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 PetscFunctionReturn(0); 134 } 135 136 /* -------------------------------------------------------------------------- */ 137 /* 138 triangulateAndFormProl 139 140 Input Parameter: 141 . selected_2 - list of selected local ID, includes selected ghosts 142 . data_stride - 143 . coords[2*data_stride] - column vector of local coordinates w/ ghosts 144 . nselected_1 - selected IDs that go with base (1) graph 145 . clid_lid_1[nselected_1] - lids of selected (c) nodes ??????????? 146 . agg_lists_1 - list of aggregates 147 . crsGID[selected.size()] - global index for prolongation operator 148 . bs - block size 149 Output Parameter: 150 . a_Prol - prolongation operator 151 . a_worst_best - measure of worst missed fine vertex, 0 is no misses 152 */ 153 #undef __FUNCT__ 154 #define __FUNCT__ "triangulateAndFormProl" 155 static PetscErrorCode triangulateAndFormProl(IS selected_2, /* list of selected local ID, includes selected ghosts */ 156 const PetscInt data_stride, 157 const PetscReal coords[], /* column vector of local coordinates w/ ghosts */ 158 const PetscInt nselected_1, /* list of selected local ID, includes selected ghosts */ 159 const PetscInt clid_lid_1[], 160 const PetscCoarsenData *agg_lists_1, /* selected_1 vertices of aggregate unselected vertices */ 161 const PetscInt crsGID[], 162 const PetscInt bs, 163 Mat a_Prol, /* prolongation operator (output) */ 164 PetscReal *a_worst_best) /* measure of worst missed fine vertex, 0 is no misses */ 165 { 166 #if defined(PETSC_HAVE_TRIANGLE) 167 PetscErrorCode ierr; 168 PetscInt jj,tid,tt,idx,nselected_2; 169 struct triangulateio in,mid; 170 const PetscInt *selected_idx_2; 171 PetscMPIInt mype,npe; 172 PetscInt Istart,Iend,nFineLoc,myFine0; 173 int kk,nPlotPts,sid; 174 MPI_Comm wcomm = ((PetscObject)a_Prol)->comm; 175 PetscReal tm; 176 177 PetscFunctionBegin; 178 ierr = MPI_Comm_rank(wcomm,&mype);CHKERRQ(ierr); 179 ierr = MPI_Comm_size(wcomm,&npe);CHKERRQ(ierr); 180 ierr = ISGetSize(selected_2, &nselected_2);CHKERRQ(ierr); 181 if (nselected_2 == 1 || nselected_2 == 2) { /* 0 happens on idle processors */ 182 *a_worst_best = 100.0; /* this will cause a stop, but not globalized (should not happen) */ 183 } else *a_worst_best = 0.0; 184 ierr = MPI_Allreduce(a_worst_best, &tm, 1, MPIU_REAL, MPIU_MAX, wcomm);CHKERRQ(ierr); 185 if (tm > 0.0) { 186 *a_worst_best = 100.0; 187 PetscFunctionReturn(0); 188 } 189 ierr = MatGetOwnershipRange(a_Prol, &Istart, &Iend);CHKERRQ(ierr); 190 nFineLoc = (Iend-Istart)/bs; myFine0 = Istart/bs; 191 nPlotPts = nFineLoc; /* locals */ 192 /* traingle */ 193 /* Define input points - in*/ 194 in.numberofpoints = nselected_2; 195 in.numberofpointattributes = 0; 196 /* get nselected points */ 197 ierr = PetscMalloc(2*(nselected_2)*sizeof(REAL), &in.pointlist);CHKERRQ(ierr); 198 ierr = ISGetIndices(selected_2, &selected_idx_2);CHKERRQ(ierr); 199 200 for (kk=0,sid=0;kk<nselected_2;kk++,sid += 2) { 201 PetscInt lid = selected_idx_2[kk]; 202 in.pointlist[sid] = coords[lid]; 203 in.pointlist[sid+1] = coords[data_stride + lid]; 204 if (lid>=nFineLoc) nPlotPts++; 205 } 206 assert(sid==2*nselected_2); 207 208 in.numberofsegments = 0; 209 in.numberofedges = 0; 210 in.numberofholes = 0; 211 in.numberofregions = 0; 212 in.trianglelist = 0; 213 in.segmentmarkerlist = 0; 214 in.pointattributelist = 0; 215 in.pointmarkerlist = 0; 216 in.triangleattributelist = 0; 217 in.trianglearealist = 0; 218 in.segmentlist = 0; 219 in.holelist = 0; 220 in.regionlist = 0; 221 in.edgelist = 0; 222 in.edgemarkerlist = 0; 223 in.normlist = 0; 224 /* triangulate */ 225 mid.pointlist = 0; /* Not needed if -N switch used. */ 226 /* Not needed if -N switch used or number of point attributes is zero: */ 227 mid.pointattributelist = 0; 228 mid.pointmarkerlist = 0; /* Not needed if -N or -B switch used. */ 229 mid.trianglelist = 0; /* Not needed if -E switch used. */ 230 /* Not needed if -E switch used or number of triangle attributes is zero: */ 231 mid.triangleattributelist = 0; 232 mid.neighborlist = 0; /* Needed only if -n switch used. */ 233 /* Needed only if segments are output (-p or -c) and -P not used: */ 234 mid.segmentlist = 0; 235 /* Needed only if segments are output (-p or -c) and -P and -B not used: */ 236 mid.segmentmarkerlist = 0; 237 mid.edgelist = 0; /* Needed only if -e switch used. */ 238 mid.edgemarkerlist = 0; /* Needed if -e used and -B not used. */ 239 mid.numberoftriangles = 0; 240 241 /* Triangulate the points. Switches are chosen to read and write a */ 242 /* PSLG (p), preserve the convex hull (c), number everything from */ 243 /* zero (z), assign a regional attribute to each element (A), and */ 244 /* produce an edge list (e), a Voronoi diagram (v), and a triangle */ 245 /* neighbor list (n). */ 246 if (nselected_2 != 0) { /* inactive processor */ 247 char args[] = "npczQ"; /* c is needed ? */ 248 triangulate(args, &in, &mid, (struct triangulateio *) NULL); 249 /* output .poly files for 'showme' */ 250 if (!PETSC_TRUE) { 251 static int level = 1; 252 FILE *file; char fname[32]; 253 254 sprintf(fname,"C%d_%d.poly",level,mype); file = fopen(fname, "w"); 255 /*First line: <# of vertices> <dimension (must be 2)> <# of attributes> <# of boundary markers (0 or 1)>*/ 256 fprintf(file, "%d %d %d %d\n",in.numberofpoints,2,0,0); 257 /*Following lines: <vertex #> <x> <y> */ 258 for (kk=0,sid=0;kk<in.numberofpoints;kk++,sid += 2) { 259 fprintf(file, "%d %e %e\n",kk,in.pointlist[sid],in.pointlist[sid+1]); 260 } 261 /*One line: <# of segments> <# of boundary markers (0 or 1)> */ 262 fprintf(file, "%d %d\n",0,0); 263 /*Following lines: <segment #> <endpoint> <endpoint> [boundary marker] */ 264 /* One line: <# of holes> */ 265 fprintf(file, "%d\n",0); 266 /* Following lines: <hole #> <x> <y> */ 267 /* Optional line: <# of regional attributes and/or area constraints> */ 268 /* Optional following lines: <region #> <x> <y> <attribute> <maximum area> */ 269 fclose(file); 270 271 /* elems */ 272 sprintf(fname,"C%d_%d.ele",level,mype); file = fopen(fname, "w"); 273 /* First line: <# of triangles> <nodes per triangle> <# of attributes> */ 274 fprintf(file, "%d %d %d\n",mid.numberoftriangles,3,0); 275 /* Remaining lines: <triangle #> <node> <node> <node> ... [attributes] */ 276 for (kk=0,sid=0;kk<mid.numberoftriangles;kk++,sid += 3) { 277 fprintf(file, "%d %d %d %d\n",kk,mid.trianglelist[sid],mid.trianglelist[sid+1],mid.trianglelist[sid+2]); 278 } 279 fclose(file); 280 281 sprintf(fname,"C%d_%d.node",level,mype); file = fopen(fname, "w"); 282 /* First line: <# of vertices> <dimension (must be 2)> <# of attributes> <# of boundary markers (0 or 1)> */ 283 /* fprintf(file, "%d %d %d %d\n",in.numberofpoints,2,0,0); */ 284 fprintf(file, "%d %d %d %d\n",nPlotPts,2,0,0); 285 /*Following lines: <vertex #> <x> <y> */ 286 for (kk=0,sid=0;kk<in.numberofpoints;kk++,sid+=2) { 287 fprintf(file, "%d %e %e\n",kk,in.pointlist[sid],in.pointlist[sid+1]); 288 } 289 290 sid /= 2; 291 for (jj=0;jj<nFineLoc;jj++) { 292 PetscBool sel = PETSC_TRUE; 293 for (kk=0 ; kk<nselected_2 && sel ; kk++) { 294 PetscInt lid = selected_idx_2[kk]; 295 if (lid == jj) sel = PETSC_FALSE; 296 } 297 if (sel) { 298 fprintf(file, "%d %e %e\n",sid++,coords[jj],coords[data_stride + jj]); 299 } 300 } 301 fclose(file); 302 assert(sid==nPlotPts); 303 level++; 304 } 305 } 306 #if defined PETSC_GAMG_USE_LOG 307 ierr = PetscLogEventBegin(petsc_gamg_setup_events[FIND_V],0,0,0,0);CHKERRQ(ierr); 308 #endif 309 { /* form P - setup some maps */ 310 PetscInt clid,mm,*nTri,*node_tri; 311 312 ierr = PetscMalloc(nselected_2*sizeof(PetscInt), &node_tri);CHKERRQ(ierr); 313 ierr = PetscMalloc(nselected_2*sizeof(PetscInt), &nTri);CHKERRQ(ierr); 314 315 /* need list of triangles on node */ 316 for (kk=0;kk<nselected_2;kk++) nTri[kk] = 0; 317 for (tid=0,kk=0;tid<mid.numberoftriangles;tid++) { 318 for (jj=0;jj<3;jj++) { 319 PetscInt cid = mid.trianglelist[kk++]; 320 if (nTri[cid] == 0) node_tri[cid] = tid; 321 nTri[cid]++; 322 } 323 } 324 #define EPS 1.e-12 325 /* find points and set prolongation */ 326 for (mm = clid = 0 ; mm < nFineLoc ; mm++) { 327 PetscBool ise; 328 ierr = PetscCDEmptyAt(agg_lists_1,mm,&ise);CHKERRQ(ierr); 329 if (!ise) { 330 const PetscInt lid = mm; 331 /* for (clid_iterator=0;clid_iterator<nselected_1;clid_iterator++) { */ 332 /* PetscInt flid = clid_lid_1[clid_iterator]; assert(flid != -1); */ 333 PetscScalar AA[3][3]; 334 PetscBLASInt N=3,NRHS=1,LDA=3,IPIV[3],LDB=3,INFO; 335 PetscCDPos pos; 336 ierr = PetscCDGetHeadPos(agg_lists_1,lid,&pos);CHKERRQ(ierr); 337 while (pos) { 338 PetscInt flid; 339 ierr = PetscLLNGetID(pos, &flid);CHKERRQ(ierr); 340 ierr = PetscCDGetNextPos(agg_lists_1,lid,&pos);CHKERRQ(ierr); 341 342 if (flid < nFineLoc) { /* could be a ghost */ 343 PetscInt bestTID = -1; PetscReal best_alpha = 1.e10; 344 const PetscInt fgid = flid + myFine0; 345 /* compute shape function for gid */ 346 const PetscReal fcoord[3] = {coords[flid],coords[data_stride+flid],1.0}; 347 PetscBool haveit=PETSC_FALSE; PetscScalar alpha[3]; PetscInt clids[3]; 348 /* look for it */ 349 for (tid = node_tri[clid], jj=0; 350 jj < 5 && !haveit && tid != -1; 351 jj++) { 352 for (tt=0;tt<3;tt++) { 353 PetscInt cid2 = mid.trianglelist[3*tid + tt]; 354 PetscInt lid2 = selected_idx_2[cid2]; 355 AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0; 356 clids[tt] = cid2; /* store for interp */ 357 } 358 359 for (tt=0;tt<3;tt++) alpha[tt] = (PetscScalar)fcoord[tt]; 360 361 /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */ 362 LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO); 363 { 364 PetscBool have=PETSC_TRUE; PetscReal lowest=1.e10; 365 for (tt = 0, idx = 0 ; tt < 3 ; tt++) { 366 if (PetscRealPart(alpha[tt]) > (1.0+EPS) || PetscRealPart(alpha[tt]) < -EPS) have = PETSC_FALSE; 367 if (PetscRealPart(alpha[tt]) < lowest) { 368 lowest = PetscRealPart(alpha[tt]); 369 idx = tt; 370 } 371 } 372 haveit = have; 373 } 374 tid = mid.neighborlist[3*tid + idx]; 375 } 376 377 if (!haveit) { 378 /* brute force */ 379 for (tid=0 ; tid<mid.numberoftriangles && !haveit ; tid++) { 380 for (tt=0;tt<3;tt++) { 381 PetscInt cid2 = mid.trianglelist[3*tid + tt]; 382 PetscInt lid2 = selected_idx_2[cid2]; 383 AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0; 384 clids[tt] = cid2; /* store for interp */ 385 } 386 for (tt=0;tt<3;tt++) alpha[tt] = fcoord[tt]; 387 /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */ 388 LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO); 389 { 390 PetscBool have=PETSC_TRUE; PetscReal worst=0.0, v; 391 for (tt=0; tt<3 && have ;tt++) { 392 if (PetscRealPart(alpha[tt]) > 1.0+EPS || PetscRealPart(alpha[tt]) < -EPS) have=PETSC_FALSE; 393 if ((v=PetscAbs(PetscRealPart(alpha[tt])-0.5)) > worst) worst = v; 394 } 395 if (worst < best_alpha) { 396 best_alpha = worst; bestTID = tid; 397 } 398 haveit = have; 399 } 400 } 401 } 402 if (!haveit) { 403 if (best_alpha > *a_worst_best) *a_worst_best = best_alpha; 404 /* use best one */ 405 for (tt=0;tt<3;tt++) { 406 PetscInt cid2 = mid.trianglelist[3*bestTID + tt]; 407 PetscInt lid2 = selected_idx_2[cid2]; 408 AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0; 409 clids[tt] = cid2; /* store for interp */ 410 } 411 for (tt=0;tt<3;tt++) alpha[tt] = fcoord[tt]; 412 /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */ 413 LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO); 414 } 415 416 /* put in row of P */ 417 for (idx=0;idx<3;idx++) { 418 PetscScalar shp = alpha[idx]; 419 if (PetscAbs(PetscRealPart(shp)) > 1.e-6) { 420 PetscInt cgid = crsGID[clids[idx]]; 421 PetscInt jj = cgid*bs, ii = fgid*bs; /* need to gloalize */ 422 for (tt=0 ; tt < bs ; tt++, ii++, jj++) { 423 ierr = MatSetValues(a_Prol,1,&ii,1,&jj,&shp,INSERT_VALUES);CHKERRQ(ierr); 424 } 425 } 426 } 427 } 428 } /* aggregates iterations */ 429 clid++; 430 } /* a coarse agg */ 431 } /* for all fine nodes */ 432 433 ierr = ISRestoreIndices(selected_2, &selected_idx_2);CHKERRQ(ierr); 434 ierr = MatAssemblyBegin(a_Prol,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 435 ierr = MatAssemblyEnd(a_Prol,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 436 437 ierr = PetscFree(node_tri);CHKERRQ(ierr); 438 ierr = PetscFree(nTri);CHKERRQ(ierr); 439 } 440 #if defined PETSC_GAMG_USE_LOG 441 ierr = PetscLogEventEnd(petsc_gamg_setup_events[FIND_V],0,0,0,0);CHKERRQ(ierr); 442 #endif 443 free(mid.trianglelist); 444 free(mid.neighborlist); 445 ierr = PetscFree(in.pointlist);CHKERRQ(ierr); 446 447 PetscFunctionReturn(0); 448 #else 449 SETERRQ(((PetscObject)a_Prol)->comm,PETSC_ERR_PLIB,"configure with TRIANGLE to use geometric MG"); 450 #endif 451 } 452 /* -------------------------------------------------------------------------- */ 453 /* 454 getGIDsOnSquareGraph - square graph, get 455 456 Input Parameter: 457 . nselected_1 - selected local indices (includes ghosts in input Gmat1) 458 . clid_lid_1 - [nselected_1] lids of selected nodes 459 . Gmat1 - graph that goes with 'selected_1' 460 Output Parameter: 461 . a_selected_2 - selected local indices (includes ghosts in output a_Gmat_2) 462 . a_Gmat_2 - graph that is squared of 'Gmat_1' 463 . a_crsGID[a_selected_2.size()] - map of global IDs of coarse grid nodes 464 */ 465 #undef __FUNCT__ 466 #define __FUNCT__ "getGIDsOnSquareGraph" 467 static PetscErrorCode getGIDsOnSquareGraph(const PetscInt nselected_1, 468 const PetscInt clid_lid_1[], 469 const Mat Gmat1, 470 IS *a_selected_2, 471 Mat *a_Gmat_2, 472 PetscInt **a_crsGID) 473 { 474 PetscErrorCode ierr; 475 PetscMPIInt mype,npe; 476 PetscInt *crsGID, kk,my0,Iend,nloc; 477 MPI_Comm wcomm = ((PetscObject)Gmat1)->comm; 478 479 PetscFunctionBegin; 480 ierr = MPI_Comm_rank(wcomm,&mype);CHKERRQ(ierr); 481 ierr = MPI_Comm_size(wcomm,&npe);CHKERRQ(ierr); 482 ierr = MatGetOwnershipRange(Gmat1,&my0,&Iend);CHKERRQ(ierr); /* AIJ */ 483 nloc = Iend - my0; /* this does not change */ 484 485 if (npe == 1) { /* not much to do in serial */ 486 ierr = PetscMalloc(nselected_1*sizeof(PetscInt), &crsGID);CHKERRQ(ierr); 487 for (kk=0;kk<nselected_1;kk++) crsGID[kk] = kk; 488 *a_Gmat_2 = 0; 489 ierr = ISCreateGeneral(PETSC_COMM_SELF,nselected_1,clid_lid_1,PETSC_COPY_VALUES,a_selected_2);CHKERRQ(ierr); 490 } else { 491 PetscInt idx,num_fine_ghosts,num_crs_ghost,myCrs0; 492 Mat_MPIAIJ *mpimat2; 493 Mat Gmat2; 494 Vec locState; 495 PetscScalar *cpcol_state; 496 497 /* scan my coarse zero gid, set 'lid_state' with coarse GID */ 498 kk = nselected_1; 499 MPI_Scan(&kk, &myCrs0, 1, MPIU_INT, MPIU_SUM, wcomm); 500 myCrs0 -= nselected_1; 501 502 if (a_Gmat_2) { /* output */ 503 /* grow graph to get wider set of selected vertices to cover fine grid, invalidates 'llist' */ 504 ierr = MatTransposeMatMult(Gmat1, Gmat1, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &Gmat2);CHKERRQ(ierr); 505 *a_Gmat_2 = Gmat2; /* output */ 506 } else Gmat2 = Gmat1; /* use local to get crsGIDs at least */ 507 /* get coarse grid GIDS for selected (locals and ghosts) */ 508 mpimat2 = (Mat_MPIAIJ*)Gmat2->data; 509 ierr = MatGetVecs(Gmat2, &locState, 0);CHKERRQ(ierr); 510 ierr = VecSet(locState, (PetscScalar)(PetscReal)(-1));CHKERRQ(ierr); /* set with UNKNOWN state */ 511 for (kk=0;kk<nselected_1;kk++) { 512 PetscInt fgid = clid_lid_1[kk] + my0; 513 PetscScalar v = (PetscScalar)(kk+myCrs0); 514 ierr = VecSetValues(locState, 1, &fgid, &v, INSERT_VALUES);CHKERRQ(ierr); /* set with PID */ 515 } 516 ierr = VecAssemblyBegin(locState);CHKERRQ(ierr); 517 ierr = VecAssemblyEnd(locState);CHKERRQ(ierr); 518 ierr = VecScatterBegin(mpimat2->Mvctx,locState,mpimat2->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 519 ierr = VecScatterEnd(mpimat2->Mvctx,locState,mpimat2->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 520 ierr = VecGetLocalSize(mpimat2->lvec, &num_fine_ghosts);CHKERRQ(ierr); 521 ierr = VecGetArray(mpimat2->lvec, &cpcol_state);CHKERRQ(ierr); 522 for (kk=0,num_crs_ghost=0;kk<num_fine_ghosts;kk++) { 523 if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) num_crs_ghost++; 524 } 525 ierr = PetscMalloc((nselected_1+num_crs_ghost)*sizeof(PetscInt), &crsGID);CHKERRQ(ierr); /* output */ 526 { 527 PetscInt *selected_set; 528 ierr = PetscMalloc((nselected_1+num_crs_ghost)*sizeof(PetscInt), &selected_set);CHKERRQ(ierr); 529 /* do ghost of 'crsGID' */ 530 for (kk=0,idx=nselected_1;kk<num_fine_ghosts;kk++) { 531 if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) { 532 PetscInt cgid = (PetscInt)PetscRealPart(cpcol_state[kk]); 533 selected_set[idx] = nloc + kk; 534 crsGID[idx++] = cgid; 535 } 536 } 537 assert(idx==(nselected_1+num_crs_ghost)); 538 ierr = VecRestoreArray(mpimat2->lvec, &cpcol_state);CHKERRQ(ierr); 539 /* do locals in 'crsGID' */ 540 ierr = VecGetArray(locState, &cpcol_state);CHKERRQ(ierr); 541 for (kk=0,idx=0;kk<nloc;kk++) { 542 if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) { 543 PetscInt cgid = (PetscInt)PetscRealPart(cpcol_state[kk]); 544 selected_set[idx] = kk; 545 crsGID[idx++] = cgid; 546 } 547 } 548 assert(idx==nselected_1); 549 ierr = VecRestoreArray(locState, &cpcol_state);CHKERRQ(ierr); 550 551 if (a_selected_2 != 0) { /* output */ 552 ierr = ISCreateGeneral(PETSC_COMM_SELF,(nselected_1+num_crs_ghost),selected_set,PETSC_OWN_POINTER,a_selected_2);CHKERRQ(ierr); 553 } else { 554 ierr = PetscFree(selected_set);CHKERRQ(ierr); 555 } 556 } 557 ierr = VecDestroy(&locState);CHKERRQ(ierr); 558 } 559 *a_crsGID = crsGID; /* output */ 560 561 PetscFunctionReturn(0); 562 } 563 564 /* -------------------------------------------------------------------------- */ 565 /* 566 PCGAMGgraph_GEO 567 568 Input Parameter: 569 . pc - this 570 . Amat - matrix on this fine level 571 Output Parameter: 572 . a_Gmat 573 */ 574 #undef __FUNCT__ 575 #define __FUNCT__ "PCGAMGgraph_GEO" 576 PetscErrorCode PCGAMGgraph_GEO(PC pc, 577 const Mat Amat, 578 Mat *a_Gmat) 579 { 580 PetscErrorCode ierr; 581 PC_MG *mg = (PC_MG*)pc->data; 582 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 583 const PetscInt verbose = pc_gamg->verbose; 584 const PetscReal vfilter = pc_gamg->threshold; 585 PetscMPIInt mype,npe; 586 MPI_Comm wcomm = ((PetscObject)Amat)->comm; 587 Mat Gmat; 588 PetscBool set,flg,symm; 589 590 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 SETERRQ(wcomm,PETSC_ERR_PLIB,"3D not implemented for 'geo' AMG"); 851 { /* create next coords - output */ 852 PetscReal *crs_crds; 853 ierr = PetscMalloc(dim*nLocalSelected*sizeof(PetscReal), &crs_crds);CHKERRQ(ierr); 854 for (kk=0;kk<nLocalSelected;kk++) {/* grab local select nodes to promote - output */ 855 PetscInt lid = clid_flid[kk]; 856 for (jj=0;jj<dim;jj++) crs_crds[jj*nLocalSelected + kk] = pc_gamg->data[jj*nloc + lid]; 857 } 858 859 ierr = PetscFree(pc_gamg->data);CHKERRQ(ierr); 860 pc_gamg->data = crs_crds; /* out */ 861 pc_gamg->data_sz = dim*nLocalSelected; 862 } 863 ierr = ISDestroy(&selected_2);CHKERRQ(ierr); 864 } 865 866 *a_P_out = Prol; /* out */ 867 ierr = PetscFree(clid_flid);CHKERRQ(ierr); 868 #if defined PETSC_USE_LOG 869 ierr = PetscLogEventEnd(PC_GAMGProlongator_GEO,0,0,0,0);CHKERRQ(ierr); 870 #endif 871 PetscFunctionReturn(0); 872 } 873 874 /* -------------------------------------------------------------------------- */ 875 /* 876 PCCreateGAMG_GEO 877 878 Input Parameter: 879 . pc - 880 */ 881 #undef __FUNCT__ 882 #define __FUNCT__ "PCCreateGAMG_GEO" 883 PetscErrorCode PCCreateGAMG_GEO(PC pc) 884 { 885 PetscErrorCode ierr; 886 PC_MG *mg = (PC_MG*)pc->data; 887 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 888 889 PetscFunctionBegin; 890 pc->ops->setfromoptions = PCSetFromOptions_GEO; 891 /* pc->ops->destroy = PCDestroy_GEO; */ 892 /* reset does not do anything; setup not virtual */ 893 894 /* set internal function pointers */ 895 pc_gamg->graph = PCGAMGgraph_GEO; 896 pc_gamg->coarsen = PCGAMGcoarsen_GEO; 897 pc_gamg->prolongator = PCGAMGProlongator_GEO; 898 pc_gamg->optprol = 0; 899 pc_gamg->formkktprol = 0; 900 901 pc_gamg->createdefaultdata = PCSetData_GEO; 902 903 ierr = PetscObjectComposeFunctionDynamic((PetscObject)pc, 904 "PCSetCoordinates_C", 905 "PCSetCoordinates_GEO", 906 PCSetCoordinates_GEO);CHKERRQ(ierr); 907 908 PetscFunctionReturn(0); 909 } 910