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 77 PetscFunctionReturn(0); 78 } 79 EXTERN_C_END 80 81 /* -------------------------------------------------------------------------- */ 82 /* 83 PCSetData_GEO 84 85 Input Parameter: 86 . pc - 87 */ 88 #undef __FUNCT__ 89 #define __FUNCT__ "PCSetData_GEO" 90 PetscErrorCode PCSetData_GEO(PC pc, Mat m) 91 { 92 PetscFunctionBegin; 93 SETERRQ(((PetscObject)pc)->comm,PETSC_ERR_PLIB,"GEO MG needs coordinates"); 94 } 95 96 /* -------------------------------------------------------------------------- */ 97 /* 98 PCSetFromOptions_GEO 99 100 Input Parameter: 101 . pc - 102 */ 103 #undef __FUNCT__ 104 #define __FUNCT__ "PCSetFromOptions_GEO" 105 PetscErrorCode PCSetFromOptions_GEO(PC pc) 106 { 107 PetscErrorCode ierr; 108 PC_MG *mg = (PC_MG*)pc->data; 109 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 110 111 PetscFunctionBegin; 112 ierr = PetscOptionsHead("GAMG-GEO options");CHKERRQ(ierr); 113 { 114 /* -pc_gamg_sa_nsmooths */ 115 /* pc_gamg_sa->smooths = 0; */ 116 /* ierr = PetscOptionsInt("-pc_gamg_agg_nsmooths", */ 117 /* "smoothing steps for smoothed aggregation, usually 1 (0)", */ 118 /* "PCGAMGSetNSmooths_AGG", */ 119 /* pc_gamg_sa->smooths, */ 120 /* &pc_gamg_sa->smooths, */ 121 /* &flag); */ 122 /* CHKERRQ(ierr); */ 123 } 124 ierr = PetscOptionsTail();CHKERRQ(ierr); 125 126 /* call base class */ 127 ierr = PCSetFromOptions_GAMG(pc);CHKERRQ(ierr); 128 129 if (pc_gamg->verbose) { 130 MPI_Comm wcomm = ((PetscObject)pc)->comm; 131 PetscPrintf(wcomm,"[%d]%s done\n",0,__FUNCT__); 132 } 133 134 PetscFunctionReturn(0); 135 } 136 137 /* -------------------------------------------------------------------------- */ 138 /* 139 triangulateAndFormProl 140 141 Input Parameter: 142 . selected_2 - list of selected local ID, includes selected ghosts 143 . data_stride - 144 . coords[2*data_stride] - column vector of local coordinates w/ ghosts 145 . nselected_1 - selected IDs that go with base (1) graph 146 . clid_lid_1[nselected_1] - lids of selected (c) nodes ??????????? 147 . agg_lists_1 - list of aggregates 148 . crsGID[selected.size()] - global index for prolongation operator 149 . bs - block size 150 Output Parameter: 151 . a_Prol - prolongation operator 152 . a_worst_best - measure of worst missed fine vertex, 0 is no misses 153 */ 154 #undef __FUNCT__ 155 #define __FUNCT__ "triangulateAndFormProl" 156 static PetscErrorCode triangulateAndFormProl(IS selected_2, /* list of selected local ID, includes selected ghosts */ 157 const PetscInt data_stride, 158 const PetscReal coords[], /* column vector of local coordinates w/ ghosts */ 159 const PetscInt nselected_1, /* list of selected local ID, includes selected ghosts */ 160 const PetscInt clid_lid_1[], 161 const PetscCoarsenData *agg_lists_1, /* selected_1 vertices of aggregate unselected vertices */ 162 const PetscInt crsGID[], 163 const PetscInt bs, 164 Mat a_Prol, /* prolongation operator (output) */ 165 PetscReal *a_worst_best) /* measure of worst missed fine vertex, 0 is no misses */ 166 { 167 #if defined(PETSC_HAVE_TRIANGLE) 168 PetscErrorCode ierr; 169 PetscInt jj,tid,tt,idx,nselected_2; 170 struct triangulateio in,mid; 171 const PetscInt *selected_idx_2; 172 PetscMPIInt mype,npe; 173 PetscInt Istart,Iend,nFineLoc,myFine0; 174 int kk,nPlotPts,sid; 175 MPI_Comm wcomm = ((PetscObject)a_Prol)->comm; 176 PetscReal tm; 177 PetscFunctionBegin; 178 179 ierr = MPI_Comm_rank(wcomm,&mype);CHKERRQ(ierr); 180 ierr = MPI_Comm_size(wcomm,&npe);CHKERRQ(ierr); 181 ierr = ISGetSize(selected_2, &nselected_2);CHKERRQ(ierr); 182 if (nselected_2 == 1 || nselected_2 == 2) { /* 0 happens on idle processors */ 183 *a_worst_best = 100.0; /* this will cause a stop, but not globalized (should not happen) */ 184 } else *a_worst_best = 0.0; 185 ierr = MPI_Allreduce(a_worst_best, &tm, 1, MPIU_REAL, MPIU_MAX, wcomm);CHKERRQ(ierr); 186 if (tm > 0.0) { 187 *a_worst_best = 100.0; 188 PetscFunctionReturn(0); 189 } 190 ierr = MatGetOwnershipRange(a_Prol, &Istart, &Iend);CHKERRQ(ierr); 191 nFineLoc = (Iend-Istart)/bs; myFine0 = Istart/bs; 192 nPlotPts = nFineLoc; /* locals */ 193 /* traingle */ 194 /* Define input points - in*/ 195 in.numberofpoints = nselected_2; 196 in.numberofpointattributes = 0; 197 /* get nselected points */ 198 ierr = PetscMalloc(2*(nselected_2)*sizeof(REAL), &in.pointlist);CHKERRQ(ierr); 199 ierr = ISGetIndices(selected_2, &selected_idx_2);CHKERRQ(ierr); 200 201 for (kk=0,sid=0;kk<nselected_2;kk++,sid += 2) { 202 PetscInt lid = selected_idx_2[kk]; 203 in.pointlist[sid] = coords[lid]; 204 in.pointlist[sid+1] = coords[data_stride + lid]; 205 if (lid>=nFineLoc) nPlotPts++; 206 } 207 assert(sid==2*nselected_2); 208 209 in.numberofsegments = 0; 210 in.numberofedges = 0; 211 in.numberofholes = 0; 212 in.numberofregions = 0; 213 in.trianglelist = 0; 214 in.segmentmarkerlist = 0; 215 in.pointattributelist = 0; 216 in.pointmarkerlist = 0; 217 in.triangleattributelist = 0; 218 in.trianglearealist = 0; 219 in.segmentlist = 0; 220 in.holelist = 0; 221 in.regionlist = 0; 222 in.edgelist = 0; 223 in.edgemarkerlist = 0; 224 in.normlist = 0; 225 /* triangulate */ 226 mid.pointlist = 0; /* Not needed if -N switch used. */ 227 /* Not needed if -N switch used or number of point attributes is zero: */ 228 mid.pointattributelist = 0; 229 mid.pointmarkerlist = 0; /* Not needed if -N or -B switch used. */ 230 mid.trianglelist = 0; /* Not needed if -E switch used. */ 231 /* Not needed if -E switch used or number of triangle attributes is zero: */ 232 mid.triangleattributelist = 0; 233 mid.neighborlist = 0; /* Needed only if -n switch used. */ 234 /* Needed only if segments are output (-p or -c) and -P not used: */ 235 mid.segmentlist = 0; 236 /* Needed only if segments are output (-p or -c) and -P and -B not used: */ 237 mid.segmentmarkerlist = 0; 238 mid.edgelist = 0; /* Needed only if -e switch used. */ 239 mid.edgemarkerlist = 0; /* Needed if -e used and -B not used. */ 240 mid.numberoftriangles = 0; 241 242 /* Triangulate the points. Switches are chosen to read and write a */ 243 /* PSLG (p), preserve the convex hull (c), number everything from */ 244 /* zero (z), assign a regional attribute to each element (A), and */ 245 /* produce an edge list (e), a Voronoi diagram (v), and a triangle */ 246 /* neighbor list (n). */ 247 if (nselected_2 != 0) { /* inactive processor */ 248 char args[] = "npczQ"; /* c is needed ? */ 249 triangulate(args, &in, &mid, (struct triangulateio *) NULL); 250 /* output .poly files for 'showme' */ 251 if (!PETSC_TRUE) { 252 static int level = 1; 253 FILE *file; char fname[32]; 254 255 sprintf(fname,"C%d_%d.poly",level,mype); file = fopen(fname, "w"); 256 /*First line: <# of vertices> <dimension (must be 2)> <# of attributes> <# of boundary markers (0 or 1)>*/ 257 fprintf(file, "%d %d %d %d\n",in.numberofpoints,2,0,0); 258 /*Following lines: <vertex #> <x> <y> */ 259 for (kk=0,sid=0;kk<in.numberofpoints;kk++,sid += 2) { 260 fprintf(file, "%d %e %e\n",kk,in.pointlist[sid],in.pointlist[sid+1]); 261 } 262 /*One line: <# of segments> <# of boundary markers (0 or 1)> */ 263 fprintf(file, "%d %d\n",0,0); 264 /*Following lines: <segment #> <endpoint> <endpoint> [boundary marker] */ 265 /* One line: <# of holes> */ 266 fprintf(file, "%d\n",0); 267 /* Following lines: <hole #> <x> <y> */ 268 /* Optional line: <# of regional attributes and/or area constraints> */ 269 /* Optional following lines: <region #> <x> <y> <attribute> <maximum area> */ 270 fclose(file); 271 272 /* elems */ 273 sprintf(fname,"C%d_%d.ele",level,mype); file = fopen(fname, "w"); 274 /* First line: <# of triangles> <nodes per triangle> <# of attributes> */ 275 fprintf(file, "%d %d %d\n",mid.numberoftriangles,3,0); 276 /* Remaining lines: <triangle #> <node> <node> <node> ... [attributes] */ 277 for (kk=0,sid=0;kk<mid.numberoftriangles;kk++,sid += 3) { 278 fprintf(file, "%d %d %d %d\n",kk,mid.trianglelist[sid],mid.trianglelist[sid+1],mid.trianglelist[sid+2]); 279 } 280 fclose(file); 281 282 sprintf(fname,"C%d_%d.node",level,mype); file = fopen(fname, "w"); 283 /* First line: <# of vertices> <dimension (must be 2)> <# of attributes> <# of boundary markers (0 or 1)> */ 284 /* fprintf(file, "%d %d %d %d\n",in.numberofpoints,2,0,0); */ 285 fprintf(file, "%d %d %d %d\n",nPlotPts,2,0,0); 286 /*Following lines: <vertex #> <x> <y> */ 287 for (kk=0,sid=0;kk<in.numberofpoints;kk++,sid+=2) { 288 fprintf(file, "%d %e %e\n",kk,in.pointlist[sid],in.pointlist[sid+1]); 289 } 290 291 sid /= 2; 292 for (jj=0;jj<nFineLoc;jj++) { 293 PetscBool sel = PETSC_TRUE; 294 for (kk=0 ; kk<nselected_2 && sel ; kk++) { 295 PetscInt lid = selected_idx_2[kk]; 296 if (lid == jj) sel = PETSC_FALSE; 297 } 298 if (sel) { 299 fprintf(file, "%d %e %e\n",sid++,coords[jj],coords[data_stride + jj]); 300 } 301 } 302 fclose(file); 303 assert(sid==nPlotPts); 304 level++; 305 } 306 } 307 #if defined PETSC_GAMG_USE_LOG 308 ierr = PetscLogEventBegin(petsc_gamg_setup_events[FIND_V],0,0,0,0);CHKERRQ(ierr); 309 #endif 310 { /* form P - setup some maps */ 311 PetscInt clid,mm,*nTri,*node_tri; 312 313 ierr = PetscMalloc(nselected_2*sizeof(PetscInt), &node_tri);CHKERRQ(ierr); 314 ierr = PetscMalloc(nselected_2*sizeof(PetscInt), &nTri);CHKERRQ(ierr); 315 316 /* need list of triangles on node */ 317 for (kk=0;kk<nselected_2;kk++) nTri[kk] = 0; 318 for (tid=0,kk=0;tid<mid.numberoftriangles;tid++) { 319 for (jj=0;jj<3;jj++) { 320 PetscInt cid = mid.trianglelist[kk++]; 321 if (nTri[cid] == 0) node_tri[cid] = tid; 322 nTri[cid]++; 323 } 324 } 325 #define EPS 1.e-12 326 /* find points and set prolongation */ 327 for (mm = clid = 0 ; mm < nFineLoc ; mm++) { 328 PetscBool ise; 329 ierr = PetscCDEmptyAt(agg_lists_1,mm,&ise);CHKERRQ(ierr); 330 if (!ise) { 331 const PetscInt lid = mm; 332 /* for (clid_iterator=0;clid_iterator<nselected_1;clid_iterator++) { */ 333 /* PetscInt flid = clid_lid_1[clid_iterator]; assert(flid != -1); */ 334 PetscScalar AA[3][3]; 335 PetscBLASInt N=3,NRHS=1,LDA=3,IPIV[3],LDB=3,INFO; 336 PetscCDPos pos; 337 ierr = PetscCDGetHeadPos(agg_lists_1,lid,&pos);CHKERRQ(ierr); 338 while (pos) { 339 PetscInt flid; 340 ierr = PetscLLNGetID(pos, &flid);CHKERRQ(ierr); 341 ierr = PetscCDGetNextPos(agg_lists_1,lid,&pos);CHKERRQ(ierr); 342 343 if (flid < nFineLoc) { /* could be a ghost */ 344 PetscInt bestTID = -1; PetscReal best_alpha = 1.e10; 345 const PetscInt fgid = flid + myFine0; 346 /* compute shape function for gid */ 347 const PetscReal fcoord[3] = {coords[flid],coords[data_stride+flid],1.0}; 348 PetscBool haveit=PETSC_FALSE; PetscScalar alpha[3]; PetscInt clids[3]; 349 /* look for it */ 350 for (tid = node_tri[clid], jj=0; 351 jj < 5 && !haveit && tid != -1; 352 jj++) { 353 for (tt=0;tt<3;tt++) { 354 PetscInt cid2 = mid.trianglelist[3*tid + tt]; 355 PetscInt lid2 = selected_idx_2[cid2]; 356 AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0; 357 clids[tt] = cid2; /* store for interp */ 358 } 359 360 for (tt=0;tt<3;tt++) alpha[tt] = (PetscScalar)fcoord[tt]; 361 362 /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */ 363 LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO); 364 { 365 PetscBool have=PETSC_TRUE; PetscReal lowest=1.e10; 366 for (tt = 0, idx = 0 ; tt < 3 ; tt++) { 367 if (PetscRealPart(alpha[tt]) > (1.0+EPS) || PetscRealPart(alpha[tt]) < -EPS) have = PETSC_FALSE; 368 if (PetscRealPart(alpha[tt]) < lowest) { 369 lowest = PetscRealPart(alpha[tt]); 370 idx = tt; 371 } 372 } 373 haveit = have; 374 } 375 tid = mid.neighborlist[3*tid + idx]; 376 } 377 378 if (!haveit) { 379 /* brute force */ 380 for (tid=0 ; tid<mid.numberoftriangles && !haveit ; tid++) { 381 for (tt=0;tt<3;tt++) { 382 PetscInt cid2 = mid.trianglelist[3*tid + 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 LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO); 390 { 391 PetscBool have=PETSC_TRUE; PetscReal worst=0.0, v; 392 for (tt=0; tt<3 && have ;tt++) { 393 if (PetscRealPart(alpha[tt]) > 1.0+EPS || PetscRealPart(alpha[tt]) < -EPS) have=PETSC_FALSE; 394 if ((v=PetscAbs(PetscRealPart(alpha[tt])-0.5)) > worst) worst = v; 395 } 396 if (worst < best_alpha) { 397 best_alpha = worst; bestTID = tid; 398 } 399 haveit = have; 400 } 401 } 402 } 403 if (!haveit) { 404 if (best_alpha > *a_worst_best) *a_worst_best = best_alpha; 405 /* use best one */ 406 for (tt=0;tt<3;tt++) { 407 PetscInt cid2 = mid.trianglelist[3*bestTID + tt]; 408 PetscInt lid2 = selected_idx_2[cid2]; 409 AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0; 410 clids[tt] = cid2; /* store for interp */ 411 } 412 for (tt=0;tt<3;tt++) alpha[tt] = fcoord[tt]; 413 /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */ 414 LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO); 415 } 416 417 /* put in row of P */ 418 for (idx=0;idx<3;idx++) { 419 PetscScalar shp = alpha[idx]; 420 if (PetscAbs(PetscRealPart(shp)) > 1.e-6) { 421 PetscInt cgid = crsGID[clids[idx]]; 422 PetscInt jj = cgid*bs, ii = fgid*bs; /* need to gloalize */ 423 for (tt=0 ; tt < bs ; tt++, ii++, jj++) { 424 ierr = MatSetValues(a_Prol,1,&ii,1,&jj,&shp,INSERT_VALUES);CHKERRQ(ierr); 425 } 426 } 427 } 428 } 429 } /* aggregates iterations */ 430 clid++; 431 } /* a coarse agg */ 432 } /* for all fine nodes */ 433 434 ierr = ISRestoreIndices(selected_2, &selected_idx_2);CHKERRQ(ierr); 435 ierr = MatAssemblyBegin(a_Prol,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 436 ierr = MatAssemblyEnd(a_Prol,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 437 438 ierr = PetscFree(node_tri);CHKERRQ(ierr); 439 ierr = PetscFree(nTri);CHKERRQ(ierr); 440 } 441 #if defined PETSC_GAMG_USE_LOG 442 ierr = PetscLogEventEnd(petsc_gamg_setup_events[FIND_V],0,0,0,0);CHKERRQ(ierr); 443 #endif 444 free(mid.trianglelist); 445 free(mid.neighborlist); 446 ierr = PetscFree(in.pointlist);CHKERRQ(ierr); 447 448 PetscFunctionReturn(0); 449 #else 450 SETERRQ(((PetscObject)a_Prol)->comm,PETSC_ERR_PLIB,"configure with TRIANGLE to use geometric MG"); 451 #endif 452 } 453 /* -------------------------------------------------------------------------- */ 454 /* 455 getGIDsOnSquareGraph - square graph, get 456 457 Input Parameter: 458 . nselected_1 - selected local indices (includes ghosts in input Gmat1) 459 . clid_lid_1 - [nselected_1] lids of selected nodes 460 . Gmat1 - graph that goes with 'selected_1' 461 Output Parameter: 462 . a_selected_2 - selected local indices (includes ghosts in output a_Gmat_2) 463 . a_Gmat_2 - graph that is squared of 'Gmat_1' 464 . a_crsGID[a_selected_2.size()] - map of global IDs of coarse grid nodes 465 */ 466 #undef __FUNCT__ 467 #define __FUNCT__ "getGIDsOnSquareGraph" 468 static PetscErrorCode getGIDsOnSquareGraph(const PetscInt nselected_1, 469 const PetscInt clid_lid_1[], 470 const Mat Gmat1, 471 IS *a_selected_2, 472 Mat *a_Gmat_2, 473 PetscInt **a_crsGID) 474 { 475 PetscErrorCode ierr; 476 PetscMPIInt mype,npe; 477 PetscInt *crsGID, kk,my0,Iend,nloc; 478 MPI_Comm wcomm = ((PetscObject)Gmat1)->comm; 479 480 PetscFunctionBegin; 481 ierr = MPI_Comm_rank(wcomm,&mype);CHKERRQ(ierr); 482 ierr = MPI_Comm_size(wcomm,&npe);CHKERRQ(ierr); 483 ierr = MatGetOwnershipRange(Gmat1,&my0,&Iend);CHKERRQ(ierr); /* AIJ */ 484 nloc = Iend - my0; /* this does not change */ 485 486 if (npe == 1) { /* not much to do in serial */ 487 ierr = PetscMalloc(nselected_1*sizeof(PetscInt), &crsGID);CHKERRQ(ierr); 488 for (kk=0;kk<nselected_1;kk++) crsGID[kk] = kk; 489 *a_Gmat_2 = 0; 490 ierr = ISCreateGeneral(PETSC_COMM_SELF,nselected_1,clid_lid_1,PETSC_COPY_VALUES,a_selected_2);CHKERRQ(ierr); 491 } else { 492 PetscInt idx,num_fine_ghosts,num_crs_ghost,myCrs0; 493 Mat_MPIAIJ *mpimat2; 494 Mat Gmat2; 495 Vec locState; 496 PetscScalar *cpcol_state; 497 498 /* scan my coarse zero gid, set 'lid_state' with coarse GID */ 499 kk = nselected_1; 500 MPI_Scan(&kk, &myCrs0, 1, MPIU_INT, MPIU_SUM, wcomm); 501 myCrs0 -= nselected_1; 502 503 if (a_Gmat_2) { /* output */ 504 /* grow graph to get wider set of selected vertices to cover fine grid, invalidates 'llist' */ 505 ierr = MatTransposeMatMult(Gmat1, Gmat1, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &Gmat2);CHKERRQ(ierr); 506 *a_Gmat_2 = Gmat2; /* output */ 507 } else Gmat2 = Gmat1; /* use local to get crsGIDs at least */ 508 /* get coarse grid GIDS for selected (locals and ghosts) */ 509 mpimat2 = (Mat_MPIAIJ*)Gmat2->data; 510 ierr = MatGetVecs(Gmat2, &locState, 0);CHKERRQ(ierr); 511 ierr = VecSet(locState, (PetscScalar)(PetscReal)(-1));CHKERRQ(ierr); /* set with UNKNOWN state */ 512 for (kk=0;kk<nselected_1;kk++) { 513 PetscInt fgid = clid_lid_1[kk] + my0; 514 PetscScalar v = (PetscScalar)(kk+myCrs0); 515 ierr = VecSetValues(locState, 1, &fgid, &v, INSERT_VALUES);CHKERRQ(ierr); /* set with PID */ 516 } 517 ierr = VecAssemblyBegin(locState);CHKERRQ(ierr); 518 ierr = VecAssemblyEnd(locState);CHKERRQ(ierr); 519 ierr = VecScatterBegin(mpimat2->Mvctx,locState,mpimat2->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 520 ierr = VecScatterEnd(mpimat2->Mvctx,locState,mpimat2->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 521 ierr = VecGetLocalSize(mpimat2->lvec, &num_fine_ghosts);CHKERRQ(ierr); 522 ierr = VecGetArray(mpimat2->lvec, &cpcol_state);CHKERRQ(ierr); 523 for (kk=0,num_crs_ghost=0;kk<num_fine_ghosts;kk++) { 524 if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) num_crs_ghost++; 525 } 526 ierr = PetscMalloc((nselected_1+num_crs_ghost)*sizeof(PetscInt), &crsGID);CHKERRQ(ierr); /* output */ 527 { 528 PetscInt *selected_set; 529 ierr = PetscMalloc((nselected_1+num_crs_ghost)*sizeof(PetscInt), &selected_set);CHKERRQ(ierr); 530 /* do ghost of 'crsGID' */ 531 for (kk=0,idx=nselected_1;kk<num_fine_ghosts;kk++) { 532 if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) { 533 PetscInt cgid = (PetscInt)PetscRealPart(cpcol_state[kk]); 534 selected_set[idx] = nloc + kk; 535 crsGID[idx++] = cgid; 536 } 537 } 538 assert(idx==(nselected_1+num_crs_ghost)); 539 ierr = VecRestoreArray(mpimat2->lvec, &cpcol_state);CHKERRQ(ierr); 540 /* do locals in 'crsGID' */ 541 ierr = VecGetArray(locState, &cpcol_state);CHKERRQ(ierr); 542 for (kk=0,idx=0;kk<nloc;kk++) { 543 if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) { 544 PetscInt cgid = (PetscInt)PetscRealPart(cpcol_state[kk]); 545 selected_set[idx] = kk; 546 crsGID[idx++] = cgid; 547 } 548 } 549 assert(idx==nselected_1); 550 ierr = VecRestoreArray(locState, &cpcol_state);CHKERRQ(ierr); 551 552 if (a_selected_2 != 0) { /* output */ 553 ierr = ISCreateGeneral(PETSC_COMM_SELF,(nselected_1+num_crs_ghost),selected_set,PETSC_OWN_POINTER,a_selected_2);CHKERRQ(ierr); 554 } else { 555 ierr = PetscFree(selected_set);CHKERRQ(ierr); 556 } 557 } 558 ierr = VecDestroy(&locState);CHKERRQ(ierr); 559 } 560 *a_crsGID = crsGID; /* output */ 561 562 PetscFunctionReturn(0); 563 } 564 565 /* -------------------------------------------------------------------------- */ 566 /* 567 PCGAMGgraph_GEO 568 569 Input Parameter: 570 . pc - this 571 . Amat - matrix on this fine level 572 Output Parameter: 573 . a_Gmat 574 */ 575 #undef __FUNCT__ 576 #define __FUNCT__ "PCGAMGgraph_GEO" 577 PetscErrorCode PCGAMGgraph_GEO(PC pc, 578 const Mat Amat, 579 Mat *a_Gmat) 580 { 581 PetscErrorCode ierr; 582 PC_MG *mg = (PC_MG*)pc->data; 583 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 584 const PetscInt verbose = pc_gamg->verbose; 585 const PetscReal vfilter = pc_gamg->threshold; 586 PetscMPIInt mype,npe; 587 MPI_Comm wcomm = ((PetscObject)Amat)->comm; 588 Mat Gmat; 589 PetscBool set,flg,symm; 590 PetscFunctionBegin; 591 #if defined PETSC_USE_LOG 592 ierr = PetscLogEventBegin(PC_GAMGGgraph_GEO,0,0,0,0);CHKERRQ(ierr); 593 #endif 594 ierr = MPI_Comm_rank(wcomm, &mype);CHKERRQ(ierr); 595 ierr = MPI_Comm_size(wcomm, &npe);CHKERRQ(ierr); 596 597 ierr = MatIsSymmetricKnown(Amat, &set, &flg);CHKERRQ(ierr); 598 symm = (PetscBool)!(set && flg); 599 600 ierr = PCGAMGCreateGraph(Amat, &Gmat);CHKERRQ(ierr); 601 ierr = PCGAMGFilterGraph(&Gmat, vfilter, symm, verbose);CHKERRQ(ierr); 602 603 *a_Gmat = Gmat; 604 #if defined PETSC_USE_LOG 605 ierr = PetscLogEventEnd(PC_GAMGGgraph_GEO,0,0,0,0);CHKERRQ(ierr); 606 #endif 607 PetscFunctionReturn(0); 608 } 609 610 /* -------------------------------------------------------------------------- */ 611 /* 612 PCGAMGcoarsen_GEO 613 614 Input Parameter: 615 . a_pc - this 616 . a_Gmat - graph 617 Output Parameter: 618 . a_llist_parent - linked list from selected indices for data locality only 619 */ 620 #undef __FUNCT__ 621 #define __FUNCT__ "PCGAMGcoarsen_GEO" 622 PetscErrorCode PCGAMGcoarsen_GEO(PC a_pc, 623 Mat *a_Gmat, 624 PetscCoarsenData **a_llist_parent) 625 { 626 PetscErrorCode ierr; 627 PC_MG *mg = (PC_MG*)a_pc->data; 628 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 629 PetscInt Istart,Iend,nloc,kk,Ii,ncols; 630 PetscMPIInt mype,npe; 631 IS perm; 632 GAMGNode *gnodes; 633 PetscInt *permute; 634 Mat Gmat = *a_Gmat; 635 MPI_Comm wcomm = ((PetscObject)Gmat)->comm; 636 MatCoarsen crs; 637 638 PetscFunctionBegin; 639 #if defined PETSC_USE_LOG 640 ierr = PetscLogEventBegin(PC_GAMGCoarsen_GEO,0,0,0,0);CHKERRQ(ierr); 641 #endif 642 ierr = MPI_Comm_rank(wcomm, &mype);CHKERRQ(ierr); 643 ierr = MPI_Comm_size(wcomm, &npe);CHKERRQ(ierr); 644 ierr = MatGetOwnershipRange(Gmat, &Istart, &Iend);CHKERRQ(ierr); 645 nloc = (Iend-Istart); 646 647 /* create random permutation with sort for geo-mg */ 648 ierr = PetscMalloc(nloc*sizeof(GAMGNode), &gnodes);CHKERRQ(ierr); 649 ierr = PetscMalloc(nloc*sizeof(PetscInt), &permute);CHKERRQ(ierr); 650 651 for (Ii=Istart; Ii<Iend; Ii++) { /* locals only? */ 652 ierr = MatGetRow(Gmat,Ii,&ncols,0,0);CHKERRQ(ierr); 653 { 654 PetscInt lid = Ii - Istart; 655 gnodes[lid].lid = lid; 656 gnodes[lid].degree = ncols; 657 } 658 ierr = MatRestoreRow(Gmat,Ii,&ncols,0,0);CHKERRQ(ierr); 659 } 660 /* randomize */ 661 srand(1); /* make deterministic */ 662 if (PETSC_TRUE) { 663 PetscBool *bIndexSet; 664 ierr = PetscMalloc(nloc*sizeof(PetscBool), &bIndexSet);CHKERRQ(ierr); 665 for (Ii = 0; Ii < nloc ; Ii++) bIndexSet[Ii] = PETSC_FALSE; 666 for (Ii = 0; Ii < nloc ; Ii++) 667 { 668 PetscInt iSwapIndex = rand()%nloc; 669 if (!bIndexSet[iSwapIndex] && iSwapIndex != Ii) 670 { 671 GAMGNode iTemp = gnodes[iSwapIndex]; 672 gnodes[iSwapIndex] = gnodes[Ii]; 673 gnodes[Ii] = iTemp; 674 bIndexSet[Ii] = PETSC_TRUE; 675 bIndexSet[iSwapIndex] = PETSC_TRUE; 676 } 677 } 678 ierr = PetscFree(bIndexSet);CHKERRQ(ierr); 679 } 680 /* only sort locals */ 681 qsort(gnodes, nloc, sizeof(GAMGNode), petsc_geo_mg_compare); 682 /* create IS of permutation */ 683 for (kk=0;kk<nloc;kk++) { /* locals only */ 684 permute[kk] = gnodes[kk].lid; 685 } 686 ierr = ISCreateGeneral(PETSC_COMM_SELF, nloc, permute, PETSC_OWN_POINTER, &perm);CHKERRQ(ierr); 687 688 ierr = PetscFree(gnodes);CHKERRQ(ierr); 689 690 /* get MIS aggs */ 691 692 ierr = MatCoarsenCreate(wcomm, &crs);CHKERRQ(ierr); 693 ierr = MatCoarsenSetType(crs, MATCOARSENMIS);CHKERRQ(ierr); 694 ierr = MatCoarsenSetGreedyOrdering(crs, perm);CHKERRQ(ierr); 695 ierr = MatCoarsenSetAdjacency(crs, Gmat);CHKERRQ(ierr); 696 ierr = MatCoarsenSetVerbose(crs, pc_gamg->verbose);CHKERRQ(ierr); 697 ierr = MatCoarsenSetStrictAggs(crs, PETSC_FALSE);CHKERRQ(ierr); 698 ierr = MatCoarsenApply(crs);CHKERRQ(ierr); 699 ierr = MatCoarsenGetData(crs, a_llist_parent);CHKERRQ(ierr); 700 ierr = MatCoarsenDestroy(&crs);CHKERRQ(ierr); 701 702 ierr = ISDestroy(&perm);CHKERRQ(ierr); 703 #if defined PETSC_USE_LOG 704 ierr = PetscLogEventEnd(PC_GAMGCoarsen_GEO,0,0,0,0);CHKERRQ(ierr); 705 #endif 706 PetscFunctionReturn(0); 707 } 708 709 /* -------------------------------------------------------------------------- */ 710 /* 711 PCGAMGProlongator_GEO 712 713 Input Parameter: 714 . pc - this 715 . Amat - matrix on this fine level 716 . Graph - used to get ghost data for nodes in 717 . selected_1 - [nselected] 718 . agg_lists - [nselected] 719 Output Parameter: 720 . a_P_out - prolongation operator to the next level 721 */ 722 #undef __FUNCT__ 723 #define __FUNCT__ "PCGAMGProlongator_GEO" 724 PetscErrorCode PCGAMGProlongator_GEO(PC pc, 725 const Mat Amat, 726 const Mat Gmat, 727 PetscCoarsenData *agg_lists, 728 Mat *a_P_out) 729 { 730 PC_MG *mg = (PC_MG*)pc->data; 731 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 732 const PetscInt verbose = pc_gamg->verbose; 733 const PetscInt dim = pc_gamg->data_cell_cols, data_cols = pc_gamg->data_cell_cols; 734 PetscErrorCode ierr; 735 PetscInt Istart,Iend,nloc,my0,jj,kk,ncols,nLocalSelected,bs,*clid_flid; 736 Mat Prol; 737 PetscMPIInt mype, npe; 738 MPI_Comm wcomm = ((PetscObject)Amat)->comm; 739 IS selected_2,selected_1; 740 const PetscInt *selected_idx; 741 742 PetscFunctionBegin; 743 #if defined PETSC_USE_LOG 744 ierr = PetscLogEventBegin(PC_GAMGProlongator_GEO,0,0,0,0);CHKERRQ(ierr); 745 #endif 746 ierr = MPI_Comm_rank(wcomm,&mype);CHKERRQ(ierr); 747 ierr = MPI_Comm_size(wcomm,&npe);CHKERRQ(ierr); 748 ierr = MatGetOwnershipRange(Amat, &Istart, &Iend);CHKERRQ(ierr); 749 ierr = MatGetBlockSize(Amat, &bs);CHKERRQ(ierr); 750 nloc = (Iend-Istart)/bs; my0 = Istart/bs; assert((Iend-Istart)%bs==0); 751 752 /* get 'nLocalSelected' */ 753 ierr = PetscCDGetMIS(agg_lists, &selected_1);CHKERRQ(ierr); 754 ierr = ISGetSize(selected_1, &jj);CHKERRQ(ierr); 755 ierr = PetscMalloc(jj*sizeof(PetscInt), &clid_flid);CHKERRQ(ierr); 756 ierr = ISGetIndices(selected_1, &selected_idx);CHKERRQ(ierr); 757 for (kk=0,nLocalSelected=0;kk<jj;kk++) { 758 PetscInt lid = selected_idx[kk]; 759 if (lid<nloc) { 760 ierr = MatGetRow(Gmat,lid+my0,&ncols,0,0);CHKERRQ(ierr); 761 if (ncols>1) { /* fiter out singletons */ 762 clid_flid[nLocalSelected++] = lid; 763 } else assert(0); /* filtered in coarsening */ 764 ierr = MatRestoreRow(Gmat,lid+my0,&ncols,0,0);CHKERRQ(ierr); 765 } 766 } 767 ierr = ISRestoreIndices(selected_1, &selected_idx);CHKERRQ(ierr); 768 ierr = ISDestroy(&selected_1);CHKERRQ(ierr); /* this is selected_1 in serial */ 769 770 /* create prolongator, create P matrix */ 771 ierr = MatCreate(wcomm, &Prol);CHKERRQ(ierr); 772 ierr = MatSetSizes(Prol,nloc*bs,nLocalSelected*bs,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 773 ierr = MatSetBlockSizes(Prol, bs, bs);CHKERRQ(ierr); 774 ierr = MatSetType(Prol, MATAIJ);CHKERRQ(ierr); 775 ierr = MatSeqAIJSetPreallocation(Prol,3*data_cols,PETSC_NULL);CHKERRQ(ierr); 776 ierr = MatMPIAIJSetPreallocation(Prol,3*data_cols,PETSC_NULL,3*data_cols,PETSC_NULL);CHKERRQ(ierr); 777 /* ierr = MatCreateAIJ(wcomm, */ 778 /* nloc*bs, nLocalSelected*bs, */ 779 /* PETSC_DETERMINE, PETSC_DETERMINE, */ 780 /* 3*data_cols, PETSC_NULL, */ 781 /* 3*data_cols, PETSC_NULL, */ 782 /* &Prol); */ 783 /* CHKERRQ(ierr); */ 784 785 /* can get all points "removed" - but not on geomg */ 786 ierr = MatGetSize(Prol, &kk, &jj);CHKERRQ(ierr); 787 if (jj==0) { 788 if (verbose) { 789 PetscPrintf(wcomm,"[%d]%s ERROE: no selected points on coarse grid\n",mype,__FUNCT__); 790 } 791 ierr = PetscFree(clid_flid);CHKERRQ(ierr); 792 ierr = MatDestroy(&Prol);CHKERRQ(ierr); 793 *a_P_out = PETSC_NULL; /* out */ 794 PetscFunctionReturn(0); 795 } 796 797 { 798 PetscReal *coords; 799 PetscInt data_stride; 800 PetscInt *crsGID = PETSC_NULL; 801 Mat Gmat2; 802 803 assert(dim==data_cols); 804 /* grow ghost data for better coarse grid cover of fine grid */ 805 #if defined PETSC_GAMG_USE_LOG 806 ierr = PetscLogEventBegin(petsc_gamg_setup_events[SET5],0,0,0,0);CHKERRQ(ierr); 807 #endif 808 /* messy method, squares graph and gets some data */ 809 ierr = getGIDsOnSquareGraph(nLocalSelected, clid_flid, Gmat, &selected_2, &Gmat2, &crsGID);CHKERRQ(ierr); 810 /* llist is now not valid wrt squared graph, but will work as iterator in 'triangulateAndFormProl' */ 811 #if defined PETSC_GAMG_USE_LOG 812 ierr = PetscLogEventEnd(petsc_gamg_setup_events[SET5],0,0,0,0);CHKERRQ(ierr); 813 #endif 814 /* create global vector of coorindates in 'coords' */ 815 if (npe > 1) { 816 ierr = PCGAMGGetDataWithGhosts(Gmat2, dim, pc_gamg->data, &data_stride, &coords);CHKERRQ(ierr); 817 } else { 818 coords = (PetscReal*)pc_gamg->data; 819 data_stride = pc_gamg->data_sz/pc_gamg->data_cell_cols; 820 } 821 ierr = MatDestroy(&Gmat2);CHKERRQ(ierr); 822 823 /* triangulate */ 824 if (dim == 2) { 825 PetscReal metric,tm; 826 #if defined PETSC_GAMG_USE_LOG 827 ierr = PetscLogEventBegin(petsc_gamg_setup_events[SET6],0,0,0,0);CHKERRQ(ierr); 828 #endif 829 ierr = triangulateAndFormProl(selected_2, data_stride, coords,nLocalSelected, clid_flid, agg_lists, crsGID, bs, Prol, &metric);CHKERRQ(ierr); 830 #if defined PETSC_GAMG_USE_LOG 831 ierr = PetscLogEventEnd(petsc_gamg_setup_events[SET6],0,0,0,0);CHKERRQ(ierr); 832 #endif 833 ierr = PetscFree(crsGID);CHKERRQ(ierr); 834 835 /* clean up and create coordinates for coarse grid (output) */ 836 if (npe > 1) ierr = PetscFree(coords);CHKERRQ(ierr); 837 838 ierr = MPI_Allreduce(&metric, &tm, 1, MPIU_REAL, MPIU_MAX, wcomm);CHKERRQ(ierr); 839 if (tm > 1.) { /* needs to be globalized - should not happen */ 840 if (verbose) { 841 PetscPrintf(wcomm,"[%d]%s failed metric for coarse grid %e\n",mype,__FUNCT__,tm); 842 } 843 ierr = MatDestroy(&Prol);CHKERRQ(ierr); 844 Prol = PETSC_NULL; 845 } else if (metric > .0) { 846 if (verbose) { 847 PetscPrintf(wcomm,"[%d]%s worst metric for coarse grid = %e\n",mype,__FUNCT__,metric); 848 } 849 } 850 } else { 851 SETERRQ(wcomm,PETSC_ERR_PLIB,"3D not implemented for 'geo' AMG"); 852 } 853 { /* create next coords - output */ 854 PetscReal *crs_crds; 855 ierr = PetscMalloc(dim*nLocalSelected*sizeof(PetscReal), &crs_crds);CHKERRQ(ierr); 856 for (kk=0;kk<nLocalSelected;kk++) {/* grab local select nodes to promote - output */ 857 PetscInt lid = clid_flid[kk]; 858 for (jj=0;jj<dim;jj++) crs_crds[jj*nLocalSelected + kk] = pc_gamg->data[jj*nloc + lid]; 859 } 860 861 ierr = PetscFree(pc_gamg->data);CHKERRQ(ierr); 862 pc_gamg->data = crs_crds; /* out */ 863 pc_gamg->data_sz = dim*nLocalSelected; 864 } 865 ierr = ISDestroy(&selected_2);CHKERRQ(ierr); 866 } 867 868 *a_P_out = Prol; /* out */ 869 ierr = PetscFree(clid_flid);CHKERRQ(ierr); 870 #if defined PETSC_USE_LOG 871 ierr = PetscLogEventEnd(PC_GAMGProlongator_GEO,0,0,0,0);CHKERRQ(ierr); 872 #endif 873 PetscFunctionReturn(0); 874 } 875 876 /* -------------------------------------------------------------------------- */ 877 /* 878 PCCreateGAMG_GEO 879 880 Input Parameter: 881 . pc - 882 */ 883 #undef __FUNCT__ 884 #define __FUNCT__ "PCCreateGAMG_GEO" 885 PetscErrorCode PCCreateGAMG_GEO(PC pc) 886 { 887 PetscErrorCode ierr; 888 PC_MG *mg = (PC_MG*)pc->data; 889 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 890 891 PetscFunctionBegin; 892 pc->ops->setfromoptions = PCSetFromOptions_GEO; 893 /* pc->ops->destroy = PCDestroy_GEO; */ 894 /* reset does not do anything; setup not virtual */ 895 896 /* set internal function pointers */ 897 pc_gamg->graph = PCGAMGgraph_GEO; 898 pc_gamg->coarsen = PCGAMGcoarsen_GEO; 899 pc_gamg->prolongator = PCGAMGProlongator_GEO; 900 pc_gamg->optprol = 0; 901 pc_gamg->formkktprol = 0; 902 903 pc_gamg->createdefaultdata = PCSetData_GEO; 904 905 ierr = PetscObjectComposeFunctionDynamic((PetscObject)pc, 906 "PCSetCoordinates_C", 907 "PCSetCoordinates_GEO", 908 PCSetCoordinates_GEO);CHKERRQ(ierr); 909 910 PetscFunctionReturn(0); 911 } 912