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 #include <petsc-private/kspimpl.h> 7 8 #if defined(PETSC_HAVE_TRIANGLE) 9 #define REAL PetscReal 10 #include <triangle.h> 11 #endif 12 13 #include <assert.h> 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 int petsc_geo_mg_compare (const void *a, const void *b) 22 { 23 return (((GAMGNode*)a)->degree - ((GAMGNode*)b)->degree); 24 } 25 26 /* -------------------------------------------------------------------------- */ 27 /* 28 PCSetCoordinates_GEO 29 30 Input Parameter: 31 . pc - the preconditioner context 32 */ 33 EXTERN_C_BEGIN 34 #undef __FUNCT__ 35 #define __FUNCT__ "PCSetCoordinates_GEO" 36 PetscErrorCode PCSetCoordinates_GEO(PC pc, PetscInt ndm, PetscInt a_nloc, PetscReal *coords) 37 { 38 PC_MG *mg = (PC_MG*)pc->data; 39 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 40 PetscErrorCode ierr; 41 PetscInt arrsz,bs,my0,kk,ii,nloc,Iend; 42 Mat Amat = pc->pmat; 43 44 PetscFunctionBegin; 45 PetscValidHeaderSpecific(Amat, MAT_CLASSID, 1); 46 ierr = MatGetBlockSize(Amat, &bs);CHKERRQ(ierr); 47 48 ierr = MatGetOwnershipRange(Amat, &my0, &Iend);CHKERRQ(ierr); 49 nloc = (Iend-my0)/bs; 50 51 if (nloc!=a_nloc)SETERRQ2(((PetscObject)Amat)->comm,PETSC_ERR_ARG_WRONG, "Stokes not supported nloc = %d %d.",a_nloc,nloc); 52 if ((Iend-my0)%bs!=0) SETERRQ1(((PetscObject)Amat)->comm,PETSC_ERR_ARG_WRONG, "Bad local size %d.",nloc); 53 54 pc_gamg->data_cell_rows = 1; 55 if (coords==0 && nloc > 0) SETERRQ(((PetscObject)Amat)->comm,PETSC_ERR_ARG_WRONG, "Need coordinates for pc_gamg_type 'geo'."); 56 pc_gamg->data_cell_cols = ndm; /* coordinates */ 57 58 arrsz = nloc*pc_gamg->data_cell_rows*pc_gamg->data_cell_cols; 59 60 /* create data - syntactic sugar that should be refactored at some point */ 61 if (pc_gamg->data==0 || (pc_gamg->data_sz != arrsz)) { 62 ierr = PetscFree(pc_gamg->data);CHKERRQ(ierr); 63 ierr = PetscMalloc((arrsz+1)*sizeof(PetscReal), &pc_gamg->data);CHKERRQ(ierr); 64 } 65 for (kk=0;kk<arrsz;kk++)pc_gamg->data[kk] = -999.; 66 pc_gamg->data[arrsz] = -99.; 67 /* copy data in - column oriented */ 68 for (kk = 0 ; kk < nloc ; kk++) { 69 for (ii = 0 ; ii < ndm ; ii++) { 70 pc_gamg->data[ii*nloc + kk] = coords[kk*ndm + ii]; 71 } 72 } 73 assert(pc_gamg->data[arrsz] == -99.); 74 75 pc_gamg->data_sz = arrsz; 76 PetscFunctionReturn(0); 77 } 78 EXTERN_C_END 79 80 /* -------------------------------------------------------------------------- */ 81 /* 82 PCSetData_GEO 83 84 Input Parameter: 85 . pc - 86 */ 87 #undef __FUNCT__ 88 #define __FUNCT__ "PCSetData_GEO" 89 PetscErrorCode PCSetData_GEO(PC pc, Mat m) 90 { 91 PetscFunctionBegin; 92 SETERRQ(((PetscObject)pc)->comm,PETSC_ERR_PLIB,"GEO MG needs coordinates"); 93 } 94 95 /* -------------------------------------------------------------------------- */ 96 /* 97 PCSetFromOptions_GEO 98 99 Input Parameter: 100 . pc - 101 */ 102 #undef __FUNCT__ 103 #define __FUNCT__ "PCSetFromOptions_GEO" 104 PetscErrorCode PCSetFromOptions_GEO(PC pc) 105 { 106 PetscErrorCode ierr; 107 PC_MG *mg = (PC_MG*)pc->data; 108 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 109 110 PetscFunctionBegin; 111 ierr = PetscOptionsHead("GAMG-GEO options");CHKERRQ(ierr); 112 { 113 /* -pc_gamg_sa_nsmooths */ 114 /* pc_gamg_sa->smooths = 0; */ 115 /* ierr = PetscOptionsInt("-pc_gamg_agg_nsmooths", */ 116 /* "smoothing steps for smoothed aggregation, usually 1 (0)", */ 117 /* "PCGAMGSetNSmooths_AGG", */ 118 /* pc_gamg_sa->smooths, */ 119 /* &pc_gamg_sa->smooths, */ 120 /* &flag); */ 121 /* CHKERRQ(ierr); */ 122 } 123 ierr = PetscOptionsTail();CHKERRQ(ierr); 124 125 /* call base class */ 126 ierr = PCSetFromOptions_GAMG(pc);CHKERRQ(ierr); 127 128 if (pc_gamg->verbose) { 129 MPI_Comm wcomm = ((PetscObject)pc)->comm; 130 PetscPrintf(wcomm,"[%d]%s done\n",0,__FUNCT__); 131 } 132 PetscFunctionReturn(0); 133 } 134 135 /* -------------------------------------------------------------------------- */ 136 /* 137 triangulateAndFormProl 138 139 Input Parameter: 140 . selected_2 - list of selected local ID, includes selected ghosts 141 . data_stride - 142 . coords[2*data_stride] - column vector of local coordinates w/ ghosts 143 . nselected_1 - selected IDs that go with base (1) graph 144 . clid_lid_1[nselected_1] - lids of selected (c) nodes ??????????? 145 . agg_lists_1 - list of aggregates 146 . crsGID[selected.size()] - global index for prolongation operator 147 . bs - block size 148 Output Parameter: 149 . a_Prol - prolongation operator 150 . a_worst_best - measure of worst missed fine vertex, 0 is no misses 151 */ 152 #undef __FUNCT__ 153 #define __FUNCT__ "triangulateAndFormProl" 154 static PetscErrorCode triangulateAndFormProl(IS selected_2, /* list of selected local ID, includes selected ghosts */ 155 const PetscInt data_stride, 156 const PetscReal coords[], /* column vector of local coordinates w/ ghosts */ 157 const PetscInt nselected_1, /* list of selected local ID, includes selected ghosts */ 158 const PetscInt clid_lid_1[], 159 const PetscCoarsenData *agg_lists_1, /* selected_1 vertices of aggregate unselected vertices */ 160 const PetscInt crsGID[], 161 const PetscInt bs, 162 Mat a_Prol, /* prolongation operator (output) */ 163 PetscReal *a_worst_best) /* measure of worst missed fine vertex, 0 is no misses */ 164 { 165 #if defined(PETSC_HAVE_TRIANGLE) 166 PetscErrorCode ierr; 167 PetscInt jj,tid,tt,idx,nselected_2; 168 struct triangulateio in,mid; 169 const PetscInt *selected_idx_2; 170 PetscMPIInt rank,size; 171 PetscInt Istart,Iend,nFineLoc,myFine0; 172 int kk,nPlotPts,sid; 173 MPI_Comm wcomm = ((PetscObject)a_Prol)->comm; 174 PetscReal tm; 175 176 PetscFunctionBegin; 177 ierr = MPI_Comm_rank(wcomm,&rank);CHKERRQ(ierr); 178 ierr = MPI_Comm_size(wcomm,&size);CHKERRQ(ierr); 179 ierr = ISGetSize(selected_2, &nselected_2);CHKERRQ(ierr); 180 if (nselected_2 == 1 || nselected_2 == 2) { /* 0 happens on idle processors */ 181 *a_worst_best = 100.0; /* this will cause a stop, but not globalized (should not happen) */ 182 } else *a_worst_best = 0.0; 183 ierr = MPI_Allreduce(a_worst_best, &tm, 1, MPIU_REAL, MPIU_MAX, wcomm);CHKERRQ(ierr); 184 if (tm > 0.0) { 185 *a_worst_best = 100.0; 186 PetscFunctionReturn(0); 187 } 188 ierr = MatGetOwnershipRange(a_Prol, &Istart, &Iend);CHKERRQ(ierr); 189 nFineLoc = (Iend-Istart)/bs; myFine0 = Istart/bs; 190 nPlotPts = nFineLoc; /* locals */ 191 /* traingle */ 192 /* Define input points - in*/ 193 in.numberofpoints = nselected_2; 194 in.numberofpointattributes = 0; 195 /* get nselected points */ 196 ierr = PetscMalloc(2*(nselected_2)*sizeof(REAL), &in.pointlist);CHKERRQ(ierr); 197 ierr = ISGetIndices(selected_2, &selected_idx_2);CHKERRQ(ierr); 198 199 for (kk=0,sid=0;kk<nselected_2;kk++,sid += 2) { 200 PetscInt lid = selected_idx_2[kk]; 201 in.pointlist[sid] = coords[lid]; 202 in.pointlist[sid+1] = coords[data_stride + lid]; 203 if (lid>=nFineLoc) nPlotPts++; 204 } 205 assert(sid==2*nselected_2); 206 207 in.numberofsegments = 0; 208 in.numberofedges = 0; 209 in.numberofholes = 0; 210 in.numberofregions = 0; 211 in.trianglelist = 0; 212 in.segmentmarkerlist = 0; 213 in.pointattributelist = 0; 214 in.pointmarkerlist = 0; 215 in.triangleattributelist = 0; 216 in.trianglearealist = 0; 217 in.segmentlist = 0; 218 in.holelist = 0; 219 in.regionlist = 0; 220 in.edgelist = 0; 221 in.edgemarkerlist = 0; 222 in.normlist = 0; 223 /* triangulate */ 224 mid.pointlist = 0; /* Not needed if -N switch used. */ 225 /* Not needed if -N switch used or number of point attributes is zero: */ 226 mid.pointattributelist = 0; 227 mid.pointmarkerlist = 0; /* Not needed if -N or -B switch used. */ 228 mid.trianglelist = 0; /* Not needed if -E switch used. */ 229 /* Not needed if -E switch used or number of triangle attributes is zero: */ 230 mid.triangleattributelist = 0; 231 mid.neighborlist = 0; /* Needed only if -n switch used. */ 232 /* Needed only if segments are output (-p or -c) and -P not used: */ 233 mid.segmentlist = 0; 234 /* Needed only if segments are output (-p or -c) and -P and -B not used: */ 235 mid.segmentmarkerlist = 0; 236 mid.edgelist = 0; /* Needed only if -e switch used. */ 237 mid.edgemarkerlist = 0; /* Needed if -e used and -B not used. */ 238 mid.numberoftriangles = 0; 239 240 /* Triangulate the points. Switches are chosen to read and write a */ 241 /* PSLG (p), preserve the convex hull (c), number everything from */ 242 /* zero (z), assign a regional attribute to each element (A), and */ 243 /* produce an edge list (e), a Voronoi diagram (v), and a triangle */ 244 /* neighbor list (n). */ 245 if (nselected_2 != 0) { /* inactive processor */ 246 char args[] = "npczQ"; /* c is needed ? */ 247 triangulate(args, &in, &mid, (struct triangulateio *) NULL); 248 /* output .poly files for 'showme' */ 249 if (!PETSC_TRUE) { 250 static int level = 1; 251 FILE *file; char fname[32]; 252 253 sprintf(fname,"C%d_%d.poly",level,rank); file = fopen(fname, "w"); 254 /*First line: <# of vertices> <dimension (must be 2)> <# of attributes> <# of boundary markers (0 or 1)>*/ 255 fprintf(file, "%d %d %d %d\n",in.numberofpoints,2,0,0); 256 /*Following lines: <vertex #> <x> <y> */ 257 for (kk=0,sid=0;kk<in.numberofpoints;kk++,sid += 2) { 258 fprintf(file, "%d %e %e\n",kk,in.pointlist[sid],in.pointlist[sid+1]); 259 } 260 /*One line: <# of segments> <# of boundary markers (0 or 1)> */ 261 fprintf(file, "%d %d\n",0,0); 262 /*Following lines: <segment #> <endpoint> <endpoint> [boundary marker] */ 263 /* One line: <# of holes> */ 264 fprintf(file, "%d\n",0); 265 /* Following lines: <hole #> <x> <y> */ 266 /* Optional line: <# of regional attributes and/or area constraints> */ 267 /* Optional following lines: <region #> <x> <y> <attribute> <maximum area> */ 268 fclose(file); 269 270 /* elems */ 271 sprintf(fname,"C%d_%d.ele",level,rank); file = fopen(fname, "w"); 272 /* First line: <# of triangles> <nodes per triangle> <# of attributes> */ 273 fprintf(file, "%d %d %d\n",mid.numberoftriangles,3,0); 274 /* Remaining lines: <triangle #> <node> <node> <node> ... [attributes] */ 275 for (kk=0,sid=0;kk<mid.numberoftriangles;kk++,sid += 3) { 276 fprintf(file, "%d %d %d %d\n",kk,mid.trianglelist[sid],mid.trianglelist[sid+1],mid.trianglelist[sid+2]); 277 } 278 fclose(file); 279 280 sprintf(fname,"C%d_%d.node",level,rank); file = fopen(fname, "w"); 281 /* First line: <# of vertices> <dimension (must be 2)> <# of attributes> <# of boundary markers (0 or 1)> */ 282 /* fprintf(file, "%d %d %d %d\n",in.numberofpoints,2,0,0); */ 283 fprintf(file, "%d %d %d %d\n",nPlotPts,2,0,0); 284 /*Following lines: <vertex #> <x> <y> */ 285 for (kk=0,sid=0;kk<in.numberofpoints;kk++,sid+=2) { 286 fprintf(file, "%d %e %e\n",kk,in.pointlist[sid],in.pointlist[sid+1]); 287 } 288 289 sid /= 2; 290 for (jj=0;jj<nFineLoc;jj++) { 291 PetscBool sel = PETSC_TRUE; 292 for (kk=0 ; kk<nselected_2 && sel ; kk++) { 293 PetscInt lid = selected_idx_2[kk]; 294 if (lid == jj) sel = PETSC_FALSE; 295 } 296 if (sel) { 297 fprintf(file, "%d %e %e\n",sid++,coords[jj],coords[data_stride + jj]); 298 } 299 } 300 fclose(file); 301 assert(sid==nPlotPts); 302 level++; 303 } 304 } 305 #if defined PETSC_GAMG_USE_LOG 306 ierr = PetscLogEventBegin(petsc_gamg_setup_events[FIND_V],0,0,0,0);CHKERRQ(ierr); 307 #endif 308 { /* form P - setup some maps */ 309 PetscInt clid,mm,*nTri,*node_tri; 310 311 ierr = PetscMalloc(nselected_2*sizeof(PetscInt), &node_tri);CHKERRQ(ierr); 312 ierr = PetscMalloc(nselected_2*sizeof(PetscInt), &nTri);CHKERRQ(ierr); 313 314 /* need list of triangles on node */ 315 for (kk=0;kk<nselected_2;kk++) nTri[kk] = 0; 316 for (tid=0,kk=0;tid<mid.numberoftriangles;tid++) { 317 for (jj=0;jj<3;jj++) { 318 PetscInt cid = mid.trianglelist[kk++]; 319 if (nTri[cid] == 0) node_tri[cid] = tid; 320 nTri[cid]++; 321 } 322 } 323 #define EPS 1.e-12 324 /* find points and set prolongation */ 325 for (mm = clid = 0 ; mm < nFineLoc ; mm++) { 326 PetscBool ise; 327 ierr = PetscCDEmptyAt(agg_lists_1,mm,&ise);CHKERRQ(ierr); 328 if (!ise) { 329 const PetscInt lid = mm; 330 /* for (clid_iterator=0;clid_iterator<nselected_1;clid_iterator++) { */ 331 /* PetscInt flid = clid_lid_1[clid_iterator]; assert(flid != -1); */ 332 PetscScalar AA[3][3]; 333 PetscBLASInt N=3,NRHS=1,LDA=3,IPIV[3],LDB=3,INFO; 334 PetscCDPos pos; 335 ierr = PetscCDGetHeadPos(agg_lists_1,lid,&pos);CHKERRQ(ierr); 336 while (pos) { 337 PetscInt flid; 338 ierr = PetscLLNGetID(pos, &flid);CHKERRQ(ierr); 339 ierr = PetscCDGetNextPos(agg_lists_1,lid,&pos);CHKERRQ(ierr); 340 341 if (flid < nFineLoc) { /* could be a ghost */ 342 PetscInt bestTID = -1; PetscReal best_alpha = 1.e10; 343 const PetscInt fgid = flid + myFine0; 344 /* compute shape function for gid */ 345 const PetscReal fcoord[3] = {coords[flid],coords[data_stride+flid],1.0}; 346 PetscBool haveit=PETSC_FALSE; PetscScalar alpha[3]; PetscInt clids[3]; 347 /* look for it */ 348 for (tid = node_tri[clid], jj=0; 349 jj < 5 && !haveit && tid != -1; 350 jj++) { 351 for (tt=0;tt<3;tt++) { 352 PetscInt cid2 = mid.trianglelist[3*tid + tt]; 353 PetscInt lid2 = selected_idx_2[cid2]; 354 AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0; 355 clids[tt] = cid2; /* store for interp */ 356 } 357 358 for (tt=0;tt<3;tt++) alpha[tt] = (PetscScalar)fcoord[tt]; 359 360 /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */ 361 LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO); 362 { 363 PetscBool have=PETSC_TRUE; PetscReal lowest=1.e10; 364 for (tt = 0, idx = 0 ; tt < 3 ; tt++) { 365 if (PetscRealPart(alpha[tt]) > (1.0+EPS) || PetscRealPart(alpha[tt]) < -EPS) have = PETSC_FALSE; 366 if (PetscRealPart(alpha[tt]) < lowest) { 367 lowest = PetscRealPart(alpha[tt]); 368 idx = tt; 369 } 370 } 371 haveit = have; 372 } 373 tid = mid.neighborlist[3*tid + idx]; 374 } 375 376 if (!haveit) { 377 /* brute force */ 378 for (tid=0 ; tid<mid.numberoftriangles && !haveit ; tid++) { 379 for (tt=0;tt<3;tt++) { 380 PetscInt cid2 = mid.trianglelist[3*tid + tt]; 381 PetscInt lid2 = selected_idx_2[cid2]; 382 AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0; 383 clids[tt] = cid2; /* store for interp */ 384 } 385 for (tt=0;tt<3;tt++) alpha[tt] = fcoord[tt]; 386 /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */ 387 LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO); 388 { 389 PetscBool have=PETSC_TRUE; PetscReal worst=0.0, v; 390 for (tt=0; tt<3 && have ;tt++) { 391 if (PetscRealPart(alpha[tt]) > 1.0+EPS || PetscRealPart(alpha[tt]) < -EPS) have=PETSC_FALSE; 392 if ((v=PetscAbs(PetscRealPart(alpha[tt])-0.5)) > worst) worst = v; 393 } 394 if (worst < best_alpha) { 395 best_alpha = worst; bestTID = tid; 396 } 397 haveit = have; 398 } 399 } 400 } 401 if (!haveit) { 402 if (best_alpha > *a_worst_best) *a_worst_best = best_alpha; 403 /* use best one */ 404 for (tt=0;tt<3;tt++) { 405 PetscInt cid2 = mid.trianglelist[3*bestTID + tt]; 406 PetscInt lid2 = selected_idx_2[cid2]; 407 AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0; 408 clids[tt] = cid2; /* store for interp */ 409 } 410 for (tt=0;tt<3;tt++) alpha[tt] = fcoord[tt]; 411 /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */ 412 LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO); 413 } 414 415 /* put in row of P */ 416 for (idx=0;idx<3;idx++) { 417 PetscScalar shp = alpha[idx]; 418 if (PetscAbs(PetscRealPart(shp)) > 1.e-6) { 419 PetscInt cgid = crsGID[clids[idx]]; 420 PetscInt jj = cgid*bs, ii = fgid*bs; /* need to gloalize */ 421 for (tt=0 ; tt < bs ; tt++, ii++, jj++) { 422 ierr = MatSetValues(a_Prol,1,&ii,1,&jj,&shp,INSERT_VALUES);CHKERRQ(ierr); 423 } 424 } 425 } 426 } 427 } /* aggregates iterations */ 428 clid++; 429 } /* a coarse agg */ 430 } /* for all fine nodes */ 431 432 ierr = ISRestoreIndices(selected_2, &selected_idx_2);CHKERRQ(ierr); 433 ierr = MatAssemblyBegin(a_Prol,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 434 ierr = MatAssemblyEnd(a_Prol,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 435 436 ierr = PetscFree(node_tri);CHKERRQ(ierr); 437 ierr = PetscFree(nTri);CHKERRQ(ierr); 438 } 439 #if defined PETSC_GAMG_USE_LOG 440 ierr = PetscLogEventEnd(petsc_gamg_setup_events[FIND_V],0,0,0,0);CHKERRQ(ierr); 441 #endif 442 free(mid.trianglelist); 443 free(mid.neighborlist); 444 ierr = PetscFree(in.pointlist);CHKERRQ(ierr); 445 PetscFunctionReturn(0); 446 #else 447 SETERRQ(((PetscObject)a_Prol)->comm,PETSC_ERR_PLIB,"configure with TRIANGLE to use geometric MG"); 448 #endif 449 } 450 /* -------------------------------------------------------------------------- */ 451 /* 452 getGIDsOnSquareGraph - square graph, get 453 454 Input Parameter: 455 . nselected_1 - selected local indices (includes ghosts in input Gmat1) 456 . clid_lid_1 - [nselected_1] lids of selected nodes 457 . Gmat1 - graph that goes with 'selected_1' 458 Output Parameter: 459 . a_selected_2 - selected local indices (includes ghosts in output a_Gmat_2) 460 . a_Gmat_2 - graph that is squared of 'Gmat_1' 461 . a_crsGID[a_selected_2.size()] - map of global IDs of coarse grid nodes 462 */ 463 #undef __FUNCT__ 464 #define __FUNCT__ "getGIDsOnSquareGraph" 465 static PetscErrorCode getGIDsOnSquareGraph(const PetscInt nselected_1, 466 const PetscInt clid_lid_1[], 467 const Mat Gmat1, 468 IS *a_selected_2, 469 Mat *a_Gmat_2, 470 PetscInt **a_crsGID) 471 { 472 PetscErrorCode ierr; 473 PetscMPIInt rank,size; 474 PetscInt *crsGID, kk,my0,Iend,nloc; 475 MPI_Comm wcomm = ((PetscObject)Gmat1)->comm; 476 477 PetscFunctionBegin; 478 ierr = MPI_Comm_rank(wcomm,&rank);CHKERRQ(ierr); 479 ierr = MPI_Comm_size(wcomm,&size);CHKERRQ(ierr); 480 ierr = MatGetOwnershipRange(Gmat1,&my0,&Iend);CHKERRQ(ierr); /* AIJ */ 481 nloc = Iend - my0; /* this does not change */ 482 483 if (size == 1) { /* not much to do in serial */ 484 ierr = PetscMalloc(nselected_1*sizeof(PetscInt), &crsGID);CHKERRQ(ierr); 485 for (kk=0;kk<nselected_1;kk++) crsGID[kk] = kk; 486 *a_Gmat_2 = 0; 487 ierr = ISCreateGeneral(PETSC_COMM_SELF,nselected_1,clid_lid_1,PETSC_COPY_VALUES,a_selected_2);CHKERRQ(ierr); 488 } else { 489 PetscInt idx,num_fine_ghosts,num_crs_ghost,myCrs0; 490 Mat_MPIAIJ *mpimat2; 491 Mat Gmat2; 492 Vec locState; 493 PetscScalar *cpcol_state; 494 495 /* scan my coarse zero gid, set 'lid_state' with coarse GID */ 496 kk = nselected_1; 497 MPI_Scan(&kk, &myCrs0, 1, MPIU_INT, MPIU_SUM, wcomm); 498 myCrs0 -= nselected_1; 499 500 if (a_Gmat_2) { /* output */ 501 /* grow graph to get wider set of selected vertices to cover fine grid, invalidates 'llist' */ 502 ierr = MatTransposeMatMult(Gmat1, Gmat1, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &Gmat2);CHKERRQ(ierr); 503 *a_Gmat_2 = Gmat2; /* output */ 504 } else Gmat2 = Gmat1; /* use local to get crsGIDs at least */ 505 /* get coarse grid GIDS for selected (locals and ghosts) */ 506 mpimat2 = (Mat_MPIAIJ*)Gmat2->data; 507 ierr = MatGetVecs(Gmat2, &locState, 0);CHKERRQ(ierr); 508 ierr = VecSet(locState, (PetscScalar)(PetscReal)(-1));CHKERRQ(ierr); /* set with UNKNOWN state */ 509 for (kk=0;kk<nselected_1;kk++) { 510 PetscInt fgid = clid_lid_1[kk] + my0; 511 PetscScalar v = (PetscScalar)(kk+myCrs0); 512 ierr = VecSetValues(locState, 1, &fgid, &v, INSERT_VALUES);CHKERRQ(ierr); /* set with PID */ 513 } 514 ierr = VecAssemblyBegin(locState);CHKERRQ(ierr); 515 ierr = VecAssemblyEnd(locState);CHKERRQ(ierr); 516 ierr = VecScatterBegin(mpimat2->Mvctx,locState,mpimat2->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 517 ierr = VecScatterEnd(mpimat2->Mvctx,locState,mpimat2->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 518 ierr = VecGetLocalSize(mpimat2->lvec, &num_fine_ghosts);CHKERRQ(ierr); 519 ierr = VecGetArray(mpimat2->lvec, &cpcol_state);CHKERRQ(ierr); 520 for (kk=0,num_crs_ghost=0;kk<num_fine_ghosts;kk++) { 521 if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) num_crs_ghost++; 522 } 523 ierr = PetscMalloc((nselected_1+num_crs_ghost)*sizeof(PetscInt), &crsGID);CHKERRQ(ierr); /* output */ 524 { 525 PetscInt *selected_set; 526 ierr = PetscMalloc((nselected_1+num_crs_ghost)*sizeof(PetscInt), &selected_set);CHKERRQ(ierr); 527 /* do ghost of 'crsGID' */ 528 for (kk=0,idx=nselected_1;kk<num_fine_ghosts;kk++) { 529 if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) { 530 PetscInt cgid = (PetscInt)PetscRealPart(cpcol_state[kk]); 531 selected_set[idx] = nloc + kk; 532 crsGID[idx++] = cgid; 533 } 534 } 535 assert(idx==(nselected_1+num_crs_ghost)); 536 ierr = VecRestoreArray(mpimat2->lvec, &cpcol_state);CHKERRQ(ierr); 537 /* do locals in 'crsGID' */ 538 ierr = VecGetArray(locState, &cpcol_state);CHKERRQ(ierr); 539 for (kk=0,idx=0;kk<nloc;kk++) { 540 if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) { 541 PetscInt cgid = (PetscInt)PetscRealPart(cpcol_state[kk]); 542 selected_set[idx] = kk; 543 crsGID[idx++] = cgid; 544 } 545 } 546 assert(idx==nselected_1); 547 ierr = VecRestoreArray(locState, &cpcol_state);CHKERRQ(ierr); 548 549 if (a_selected_2 != 0) { /* output */ 550 ierr = ISCreateGeneral(PETSC_COMM_SELF,(nselected_1+num_crs_ghost),selected_set,PETSC_OWN_POINTER,a_selected_2);CHKERRQ(ierr); 551 } else { 552 ierr = PetscFree(selected_set);CHKERRQ(ierr); 553 } 554 } 555 ierr = VecDestroy(&locState);CHKERRQ(ierr); 556 } 557 *a_crsGID = crsGID; /* output */ 558 PetscFunctionReturn(0); 559 } 560 561 /* -------------------------------------------------------------------------- */ 562 /* 563 PCGAMGgraph_GEO 564 565 Input Parameter: 566 . pc - this 567 . Amat - matrix on this fine level 568 Output Parameter: 569 . a_Gmat 570 */ 571 #undef __FUNCT__ 572 #define __FUNCT__ "PCGAMGgraph_GEO" 573 PetscErrorCode PCGAMGgraph_GEO(PC pc, 574 const Mat Amat, 575 Mat *a_Gmat) 576 { 577 PetscErrorCode ierr; 578 PC_MG *mg = (PC_MG*)pc->data; 579 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 580 const PetscInt verbose = pc_gamg->verbose; 581 const PetscReal vfilter = pc_gamg->threshold; 582 PetscMPIInt rank,size; 583 MPI_Comm wcomm = ((PetscObject)Amat)->comm; 584 Mat Gmat; 585 PetscBool set,flg,symm; 586 587 PetscFunctionBegin; 588 #if defined PETSC_USE_LOG 589 ierr = PetscLogEventBegin(PC_GAMGGgraph_GEO,0,0,0,0);CHKERRQ(ierr); 590 #endif 591 ierr = MPI_Comm_rank(wcomm, &rank);CHKERRQ(ierr); 592 ierr = MPI_Comm_size(wcomm, &size);CHKERRQ(ierr); 593 594 ierr = MatIsSymmetricKnown(Amat, &set, &flg);CHKERRQ(ierr); 595 symm = (PetscBool)!(set && flg); 596 597 ierr = PCGAMGCreateGraph(Amat, &Gmat);CHKERRQ(ierr); 598 ierr = PCGAMGFilterGraph(&Gmat, vfilter, symm, verbose);CHKERRQ(ierr); 599 600 *a_Gmat = Gmat; 601 #if defined PETSC_USE_LOG 602 ierr = PetscLogEventEnd(PC_GAMGGgraph_GEO,0,0,0,0);CHKERRQ(ierr); 603 #endif 604 PetscFunctionReturn(0); 605 } 606 607 /* -------------------------------------------------------------------------- */ 608 /* 609 PCGAMGcoarsen_GEO 610 611 Input Parameter: 612 . a_pc - this 613 . a_Gmat - graph 614 Output Parameter: 615 . a_llist_parent - linked list from selected indices for data locality only 616 */ 617 #undef __FUNCT__ 618 #define __FUNCT__ "PCGAMGcoarsen_GEO" 619 PetscErrorCode PCGAMGcoarsen_GEO(PC a_pc, 620 Mat *a_Gmat, 621 PetscCoarsenData **a_llist_parent) 622 { 623 PetscErrorCode ierr; 624 PC_MG *mg = (PC_MG*)a_pc->data; 625 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 626 PetscInt Istart,Iend,nloc,kk,Ii,ncols; 627 PetscMPIInt rank,size; 628 IS perm; 629 GAMGNode *gnodes; 630 PetscInt *permute; 631 Mat Gmat = *a_Gmat; 632 MPI_Comm wcomm = ((PetscObject)Gmat)->comm; 633 MatCoarsen crs; 634 635 PetscFunctionBegin; 636 #if defined PETSC_USE_LOG 637 ierr = PetscLogEventBegin(PC_GAMGCoarsen_GEO,0,0,0,0);CHKERRQ(ierr); 638 #endif 639 ierr = MPI_Comm_rank(wcomm, &rank);CHKERRQ(ierr); 640 ierr = MPI_Comm_size(wcomm, &size);CHKERRQ(ierr); 641 ierr = MatGetOwnershipRange(Gmat, &Istart, &Iend);CHKERRQ(ierr); 642 nloc = (Iend-Istart); 643 644 /* create random permutation with sort for geo-mg */ 645 ierr = PetscMalloc(nloc*sizeof(GAMGNode), &gnodes);CHKERRQ(ierr); 646 ierr = PetscMalloc(nloc*sizeof(PetscInt), &permute);CHKERRQ(ierr); 647 648 for (Ii=Istart; Ii<Iend; Ii++) { /* locals only? */ 649 ierr = MatGetRow(Gmat,Ii,&ncols,0,0);CHKERRQ(ierr); 650 { 651 PetscInt lid = Ii - Istart; 652 gnodes[lid].lid = lid; 653 gnodes[lid].degree = ncols; 654 } 655 ierr = MatRestoreRow(Gmat,Ii,&ncols,0,0);CHKERRQ(ierr); 656 } 657 /* randomize */ 658 srand(1); /* make deterministic */ 659 if (PETSC_TRUE) { 660 PetscBool *bIndexSet; 661 ierr = PetscMalloc(nloc*sizeof(PetscBool), &bIndexSet);CHKERRQ(ierr); 662 for (Ii = 0; Ii < nloc ; Ii++) bIndexSet[Ii] = PETSC_FALSE; 663 for (Ii = 0; Ii < nloc ; Ii++) 664 { 665 PetscInt iSwapIndex = rand()%nloc; 666 if (!bIndexSet[iSwapIndex] && iSwapIndex != Ii) 667 { 668 GAMGNode iTemp = gnodes[iSwapIndex]; 669 gnodes[iSwapIndex] = gnodes[Ii]; 670 gnodes[Ii] = iTemp; 671 bIndexSet[Ii] = PETSC_TRUE; 672 bIndexSet[iSwapIndex] = PETSC_TRUE; 673 } 674 } 675 ierr = PetscFree(bIndexSet);CHKERRQ(ierr); 676 } 677 /* only sort locals */ 678 qsort(gnodes, nloc, sizeof(GAMGNode), petsc_geo_mg_compare); 679 /* create IS of permutation */ 680 for (kk=0;kk<nloc;kk++) { /* locals only */ 681 permute[kk] = gnodes[kk].lid; 682 } 683 ierr = ISCreateGeneral(PETSC_COMM_SELF, nloc, permute, PETSC_OWN_POINTER, &perm);CHKERRQ(ierr); 684 685 ierr = PetscFree(gnodes);CHKERRQ(ierr); 686 687 /* get MIS aggs */ 688 689 ierr = MatCoarsenCreate(wcomm, &crs);CHKERRQ(ierr); 690 ierr = MatCoarsenSetType(crs, MATCOARSENMIS);CHKERRQ(ierr); 691 ierr = MatCoarsenSetGreedyOrdering(crs, perm);CHKERRQ(ierr); 692 ierr = MatCoarsenSetAdjacency(crs, Gmat);CHKERRQ(ierr); 693 ierr = MatCoarsenSetVerbose(crs, pc_gamg->verbose);CHKERRQ(ierr); 694 ierr = MatCoarsenSetStrictAggs(crs, PETSC_FALSE);CHKERRQ(ierr); 695 ierr = MatCoarsenApply(crs);CHKERRQ(ierr); 696 ierr = MatCoarsenGetData(crs, a_llist_parent);CHKERRQ(ierr); 697 ierr = MatCoarsenDestroy(&crs);CHKERRQ(ierr); 698 699 ierr = ISDestroy(&perm);CHKERRQ(ierr); 700 #if defined PETSC_USE_LOG 701 ierr = PetscLogEventEnd(PC_GAMGCoarsen_GEO,0,0,0,0);CHKERRQ(ierr); 702 #endif 703 PetscFunctionReturn(0); 704 } 705 706 /* -------------------------------------------------------------------------- */ 707 /* 708 PCGAMGProlongator_GEO 709 710 Input Parameter: 711 . pc - this 712 . Amat - matrix on this fine level 713 . Graph - used to get ghost data for nodes in 714 . selected_1 - [nselected] 715 . agg_lists - [nselected] 716 Output Parameter: 717 . a_P_out - prolongation operator to the next level 718 */ 719 #undef __FUNCT__ 720 #define __FUNCT__ "PCGAMGProlongator_GEO" 721 PetscErrorCode PCGAMGProlongator_GEO(PC pc, 722 const Mat Amat, 723 const Mat Gmat, 724 PetscCoarsenData *agg_lists, 725 Mat *a_P_out) 726 { 727 PC_MG *mg = (PC_MG*)pc->data; 728 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 729 const PetscInt verbose = pc_gamg->verbose; 730 const PetscInt dim = pc_gamg->data_cell_cols, data_cols = pc_gamg->data_cell_cols; 731 PetscErrorCode ierr; 732 PetscInt Istart,Iend,nloc,my0,jj,kk,ncols,nLocalSelected,bs,*clid_flid; 733 Mat Prol; 734 PetscMPIInt rank, size; 735 MPI_Comm wcomm = ((PetscObject)Amat)->comm; 736 IS selected_2,selected_1; 737 const PetscInt *selected_idx; 738 739 PetscFunctionBegin; 740 #if defined PETSC_USE_LOG 741 ierr = PetscLogEventBegin(PC_GAMGProlongator_GEO,0,0,0,0);CHKERRQ(ierr); 742 #endif 743 ierr = MPI_Comm_rank(wcomm,&rank);CHKERRQ(ierr); 744 ierr = MPI_Comm_size(wcomm,&size);CHKERRQ(ierr); 745 ierr = MatGetOwnershipRange(Amat, &Istart, &Iend);CHKERRQ(ierr); 746 ierr = MatGetBlockSize(Amat, &bs);CHKERRQ(ierr); 747 nloc = (Iend-Istart)/bs; my0 = Istart/bs; assert((Iend-Istart)%bs==0); 748 749 /* get 'nLocalSelected' */ 750 ierr = PetscCDGetMIS(agg_lists, &selected_1);CHKERRQ(ierr); 751 ierr = ISGetSize(selected_1, &jj);CHKERRQ(ierr); 752 ierr = PetscMalloc(jj*sizeof(PetscInt), &clid_flid);CHKERRQ(ierr); 753 ierr = ISGetIndices(selected_1, &selected_idx);CHKERRQ(ierr); 754 for (kk=0,nLocalSelected=0;kk<jj;kk++) { 755 PetscInt lid = selected_idx[kk]; 756 if (lid<nloc) { 757 ierr = MatGetRow(Gmat,lid+my0,&ncols,0,0);CHKERRQ(ierr); 758 if (ncols>1) { /* fiter out singletons */ 759 clid_flid[nLocalSelected++] = lid; 760 } else assert(0); /* filtered in coarsening */ 761 ierr = MatRestoreRow(Gmat,lid+my0,&ncols,0,0);CHKERRQ(ierr); 762 } 763 } 764 ierr = ISRestoreIndices(selected_1, &selected_idx);CHKERRQ(ierr); 765 ierr = ISDestroy(&selected_1);CHKERRQ(ierr); /* this is selected_1 in serial */ 766 767 /* create prolongator, create P matrix */ 768 ierr = MatCreate(wcomm, &Prol);CHKERRQ(ierr); 769 ierr = MatSetSizes(Prol,nloc*bs,nLocalSelected*bs,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 770 ierr = MatSetBlockSizes(Prol, bs, bs);CHKERRQ(ierr); 771 ierr = MatSetType(Prol, MATAIJ);CHKERRQ(ierr); 772 ierr = MatSeqAIJSetPreallocation(Prol,3*data_cols,PETSC_NULL);CHKERRQ(ierr); 773 ierr = MatMPIAIJSetPreallocation(Prol,3*data_cols,PETSC_NULL,3*data_cols,PETSC_NULL);CHKERRQ(ierr); 774 /* ierr = MatCreateAIJ(wcomm, */ 775 /* nloc*bs, nLocalSelected*bs, */ 776 /* PETSC_DETERMINE, PETSC_DETERMINE, */ 777 /* 3*data_cols, PETSC_NULL, */ 778 /* 3*data_cols, PETSC_NULL, */ 779 /* &Prol); */ 780 /* CHKERRQ(ierr); */ 781 782 /* can get all points "removed" - but not on geomg */ 783 ierr = MatGetSize(Prol, &kk, &jj);CHKERRQ(ierr); 784 if (jj==0) { 785 if (verbose) { 786 PetscPrintf(wcomm,"[%d]%s ERROE: no selected points on coarse grid\n",rank,__FUNCT__); 787 } 788 ierr = PetscFree(clid_flid);CHKERRQ(ierr); 789 ierr = MatDestroy(&Prol);CHKERRQ(ierr); 790 *a_P_out = PETSC_NULL; /* out */ 791 PetscFunctionReturn(0); 792 } 793 794 { 795 PetscReal *coords; 796 PetscInt data_stride; 797 PetscInt *crsGID = PETSC_NULL; 798 Mat Gmat2; 799 800 assert(dim==data_cols); 801 /* grow ghost data for better coarse grid cover of fine grid */ 802 #if defined PETSC_GAMG_USE_LOG 803 ierr = PetscLogEventBegin(petsc_gamg_setup_events[SET5],0,0,0,0);CHKERRQ(ierr); 804 #endif 805 /* messy method, squares graph and gets some data */ 806 ierr = getGIDsOnSquareGraph(nLocalSelected, clid_flid, Gmat, &selected_2, &Gmat2, &crsGID);CHKERRQ(ierr); 807 /* llist is now not valid wrt squared graph, but will work as iterator in 'triangulateAndFormProl' */ 808 #if defined PETSC_GAMG_USE_LOG 809 ierr = PetscLogEventEnd(petsc_gamg_setup_events[SET5],0,0,0,0);CHKERRQ(ierr); 810 #endif 811 /* create global vector of coorindates in 'coords' */ 812 if (size > 1) { 813 ierr = PCGAMGGetDataWithGhosts(Gmat2, dim, pc_gamg->data, &data_stride, &coords);CHKERRQ(ierr); 814 } else { 815 coords = (PetscReal*)pc_gamg->data; 816 data_stride = pc_gamg->data_sz/pc_gamg->data_cell_cols; 817 } 818 ierr = MatDestroy(&Gmat2);CHKERRQ(ierr); 819 820 /* triangulate */ 821 if (dim == 2) { 822 PetscReal metric,tm; 823 #if defined PETSC_GAMG_USE_LOG 824 ierr = PetscLogEventBegin(petsc_gamg_setup_events[SET6],0,0,0,0);CHKERRQ(ierr); 825 #endif 826 ierr = triangulateAndFormProl(selected_2, data_stride, coords,nLocalSelected, clid_flid, agg_lists, crsGID, bs, Prol, &metric);CHKERRQ(ierr); 827 #if defined PETSC_GAMG_USE_LOG 828 ierr = PetscLogEventEnd(petsc_gamg_setup_events[SET6],0,0,0,0);CHKERRQ(ierr); 829 #endif 830 ierr = PetscFree(crsGID);CHKERRQ(ierr); 831 832 /* clean up and create coordinates for coarse grid (output) */ 833 if (size > 1) ierr = PetscFree(coords);CHKERRQ(ierr); 834 835 ierr = MPI_Allreduce(&metric, &tm, 1, MPIU_REAL, MPIU_MAX, wcomm);CHKERRQ(ierr); 836 if (tm > 1.) { /* needs to be globalized - should not happen */ 837 if (verbose) { 838 PetscPrintf(wcomm,"[%d]%s failed metric for coarse grid %e\n",rank,__FUNCT__,tm); 839 } 840 ierr = MatDestroy(&Prol);CHKERRQ(ierr); 841 Prol = PETSC_NULL; 842 } else if (metric > .0) { 843 if (verbose) { 844 PetscPrintf(wcomm,"[%d]%s worst metric for coarse grid = %e\n",rank,__FUNCT__,metric); 845 } 846 } 847 } else SETERRQ(wcomm,PETSC_ERR_PLIB,"3D not implemented for 'geo' AMG"); 848 { /* create next coords - output */ 849 PetscReal *crs_crds; 850 ierr = PetscMalloc(dim*nLocalSelected*sizeof(PetscReal), &crs_crds);CHKERRQ(ierr); 851 for (kk=0;kk<nLocalSelected;kk++) {/* grab local select nodes to promote - output */ 852 PetscInt lid = clid_flid[kk]; 853 for (jj=0;jj<dim;jj++) crs_crds[jj*nLocalSelected + kk] = pc_gamg->data[jj*nloc + lid]; 854 } 855 856 ierr = PetscFree(pc_gamg->data);CHKERRQ(ierr); 857 pc_gamg->data = crs_crds; /* out */ 858 pc_gamg->data_sz = dim*nLocalSelected; 859 } 860 ierr = ISDestroy(&selected_2);CHKERRQ(ierr); 861 } 862 863 *a_P_out = Prol; /* out */ 864 ierr = PetscFree(clid_flid);CHKERRQ(ierr); 865 #if defined PETSC_USE_LOG 866 ierr = PetscLogEventEnd(PC_GAMGProlongator_GEO,0,0,0,0);CHKERRQ(ierr); 867 #endif 868 PetscFunctionReturn(0); 869 } 870 871 /* -------------------------------------------------------------------------- */ 872 /* 873 PCCreateGAMG_GEO 874 875 Input Parameter: 876 . pc - 877 */ 878 #undef __FUNCT__ 879 #define __FUNCT__ "PCCreateGAMG_GEO" 880 PetscErrorCode PCCreateGAMG_GEO(PC pc) 881 { 882 PetscErrorCode ierr; 883 PC_MG *mg = (PC_MG*)pc->data; 884 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 885 886 PetscFunctionBegin; 887 pc->ops->setfromoptions = PCSetFromOptions_GEO; 888 /* pc->ops->destroy = PCDestroy_GEO; */ 889 /* reset does not do anything; setup not virtual */ 890 891 /* set internal function pointers */ 892 pc_gamg->graph = PCGAMGgraph_GEO; 893 pc_gamg->coarsen = PCGAMGcoarsen_GEO; 894 pc_gamg->prolongator = PCGAMGProlongator_GEO; 895 pc_gamg->optprol = 0; 896 pc_gamg->formkktprol = 0; 897 898 pc_gamg->createdefaultdata = PCSetData_GEO; 899 900 ierr = PetscObjectComposeFunctionDynamic((PetscObject)pc, 901 "PCSetCoordinates_C", 902 "PCSetCoordinates_GEO", 903 PCSetCoordinates_GEO);CHKERRQ(ierr); 904 PetscFunctionReturn(0); 905 } 906