1 /* 2 GAMG geometric-algebric multiogrid PC - Mark Adams 2011 3 */ 4 5 #include <../src/ksp/pc/impls/gamg/gamg.h> /*I "petscpc.h" I*/ 6 7 #if defined(PETSC_HAVE_TRIANGLE) 8 #define REAL PetscReal 9 #include <triangle.h> 10 #endif 11 12 #include <petscblaslapack.h> 13 14 /* Private context for the GAMG preconditioner */ 15 typedef struct { 16 PetscInt lid; /* local vertex index */ 17 PetscInt degree; /* vertex degree */ 18 } GAMGNode; 19 20 int petsc_geo_mg_compare(const void *a, const void *b) 21 { 22 return (((GAMGNode*)a)->degree - ((GAMGNode*)b)->degree); 23 } 24 25 /* -------------------------------------------------------------------------- */ 26 /* 27 PCSetCoordinates_GEO 28 29 Input Parameter: 30 . pc - the preconditioner context 31 */ 32 #undef __FUNCT__ 33 #define __FUNCT__ "PCSetCoordinates_GEO" 34 PetscErrorCode PCSetCoordinates_GEO(PC pc, PetscInt ndm, PetscInt a_nloc, PetscReal *coords) 35 { 36 PC_MG *mg = (PC_MG*)pc->data; 37 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 38 PetscErrorCode ierr; 39 PetscInt arrsz,bs,my0,kk,ii,nloc,Iend; 40 Mat Amat = pc->pmat; 41 42 PetscFunctionBegin; 43 PetscValidHeaderSpecific(Amat, MAT_CLASSID, 1); 44 ierr = MatGetBlockSize(Amat, &bs);CHKERRQ(ierr); 45 46 ierr = MatGetOwnershipRange(Amat, &my0, &Iend);CHKERRQ(ierr); 47 nloc = (Iend-my0)/bs; 48 49 if (nloc!=a_nloc) SETERRQ2(PetscObjectComm((PetscObject)Amat),PETSC_ERR_ARG_WRONG, "Stokes not supported nloc = %d %d.",a_nloc,nloc); 50 if ((Iend-my0)%bs!=0) SETERRQ1(PetscObjectComm((PetscObject)Amat),PETSC_ERR_ARG_WRONG, "Bad local size %d.",nloc); 51 52 pc_gamg->data_cell_rows = 1; 53 if (!coords && nloc > 0) SETERRQ(PetscObjectComm((PetscObject)Amat),PETSC_ERR_ARG_WRONG, "Need coordinates for pc_gamg_type 'geo'."); 54 pc_gamg->data_cell_cols = ndm; /* coordinates */ 55 56 arrsz = nloc*pc_gamg->data_cell_rows*pc_gamg->data_cell_cols; 57 58 /* create data - syntactic sugar that should be refactored at some point */ 59 if (!pc_gamg->data || (pc_gamg->data_sz != arrsz)) { 60 ierr = PetscFree(pc_gamg->data);CHKERRQ(ierr); 61 ierr = PetscMalloc1(arrsz+1, &pc_gamg->data);CHKERRQ(ierr); 62 } 63 for (kk=0; kk<arrsz; kk++) pc_gamg->data[kk] = -999.; 64 pc_gamg->data[arrsz] = -99.; 65 /* copy data in - column oriented */ 66 for (kk = 0; kk < nloc; kk++) { 67 for (ii = 0; ii < ndm; ii++) { 68 pc_gamg->data[ii*nloc + kk] = coords[kk*ndm + ii]; 69 } 70 } 71 if (pc_gamg->data[arrsz] != -99.) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"pc_gamg->data[arrsz %D] %g != -99.",arrsz,pc_gamg->data[arrsz]); 72 pc_gamg->data_sz = arrsz; 73 PetscFunctionReturn(0); 74 } 75 76 /* -------------------------------------------------------------------------- */ 77 /* 78 PCSetData_GEO 79 80 Input Parameter: 81 . pc - 82 */ 83 #undef __FUNCT__ 84 #define __FUNCT__ "PCSetData_GEO" 85 PetscErrorCode PCSetData_GEO(PC pc, Mat m) 86 { 87 PetscFunctionBegin; 88 SETERRQ(PetscObjectComm((PetscObject)pc),PETSC_ERR_PLIB,"GEO MG needs coordinates"); 89 } 90 91 /* -------------------------------------------------------------------------- */ 92 /* 93 PCSetFromOptions_GEO 94 95 Input Parameter: 96 . pc - 97 */ 98 #undef __FUNCT__ 99 #define __FUNCT__ "PCSetFromOptions_GEO" 100 PetscErrorCode PCSetFromOptions_GEO(PetscOptionItems *PetscOptionsObject,PC pc) 101 { 102 PetscErrorCode ierr; 103 104 PetscFunctionBegin; 105 ierr = PetscOptionsHead(PetscOptionsObject,"GAMG-GEO options");CHKERRQ(ierr); 106 { 107 /* -pc_gamg_sa_nsmooths */ 108 /* pc_gamg_sa->smooths = 0; */ 109 /* ierr = PetscOptionsInt("-pc_gamg_agg_nsmooths", */ 110 /* "smoothing steps for smoothed aggregation, usually 1 (0)", */ 111 /* "PCGAMGSetNSmooths_AGG", */ 112 /* pc_gamg_sa->smooths, */ 113 /* &pc_gamg_sa->smooths, */ 114 /* &flag); */ 115 /* CHKERRQ(ierr); */ 116 } 117 ierr = PetscOptionsTail();CHKERRQ(ierr); 118 PetscFunctionReturn(0); 119 } 120 121 /* -------------------------------------------------------------------------- */ 122 /* 123 triangulateAndFormProl 124 125 Input Parameter: 126 . selected_2 - list of selected local ID, includes selected ghosts 127 . data_stride - 128 . coords[2*data_stride] - column vector of local coordinates w/ ghosts 129 . nselected_1 - selected IDs that go with base (1) graph includes selected ghosts 130 . clid_lid_1[nselected_1] - lids of selected (c) nodes ??????????? 131 . agg_lists_1 - list of aggregates selected_1 vertices of aggregate unselected vertices 132 . crsGID[selected.size()] - global index for prolongation operator 133 . bs - block size 134 Output Parameter: 135 . a_Prol - prolongation operator 136 . a_worst_best - measure of worst missed fine vertex, 0 is no misses 137 */ 138 #undef __FUNCT__ 139 #define __FUNCT__ "triangulateAndFormProl" 140 static PetscErrorCode triangulateAndFormProl(IS selected_2,PetscInt data_stride,PetscReal coords[],PetscInt nselected_1,const PetscInt clid_lid_1[],const PetscCoarsenData *agg_lists_1, 141 const PetscInt crsGID[],PetscInt bs,Mat a_Prol,PetscReal *a_worst_best) 142 { 143 #if defined(PETSC_HAVE_TRIANGLE) 144 PetscErrorCode ierr; 145 PetscInt jj,tid,tt,idx,nselected_2; 146 struct triangulateio in,mid; 147 const PetscInt *selected_idx_2; 148 PetscMPIInt rank; 149 PetscInt Istart,Iend,nFineLoc,myFine0; 150 int kk,nPlotPts,sid; 151 MPI_Comm comm; 152 PetscReal tm; 153 154 PetscFunctionBegin; 155 ierr = PetscObjectGetComm((PetscObject)a_Prol,&comm);CHKERRQ(ierr); 156 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 157 ierr = ISGetSize(selected_2, &nselected_2);CHKERRQ(ierr); 158 if (nselected_2 == 1 || nselected_2 == 2) { /* 0 happens on idle processors */ 159 *a_worst_best = 100.0; /* this will cause a stop, but not globalized (should not happen) */ 160 } else *a_worst_best = 0.0; 161 ierr = MPIU_Allreduce(a_worst_best, &tm, 1, MPIU_REAL, MPIU_MAX, comm);CHKERRQ(ierr); 162 if (tm > 0.0) { 163 *a_worst_best = 100.0; 164 PetscFunctionReturn(0); 165 } 166 ierr = MatGetOwnershipRange(a_Prol, &Istart, &Iend);CHKERRQ(ierr); 167 nFineLoc = (Iend-Istart)/bs; myFine0 = Istart/bs; 168 nPlotPts = nFineLoc; /* locals */ 169 /* traingle */ 170 /* Define input points - in*/ 171 in.numberofpoints = nselected_2; 172 in.numberofpointattributes = 0; 173 /* get nselected points */ 174 ierr = PetscMalloc1(2*nselected_2, &in.pointlist);CHKERRQ(ierr); 175 ierr = ISGetIndices(selected_2, &selected_idx_2);CHKERRQ(ierr); 176 177 for (kk=0,sid=0; kk<nselected_2; kk++,sid += 2) { 178 PetscInt lid = selected_idx_2[kk]; 179 in.pointlist[sid] = coords[lid]; 180 in.pointlist[sid+1] = coords[data_stride + lid]; 181 if (lid>=nFineLoc) nPlotPts++; 182 } 183 if (sid != 2*nselected_2) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"sid %D != 2*nselected_2 %D",sid,nselected_2); 184 185 in.numberofsegments = 0; 186 in.numberofedges = 0; 187 in.numberofholes = 0; 188 in.numberofregions = 0; 189 in.trianglelist = 0; 190 in.segmentmarkerlist = 0; 191 in.pointattributelist = 0; 192 in.pointmarkerlist = 0; 193 in.triangleattributelist = 0; 194 in.trianglearealist = 0; 195 in.segmentlist = 0; 196 in.holelist = 0; 197 in.regionlist = 0; 198 in.edgelist = 0; 199 in.edgemarkerlist = 0; 200 in.normlist = 0; 201 202 /* triangulate */ 203 mid.pointlist = 0; /* Not needed if -N switch used. */ 204 /* Not needed if -N switch used or number of point attributes is zero: */ 205 mid.pointattributelist = 0; 206 mid.pointmarkerlist = 0; /* Not needed if -N or -B switch used. */ 207 mid.trianglelist = 0; /* Not needed if -E switch used. */ 208 /* Not needed if -E switch used or number of triangle attributes is zero: */ 209 mid.triangleattributelist = 0; 210 mid.neighborlist = 0; /* Needed only if -n switch used. */ 211 /* Needed only if segments are output (-p or -c) and -P not used: */ 212 mid.segmentlist = 0; 213 /* Needed only if segments are output (-p or -c) and -P and -B not used: */ 214 mid.segmentmarkerlist = 0; 215 mid.edgelist = 0; /* Needed only if -e switch used. */ 216 mid.edgemarkerlist = 0; /* Needed if -e used and -B not used. */ 217 mid.numberoftriangles = 0; 218 219 /* Triangulate the points. Switches are chosen to read and write a */ 220 /* PSLG (p), preserve the convex hull (c), number everything from */ 221 /* zero (z), assign a regional attribute to each element (A), and */ 222 /* produce an edge list (e), a Voronoi diagram (v), and a triangle */ 223 /* neighbor list (n). */ 224 if (nselected_2 != 0) { /* inactive processor */ 225 char args[] = "npczQ"; /* c is needed ? */ 226 triangulate(args, &in, &mid, (struct triangulateio*) NULL); 227 /* output .poly files for 'showme' */ 228 if (!PETSC_TRUE) { 229 static int level = 1; 230 FILE *file; char fname[32]; 231 232 sprintf(fname,"C%d_%d.poly",level,rank); file = fopen(fname, "w"); 233 /*First line: <# of vertices> <dimension (must be 2)> <# of attributes> <# of boundary markers (0 or 1)>*/ 234 fprintf(file, "%d %d %d %d\n",in.numberofpoints,2,0,0); 235 /*Following lines: <vertex #> <x> <y> */ 236 for (kk=0,sid=0; kk<in.numberofpoints; kk++,sid += 2) { 237 fprintf(file, "%d %e %e\n",kk,in.pointlist[sid],in.pointlist[sid+1]); 238 } 239 /*One line: <# of segments> <# of boundary markers (0 or 1)> */ 240 fprintf(file, "%d %d\n",0,0); 241 /*Following lines: <segment #> <endpoint> <endpoint> [boundary marker] */ 242 /* One line: <# of holes> */ 243 fprintf(file, "%d\n",0); 244 /* Following lines: <hole #> <x> <y> */ 245 /* Optional line: <# of regional attributes and/or area constraints> */ 246 /* Optional following lines: <region #> <x> <y> <attribute> <maximum area> */ 247 fclose(file); 248 249 /* elems */ 250 sprintf(fname,"C%d_%d.ele",level,rank); file = fopen(fname, "w"); 251 /* First line: <# of triangles> <nodes per triangle> <# of attributes> */ 252 fprintf(file, "%d %d %d\n",mid.numberoftriangles,3,0); 253 /* Remaining lines: <triangle #> <node> <node> <node> ... [attributes] */ 254 for (kk=0,sid=0; kk<mid.numberoftriangles; kk++,sid += 3) { 255 fprintf(file, "%d %d %d %d\n",kk,mid.trianglelist[sid],mid.trianglelist[sid+1],mid.trianglelist[sid+2]); 256 } 257 fclose(file); 258 259 sprintf(fname,"C%d_%d.node",level,rank); file = fopen(fname, "w"); 260 /* First line: <# of vertices> <dimension (must be 2)> <# of attributes> <# of boundary markers (0 or 1)> */ 261 /* fprintf(file, "%d %d %d %d\n",in.numberofpoints,2,0,0); */ 262 fprintf(file, "%d %d %d %d\n",nPlotPts,2,0,0); 263 /*Following lines: <vertex #> <x> <y> */ 264 for (kk=0,sid=0; kk<in.numberofpoints; kk++,sid+=2) { 265 fprintf(file, "%d %e %e\n",kk,in.pointlist[sid],in.pointlist[sid+1]); 266 } 267 268 sid /= 2; 269 for (jj=0; jj<nFineLoc; jj++) { 270 PetscBool sel = PETSC_TRUE; 271 for (kk=0; kk<nselected_2 && sel; kk++) { 272 PetscInt lid = selected_idx_2[kk]; 273 if (lid == jj) sel = PETSC_FALSE; 274 } 275 if (sel) fprintf(file, "%d %e %e\n",sid++,coords[jj],coords[data_stride + jj]); 276 } 277 fclose(file); 278 if (sid != nPlotPts) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"sid %D != nPlotPts %D",sid,nPlotPts); 279 level++; 280 } 281 } 282 #if defined PETSC_GAMG_USE_LOG 283 ierr = PetscLogEventBegin(petsc_gamg_setup_events[FIND_V],0,0,0,0);CHKERRQ(ierr); 284 #endif 285 { /* form P - setup some maps */ 286 PetscInt clid,mm,*nTri,*node_tri; 287 288 ierr = PetscMalloc2(nselected_2, &node_tri,nselected_2, &nTri);CHKERRQ(ierr); 289 290 /* need list of triangles on node */ 291 for (kk=0; kk<nselected_2; kk++) nTri[kk] = 0; 292 for (tid=0,kk=0; tid<mid.numberoftriangles; tid++) { 293 for (jj=0; jj<3; jj++) { 294 PetscInt cid = mid.trianglelist[kk++]; 295 if (nTri[cid] == 0) node_tri[cid] = tid; 296 nTri[cid]++; 297 } 298 } 299 #define EPS 1.e-12 300 /* find points and set prolongation */ 301 for (mm = clid = 0; mm < nFineLoc; mm++) { 302 PetscBool ise; 303 ierr = PetscCDEmptyAt(agg_lists_1,mm,&ise);CHKERRQ(ierr); 304 if (!ise) { 305 const PetscInt lid = mm; 306 PetscScalar AA[3][3]; 307 PetscBLASInt N=3,NRHS=1,LDA=3,IPIV[3],LDB=3,INFO; 308 PetscCDIntNd *pos; 309 310 ierr = PetscCDGetHeadPos(agg_lists_1,lid,&pos);CHKERRQ(ierr); 311 while (pos) { 312 PetscInt flid; 313 ierr = PetscCDIntNdGetID(pos, &flid);CHKERRQ(ierr); 314 ierr = PetscCDGetNextPos(agg_lists_1,lid,&pos);CHKERRQ(ierr); 315 316 if (flid < nFineLoc) { /* could be a ghost */ 317 PetscInt bestTID = -1; PetscReal best_alpha = 1.e10; 318 const PetscInt fgid = flid + myFine0; 319 /* compute shape function for gid */ 320 const PetscReal fcoord[3] = {coords[flid],coords[data_stride+flid],1.0}; 321 PetscBool haveit =PETSC_FALSE; PetscScalar alpha[3]; PetscInt clids[3]; 322 323 /* look for it */ 324 for (tid = node_tri[clid], jj=0; 325 jj < 5 && !haveit && tid != -1; 326 jj++) { 327 for (tt=0; tt<3; tt++) { 328 PetscInt cid2 = mid.trianglelist[3*tid + tt]; 329 PetscInt lid2 = selected_idx_2[cid2]; 330 AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0; 331 clids[tt] = cid2; /* store for interp */ 332 } 333 334 for (tt=0; tt<3; tt++) alpha[tt] = (PetscScalar)fcoord[tt]; 335 336 /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */ 337 PetscStackCallBLAS("LAPACKgesv",LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO)); 338 { 339 PetscBool have=PETSC_TRUE; PetscReal lowest=1.e10; 340 for (tt = 0, idx = 0; tt < 3; tt++) { 341 if (PetscRealPart(alpha[tt]) > (1.0+EPS) || PetscRealPart(alpha[tt]) < -EPS) have = PETSC_FALSE; 342 if (PetscRealPart(alpha[tt]) < lowest) { 343 lowest = PetscRealPart(alpha[tt]); 344 idx = tt; 345 } 346 } 347 haveit = have; 348 } 349 tid = mid.neighborlist[3*tid + idx]; 350 } 351 352 if (!haveit) { 353 /* brute force */ 354 for (tid=0; tid<mid.numberoftriangles && !haveit; tid++) { 355 for (tt=0; tt<3; tt++) { 356 PetscInt cid2 = mid.trianglelist[3*tid + tt]; 357 PetscInt lid2 = selected_idx_2[cid2]; 358 AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0; 359 clids[tt] = cid2; /* store for interp */ 360 } 361 for (tt=0; tt<3; tt++) alpha[tt] = fcoord[tt]; 362 /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */ 363 PetscStackCallBLAS("LAPACKgesv",LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO)); 364 { 365 PetscBool have=PETSC_TRUE; PetscReal worst=0.0, v; 366 for (tt=0; tt<3 && have; tt++) { 367 if (PetscRealPart(alpha[tt]) > 1.0+EPS || PetscRealPart(alpha[tt]) < -EPS) have=PETSC_FALSE; 368 if ((v=PetscAbs(PetscRealPart(alpha[tt])-0.5)) > worst) worst = v; 369 } 370 if (worst < best_alpha) { 371 best_alpha = worst; bestTID = tid; 372 } 373 haveit = have; 374 } 375 } 376 } 377 if (!haveit) { 378 if (best_alpha > *a_worst_best) *a_worst_best = best_alpha; 379 /* use best one */ 380 for (tt=0; tt<3; tt++) { 381 PetscInt cid2 = mid.trianglelist[3*bestTID + 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 PetscStackCallBLAS("LAPACKgesv",LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO)); 389 } 390 391 /* put in row of P */ 392 for (idx=0; idx<3; idx++) { 393 PetscScalar shp = alpha[idx]; 394 if (PetscAbs(PetscRealPart(shp)) > 1.e-6) { 395 PetscInt cgid = crsGID[clids[idx]]; 396 PetscInt jj = cgid*bs, ii = fgid*bs; /* need to gloalize */ 397 for (tt=0; tt < bs; tt++, ii++, jj++) { 398 ierr = MatSetValues(a_Prol,1,&ii,1,&jj,&shp,INSERT_VALUES);CHKERRQ(ierr); 399 } 400 } 401 } 402 } 403 } /* aggregates iterations */ 404 clid++; 405 } /* a coarse agg */ 406 } /* for all fine nodes */ 407 408 ierr = ISRestoreIndices(selected_2, &selected_idx_2);CHKERRQ(ierr); 409 ierr = MatAssemblyBegin(a_Prol,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 410 ierr = MatAssemblyEnd(a_Prol,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 411 412 ierr = PetscFree2(node_tri,nTri);CHKERRQ(ierr); 413 } 414 #if defined PETSC_GAMG_USE_LOG 415 ierr = PetscLogEventEnd(petsc_gamg_setup_events[FIND_V],0,0,0,0);CHKERRQ(ierr); 416 #endif 417 free(mid.trianglelist); 418 free(mid.neighborlist); 419 ierr = PetscFree(in.pointlist);CHKERRQ(ierr); 420 PetscFunctionReturn(0); 421 #else 422 SETERRQ(PetscObjectComm((PetscObject)a_Prol),PETSC_ERR_PLIB,"configure with TRIANGLE to use geometric MG"); 423 #endif 424 } 425 /* -------------------------------------------------------------------------- */ 426 /* 427 getGIDsOnSquareGraph - square graph, get 428 429 Input Parameter: 430 . nselected_1 - selected local indices (includes ghosts in input Gmat1) 431 . clid_lid_1 - [nselected_1] lids of selected nodes 432 . Gmat1 - graph that goes with 'selected_1' 433 Output Parameter: 434 . a_selected_2 - selected local indices (includes ghosts in output a_Gmat_2) 435 . a_Gmat_2 - graph that is squared of 'Gmat_1' 436 . a_crsGID[a_selected_2.size()] - map of global IDs of coarse grid nodes 437 */ 438 #undef __FUNCT__ 439 #define __FUNCT__ "getGIDsOnSquareGraph" 440 static PetscErrorCode getGIDsOnSquareGraph(PetscInt nselected_1,const PetscInt clid_lid_1[],const Mat Gmat1,IS *a_selected_2,Mat *a_Gmat_2,PetscInt **a_crsGID) 441 { 442 PetscErrorCode ierr; 443 PetscMPIInt size; 444 PetscInt *crsGID, kk,my0,Iend,nloc; 445 MPI_Comm comm; 446 447 PetscFunctionBegin; 448 ierr = PetscObjectGetComm((PetscObject)Gmat1,&comm);CHKERRQ(ierr); 449 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 450 ierr = MatGetOwnershipRange(Gmat1,&my0,&Iend);CHKERRQ(ierr); /* AIJ */ 451 nloc = Iend - my0; /* this does not change */ 452 453 if (size == 1) { /* not much to do in serial */ 454 ierr = PetscMalloc1(nselected_1, &crsGID);CHKERRQ(ierr); 455 for (kk=0; kk<nselected_1; kk++) crsGID[kk] = kk; 456 *a_Gmat_2 = 0; 457 ierr = ISCreateGeneral(PETSC_COMM_SELF,nselected_1,clid_lid_1,PETSC_COPY_VALUES,a_selected_2);CHKERRQ(ierr); 458 } else { 459 PetscInt idx,num_fine_ghosts,num_crs_ghost,myCrs0; 460 Mat_MPIAIJ *mpimat2; 461 Mat Gmat2; 462 Vec locState; 463 PetscScalar *cpcol_state; 464 465 /* scan my coarse zero gid, set 'lid_state' with coarse GID */ 466 kk = nselected_1; 467 ierr = MPI_Scan(&kk, &myCrs0, 1, MPIU_INT, MPI_SUM, comm);CHKERRQ(ierr); 468 myCrs0 -= nselected_1; 469 470 if (a_Gmat_2) { /* output */ 471 /* grow graph to get wider set of selected vertices to cover fine grid, invalidates 'llist' */ 472 ierr = MatTransposeMatMult(Gmat1, Gmat1, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &Gmat2);CHKERRQ(ierr); 473 *a_Gmat_2 = Gmat2; /* output */ 474 } else Gmat2 = Gmat1; /* use local to get crsGIDs at least */ 475 /* get coarse grid GIDS for selected (locals and ghosts) */ 476 mpimat2 = (Mat_MPIAIJ*)Gmat2->data; 477 ierr = MatCreateVecs(Gmat2, &locState, 0);CHKERRQ(ierr); 478 ierr = VecSet(locState, (PetscScalar)(PetscReal)(-1));CHKERRQ(ierr); /* set with UNKNOWN state */ 479 for (kk=0; kk<nselected_1; kk++) { 480 PetscInt fgid = clid_lid_1[kk] + my0; 481 PetscScalar v = (PetscScalar)(kk+myCrs0); 482 ierr = VecSetValues(locState, 1, &fgid, &v, INSERT_VALUES);CHKERRQ(ierr); /* set with PID */ 483 } 484 ierr = VecAssemblyBegin(locState);CHKERRQ(ierr); 485 ierr = VecAssemblyEnd(locState);CHKERRQ(ierr); 486 ierr = VecScatterBegin(mpimat2->Mvctx,locState,mpimat2->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 487 ierr = VecScatterEnd(mpimat2->Mvctx,locState,mpimat2->lvec,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr); 488 ierr = VecGetLocalSize(mpimat2->lvec, &num_fine_ghosts);CHKERRQ(ierr); 489 ierr = VecGetArray(mpimat2->lvec, &cpcol_state);CHKERRQ(ierr); 490 for (kk=0,num_crs_ghost=0; kk<num_fine_ghosts; kk++) { 491 if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) num_crs_ghost++; 492 } 493 ierr = PetscMalloc1(nselected_1+num_crs_ghost, &crsGID);CHKERRQ(ierr); /* output */ 494 { 495 PetscInt *selected_set; 496 ierr = PetscMalloc1(nselected_1+num_crs_ghost, &selected_set);CHKERRQ(ierr); 497 /* do ghost of 'crsGID' */ 498 for (kk=0,idx=nselected_1; kk<num_fine_ghosts; kk++) { 499 if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) { 500 PetscInt cgid = (PetscInt)PetscRealPart(cpcol_state[kk]); 501 selected_set[idx] = nloc + kk; 502 crsGID[idx++] = cgid; 503 } 504 } 505 if (idx != (nselected_1+num_crs_ghost)) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"idx %D != (nselected_1 %D + num_crs_ghost %D)",idx,nselected_1,num_crs_ghost); 506 ierr = VecRestoreArray(mpimat2->lvec, &cpcol_state);CHKERRQ(ierr); 507 /* do locals in 'crsGID' */ 508 ierr = VecGetArray(locState, &cpcol_state);CHKERRQ(ierr); 509 for (kk=0,idx=0; kk<nloc; kk++) { 510 if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) { 511 PetscInt cgid = (PetscInt)PetscRealPart(cpcol_state[kk]); 512 selected_set[idx] = kk; 513 crsGID[idx++] = cgid; 514 } 515 } 516 if (idx != nselected_1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"idx %D != nselected_1 %D",idx,nselected_1); 517 ierr = VecRestoreArray(locState, &cpcol_state);CHKERRQ(ierr); 518 519 if (a_selected_2 != 0) { /* output */ 520 ierr = ISCreateGeneral(PETSC_COMM_SELF,(nselected_1+num_crs_ghost),selected_set,PETSC_OWN_POINTER,a_selected_2);CHKERRQ(ierr); 521 } else { 522 ierr = PetscFree(selected_set);CHKERRQ(ierr); 523 } 524 } 525 ierr = VecDestroy(&locState);CHKERRQ(ierr); 526 } 527 *a_crsGID = crsGID; /* output */ 528 PetscFunctionReturn(0); 529 } 530 531 /* -------------------------------------------------------------------------- */ 532 /* 533 PCGAMGGraph_GEO 534 535 Input Parameter: 536 . pc - this 537 . Amat - matrix on this fine level 538 Output Parameter: 539 . a_Gmat 540 */ 541 #undef __FUNCT__ 542 #define __FUNCT__ "PCGAMGGraph_GEO" 543 PetscErrorCode PCGAMGGraph_GEO(PC pc,Mat Amat,Mat *a_Gmat) 544 { 545 PetscErrorCode ierr; 546 PC_MG *mg = (PC_MG*)pc->data; 547 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 548 const PetscReal vfilter = pc_gamg->threshold; 549 MPI_Comm comm; 550 Mat Gmat; 551 PetscBool set,flg,symm; 552 553 PetscFunctionBegin; 554 ierr = PetscObjectGetComm((PetscObject)Amat,&comm);CHKERRQ(ierr); 555 ierr = PetscLogEventBegin(PC_GAMGGraph_GEO,0,0,0,0);CHKERRQ(ierr); 556 557 ierr = MatIsSymmetricKnown(Amat, &set, &flg);CHKERRQ(ierr); 558 symm = (PetscBool)!(set && flg); 559 560 ierr = PCGAMGCreateGraph(Amat, &Gmat);CHKERRQ(ierr); 561 ierr = PCGAMGFilterGraph(&Gmat, vfilter, symm);CHKERRQ(ierr); 562 563 *a_Gmat = Gmat; 564 ierr = PetscLogEventEnd(PC_GAMGGraph_GEO,0,0,0,0);CHKERRQ(ierr); 565 PetscFunctionReturn(0); 566 } 567 568 /* -------------------------------------------------------------------------- */ 569 /* 570 PCGAMGCoarsen_GEO 571 572 Input Parameter: 573 . a_pc - this 574 . a_Gmat - graph 575 Output Parameter: 576 . a_llist_parent - linked list from selected indices for data locality only 577 */ 578 #undef __FUNCT__ 579 #define __FUNCT__ "PCGAMGCoarsen_GEO" 580 PetscErrorCode PCGAMGCoarsen_GEO(PC a_pc,Mat *a_Gmat,PetscCoarsenData **a_llist_parent) 581 { 582 PetscErrorCode ierr; 583 PetscInt Istart,Iend,nloc,kk,Ii,ncols; 584 IS perm; 585 GAMGNode *gnodes; 586 PetscInt *permute; 587 Mat Gmat = *a_Gmat; 588 MPI_Comm comm; 589 MatCoarsen crs; 590 591 PetscFunctionBegin; 592 ierr = PetscObjectGetComm((PetscObject)a_pc,&comm);CHKERRQ(ierr); 593 ierr = PetscLogEventBegin(PC_GAMGCoarsen_GEO,0,0,0,0);CHKERRQ(ierr); 594 ierr = MatGetOwnershipRange(Gmat, &Istart, &Iend);CHKERRQ(ierr); 595 nloc = (Iend-Istart); 596 597 /* create random permutation with sort for geo-mg */ 598 ierr = PetscMalloc1(nloc, &gnodes);CHKERRQ(ierr); 599 ierr = PetscMalloc1(nloc, &permute);CHKERRQ(ierr); 600 601 for (Ii=Istart; Ii<Iend; Ii++) { /* locals only? */ 602 ierr = MatGetRow(Gmat,Ii,&ncols,0,0);CHKERRQ(ierr); 603 { 604 PetscInt lid = Ii - Istart; 605 gnodes[lid].lid = lid; 606 gnodes[lid].degree = ncols; 607 } 608 ierr = MatRestoreRow(Gmat,Ii,&ncols,0,0);CHKERRQ(ierr); 609 } 610 if (PETSC_TRUE) { 611 PetscRandom rand; 612 PetscBool *bIndexSet; 613 PetscReal rr; 614 PetscInt iSwapIndex; 615 616 ierr = PetscRandomCreate(comm,&rand);CHKERRQ(ierr); 617 ierr = PetscCalloc1(nloc, &bIndexSet);CHKERRQ(ierr); 618 for (Ii = 0; Ii < nloc; Ii++) { 619 ierr = PetscRandomGetValueReal(rand,&rr);CHKERRQ(ierr); 620 iSwapIndex = (PetscInt) (rr*nloc); 621 if (!bIndexSet[iSwapIndex] && iSwapIndex != Ii) { 622 GAMGNode iTemp = gnodes[iSwapIndex]; 623 gnodes[iSwapIndex] = gnodes[Ii]; 624 gnodes[Ii] = iTemp; 625 bIndexSet[Ii] = PETSC_TRUE; 626 bIndexSet[iSwapIndex] = PETSC_TRUE; 627 } 628 } 629 ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr); 630 ierr = PetscFree(bIndexSet);CHKERRQ(ierr); 631 } 632 /* only sort locals */ 633 qsort(gnodes, nloc, sizeof(GAMGNode), petsc_geo_mg_compare); 634 /* create IS of permutation */ 635 for (kk=0; kk<nloc; kk++) permute[kk] = gnodes[kk].lid; /* locals only */ 636 ierr = ISCreateGeneral(PETSC_COMM_SELF, nloc, permute, PETSC_OWN_POINTER, &perm);CHKERRQ(ierr); 637 638 ierr = PetscFree(gnodes);CHKERRQ(ierr); 639 640 /* get MIS aggs */ 641 642 ierr = MatCoarsenCreate(comm, &crs);CHKERRQ(ierr); 643 ierr = MatCoarsenSetType(crs, MATCOARSENMIS);CHKERRQ(ierr); 644 ierr = MatCoarsenSetGreedyOrdering(crs, perm);CHKERRQ(ierr); 645 ierr = MatCoarsenSetAdjacency(crs, Gmat);CHKERRQ(ierr); 646 ierr = MatCoarsenSetStrictAggs(crs, PETSC_FALSE);CHKERRQ(ierr); 647 ierr = MatCoarsenApply(crs);CHKERRQ(ierr); 648 ierr = MatCoarsenGetData(crs, a_llist_parent);CHKERRQ(ierr); 649 ierr = MatCoarsenDestroy(&crs);CHKERRQ(ierr); 650 651 ierr = ISDestroy(&perm);CHKERRQ(ierr); 652 ierr = PetscLogEventEnd(PC_GAMGCoarsen_GEO,0,0,0,0);CHKERRQ(ierr); 653 PetscFunctionReturn(0); 654 } 655 656 /* -------------------------------------------------------------------------- */ 657 /* 658 PCGAMGProlongator_GEO 659 660 Input Parameter: 661 . pc - this 662 . Amat - matrix on this fine level 663 . Graph - used to get ghost data for nodes in 664 . selected_1 - [nselected] 665 . agg_lists - [nselected] 666 Output Parameter: 667 . a_P_out - prolongation operator to the next level 668 */ 669 #undef __FUNCT__ 670 #define __FUNCT__ "PCGAMGProlongator_GEO" 671 PetscErrorCode PCGAMGProlongator_GEO(PC pc,Mat Amat,Mat Gmat,PetscCoarsenData *agg_lists,Mat *a_P_out) 672 { 673 PC_MG *mg = (PC_MG*)pc->data; 674 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 675 const PetscInt dim = pc_gamg->data_cell_cols, data_cols = pc_gamg->data_cell_cols; 676 PetscErrorCode ierr; 677 PetscInt Istart,Iend,nloc,my0,jj,kk,ncols,nLocalSelected,bs,*clid_flid; 678 Mat Prol; 679 PetscMPIInt rank, size; 680 MPI_Comm comm; 681 IS selected_2,selected_1; 682 const PetscInt *selected_idx; 683 MatType mtype; 684 685 PetscFunctionBegin; 686 ierr = PetscObjectGetComm((PetscObject)Amat,&comm);CHKERRQ(ierr); 687 ierr = PetscLogEventBegin(PC_GAMGProlongator_GEO,0,0,0,0);CHKERRQ(ierr); 688 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 689 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 690 ierr = MatGetOwnershipRange(Amat, &Istart, &Iend);CHKERRQ(ierr); 691 ierr = MatGetBlockSize(Amat, &bs);CHKERRQ(ierr); 692 nloc = (Iend-Istart)/bs; my0 = Istart/bs; 693 if ((Iend-Istart) % bs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"(Iend %D - Istart %D) % bs %D",Iend,Istart,bs); 694 695 /* get 'nLocalSelected' */ 696 ierr = PetscCDGetMIS(agg_lists, &selected_1);CHKERRQ(ierr); 697 ierr = ISGetSize(selected_1, &jj);CHKERRQ(ierr); 698 ierr = PetscMalloc1(jj, &clid_flid);CHKERRQ(ierr); 699 ierr = ISGetIndices(selected_1, &selected_idx);CHKERRQ(ierr); 700 for (kk=0,nLocalSelected=0; kk<jj; kk++) { 701 PetscInt lid = selected_idx[kk]; 702 if (lid<nloc) { 703 ierr = MatGetRow(Gmat,lid+my0,&ncols,0,0);CHKERRQ(ierr); 704 if (ncols>1) clid_flid[nLocalSelected++] = lid; /* fiter out singletons */ 705 ierr = MatRestoreRow(Gmat,lid+my0,&ncols,0,0);CHKERRQ(ierr); 706 } 707 } 708 ierr = ISRestoreIndices(selected_1, &selected_idx);CHKERRQ(ierr); 709 ierr = ISDestroy(&selected_1);CHKERRQ(ierr); /* this is selected_1 in serial */ 710 711 /* create prolongator matrix */ 712 ierr = MatGetType(Amat,&mtype);CHKERRQ(ierr); 713 ierr = MatCreate(comm, &Prol);CHKERRQ(ierr); 714 ierr = MatSetSizes(Prol,nloc*bs,nLocalSelected*bs,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr); 715 ierr = MatSetBlockSizes(Prol, bs, bs);CHKERRQ(ierr); 716 ierr = MatSetType(Prol, mtype);CHKERRQ(ierr); 717 ierr = MatSeqAIJSetPreallocation(Prol,3*data_cols,NULL);CHKERRQ(ierr); 718 ierr = MatMPIAIJSetPreallocation(Prol,3*data_cols,NULL,3*data_cols,NULL);CHKERRQ(ierr); 719 720 /* can get all points "removed" - but not on geomg */ 721 ierr = MatGetSize(Prol, &kk, &jj);CHKERRQ(ierr); 722 if (!jj) { 723 ierr = PetscInfo(pc,"ERROE: no selected points on coarse grid\n");CHKERRQ(ierr); 724 ierr = PetscFree(clid_flid);CHKERRQ(ierr); 725 ierr = MatDestroy(&Prol);CHKERRQ(ierr); 726 *a_P_out = NULL; /* out */ 727 PetscFunctionReturn(0); 728 } 729 730 { 731 PetscReal *coords; 732 PetscInt data_stride; 733 PetscInt *crsGID = NULL; 734 Mat Gmat2; 735 736 if (dim != data_cols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"dim %D != data_cols %D",dim,data_cols); 737 /* grow ghost data for better coarse grid cover of fine grid */ 738 #if defined PETSC_GAMG_USE_LOG 739 ierr = PetscLogEventBegin(petsc_gamg_setup_events[SET5],0,0,0,0);CHKERRQ(ierr); 740 #endif 741 /* messy method, squares graph and gets some data */ 742 ierr = getGIDsOnSquareGraph(nLocalSelected, clid_flid, Gmat, &selected_2, &Gmat2, &crsGID);CHKERRQ(ierr); 743 /* llist is now not valid wrt squared graph, but will work as iterator in 'triangulateAndFormProl' */ 744 #if defined PETSC_GAMG_USE_LOG 745 ierr = PetscLogEventEnd(petsc_gamg_setup_events[SET5],0,0,0,0);CHKERRQ(ierr); 746 #endif 747 /* create global vector of coorindates in 'coords' */ 748 if (size > 1) { 749 ierr = PCGAMGGetDataWithGhosts(Gmat2, dim, pc_gamg->data, &data_stride, &coords);CHKERRQ(ierr); 750 } else { 751 coords = (PetscReal*)pc_gamg->data; 752 data_stride = pc_gamg->data_sz/pc_gamg->data_cell_cols; 753 } 754 ierr = MatDestroy(&Gmat2);CHKERRQ(ierr); 755 756 /* triangulate */ 757 if (dim == 2) { 758 PetscReal metric,tm; 759 #if defined PETSC_GAMG_USE_LOG 760 ierr = PetscLogEventBegin(petsc_gamg_setup_events[SET6],0,0,0,0);CHKERRQ(ierr); 761 #endif 762 ierr = triangulateAndFormProl(selected_2, data_stride, coords,nLocalSelected, clid_flid, agg_lists, crsGID, bs, Prol, &metric);CHKERRQ(ierr); 763 #if defined PETSC_GAMG_USE_LOG 764 ierr = PetscLogEventEnd(petsc_gamg_setup_events[SET6],0,0,0,0);CHKERRQ(ierr); 765 #endif 766 ierr = PetscFree(crsGID);CHKERRQ(ierr); 767 768 /* clean up and create coordinates for coarse grid (output) */ 769 if (size > 1) ierr = PetscFree(coords);CHKERRQ(ierr); 770 771 ierr = MPIU_Allreduce(&metric, &tm, 1, MPIU_REAL, MPIU_MAX, comm);CHKERRQ(ierr); 772 if (tm > 1.) { /* needs to be globalized - should not happen */ 773 ierr = PetscInfo1(pc," failed metric for coarse grid %e\n",(double)tm);CHKERRQ(ierr); 774 ierr = MatDestroy(&Prol);CHKERRQ(ierr); 775 } else if (metric > .0) { 776 ierr = PetscInfo1(pc,"worst metric for coarse grid = %e\n",(double)metric);CHKERRQ(ierr); 777 } 778 } else SETERRQ(comm,PETSC_ERR_PLIB,"3D not implemented for 'geo' AMG"); 779 { /* create next coords - output */ 780 PetscReal *crs_crds; 781 ierr = PetscMalloc1(dim*nLocalSelected, &crs_crds);CHKERRQ(ierr); 782 for (kk=0; kk<nLocalSelected; kk++) { /* grab local select nodes to promote - output */ 783 PetscInt lid = clid_flid[kk]; 784 for (jj=0; jj<dim; jj++) crs_crds[jj*nLocalSelected + kk] = pc_gamg->data[jj*nloc + lid]; 785 } 786 787 ierr = PetscFree(pc_gamg->data);CHKERRQ(ierr); 788 pc_gamg->data = crs_crds; /* out */ 789 pc_gamg->data_sz = dim*nLocalSelected; 790 } 791 ierr = ISDestroy(&selected_2);CHKERRQ(ierr); 792 } 793 794 *a_P_out = Prol; /* out */ 795 ierr = PetscFree(clid_flid);CHKERRQ(ierr); 796 ierr = PetscLogEventEnd(PC_GAMGProlongator_GEO,0,0,0,0);CHKERRQ(ierr); 797 PetscFunctionReturn(0); 798 } 799 800 #undef __FUNCT__ 801 #define __FUNCT__ "PCDestroy_GAMG_GEO" 802 static PetscErrorCode PCDestroy_GAMG_GEO(PC pc) 803 { 804 PetscErrorCode ierr; 805 806 PetscFunctionBegin; 807 ierr = PetscObjectComposeFunction((PetscObject)pc,"PCSetCoordinates_C",NULL);CHKERRQ(ierr); 808 PetscFunctionReturn(0); 809 } 810 811 /* -------------------------------------------------------------------------- */ 812 /* 813 PCCreateGAMG_GEO 814 815 Input Parameter: 816 . pc - 817 */ 818 #undef __FUNCT__ 819 #define __FUNCT__ "PCCreateGAMG_GEO" 820 PetscErrorCode PCCreateGAMG_GEO(PC pc) 821 { 822 PetscErrorCode ierr; 823 PC_MG *mg = (PC_MG*)pc->data; 824 PC_GAMG *pc_gamg = (PC_GAMG*)mg->innerctx; 825 826 PetscFunctionBegin; 827 pc_gamg->ops->setfromoptions = PCSetFromOptions_GEO; 828 pc_gamg->ops->destroy = PCDestroy_GAMG_GEO; 829 /* reset does not do anything; setup not virtual */ 830 831 /* set internal function pointers */ 832 pc_gamg->ops->graph = PCGAMGGraph_GEO; 833 pc_gamg->ops->coarsen = PCGAMGCoarsen_GEO; 834 pc_gamg->ops->prolongator = PCGAMGProlongator_GEO; 835 pc_gamg->ops->optprolongator = NULL; 836 pc_gamg->ops->createdefaultdata = PCSetData_GEO; 837 838 ierr = PetscObjectComposeFunction((PetscObject)pc,"PCSetCoordinates_C",PCSetCoordinates_GEO);CHKERRQ(ierr); 839 PetscFunctionReturn(0); 840 } 841