 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 974 ierr = MatGetOwnershipRange(Amat, &Istart, &Iend);CHKERRQ(ierr); 975 ierr = MatGetBlockSize(Amat, &bs);CHKERRQ(ierr); 976 nloc = (Iend-Istart)/bs; my0 = Istart/bs; 977 if ((Iend-Istart) % bs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"(Iend %D - Istart %D) not divisible by bs %D",Iend,Istart,bs); 978 979 /* get 'nLocalSelected' */ 980 for (ii=0, nLocalSelected = 0; ii < nloc; ii++) { 981 PetscBool ise; 982 /* filter out singletons 0 or 1? */ 983 ierr = PetscCDEmptyAt(agg_lists, ii, &ise);CHKERRQ(ierr); 984 if (!ise) nLocalSelected++; 985 } 986 987 /* create prolongator, create P matrix */ 988 ierr = MatGetType(Amat,&mtype);CHKERRQ(ierr); 989 ierr = MatCreate(comm, &Prol);CHKERRQ(ierr); 990 ierr = MatSetSizes(Prol,nloc*bs,nLocalSelected*col_bs,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 991 ierr = MatSetBlockSizes(Prol, bs, col_bs);CHKERRQ(ierr); 992 ierr = MatSetType(Prol, mtype);CHKERRQ(ierr); 993 ierr = MatSeqAIJSetPreallocation(Prol, col_bs, NULL);CHKERRQ(ierr); 994 ierr = MatMPIAIJSetPreallocation(Prol,col_bs, NULL,col_bs, NULL);CHKERRQ(ierr); 995 996 /* can get all points "removed" */ 997 ierr = MatGetSize(Prol, &kk, &ii);CHKERRQ(ierr); 998 if (!ii) { 999 ierr = PetscInfo(pc,"No selected points on coarse grid\n");CHKERRQ(ierr); 1000 ierr = MatDestroy(&Prol);CHKERRQ(ierr); 1001 *a_P_out = NULL; /* out */ 1002 ierr = PetscLogEventEnd(PC_GAMGProlongator_AGG,0,0,0,0);CHKERRQ(ierr); 1003 PetscFunctionReturn(0); 1004 } 1005 ierr = PetscInfo1(pc,"New grid %D nodes\n",ii/col_bs);CHKERRQ(ierr); 1006 ierr = MatGetOwnershipRangeColumn(Prol, &myCrs0, &kk);CHKERRQ(ierr); 1007 1008 if ((kk-myCrs0) % col_bs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"(kk %D -myCrs0 %D) not divisible by col_bs %D",kk,myCrs0,col_bs); 1009 myCrs0 = myCrs0/col_bs; 1010 if ((kk/col_bs-myCrs0) != nLocalSelected) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_PLIB,"(kk %D/col_bs %D - myCrs0 %D) != nLocalSelected %D)",kk,col_bs,myCrs0,nLocalSelected); 1011 1012 /* create global vector of data in 'data_w_ghost' */ 1013 #if defined PETSC_GAMG_USE_LOG 1014 ierr = PetscLogEventBegin(petsc_gamg_setup_events[SET7],0,0,0,0);CHKERRQ(ierr); 1015 #endif 1016 if (size > 1) { /* */ 1017 PetscReal *tmp_gdata,*tmp_ldata,*tp2; 1018 ierr = PetscMalloc1(nloc, &tmp_ldata);CHKERRQ(ierr); 1019 for (jj = 0; jj < col_bs; jj++) { 1020 for (kk = 0; kk < bs; kk++) { 1021 PetscInt ii,stride; 1022 const PetscReal *tp = pc_gamg->data + jj*bs*nloc + kk; 1023 for (ii = 0; ii < nloc; ii++, tp += bs) tmp_ldata[ii] = *tp; 1024 1025 ierr = PCGAMGGetDataWithGhosts(Gmat, 1, tmp_ldata, &stride, &tmp_gdata);CHKERRQ(ierr); 1026 1027 if (!jj && !kk) { /* now I know how many todal nodes - allocate */ 1028 ierr = PetscMalloc1(stride*bs*col_bs, &data_w_ghost);CHKERRQ(ierr); 1029 nbnodes = bs*stride; 1030 } 1031 tp2 = data_w_ghost + jj*bs*stride + kk; 1032 for (ii = 0; ii < stride; ii++, tp2 += bs) *tp2 = tmp_gdata[ii]; 1033 ierr = PetscFree(tmp_gdata);CHKERRQ(ierr); 1034 } 1035 } 1036 ierr = PetscFree(tmp_ldata);CHKERRQ(ierr); 1037 } else { 1038 nbnodes = bs*nloc; 1039 data_w_ghost = (PetscReal*)pc_gamg->data; 1040 } 1041 1042 /* get P0 */ 1043 if (size > 1) { 1044 PetscReal *fid_glid_loc,*fiddata; 1045 PetscInt stride; 1046 1047 ierr = PetscMalloc1(nloc, &fid_glid_loc);CHKERRQ(ierr); 1048 for (kk=0; kk<nloc; kk++) fid_glid_loc[kk] = (PetscReal)(my0+kk); 1049 ierr = PCGAMGGetDataWithGhosts(Gmat, 1, fid_glid_loc, &stride, &fiddata);CHKERRQ(ierr); 1050 ierr = PetscMalloc1(stride, &flid_fgid);CHKERRQ(ierr); 1051 for (kk=0; kk<stride; kk++) flid_fgid[kk] = (PetscInt)fiddata[kk]; 1052 ierr = PetscFree(fiddata);CHKERRQ(ierr); 1053 1054 if (stride != nbnodes/bs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"stride %D != nbnodes %D/bs %D",stride,nbnodes,bs); 1055 ierr = PetscFree(fid_glid_loc);CHKERRQ(ierr); 1056 } else { 1057 ierr = PetscMalloc1(nloc, &flid_fgid);CHKERRQ(ierr); 1058 for (kk=0; kk<nloc; kk++) flid_fgid[kk] = my0 + kk; 1059 } 1060 #if defined PETSC_GAMG_USE_LOG 1061 ierr = PetscLogEventEnd(petsc_gamg_setup_events[SET7],0,0,0,0);CHKERRQ(ierr); 1062 ierr = PetscLogEventBegin(petsc_gamg_setup_events[SET8],0,0,0,0);CHKERRQ(ierr); 1063 #endif 1064 { 1065 PetscReal *data_out = NULL; 1066 ierr = formProl0(agg_lists, bs, col_bs, myCrs0, nbnodes,data_w_ghost, flid_fgid, &data_out, Prol);CHKERRQ(ierr); 1067 ierr = PetscFree(pc_gamg->data);CHKERRQ(ierr); 1068 1069 pc_gamg->data = data_out; 1070 pc_gamg->data_cell_rows = col_bs; 1071 pc_gamg->data_sz = col_bs*col_bs*nLocalSelected; 1072 } 1073 #if defined PETSC_GAMG_USE_LOG 1074 ierr = PetscLogEventEnd(petsc_gamg_setup_events[SET8],0,0,0,0);CHKERRQ(ierr); 1075 #endif 1076 if (size > 1) {ierr = PetscFree(data_w_ghost);CHKERRQ(ierr);} 1077 ierr = PetscFree(flid_fgid);CHKERRQ(ierr); 1078 1079 *a_P_out = Prol; /* out */ 1080 1081 ierr = PetscLogEventEnd(PC_GAMGProlongator_AGG,0,0,0,0);CHKERRQ(ierr); 1082 PetscFunctionReturn(0); 1083 } 1084 1085 /* -------------------------------------------------------------------------- */ 1086 /* 1087 PCGAMGOptProlongator_AGG 1088 1089 Input Parameter: 1090 . pc - this 1091 . Amat - matrix on this fine level 1092 In/Output Parameter: 1093 . a_P - prolongation operator to the next level 1094 */ 1095 static PetscErrorCode PCGAMGOptProlongator_AGG(PC pc,Mat Amat,Mat *a_P) 1096 { 1097 PetscErrorCode ierr; 1098 PC_MG *mg = (PC_MG*)pc->data; 1099 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 1100 PC_GAMG_AGG *pc_gamg_agg = (PC_GAMG_AGG*)pc_gamg->subctx; 1101 PetscInt jj; 1102 Mat Prol = *a_P; 1103 MPI_Comm comm; 1104 KSP eksp; 1105 Vec bb, xx; 1106 PC epc; 1107 PetscReal alpha, emax, emin; 1108 PetscRandom random; 1109 1110 PetscFunctionBegin; 1111 ierr = PetscObjectGetComm((PetscObject)Amat,&comm);CHKERRQ(ierr); 1112 ierr = PetscLogEventBegin(PC_GAMGOptProlongator_AGG,0,0,0,0);CHKERRQ(ierr); 1113 1114 /* compute maximum value of operator to be used in smoother */ 1115 if (0 < pc_gamg_agg->nsmooths) { 1116 ierr = MatCreateVecs(Amat, &bb, 0);CHKERRQ(ierr); 1117 ierr = MatCreateVecs(Amat, &xx, 0);CHKERRQ(ierr); 1118 ierr = PetscRandomCreate(PETSC_COMM_SELF,&random);CHKERRQ(ierr); 1119 ierr = VecSetRandom(bb,random);CHKERRQ(ierr); 1120 ierr = PetscRandomDestroy(&random);CHKERRQ(ierr); 1121 1122 ierr = KSPCreate(comm,&eksp);CHKERRQ(ierr); 1123 ierr = KSPSetTolerances(eksp,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,10);CHKERRQ(ierr); 1124 ierr = KSPSetNormType(eksp, KSP_NORM_NONE);CHKERRQ(ierr); 1125 ierr = KSPSetErrorIfNotConverged(eksp,PETSC_FALSE);CHKERRQ(ierr); 1126 1127 ierr = KSPSetInitialGuessNonzero(eksp, PETSC_FALSE);CHKERRQ(ierr); 1128 ierr = KSPSetOperators(eksp, Amat, Amat);CHKERRQ(ierr); 1129 ierr = KSPSetComputeSingularValues(eksp,PETSC_TRUE);CHKERRQ(ierr); 1130 1131 ierr = KSPGetPC(eksp, &epc);CHKERRQ(ierr); 1132 ierr = PCSetType(epc, PCJACOBI);CHKERRQ(ierr); /* smoother in smoothed agg. */ 1133 1134 ierr = KSPSetOptionsPrefix(eksp,((PetscObject)pc)->prefix);CHKERRQ(ierr); 1135 ierr = KSPAppendOptionsPrefix(eksp, "gamg_est_");CHKERRQ(ierr); 1136 ierr = KSPSetFromOptions(eksp);CHKERRQ(ierr); 1137 1138 /* solve - keep stuff out of logging */ 1139 ierr = PetscLogEventDeactivate(KSP_Solve);CHKERRQ(ierr); 1140 ierr = PetscLogEventDeactivate(PC_Apply);CHKERRQ(ierr); 1141 ierr = KSPSolve(eksp, bb, xx);CHKERRQ(ierr); 1142 ierr = PetscLogEventActivate(KSP_Solve);CHKERRQ(ierr); 1143 ierr = PetscLogEventActivate(PC_Apply);CHKERRQ(ierr); 1144 1145 ierr = KSPComputeExtremeSingularValues(eksp, &emax, &emin);CHKERRQ(ierr); 1146 ierr = PetscInfo3(pc,"Smooth P0: max eigen=%e min=%e PC=%s\n",emax,emin,PCJACOBI);CHKERRQ(ierr); 1147 ierr = VecDestroy(&xx);CHKERRQ(ierr); 1148 ierr = VecDestroy(&bb);CHKERRQ(ierr); 1149 ierr = KSPDestroy(&eksp);CHKERRQ(ierr); 1150 } 1151 1152 /* smooth P0 */ 1153 for (jj = 0; jj < pc_gamg_agg->nsmooths; jj++) { 1154 Mat tMat; 1155 Vec diag; 1156 1157 #if defined PETSC_GAMG_USE_LOG 1158 ierr = PetscLogEventBegin(petsc_gamg_setup_events[SET9],0,0,0,0);CHKERRQ(ierr); 1159 #endif 1160 1161 /* smooth P1 := (I - omega/lam D^{-1}A)P0 */ 1162 ierr = MatMatMult(Amat, Prol, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &tMat);CHKERRQ(ierr); 1163 ierr = MatCreateVecs(Amat, &diag, 0);CHKERRQ(ierr); 1164 ierr = MatGetDiagonal(Amat, diag);CHKERRQ(ierr); /* effectively PCJACOBI */ 1165 ierr = VecReciprocal(diag);CHKERRQ(ierr); 1166 ierr = MatDiagonalScale(tMat, diag, 0);CHKERRQ(ierr); 1167 ierr = VecDestroy(&diag);CHKERRQ(ierr); 1168 alpha = -1.4/emax; 1169 ierr = MatAYPX(tMat, alpha, Prol, SUBSET_NONZERO_PATTERN);CHKERRQ(ierr); 1170 ierr = MatDestroy(&Prol);CHKERRQ(ierr); 1171 Prol = tMat; 1172 #if defined PETSC_GAMG_USE_LOG 1173 ierr = PetscLogEventEnd(petsc_gamg_setup_events[SET9],0,0,0,0);CHKERRQ(ierr); 1174 #endif 1175 } 1176 ierr = PetscLogEventEnd(PC_GAMGOptProlongator_AGG,0,0,0,0);CHKERRQ(ierr); 1177 *a_P = Prol; 1178 PetscFunctionReturn(0); 1179 } 1180 1181 /* -------------------------------------------------------------------------- */ 1182 /* 1183 PCCreateGAMG_AGG 1184 1185 Input Parameter: 1186 . pc - 1187 */ 1188 PetscErrorCode PCCreateGAMG_AGG(PC pc) 1189 { 1190 PetscErrorCode ierr; 1191 PC_MG *mg = (PC_MG*)pc->data; 1192 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 1193 PC_GAMG_AGG *pc_gamg_agg; 1194 1195 PetscFunctionBegin; 1196 /* create sub context for SA */ 1197 ierr = PetscNewLog(pc,&pc_gamg_agg);CHKERRQ(ierr); 1198 pc_gamg->subctx = pc_gamg_agg; 1199 1200 pc_gamg->ops->setfromoptions = PCSetFromOptions_GAMG_AGG; 1201 pc_gamg->ops->destroy = PCDestroy_GAMG_AGG; 1202 /* reset does not do anything; setup not virtual */ 1203 1204 /* set internal function pointers */ 1205 pc_gamg->ops->graph = PCGAMGGraph_AGG; 1206 pc_gamg->ops->coarsen = PCGAMGCoarsen_AGG; 1207 pc_gamg->ops->prolongator = PCGAMGProlongator_AGG; 1208 pc_gamg->ops->optprolongator = PCGAMGOptProlongator_AGG; 1209 pc_gamg->ops->createdefaultdata = PCSetData_AGG; 1210 pc_gamg->ops->view = PCView_GAMG_AGG; 1211 1212 pc_gamg_agg->square_graph = 1; 1213 pc_gamg_agg->sym_graph = PETSC_FALSE; 1214 pc_gamg_agg->nsmooths = 1; 1215 1216 ierr = PetscObjectComposeFunction((PetscObject)pc,"PCGAMGSetNSmooths_C",PCGAMGSetNSmooths_AGG);CHKERRQ(ierr); 1217 ierr = PetscObjectComposeFunction((PetscObject)pc,"PCGAMGSetSymGraph_C",PCGAMGSetSymGraph_AGG);CHKERRQ(ierr); 1218 ierr = PetscObjectComposeFunction((PetscObject)pc,"PCGAMGSetSquareGraph_C",PCGAMGSetSquareGraph_AGG);CHKERRQ(ierr); 1219 ierr = PetscObjectComposeFunction((PetscObject)pc,"PCSetCoordinates_C",PCSetCoordinates_AGG);CHKERRQ(ierr); 1220 PetscFunctionReturn(0); 1221 } 1222