1 /* 2 GAMG geometric-algebric multiogrid PC - Mark Adams 2011 3 */ 4 5 #include <../src/ksp/pc/impls/gamg/gamg.h> /*I "petscpc.h" I*/ 6 7 #if defined(PETSC_HAVE_TRIANGLE) 8 #if !defined(ANSI_DECLARATORS) 9 #define ANSI_DECLARATORS 10 #endif 11 #include <triangle.h> 12 #endif 13 14 #include <petscblaslapack.h> 15 16 /* Private context for the GAMG preconditioner */ 17 typedef struct { 18 PetscInt lid; /* local vertex index */ 19 PetscInt degree; /* vertex degree */ 20 } GAMGNode; 21 22 PETSC_STATIC_INLINE int petsc_geo_mg_compare(const void *a, const void *b) 23 { 24 return (((GAMGNode*)a)->degree - ((GAMGNode*)b)->degree); 25 } 26 27 /* -------------------------------------------------------------------------- */ 28 /* 29 PCSetCoordinates_GEO 30 31 Input Parameter: 32 . pc - the preconditioner context 33 */ 34 PetscErrorCode PCSetCoordinates_GEO(PC pc, PetscInt ndm, PetscInt a_nloc, PetscReal *coords) 35 { 36 PC_MG *mg = (PC_MG*)pc->data; 37 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 38 PetscErrorCode ierr; 39 PetscInt arrsz,bs,my0,kk,ii,nloc,Iend,aloc; 40 Mat Amat = pc->pmat; 41 42 PetscFunctionBegin; 43 PetscValidHeaderSpecific(Amat, MAT_CLASSID, 1); 44 ierr = MatGetBlockSize(Amat, &bs);CHKERRQ(ierr); 45 ierr = MatGetOwnershipRange(Amat, &my0, &Iend);CHKERRQ(ierr); 46 aloc = (Iend-my0); 47 nloc = (Iend-my0)/bs; 48 49 if (nloc!=a_nloc && aloc!=a_nloc) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Number of local blocks %D must be %D or %D.",a_nloc,nloc,aloc); 50 51 pc_gamg->data_cell_rows = 1; 52 if (!coords && nloc > 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG, "Need coordinates for pc_gamg_type 'geo'."); 53 pc_gamg->data_cell_cols = ndm; /* coordinates */ 54 55 arrsz = nloc*pc_gamg->data_cell_rows*pc_gamg->data_cell_cols; 56 57 /* create data - syntactic sugar that should be refactored at some point */ 58 if (!pc_gamg->data || (pc_gamg->data_sz != arrsz)) { 59 ierr = PetscFree(pc_gamg->data);CHKERRQ(ierr); 60 ierr = PetscMalloc1(arrsz+1, &pc_gamg->data);CHKERRQ(ierr); 61 } 62 for (kk=0; kk<arrsz; kk++) pc_gamg->data[kk] = -999.; 63 pc_gamg->data[arrsz] = -99.; 64 /* copy data in - column oriented */ 65 if (nloc == a_nloc) { 66 for (kk = 0; kk < nloc; kk++) { 67 for (ii = 0; ii < ndm; ii++) { 68 pc_gamg->data[ii*nloc + kk] = coords[kk*ndm + ii]; 69 } 70 } 71 } else { /* assumes the coordinates are blocked */ 72 for (kk = 0; kk < nloc; kk++) { 73 for (ii = 0; ii < ndm; ii++) { 74 pc_gamg->data[ii*nloc + kk] = coords[bs*kk*ndm + ii]; 75 } 76 } 77 } 78 if (pc_gamg->data[arrsz] != -99.) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"pc_gamg->data[arrsz %D] %g != -99.",arrsz,pc_gamg->data[arrsz]); 79 pc_gamg->data_sz = arrsz; 80 PetscFunctionReturn(0); 81 } 82 83 /* -------------------------------------------------------------------------- */ 84 /* 85 PCSetData_GEO 86 87 Input Parameter: 88 . pc - 89 */ 90 PetscErrorCode PCSetData_GEO(PC pc, Mat m) 91 { 92 PetscFunctionBegin; 93 SETERRQ(PetscObjectComm((PetscObject)pc),PETSC_ERR_PLIB,"GEO MG needs coordinates"); 94 } 95 96 /* -------------------------------------------------------------------------- */ 97 /* 98 PCSetFromOptions_GEO 99 100 Input Parameter: 101 . pc - 102 */ 103 PetscErrorCode PCSetFromOptions_GEO(PetscOptionItems *PetscOptionsObject,PC pc) 104 { 105 PetscErrorCode ierr; 106 107 PetscFunctionBegin; 108 ierr = PetscOptionsHead(PetscOptionsObject,"GAMG-GEO options");CHKERRQ(ierr); 109 { 110 /* -pc_gamg_sa_nsmooths */ 111 /* pc_gamg_sa->smooths = 0; */ 112 /* ierr = PetscOptionsInt("-pc_gamg_agg_nsmooths", */ 113 /* "smoothing steps for smoothed aggregation, usually 1 (0)", */ 114 /* "PCGAMGSetNSmooths_AGG", */ 115 /* pc_gamg_sa->smooths, */ 116 /* &pc_gamg_sa->smooths, */ 117 /* &flag); */ 118 /* CHKERRQ(ierr); */ 119 } 120 ierr = PetscOptionsTail();CHKERRQ(ierr); 121 PetscFunctionReturn(0); 122 } 123 124 /* -------------------------------------------------------------------------- */ 125 /* 126 triangulateAndFormProl 127 128 Input Parameter: 129 . selected_2 - list of selected local ID, includes selected ghosts 130 . data_stride - 131 . coords[2*data_stride] - column vector of local coordinates w/ ghosts 132 . nselected_1 - selected IDs that go with base (1) graph includes selected ghosts 133 . clid_lid_1[nselected_1] - lids of selected (c) nodes ??????????? 134 . agg_lists_1 - list of aggregates selected_1 vertices of aggregate unselected vertices 135 . crsGID[selected.size()] - global index for prolongation operator 136 . bs - block size 137 Output Parameter: 138 . a_Prol - prolongation operator 139 . a_worst_best - measure of worst missed fine vertex, 0 is no misses 140 */ 141 static PetscErrorCode triangulateAndFormProl(IS selected_2,PetscInt data_stride,PetscReal coords[],PetscInt nselected_1,const PetscInt clid_lid_1[],const PetscCoarsenData *agg_lists_1, 142 const PetscInt crsGID[],PetscInt bs,Mat a_Prol,PetscReal *a_worst_best) 143 { 144 #if defined(PETSC_HAVE_TRIANGLE) 145 PetscErrorCode ierr; 146 PetscInt jj,tid,tt,idx,nselected_2; 147 struct triangulateio in,mid; 148 const PetscInt *selected_idx_2; 149 PetscMPIInt rank; 150 PetscInt Istart,Iend,nFineLoc,myFine0; 151 int kk,nPlotPts,sid; 152 MPI_Comm comm; 153 PetscReal tm; 154 155 PetscFunctionBegin; 156 ierr = PetscObjectGetComm((PetscObject)a_Prol,&comm);CHKERRQ(ierr); 157 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 158 ierr = ISGetSize(selected_2, &nselected_2);CHKERRQ(ierr); 159 if (nselected_2 == 1 || nselected_2 == 2) { /* 0 happens on idle processors */ 160 *a_worst_best = 100.0; /* this will cause a stop, but not globalized (should not happen) */ 161 } else *a_worst_best = 0.0; 162 ierr = MPIU_Allreduce(a_worst_best, &tm, 1, MPIU_REAL, MPIU_MAX, comm);CHKERRQ(ierr); 163 if (tm > 0.0) { 164 *a_worst_best = 100.0; 165 PetscFunctionReturn(0); 166 } 167 ierr = MatGetOwnershipRange(a_Prol, &Istart, &Iend);CHKERRQ(ierr); 168 nFineLoc = (Iend-Istart)/bs; myFine0 = Istart/bs; 169 nPlotPts = nFineLoc; /* locals */ 170 /* traingle */ 171 /* Define input points - in*/ 172 in.numberofpoints = nselected_2; 173 in.numberofpointattributes = 0; 174 /* get nselected points */ 175 ierr = PetscMalloc1(2*nselected_2, &in.pointlist);CHKERRQ(ierr); 176 ierr = ISGetIndices(selected_2, &selected_idx_2);CHKERRQ(ierr); 177 178 for (kk=0,sid=0; kk<nselected_2; kk++,sid += 2) { 179 PetscInt lid = selected_idx_2[kk]; 180 in.pointlist[sid] = coords[lid]; 181 in.pointlist[sid+1] = coords[data_stride + lid]; 182 if (lid>=nFineLoc) nPlotPts++; 183 } 184 if (sid != 2*nselected_2) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"sid %D != 2*nselected_2 %D",sid,nselected_2); 185 186 in.numberofsegments = 0; 187 in.numberofedges = 0; 188 in.numberofholes = 0; 189 in.numberofregions = 0; 190 in.trianglelist = 0; 191 in.segmentmarkerlist = 0; 192 in.pointattributelist = 0; 193 in.pointmarkerlist = 0; 194 in.triangleattributelist = 0; 195 in.trianglearealist = 0; 196 in.segmentlist = 0; 197 in.holelist = 0; 198 in.regionlist = 0; 199 in.edgelist = 0; 200 in.edgemarkerlist = 0; 201 in.normlist = 0; 202 203 /* triangulate */ 204 mid.pointlist = 0; /* Not needed if -N switch used. */ 205 /* Not needed if -N switch used or number of point attributes is zero: */ 206 mid.pointattributelist = 0; 207 mid.pointmarkerlist = 0; /* Not needed if -N or -B switch used. */ 208 mid.trianglelist = 0; /* Not needed if -E switch used. */ 209 /* Not needed if -E switch used or number of triangle attributes is zero: */ 210 mid.triangleattributelist = 0; 211 mid.neighborlist = 0; /* Needed only if -n switch used. */ 212 /* Needed only if segments are output (-p or -c) and -P not used: */ 213 mid.segmentlist = 0; 214 /* Needed only if segments are output (-p or -c) and -P and -B not used: */ 215 mid.segmentmarkerlist = 0; 216 mid.edgelist = 0; /* Needed only if -e switch used. */ 217 mid.edgemarkerlist = 0; /* Needed if -e used and -B not used. */ 218 mid.numberoftriangles = 0; 219 220 /* Triangulate the points. Switches are chosen to read and write a */ 221 /* PSLG (p), preserve the convex hull (c), number everything from */ 222 /* zero (z), assign a regional attribute to each element (A), and */ 223 /* produce an edge list (e), a Voronoi diagram (v), and a triangle */ 224 /* neighbor list (n). */ 225 if (nselected_2 != 0) { /* inactive processor */ 226 char args[] = "npczQ"; /* c is needed ? */ 227 triangulate(args, &in, &mid, (struct triangulateio*) NULL); 228 /* output .poly files for 'showme' */ 229 if (!PETSC_TRUE) { 230 static int level = 1; 231 FILE *file; char fname[32]; 232 233 sprintf(fname,"C%d_%d.poly",level,rank); file = fopen(fname, "w"); 234 /*First line: <# of vertices> <dimension (must be 2)> <# of attributes> <# of boundary markers (0 or 1)>*/ 235 fprintf(file, "%d %d %d %d\n",in.numberofpoints,2,0,0); 236 /*Following lines: <vertex #> <x> <y> */ 237 for (kk=0,sid=0; kk<in.numberofpoints; kk++,sid += 2) { 238 fprintf(file, "%d %e %e\n",kk,in.pointlist[sid],in.pointlist[sid+1]); 239 } 240 /*One line: <# of segments> <# of boundary markers (0 or 1)> */ 241 fprintf(file, "%d %d\n",0,0); 242 /*Following lines: <segment #> <endpoint> <endpoint> [boundary marker] */ 243 /* One line: <# of holes> */ 244 fprintf(file, "%d\n",0); 245 /* Following lines: <hole #> <x> <y> */ 246 /* Optional line: <# of regional attributes and/or area constraints> */ 247 /* Optional following lines: <region #> <x> <y> <attribute> <maximum area> */ 248 fclose(file); 249 250 /* elems */ 251 sprintf(fname,"C%d_%d.ele",level,rank); file = fopen(fname, "w"); 252 /* First line: <# of triangles> <nodes per triangle> <# of attributes> */ 253 fprintf(file, "%d %d %d\n",mid.numberoftriangles,3,0); 254 /* Remaining lines: <triangle #> <node> <node> <node> ... [attributes] */ 255 for (kk=0,sid=0; kk<mid.numberoftriangles; kk++,sid += 3) { 256 fprintf(file, "%d %d %d %d\n",kk,mid.trianglelist[sid],mid.trianglelist[sid+1],mid.trianglelist[sid+2]); 257 } 258 fclose(file); 259 260 sprintf(fname,"C%d_%d.node",level,rank); file = fopen(fname, "w"); 261 /* First line: <# of vertices> <dimension (must be 2)> <# of attributes> <# of boundary markers (0 or 1)> */ 262 /* fprintf(file, "%d %d %d %d\n",in.numberofpoints,2,0,0); */ 263 fprintf(file, "%d %d %d %d\n",nPlotPts,2,0,0); 264 /*Following lines: <vertex #> <x> <y> */ 265 for (kk=0,sid=0; kk<in.numberofpoints; kk++,sid+=2) { 266 fprintf(file, "%d %e %e\n",kk,in.pointlist[sid],in.pointlist[sid+1]); 267 } 268 269 sid /= 2; 270 for (jj=0; jj<nFineLoc; jj++) { 271 PetscBool sel = PETSC_TRUE; 272 for (kk=0; kk<nselected_2 && sel; kk++) { 273 PetscInt lid = selected_idx_2[kk]; 274 if (lid == jj) sel = PETSC_FALSE; 275 } 276 if (sel) fprintf(file, "%d %e %e\n",sid++,coords[jj],coords[data_stride + jj]); 277 } 278 fclose(file); 279 if (sid != nPlotPts) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"sid %D != nPlotPts %D",sid,nPlotPts); 280 level++; 281 } 282 } 283 #if defined PETSC_GAMG_USE_LOG 284 ierr = PetscLogEventBegin(petsc_gamg_setup_events[FIND_V],0,0,0,0);CHKERRQ(ierr); 285 #endif 286 { /* form P - setup some maps */ 287 PetscInt clid,mm,*nTri,*node_tri; 288 289 ierr = PetscMalloc2(nselected_2, &node_tri,nselected_2, &nTri);CHKERRQ(ierr); 290 291 /* need list of triangles on node */ 292 for (kk=0; kk<nselected_2; kk++) nTri[kk] = 0; 293 for (tid=0,kk=0; tid<mid.numberoftriangles; tid++) { 294 for (jj=0; jj<3; jj++) { 295 PetscInt cid = mid.trianglelist[kk++]; 296 if (nTri[cid] == 0) node_tri[cid] = tid; 297 nTri[cid]++; 298 } 299 } 300 #define EPS 1.e-12 301 /* find points and set prolongation */ 302 for (mm = clid = 0; mm < nFineLoc; mm++) { 303 PetscBool ise; 304 ierr = PetscCDEmptyAt(agg_lists_1,mm,&ise);CHKERRQ(ierr); 305 if (!ise) { 306 const PetscInt lid = mm; 307 PetscScalar AA[3][3]; 308 PetscBLASInt N=3,NRHS=1,LDA=3,IPIV[3],LDB=3,INFO; 309 PetscCDIntNd *pos; 310 311 ierr = PetscCDGetHeadPos(agg_lists_1,lid,&pos);CHKERRQ(ierr); 312 while (pos) { 313 PetscInt flid; 314 ierr = PetscCDIntNdGetID(pos, &flid);CHKERRQ(ierr); 315 ierr = PetscCDGetNextPos(agg_lists_1,lid,&pos);CHKERRQ(ierr); 316 317 if (flid < nFineLoc) { /* could be a ghost */ 318 PetscInt bestTID = -1; PetscReal best_alpha = 1.e10; 319 const PetscInt fgid = flid + myFine0; 320 /* compute shape function for gid */ 321 const PetscReal fcoord[3] = {coords[flid],coords[data_stride+flid],1.0}; 322 PetscBool haveit =PETSC_FALSE; PetscScalar alpha[3]; PetscInt clids[3]; 323 324 /* look for it */ 325 for (tid = node_tri[clid], jj=0; 326 jj < 5 && !haveit && tid != -1; 327 jj++) { 328 for (tt=0; tt<3; tt++) { 329 PetscInt cid2 = mid.trianglelist[3*tid + tt]; 330 PetscInt lid2 = selected_idx_2[cid2]; 331 AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0; 332 clids[tt] = cid2; /* store for interp */ 333 } 334 335 for (tt=0; tt<3; tt++) alpha[tt] = (PetscScalar)fcoord[tt]; 336 337 /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */ 338 PetscStackCallBLAS("LAPACKgesv",LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO)); 339 { 340 PetscBool have=PETSC_TRUE; PetscReal lowest=1.e10; 341 for (tt = 0, idx = 0; tt < 3; tt++) { 342 if (PetscRealPart(alpha[tt]) > (1.0+EPS) || PetscRealPart(alpha[tt]) < -EPS) have = PETSC_FALSE; 343 if (PetscRealPart(alpha[tt]) < lowest) { 344 lowest = PetscRealPart(alpha[tt]); 345 idx = tt; 346 } 347 } 348 haveit = have; 349 } 350 tid = mid.neighborlist[3*tid + idx]; 351 } 352 353 if (!haveit) { 354 /* brute force */ 355 for (tid=0; tid<mid.numberoftriangles && !haveit; tid++) { 356 for (tt=0; tt<3; tt++) { 357 PetscInt cid2 = mid.trianglelist[3*tid + tt]; 358 PetscInt lid2 = selected_idx_2[cid2]; 359 AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0; 360 clids[tt] = cid2; /* store for interp */ 361 } 362 for (tt=0; tt<3; tt++) alpha[tt] = fcoord[tt]; 363 /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */ 364 PetscStackCallBLAS("LAPACKgesv",LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO)); 365 { 366 PetscBool have=PETSC_TRUE; PetscReal worst=0.0, v; 367 for (tt=0; tt<3 && have; tt++) { 368 if (PetscRealPart(alpha[tt]) > 1.0+EPS || PetscRealPart(alpha[tt]) < -EPS) have=PETSC_FALSE; 369 if ((v=PetscAbs(PetscRealPart(alpha[tt])-0.5)) > worst) worst = v; 370 } 371 if (worst < best_alpha) { 372 best_alpha = worst; bestTID = tid; 373 } 374 haveit = have; 375 } 376 } 377 } 378 if (!haveit) { 379 if (best_alpha > *a_worst_best) *a_worst_best = best_alpha; 380 /* use best one */ 381 for (tt=0; tt<3; tt++) { 382 PetscInt cid2 = mid.trianglelist[3*bestTID + tt]; 383 PetscInt lid2 = selected_idx_2[cid2]; 384 AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0; 385 clids[tt] = cid2; /* store for interp */ 386 } 387 for (tt=0; tt<3; tt++) alpha[tt] = fcoord[tt]; 388 /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */ 389 PetscStackCallBLAS("LAPACKgesv",LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO)); 390 } 391 392 /* put in row of P */ 393 for (idx=0; idx<3; idx++) { 394 PetscScalar shp = alpha[idx]; 395 if (PetscAbs(PetscRealPart(shp)) > 1.e-6) { 396 PetscInt cgid = crsGID[clids[idx]]; 397 PetscInt jj = cgid*bs, ii = fgid*bs; /* need to gloalize */ 398 for (tt=0; tt < bs; tt++, ii++, jj++) { 399 ierr = MatSetValues(a_Prol,1,&ii,1,&jj,&shp,INSERT_VALUES);CHKERRQ(ierr); 400 } 401 } 402 } 403 } 404 } /* aggregates iterations */ 405 clid++; 406 } /* a coarse agg */ 407 } /* for all fine nodes */ 408 409 ierr = ISRestoreIndices(selected_2, &selected_idx_2);CHKERRQ(ierr); 410 ierr = MatAssemblyBegin(a_Prol,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 411 ierr = MatAssemblyEnd(a_Prol,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 412 413 ierr = PetscFree2(node_tri,nTri);CHKERRQ(ierr); 414 } 415 #if defined PETSC_GAMG_USE_LOG 416 ierr = PetscLogEventEnd(petsc_gamg_setup_events[FIND_V],0,0,0,0);CHKERRQ(ierr); 417 #endif 418 free(mid.trianglelist); 419 free(mid.neighborlist); 420 ierr = PetscFree(in.pointlist);CHKERRQ(ierr); 421 PetscFunctionReturn(0); 422 #else 423 SETERRQ(PetscObjectComm((PetscObject)a_Prol),PETSC_ERR_PLIB,"configure with TRIANGLE to use geometric MG"); 424 #endif 425 } 426 /* -------------------------------------------------------------------------- */ 427 /* 428 getGIDsOnSquareGraph - square graph, get 429 430 Input Parameter: 431 . nselected_1 - selected local indices (includes ghosts in input Gmat1) 432 . clid_lid_1 - [nselected_1] lids of selected nodes 433 . Gmat1 - graph that goes with 'selected_1' 434 Output Parameter: 435 . a_selected_2 - selected local indices (includes ghosts in output a_Gmat_2) 436 . a_Gmat_2 - graph that is squared of 'Gmat_1' 437 . a_crsGID[a_selected_2.size()] - map of global IDs of coarse grid nodes 438 */ 439 static PetscErrorCode getGIDsOnSquareGraph(PetscInt nselected_1,const PetscInt clid_lid_1[],const Mat Gmat1,IS *a_selected_2,Mat *a_Gmat_2,PetscInt **a_crsGID) 440 { 441 PetscErrorCode ierr; 442 PetscMPIInt size; 443 PetscInt *crsGID, kk,my0,Iend,nloc; 444 MPI_Comm comm; 445 446 PetscFunctionBegin; 447 ierr = PetscObjectGetComm((PetscObject)Gmat1,&comm);CHKERRQ(ierr); 448 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 449 ierr = MatGetOwnershipRange(Gmat1,&my0,&Iend);CHKERRQ(ierr); /* AIJ */ 450 nloc = Iend - my0; /* this does not change */ 451 452 if (size == 1) { /* not much to do in serial */ 453 ierr = PetscMalloc1(nselected_1, &crsGID);CHKERRQ(ierr); 454 for (kk=0; kk<nselected_1; kk++) crsGID[kk] = kk; 455 *a_Gmat_2 = 0; 456 ierr = ISCreateGeneral(PETSC_COMM_SELF,nselected_1,clid_lid_1,PETSC_COPY_VALUES,a_selected_2);CHKERRQ(ierr); 457 } else { 458 PetscInt idx,num_fine_ghosts,num_crs_ghost,myCrs0; 459 Mat_MPIAIJ *mpimat2; 460 Mat Gmat2; 461 Vec locState; 462 PetscScalar *cpcol_state; 463 464 /* scan my coarse zero gid, set 'lid_state' with coarse GID */ 465 kk = nselected_1; 466 ierr = MPI_Scan(&kk, &myCrs0, 1, MPIU_INT, MPI_SUM, comm);CHKERRQ(ierr); 467 myCrs0 -= nselected_1; 468 469 if (a_Gmat_2) { /* output */ 470 /* grow graph to get wider set of selected vertices to cover fine grid, invalidates 'llist' */ 471 ierr = MatTransposeMatMult(Gmat1, Gmat1, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &Gmat2);CHKERRQ(ierr); 472 *a_Gmat_2 = Gmat2; /* output */ 473 } else Gmat2 = Gmat1; /* use local to get crsGIDs at least */ 474 /* get coarse grid GIDS for selected (locals and ghosts) */ 475 mpimat2 = (Mat_MPIAIJ*)Gmat2->data; 476 ierr = MatCreateVecs(Gmat2, &locState, 0);CHKERRQ(ierr); 477 ierr = VecSet(locState, (PetscScalar)(PetscReal)(-1));CHKERRQ(ierr); /* set with UNKNOWN state */ 478 for (kk=0; kk<nselected_1; kk++) { 479 PetscInt fgid = clid_lid_1[kk] + my0; 480 PetscScalar v = (PetscScalar)(kk+myCrs0); 481 ierr = VecSetValues(locState, 1, &fgid, &v, INSERT_VALUES);CHKERRQ(ierr); /* set with PID */ 482 } 483 ierr = VecAssemblyBegin(locState);CHKERRQ(ierr); 484 ierr = VecAssemblyEnd(locState);CHKERRQ(ierr); 485 ierr = VecScatterBegin(mpimat2->Mvctx,locState,mpimat2->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 486 ierr = VecScatterEnd(mpimat2->Mvctx,locState,mpimat2->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 487 ierr = VecGetLocalSize(mpimat2->lvec, &num_fine_ghosts);CHKERRQ(ierr); 488 ierr = VecGetArray(mpimat2->lvec, &cpcol_state);CHKERRQ(ierr); 489 for (kk=0,num_crs_ghost=0; kk<num_fine_ghosts; kk++) { 490 if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) num_crs_ghost++; 491 } 492 ierr = PetscMalloc1(nselected_1+num_crs_ghost, &crsGID);CHKERRQ(ierr); /* output */ 493 { 494 PetscInt *selected_set; 495 ierr = PetscMalloc1(nselected_1+num_crs_ghost, &selected_set);CHKERRQ(ierr); 496 /* do ghost of 'crsGID' */ 497 for (kk=0,idx=nselected_1; kk<num_fine_ghosts; kk++) { 498 if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) { 499 PetscInt cgid = (PetscInt)PetscRealPart(cpcol_state[kk]); 500 selected_set[idx] = nloc + kk; 501 crsGID[idx++] = cgid; 502 } 503 } 504 if (idx != (nselected_1+num_crs_ghost)) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"idx %D != (nselected_1 %D + num_crs_ghost %D)",idx,nselected_1,num_crs_ghost); 505 ierr = VecRestoreArray(mpimat2->lvec, &cpcol_state);CHKERRQ(ierr); 506 /* do locals in 'crsGID' */ 507 ierr = VecGetArray(locState, &cpcol_state);CHKERRQ(ierr); 508 for (kk=0,idx=0; kk<nloc; kk++) { 509 if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) { 510 PetscInt cgid = (PetscInt)PetscRealPart(cpcol_state[kk]); 511 selected_set[idx] = kk; 512 crsGID[idx++] = cgid; 513 } 514 } 515 if (idx != nselected_1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"idx %D != nselected_1 %D",idx,nselected_1); 516 ierr = VecRestoreArray(locState, &cpcol_state);CHKERRQ(ierr); 517 518 if (a_selected_2 != 0) { /* output */ 519 ierr = ISCreateGeneral(PETSC_COMM_SELF,(nselected_1+num_crs_ghost),selected_set,PETSC_OWN_POINTER,a_selected_2);CHKERRQ(ierr); 520 } else { 521 ierr = PetscFree(selected_set);CHKERRQ(ierr); 522 } 523 } 524 ierr = VecDestroy(&locState);CHKERRQ(ierr); 525 } 526 *a_crsGID = crsGID; /* output */ 527 PetscFunctionReturn(0); 528 } 529 530 /* -------------------------------------------------------------------------- */ 531 /* 532 PCGAMGGraph_GEO 533 534 Input Parameter: 535 . pc - this 536 . Amat - matrix on this fine level 537 Output Parameter: 538 . a_Gmat 539 */ 540 PetscErrorCode PCGAMGGraph_GEO(PC pc,Mat Amat,Mat *a_Gmat) 541 { 542 PetscErrorCode ierr; 543 PC_MG *mg = (PC_MG*)pc->data; 544 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 545 const PetscReal vfilter = pc_gamg->threshold[0]; 546 MPI_Comm comm; 547 Mat Gmat; 548 PetscBool set,flg,symm; 549 550 PetscFunctionBegin; 551 ierr = PetscObjectGetComm((PetscObject)Amat,&comm);CHKERRQ(ierr); 552 ierr = PetscLogEventBegin(PC_GAMGGraph_GEO,0,0,0,0);CHKERRQ(ierr); 553 554 ierr = MatIsSymmetricKnown(Amat, &set, &flg);CHKERRQ(ierr); 555 symm = (PetscBool)!(set && flg); 556 557 ierr = PCGAMGCreateGraph(Amat, &Gmat);CHKERRQ(ierr); 558 ierr = PCGAMGFilterGraph(&Gmat, vfilter, symm);CHKERRQ(ierr); 559 560 *a_Gmat = Gmat; 561 ierr = PetscLogEventEnd(PC_GAMGGraph_GEO,0,0,0,0);CHKERRQ(ierr); 562 PetscFunctionReturn(0); 563 } 564 565 /* -------------------------------------------------------------------------- */ 566 /* 567 PCGAMGCoarsen_GEO 568 569 Input Parameter: 570 . a_pc - this 571 . a_Gmat - graph 572 Output Parameter: 573 . a_llist_parent - linked list from selected indices for data locality only 574 */ 575 PetscErrorCode PCGAMGCoarsen_GEO(PC a_pc,Mat *a_Gmat,PetscCoarsenData **a_llist_parent) 576 { 577 PetscErrorCode ierr; 578 PetscInt Istart,Iend,nloc,kk,Ii,ncols; 579 IS perm; 580 GAMGNode *gnodes; 581 PetscInt *permute; 582 Mat Gmat = *a_Gmat; 583 MPI_Comm comm; 584 MatCoarsen crs; 585 586 PetscFunctionBegin; 587 ierr = PetscObjectGetComm((PetscObject)a_pc,&comm);CHKERRQ(ierr); 588 ierr = PetscLogEventBegin(PC_GAMGCoarsen_GEO,0,0,0,0);CHKERRQ(ierr); 589 ierr = MatGetOwnershipRange(Gmat, &Istart, &Iend);CHKERRQ(ierr); 590 nloc = (Iend-Istart); 591 592 /* create random permutation with sort for geo-mg */ 593 ierr = PetscMalloc1(nloc, &gnodes);CHKERRQ(ierr); 594 ierr = PetscMalloc1(nloc, &permute);CHKERRQ(ierr); 595 596 for (Ii=Istart; Ii<Iend; Ii++) { /* locals only? */ 597 ierr = MatGetRow(Gmat,Ii,&ncols,0,0);CHKERRQ(ierr); 598 { 599 PetscInt lid = Ii - Istart; 600 gnodes[lid].lid = lid; 601 gnodes[lid].degree = ncols; 602 } 603 ierr = MatRestoreRow(Gmat,Ii,&ncols,0,0);CHKERRQ(ierr); 604 } 605 if (PETSC_TRUE) { 606 PetscRandom rand; 607 PetscBool *bIndexSet; 608 PetscReal rr; 609 PetscInt iSwapIndex; 610 611 ierr = PetscRandomCreate(comm,&rand);CHKERRQ(ierr); 612 ierr = PetscCalloc1(nloc, &bIndexSet);CHKERRQ(ierr); 613 for (Ii = 0; Ii < nloc; Ii++) { 614 ierr = PetscRandomGetValueReal(rand,&rr);CHKERRQ(ierr); 615 iSwapIndex = (PetscInt) (rr*nloc); 616 if (!bIndexSet[iSwapIndex] && iSwapIndex != Ii) { 617 GAMGNode iTemp = gnodes[iSwapIndex]; 618 gnodes[iSwapIndex] = gnodes[Ii]; 619 gnodes[Ii] = iTemp; 620 bIndexSet[Ii] = PETSC_TRUE; 621 bIndexSet[iSwapIndex] = PETSC_TRUE; 622 } 623 } 624 ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr); 625 ierr = PetscFree(bIndexSet);CHKERRQ(ierr); 626 } 627 /* only sort locals */ 628 qsort(gnodes, nloc, sizeof(GAMGNode), petsc_geo_mg_compare); 629 /* create IS of permutation */ 630 for (kk=0; kk<nloc; kk++) permute[kk] = gnodes[kk].lid; /* locals only */ 631 ierr = PetscFree(gnodes);CHKERRQ(ierr); 632 ierr = ISCreateGeneral(PETSC_COMM_SELF, nloc, permute, PETSC_OWN_POINTER, &perm);CHKERRQ(ierr); 633 634 /* get MIS aggs */ 635 636 ierr = MatCoarsenCreate(comm, &crs);CHKERRQ(ierr); 637 ierr = MatCoarsenSetType(crs, MATCOARSENMIS);CHKERRQ(ierr); 638 ierr = MatCoarsenSetGreedyOrdering(crs, perm);CHKERRQ(ierr); 639 ierr = MatCoarsenSetAdjacency(crs, Gmat);CHKERRQ(ierr); 640 ierr = MatCoarsenSetStrictAggs(crs, PETSC_FALSE);CHKERRQ(ierr); 641 ierr = MatCoarsenApply(crs);CHKERRQ(ierr); 642 ierr = MatCoarsenGetData(crs, a_llist_parent);CHKERRQ(ierr); 643 ierr = MatCoarsenDestroy(&crs);CHKERRQ(ierr); 644 645 ierr = ISDestroy(&perm);CHKERRQ(ierr); 646 ierr = PetscLogEventEnd(PC_GAMGCoarsen_GEO,0,0,0,0);CHKERRQ(ierr); 647 PetscFunctionReturn(0); 648 } 649 650 /* -------------------------------------------------------------------------- */ 651 /* 652 PCGAMGProlongator_GEO 653 654 Input Parameter: 655 . pc - this 656 . Amat - matrix on this fine level 657 . Graph - used to get ghost data for nodes in 658 . selected_1 - [nselected] 659 . agg_lists - [nselected] 660 Output Parameter: 661 . a_P_out - prolongation operator to the next level 662 */ 663 PetscErrorCode PCGAMGProlongator_GEO(PC pc,Mat Amat,Mat Gmat,PetscCoarsenData *agg_lists,Mat *a_P_out) 664 { 665 PC_MG *mg = (PC_MG*)pc->data; 666 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 667 const PetscInt dim = pc_gamg->data_cell_cols, data_cols = pc_gamg->data_cell_cols; 668 PetscErrorCode ierr; 669 PetscInt Istart,Iend,nloc,my0,jj,kk,ncols,nLocalSelected,bs,*clid_flid; 670 Mat Prol; 671 PetscMPIInt rank, size; 672 MPI_Comm comm; 673 IS selected_2,selected_1; 674 const PetscInt *selected_idx; 675 MatType mtype; 676 677 PetscFunctionBegin; 678 ierr = PetscObjectGetComm((PetscObject)Amat,&comm);CHKERRQ(ierr); 679 ierr = PetscLogEventBegin(PC_GAMGProlongator_GEO,0,0,0,0);CHKERRQ(ierr); 680 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 681 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 682 ierr = MatGetOwnershipRange(Amat, &Istart, &Iend);CHKERRQ(ierr); 683 ierr = MatGetBlockSize(Amat, &bs);CHKERRQ(ierr); 684 nloc = (Iend-Istart)/bs; my0 = Istart/bs; 685 if ((Iend-Istart) % bs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"(Iend %D - Istart %D) % bs %D",Iend,Istart,bs); 686 687 /* get 'nLocalSelected' */ 688 ierr = PetscCDGetMIS(agg_lists, &selected_1);CHKERRQ(ierr); 689 ierr = ISGetSize(selected_1, &jj);CHKERRQ(ierr); 690 ierr = PetscMalloc1(jj, &clid_flid);CHKERRQ(ierr); 691 ierr = ISGetIndices(selected_1, &selected_idx);CHKERRQ(ierr); 692 for (kk=0,nLocalSelected=0; kk<jj; kk++) { 693 PetscInt lid = selected_idx[kk]; 694 if (lid<nloc) { 695 ierr = MatGetRow(Gmat,lid+my0,&ncols,0,0);CHKERRQ(ierr); 696 if (ncols>1) clid_flid[nLocalSelected++] = lid; /* fiter out singletons */ 697 ierr = MatRestoreRow(Gmat,lid+my0,&ncols,0,0);CHKERRQ(ierr); 698 } 699 } 700 ierr = ISRestoreIndices(selected_1, &selected_idx);CHKERRQ(ierr); 701 ierr = ISDestroy(&selected_1);CHKERRQ(ierr); /* this is selected_1 in serial */ 702 703 /* create prolongator matrix */ 704 ierr = MatGetType(Amat,&mtype);CHKERRQ(ierr); 705 ierr = MatCreate(comm, &Prol);CHKERRQ(ierr); 706 ierr = MatSetSizes(Prol,nloc*bs,nLocalSelected*bs,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 707 ierr = MatSetBlockSizes(Prol, bs, bs);CHKERRQ(ierr); 708 ierr = MatSetType(Prol, mtype);CHKERRQ(ierr); 709 ierr = MatSeqAIJSetPreallocation(Prol,3*data_cols,NULL);CHKERRQ(ierr); 710 ierr = MatMPIAIJSetPreallocation(Prol,3*data_cols,NULL,3*data_cols,NULL);CHKERRQ(ierr); 711 712 /* can get all points "removed" - but not on geomg */ 713 ierr = MatGetSize(Prol, &kk, &jj);CHKERRQ(ierr); 714 if (!jj) { 715 ierr = PetscInfo(pc,"ERROE: no selected points on coarse grid\n");CHKERRQ(ierr); 716 ierr = PetscFree(clid_flid);CHKERRQ(ierr); 717 ierr = MatDestroy(&Prol);CHKERRQ(ierr); 718 *a_P_out = NULL; /* out */ 719 PetscFunctionReturn(0); 720 } 721 722 { 723 PetscReal *coords; 724 PetscInt data_stride; 725 PetscInt *crsGID = NULL; 726 Mat Gmat2; 727 728 if (dim != data_cols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"dim %D != data_cols %D",dim,data_cols); 729 /* grow ghost data for better coarse grid cover of fine grid */ 730 #if defined PETSC_GAMG_USE_LOG 731 ierr = PetscLogEventBegin(petsc_gamg_setup_events[SET5],0,0,0,0);CHKERRQ(ierr); 732 #endif 733 /* messy method, squares graph and gets some data */ 734 ierr = getGIDsOnSquareGraph(nLocalSelected, clid_flid, Gmat, &selected_2, &Gmat2, &crsGID);CHKERRQ(ierr); 735 /* llist is now not valid wrt squared graph, but will work as iterator in 'triangulateAndFormProl' */ 736 #if defined PETSC_GAMG_USE_LOG 737 ierr = PetscLogEventEnd(petsc_gamg_setup_events[SET5],0,0,0,0);CHKERRQ(ierr); 738 #endif 739 /* create global vector of coorindates in 'coords' */ 740 if (size > 1) { 741 ierr = PCGAMGGetDataWithGhosts(Gmat2, dim, pc_gamg->data, &data_stride, &coords);CHKERRQ(ierr); 742 } else { 743 coords = (PetscReal*)pc_gamg->data; 744 data_stride = pc_gamg->data_sz/pc_gamg->data_cell_cols; 745 } 746 ierr = MatDestroy(&Gmat2);CHKERRQ(ierr); 747 748 /* triangulate */ 749 if (dim == 2) { 750 PetscReal metric,tm; 751 #if defined PETSC_GAMG_USE_LOG 752 ierr = PetscLogEventBegin(petsc_gamg_setup_events[SET6],0,0,0,0);CHKERRQ(ierr); 753 #endif 754 ierr = triangulateAndFormProl(selected_2, data_stride, coords,nLocalSelected, clid_flid, agg_lists, crsGID, bs, Prol, &metric);CHKERRQ(ierr); 755 #if defined PETSC_GAMG_USE_LOG 756 ierr = PetscLogEventEnd(petsc_gamg_setup_events[SET6],0,0,0,0);CHKERRQ(ierr); 757 #endif 758 ierr = PetscFree(crsGID);CHKERRQ(ierr); 759 760 /* clean up and create coordinates for coarse grid (output) */ 761 if (size > 1) ierr = PetscFree(coords);CHKERRQ(ierr); 762 763 ierr = MPIU_Allreduce(&metric, &tm, 1, MPIU_REAL, MPIU_MAX, comm);CHKERRQ(ierr); 764 if (tm > 1.) { /* needs to be globalized - should not happen */ 765 ierr = PetscInfo1(pc," failed metric for coarse grid %e\n",(double)tm);CHKERRQ(ierr); 766 ierr = MatDestroy(&Prol);CHKERRQ(ierr); 767 } else if (metric > .0) { 768 ierr = PetscInfo1(pc,"worst metric for coarse grid = %e\n",(double)metric);CHKERRQ(ierr); 769 } 770 } else SETERRQ(comm,PETSC_ERR_PLIB,"3D not implemented for 'geo' AMG"); 771 { /* create next coords - output */ 772 PetscReal *crs_crds; 773 ierr = PetscMalloc1(dim*nLocalSelected, &crs_crds);CHKERRQ(ierr); 774 for (kk=0; kk<nLocalSelected; kk++) { /* grab local select nodes to promote - output */ 775 PetscInt lid = clid_flid[kk]; 776 for (jj=0; jj<dim; jj++) crs_crds[jj*nLocalSelected + kk] = pc_gamg->data[jj*nloc + lid]; 777 } 778 779 ierr = PetscFree(pc_gamg->data);CHKERRQ(ierr); 780 pc_gamg->data = crs_crds; /* out */ 781 pc_gamg->data_sz = dim*nLocalSelected; 782 } 783 ierr = ISDestroy(&selected_2);CHKERRQ(ierr); 784 } 785 786 *a_P_out = Prol; /* out */ 787 ierr = PetscFree(clid_flid);CHKERRQ(ierr); 788 ierr = PetscLogEventEnd(PC_GAMGProlongator_GEO,0,0,0,0);CHKERRQ(ierr); 789 PetscFunctionReturn(0); 790 } 791 792 static PetscErrorCode PCDestroy_GAMG_GEO(PC pc) 793 { 794 PetscErrorCode ierr; 795 796 PetscFunctionBegin; 797 ierr = PetscObjectComposeFunction((PetscObject)pc,"PCSetCoordinates_C",NULL);CHKERRQ(ierr); 798 PetscFunctionReturn(0); 799 } 800 801 /* -------------------------------------------------------------------------- */ 802 /* 803 PCCreateGAMG_GEO 804 805 Input Parameter: 806 . pc - 807 */ 808 PetscErrorCode PCCreateGAMG_GEO(PC pc) 809 { 810 PetscErrorCode ierr; 811 PC_MG *mg = (PC_MG*)pc->data; 812 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 813 814 PetscFunctionBegin; 815 pc_gamg->ops->setfromoptions = PCSetFromOptions_GEO; 816 pc_gamg->ops->destroy = PCDestroy_GAMG_GEO; 817 /* reset does not do anything; setup not virtual */ 818 819 /* set internal function pointers */ 820 pc_gamg->ops->graph = PCGAMGGraph_GEO; 821 pc_gamg->ops->coarsen = PCGAMGCoarsen_GEO; 822 pc_gamg->ops->prolongator = PCGAMGProlongator_GEO; 823 pc_gamg->ops->optprolongator = NULL; 824 pc_gamg->ops->createdefaultdata = PCSetData_GEO; 825 826 ierr = PetscObjectComposeFunction((PetscObject)pc,"PCSetCoordinates_C",PCSetCoordinates_GEO);CHKERRQ(ierr); 827 PetscFunctionReturn(0); 828 } 829