Actual source code: geo.c

  1: /*
  2:  GAMG geometric-algebric multiogrid PC - Mark Adams 2011
  3:  */

  5: #include <../src/ksp/pc/impls/gamg/gamg.h>

  7: #if defined(PETSC_HAVE_TRIANGLE)
  8: #if !defined(ANSI_DECLARATORS)
  9: #define ANSI_DECLARATORS
 10: #endif
 11: #include <triangle.h>
 12: #endif

 14: #include <petscblaslapack.h>

 16: /* Private context for the GAMG preconditioner */
 17: typedef struct {
 18:   PetscInt lid;            /* local vertex index */
 19:   PetscInt degree;         /* vertex degree */
 20: } GAMGNode;

 22: static inline int petsc_geo_mg_compare(const void *a, const void *b)
 23: {
 24:   return (((GAMGNode*)a)->degree - ((GAMGNode*)b)->degree);
 25: }

 27: /* -------------------------------------------------------------------------- */
 28: /*
 29:    PCSetCoordinates_GEO

 31:    Input Parameter:
 32:    .  pc - the preconditioner context
 33: */
 34: PetscErrorCode PCSetCoordinates_GEO(PC pc, PetscInt ndm, PetscInt a_nloc, PetscReal *coords)
 35: {
 36:   PC_MG          *mg      = (PC_MG*)pc->data;
 37:   PC_GAMG        *pc_gamg = (PC_GAMG*)mg->innerctx;
 38:   PetscInt       arrsz,bs,my0,kk,ii,nloc,Iend,aloc;
 39:   Mat            Amat = pc->pmat;

 42:   MatGetBlockSize(Amat, &bs);
 43:   MatGetOwnershipRange(Amat, &my0, &Iend);
 44:   aloc = (Iend-my0);
 45:   nloc = (Iend-my0)/bs;


 49:   pc_gamg->data_cell_rows = 1;
 51:   pc_gamg->data_cell_cols = ndm; /* coordinates */

 53:   arrsz = nloc*pc_gamg->data_cell_rows*pc_gamg->data_cell_cols;

 55:   /* create data - syntactic sugar that should be refactored at some point */
 56:   if (!pc_gamg->data || (pc_gamg->data_sz != arrsz)) {
 57:     PetscFree(pc_gamg->data);
 58:     PetscMalloc1(arrsz+1, &pc_gamg->data);
 59:   }
 60:   for (kk=0; kk<arrsz; kk++) pc_gamg->data[kk] = -999.;
 61:   pc_gamg->data[arrsz] = -99.;
 62:   /* copy data in - column oriented */
 63:   if (nloc == a_nloc) {
 64:     for (kk = 0; kk < nloc; kk++) {
 65:       for (ii = 0; ii < ndm; ii++) {
 66:         pc_gamg->data[ii*nloc + kk] =  coords[kk*ndm + ii];
 67:       }
 68:     }
 69:   } else { /* assumes the coordinates are blocked */
 70:     for (kk = 0; kk < nloc; kk++) {
 71:       for (ii = 0; ii < ndm; ii++) {
 72:         pc_gamg->data[ii*nloc + kk] =  coords[bs*kk*ndm + ii];
 73:       }
 74:     }
 75:   }
 77:   pc_gamg->data_sz = arrsz;
 78:   return 0;
 79: }

 81: /* -------------------------------------------------------------------------- */
 82: /*
 83:    PCSetData_GEO

 85:   Input Parameter:
 86:    . pc -
 87: */
 88: PetscErrorCode PCSetData_GEO(PC pc, Mat m)
 89: {
 90:   SETERRQ(PetscObjectComm((PetscObject)pc),PETSC_ERR_PLIB,"GEO MG needs coordinates");
 91: }

 93: /* -------------------------------------------------------------------------- */
 94: /*
 95:    PCSetFromOptions_GEO

 97:   Input Parameter:
 98:    . pc -
 99: */
100: PetscErrorCode PCSetFromOptions_GEO(PetscOptionItems *PetscOptionsObject,PC pc)
101: {
102:   PetscOptionsHead(PetscOptionsObject,"GAMG-GEO options");
103:   {
104:     /* -pc_gamg_sa_nsmooths */
105:     /* pc_gamg_sa->smooths = 0; */
106:     /* PetscOptionsInt("-pc_gamg_agg_nsmooths", */
107:     /*                        "smoothing steps for smoothed aggregation, usually 1 (0)", */
108:     /*                        "PCGAMGSetNSmooths_AGG", */
109:     /*                        pc_gamg_sa->smooths, */
110:     /*                        &pc_gamg_sa->smooths, */
111:     /*                        &flag);  */
112:   }
113:   PetscOptionsTail();
114:   return 0;
115: }

117: /* -------------------------------------------------------------------------- */
118: /*
119:  triangulateAndFormProl

121:    Input Parameter:
122:    . selected_2 - list of selected local ID, includes selected ghosts
123:    . data_stride -
124:    . coords[2*data_stride] - column vector of local coordinates w/ ghosts
125:    . nselected_1 - selected IDs that go with base (1) graph includes selected ghosts
126:    . clid_lid_1[nselected_1] - lids of selected (c) nodes   ???????????
127:    . agg_lists_1 - list of aggregates selected_1 vertices of aggregate unselected vertices
128:    . crsGID[selected.size()] - global index for prolongation operator
129:    . bs - block size
130:   Output Parameter:
131:    . a_Prol - prolongation operator
132:    . a_worst_best - measure of worst missed fine vertex, 0 is no misses
133: */
134: static PetscErrorCode triangulateAndFormProl(IS selected_2,PetscInt data_stride,PetscReal coords[],PetscInt nselected_1,const PetscInt clid_lid_1[],const PetscCoarsenData *agg_lists_1,
135:                                              const PetscInt crsGID[],PetscInt bs,Mat a_Prol,PetscReal *a_worst_best)
136: {
137: #if defined(PETSC_HAVE_TRIANGLE)
138:   PetscInt             jj,tid,tt,idx,nselected_2;
139:   struct triangulateio in,mid;
140:   const PetscInt       *selected_idx_2;
141:   PetscMPIInt          rank;
142:   PetscInt             Istart,Iend,nFineLoc,myFine0;
143:   int                  kk,nPlotPts,sid;
144:   MPI_Comm             comm;
145:   PetscReal            tm;

147:   PetscObjectGetComm((PetscObject)a_Prol,&comm);
148:   MPI_Comm_rank(comm,&rank);
149:   ISGetSize(selected_2, &nselected_2);
150:   if (nselected_2 == 1 || nselected_2 == 2) { /* 0 happens on idle processors */
151:     *a_worst_best = 100.0; /* this will cause a stop, but not globalized (should not happen) */
152:   } else *a_worst_best = 0.0;
153:   MPIU_Allreduce(a_worst_best, &tm, 1, MPIU_REAL, MPIU_MAX, comm);
154:   if (tm > 0.0) {
155:     *a_worst_best = 100.0;
156:     return 0;
157:   }
158:   MatGetOwnershipRange(a_Prol, &Istart, &Iend);
159:   nFineLoc = (Iend-Istart)/bs; myFine0 = Istart/bs;
160:   nPlotPts = nFineLoc; /* locals */
161:   /* triangle */
162:   /* Define input points - in*/
163:   in.numberofpoints          = nselected_2;
164:   in.numberofpointattributes = 0;
165:   /* get nselected points */
166:   PetscMalloc1(2*nselected_2, &in.pointlist);
167:   ISGetIndices(selected_2, &selected_idx_2);

169:   for (kk=0,sid=0; kk<nselected_2; kk++,sid += 2) {
170:     PetscInt lid = selected_idx_2[kk];
171:     in.pointlist[sid]   = coords[lid];
172:     in.pointlist[sid+1] = coords[data_stride + lid];
173:     if (lid>=nFineLoc) nPlotPts++;
174:   }

177:   in.numberofsegments      = 0;
178:   in.numberofedges         = 0;
179:   in.numberofholes         = 0;
180:   in.numberofregions       = 0;
181:   in.trianglelist          = NULL;
182:   in.segmentmarkerlist     = NULL;
183:   in.pointattributelist    = NULL;
184:   in.pointmarkerlist       = NULL;
185:   in.triangleattributelist = NULL;
186:   in.trianglearealist      = NULL;
187:   in.segmentlist           = NULL;
188:   in.holelist              = NULL;
189:   in.regionlist            = NULL;
190:   in.edgelist              = NULL;
191:   in.edgemarkerlist        = NULL;
192:   in.normlist              = NULL;

194:   /* triangulate */
195:   mid.pointlist = NULL;          /* Not needed if -N switch used. */
196:   /* Not needed if -N switch used or number of point attributes is zero: */
197:   mid.pointattributelist = NULL;
198:   mid.pointmarkerlist    = NULL; /* Not needed if -N or -B switch used. */
199:   mid.trianglelist       = NULL; /* Not needed if -E switch used. */
200:   /* Not needed if -E switch used or number of triangle attributes is zero: */
201:   mid.triangleattributelist = NULL;
202:   mid.neighborlist          = NULL; /* Needed only if -n switch used. */
203:   /* Needed only if segments are output (-p or -c) and -P not used: */
204:   mid.segmentlist = NULL;
205:   /* Needed only if segments are output (-p or -c) and -P and -B not used: */
206:   mid.segmentmarkerlist = NULL;
207:   mid.edgelist          = NULL; /* Needed only if -e switch used. */
208:   mid.edgemarkerlist    = NULL; /* Needed if -e used and -B not used. */
209:   mid.numberoftriangles = 0;

211:   /* Triangulate the points.  Switches are chosen to read and write a  */
212:   /*   PSLG (p), preserve the convex hull (c), number everything from  */
213:   /*   zero (z), assign a regional attribute to each element (A), and  */
214:   /*   produce an edge list (e), a Voronoi diagram (v), and a triangle */
215:   /*   neighbor list (n).                                            */
216:   if (nselected_2 != 0) { /* inactive processor */
217:     char args[] = "npczQ"; /* c is needed ? */
218:     triangulate(args, &in, &mid, (struct triangulateio*) NULL);
219:     /* output .poly files for 'showme' */
220:     if (!PETSC_TRUE) {
221:       static int level = 1;
222:       FILE       *file; char fname[32];

224:       sprintf(fname,"C%d_%d.poly",level,rank); file = fopen(fname, "w");
225:       /*First line: <# of vertices> <dimension (must be 2)> <# of attributes> <# of boundary markers (0 or 1)>*/
226:       fprintf(file, "%d  %d  %d  %d\n",in.numberofpoints,2,0,0);
227:       /*Following lines: <vertex #> <x> <y> */
228:       for (kk=0,sid=0; kk<in.numberofpoints; kk++,sid += 2) {
229:         fprintf(file, "%d %e %e\n",kk,in.pointlist[sid],in.pointlist[sid+1]);
230:       }
231:       /*One line: <# of segments> <# of boundary markers (0 or 1)> */
232:       fprintf(file, "%d  %d\n",0,0);
233:       /*Following lines: <segment #> <endpoint> <endpoint> [boundary marker] */
234:       /* One line: <# of holes> */
235:       fprintf(file, "%d\n",0);
236:       /* Following lines: <hole #> <x> <y> */
237:       /* Optional line: <# of regional attributes and/or area constraints> */
238:       /* Optional following lines: <region #> <x> <y> <attribute> <maximum area> */
239:       fclose(file);

241:       /* elems */
242:       sprintf(fname,"C%d_%d.ele",level,rank); file = fopen(fname, "w");
243:       /* First line: <# of triangles> <nodes per triangle> <# of attributes> */
244:       fprintf(file, "%d %d %d\n",mid.numberoftriangles,3,0);
245:       /* Remaining lines: <triangle #> <node> <node> <node> ... [attributes] */
246:       for (kk=0,sid=0; kk<mid.numberoftriangles; kk++,sid += 3) {
247:         fprintf(file, "%d %d %d %d\n",kk,mid.trianglelist[sid],mid.trianglelist[sid+1],mid.trianglelist[sid+2]);
248:       }
249:       fclose(file);

251:       sprintf(fname,"C%d_%d.node",level,rank); file = fopen(fname, "w");
252:       /* First line: <# of vertices> <dimension (must be 2)> <# of attributes> <# of boundary markers (0 or 1)> */
253:       /* fprintf(file, "%d  %d  %d  %d\n",in.numberofpoints,2,0,0); */
254:       fprintf(file, "%d  %d  %d  %d\n",nPlotPts,2,0,0);
255:       /*Following lines: <vertex #> <x> <y> */
256:       for (kk=0,sid=0; kk<in.numberofpoints; kk++,sid+=2) {
257:         fprintf(file, "%d %e %e\n",kk,in.pointlist[sid],in.pointlist[sid+1]);
258:       }

260:       sid /= 2;
261:       for (jj=0; jj<nFineLoc; jj++) {
262:         PetscBool sel = PETSC_TRUE;
263:         for (kk=0; kk<nselected_2 && sel; kk++) {
264:           PetscInt lid = selected_idx_2[kk];
265:           if (lid == jj) sel = PETSC_FALSE;
266:         }
267:         if (sel) fprintf(file, "%d %e %e\n",sid++,coords[jj],coords[data_stride + jj]);
268:       }
269:       fclose(file);
271:       level++;
272:     }
273:   }
274:   PetscLogEventBegin(petsc_gamg_setup_events[FIND_V],0,0,0,0);
275:   { /* form P - setup some maps */
276:     PetscInt clid,mm,*nTri,*node_tri;

278:     PetscMalloc2(nselected_2, &node_tri,nselected_2, &nTri);

280:     /* need list of triangles on node */
281:     for (kk=0; kk<nselected_2; kk++) nTri[kk] = 0;
282:     for (tid=0,kk=0; tid<mid.numberoftriangles; tid++) {
283:       for (jj=0; jj<3; jj++) {
284:         PetscInt cid = mid.trianglelist[kk++];
285:         if (nTri[cid] == 0) node_tri[cid] = tid;
286:         nTri[cid]++;
287:       }
288:     }
289: #define EPS 1.e-12
290:     /* find points and set prolongation */
291:     for (mm = clid = 0; mm < nFineLoc; mm++) {
292:       PetscBool ise;
293:       PetscCDEmptyAt(agg_lists_1,mm,&ise);
294:       if (!ise) {
295:         const PetscInt lid = mm;
296:         PetscScalar    AA[3][3];
297:         PetscBLASInt   N=3,NRHS=1,LDA=3,IPIV[3],LDB=3,INFO;
298:         PetscCDIntNd   *pos;

300:         PetscCDGetHeadPos(agg_lists_1,lid,&pos);
301:         while (pos) {
302:           PetscInt flid;
303:           PetscCDIntNdGetID(pos, &flid);
304:           PetscCDGetNextPos(agg_lists_1,lid,&pos);

306:           if (flid < nFineLoc) {  /* could be a ghost */
307:             PetscInt       bestTID = -1; PetscReal best_alpha = 1.e10;
308:             const PetscInt fgid    = flid + myFine0;
309:             /* compute shape function for gid */
310:             const PetscReal fcoord[3] = {coords[flid],coords[data_stride+flid],1.0};
311:             PetscBool       haveit    =PETSC_FALSE; PetscScalar alpha[3]; PetscInt clids[3];

313:             /* look for it */
314:             for (tid = node_tri[clid], jj=0;
315:                  jj < 5 && !haveit && tid != -1;
316:                  jj++) {
317:               for (tt=0; tt<3; tt++) {
318:                 PetscInt cid2 = mid.trianglelist[3*tid + tt];
319:                 PetscInt lid2 = selected_idx_2[cid2];
320:                 AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0;
321:                 clids[tt] = cid2; /* store for interp */
322:               }

324:               for (tt=0; tt<3; tt++) alpha[tt] = (PetscScalar)fcoord[tt];

326:               /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */
327:               PetscStackCallBLAS("LAPACKgesv",LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO));
328:               {
329:                 PetscBool have=PETSC_TRUE;  PetscReal lowest=1.e10;
330:                 for (tt = 0, idx = 0; tt < 3; tt++) {
331:                   if (PetscRealPart(alpha[tt]) > (1.0+EPS) || PetscRealPart(alpha[tt]) < -EPS) have = PETSC_FALSE;
332:                   if (PetscRealPart(alpha[tt]) < lowest) {
333:                     lowest = PetscRealPart(alpha[tt]);
334:                     idx    = tt;
335:                   }
336:                 }
337:                 haveit = have;
338:               }
339:               tid = mid.neighborlist[3*tid + idx];
340:             }

342:             if (!haveit) {
343:               /* brute force */
344:               for (tid=0; tid<mid.numberoftriangles && !haveit; tid++) {
345:                 for (tt=0; tt<3; tt++) {
346:                   PetscInt cid2 = mid.trianglelist[3*tid + tt];
347:                   PetscInt lid2 = selected_idx_2[cid2];
348:                   AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0;
349:                   clids[tt] = cid2; /* store for interp */
350:                 }
351:                 for (tt=0; tt<3; tt++) alpha[tt] = fcoord[tt];
352:                 /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */
353:                 PetscStackCallBLAS("LAPACKgesv",LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO));
354:                 {
355:                   PetscBool have=PETSC_TRUE;  PetscReal worst=0.0, v;
356:                   for (tt=0; tt<3 && have; tt++) {
357:                     if (PetscRealPart(alpha[tt]) > 1.0+EPS || PetscRealPart(alpha[tt]) < -EPS) have=PETSC_FALSE;
358:                     if ((v=PetscAbs(PetscRealPart(alpha[tt])-0.5)) > worst) worst = v;
359:                   }
360:                   if (worst < best_alpha) {
361:                     best_alpha = worst; bestTID = tid;
362:                   }
363:                   haveit = have;
364:                 }
365:               }
366:             }
367:             if (!haveit) {
368:               if (best_alpha > *a_worst_best) *a_worst_best = best_alpha;
369:               /* use best one */
370:               for (tt=0; tt<3; tt++) {
371:                 PetscInt cid2 = mid.trianglelist[3*bestTID + tt];
372:                 PetscInt lid2 = selected_idx_2[cid2];
373:                 AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0;
374:                 clids[tt] = cid2; /* store for interp */
375:               }
376:               for (tt=0; tt<3; tt++) alpha[tt] = fcoord[tt];
377:               /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */
378:               PetscStackCallBLAS("LAPACKgesv",LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO));
379:             }

381:             /* put in row of P */
382:             for (idx=0; idx<3; idx++) {
383:               PetscScalar shp = alpha[idx];
384:               if (PetscAbs(PetscRealPart(shp)) > 1.e-6) {
385:                 PetscInt cgid = crsGID[clids[idx]];
386:                 PetscInt jj   = cgid*bs, ii = fgid*bs; /* need to gloalize */
387:                 for (tt=0; tt < bs; tt++, ii++, jj++) {
388:                   MatSetValues(a_Prol,1,&ii,1,&jj,&shp,INSERT_VALUES);
389:                 }
390:               }
391:             }
392:           }
393:         } /* aggregates iterations */
394:         clid++;
395:       } /* a coarse agg */
396:     } /* for all fine nodes */

398:     ISRestoreIndices(selected_2, &selected_idx_2);
399:     MatAssemblyBegin(a_Prol,MAT_FINAL_ASSEMBLY);
400:     MatAssemblyEnd(a_Prol,MAT_FINAL_ASSEMBLY);

402:     PetscFree2(node_tri,nTri);
403:   }
404:   PetscLogEventEnd(petsc_gamg_setup_events[FIND_V],0,0,0,0);
405:   free(mid.trianglelist);
406:   free(mid.neighborlist);
407:   free(mid.segmentlist);
408:   free(mid.segmentmarkerlist);
409:   free(mid.pointlist);
410:   free(mid.pointmarkerlist);
411:   PetscFree(in.pointlist);
412:   return 0;
413: #else
414:   SETERRQ(PetscObjectComm((PetscObject)a_Prol),PETSC_ERR_PLIB,"configure with TRIANGLE to use geometric MG");
415: #endif
416: }
417: /* -------------------------------------------------------------------------- */
418: /*
419:    getGIDsOnSquareGraph - square graph, get

421:    Input Parameter:
422:    . nselected_1 - selected local indices (includes ghosts in input Gmat1)
423:    . clid_lid_1 - [nselected_1] lids of selected nodes
424:    . Gmat1 - graph that goes with 'selected_1'
425:    Output Parameter:
426:    . a_selected_2 - selected local indices (includes ghosts in output a_Gmat_2)
427:    . a_Gmat_2 - graph that is squared of 'Gmat_1'
428:    . a_crsGID[a_selected_2.size()] - map of global IDs of coarse grid nodes
429: */
430: static PetscErrorCode getGIDsOnSquareGraph(PC pc, PetscInt nselected_1,const PetscInt clid_lid_1[],const Mat Gmat1,IS *a_selected_2,Mat *a_Gmat_2,PetscInt **a_crsGID)
431: {
432:   PetscMPIInt    size;
433:   PetscInt       *crsGID, kk,my0,Iend,nloc;
434:   MPI_Comm       comm;

436:   PetscObjectGetComm((PetscObject)Gmat1,&comm);
437:   MPI_Comm_size(comm,&size);
438:   MatGetOwnershipRange(Gmat1,&my0,&Iend); /* AIJ */
439:   nloc = Iend - my0; /* this does not change */

441:   if (size == 1) { /* not much to do in serial */
442:     PetscMalloc1(nselected_1, &crsGID);
443:     for (kk=0; kk<nselected_1; kk++) crsGID[kk] = kk;
444:     *a_Gmat_2 = NULL;
445:     ISCreateGeneral(PETSC_COMM_SELF,nselected_1,clid_lid_1,PETSC_COPY_VALUES,a_selected_2);
446:   } else {
447:     PetscInt    idx,num_fine_ghosts,num_crs_ghost,myCrs0;
448:     Mat_MPIAIJ  *mpimat2;
449:     Mat         Gmat2;
450:     Vec         locState;
451:     PetscScalar *cpcol_state;

453:     /* scan my coarse zero gid, set 'lid_state' with coarse GID */
454:     kk = nselected_1;
455:     MPI_Scan(&kk, &myCrs0, 1, MPIU_INT, MPI_SUM, comm);
456:     myCrs0 -= nselected_1;

458:     if (a_Gmat_2) { /* output */
459:       /* grow graph to get wider set of selected vertices to cover fine grid, invalidates 'llist' */
460:       PCGAMGSquareGraph_GAMG(pc,Gmat1,&Gmat2);
461:       *a_Gmat_2 = Gmat2; /* output */
462:     } else Gmat2 = Gmat1;  /* use local to get crsGIDs at least */
463:     /* get coarse grid GIDS for selected (locals and ghosts) */
464:     mpimat2 = (Mat_MPIAIJ*)Gmat2->data;
465:     MatCreateVecs(Gmat2, &locState, NULL);
466:     VecSet(locState, (PetscScalar)(PetscReal)(-1)); /* set with UNKNOWN state */
467:     for (kk=0; kk<nselected_1; kk++) {
468:       PetscInt    fgid = clid_lid_1[kk] + my0;
469:       PetscScalar v    = (PetscScalar)(kk+myCrs0);
470:       VecSetValues(locState, 1, &fgid, &v, INSERT_VALUES); /* set with PID */
471:     }
472:     VecAssemblyBegin(locState);
473:     VecAssemblyEnd(locState);
474:     VecScatterBegin(mpimat2->Mvctx,locState,mpimat2->lvec,INSERT_VALUES,SCATTER_FORWARD);
475:     VecScatterEnd(mpimat2->Mvctx,locState,mpimat2->lvec,INSERT_VALUES,SCATTER_FORWARD);
476:     VecGetLocalSize(mpimat2->lvec, &num_fine_ghosts);
477:     VecGetArray(mpimat2->lvec, &cpcol_state);
478:     for (kk=0,num_crs_ghost=0; kk<num_fine_ghosts; kk++) {
479:       if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) num_crs_ghost++;
480:     }
481:     PetscMalloc1(nselected_1+num_crs_ghost, &crsGID); /* output */
482:     {
483:       PetscInt *selected_set;
484:       PetscMalloc1(nselected_1+num_crs_ghost, &selected_set);
485:       /* do ghost of 'crsGID' */
486:       for (kk=0,idx=nselected_1; kk<num_fine_ghosts; kk++) {
487:         if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) {
488:           PetscInt cgid = (PetscInt)PetscRealPart(cpcol_state[kk]);
489:           selected_set[idx] = nloc + kk;
490:           crsGID[idx++]     = cgid;
491:         }
492:       }
494:       VecRestoreArray(mpimat2->lvec, &cpcol_state);
495:       /* do locals in 'crsGID' */
496:       VecGetArray(locState, &cpcol_state);
497:       for (kk=0,idx=0; kk<nloc; kk++) {
498:         if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) {
499:           PetscInt cgid = (PetscInt)PetscRealPart(cpcol_state[kk]);
500:           selected_set[idx] = kk;
501:           crsGID[idx++]     = cgid;
502:         }
503:       }
505:       VecRestoreArray(locState, &cpcol_state);

507:       if (a_selected_2 != NULL) { /* output */
508:         ISCreateGeneral(PETSC_COMM_SELF,(nselected_1+num_crs_ghost),selected_set,PETSC_OWN_POINTER,a_selected_2);
509:       } else {
510:         PetscFree(selected_set);
511:       }
512:     }
513:     VecDestroy(&locState);
514:   }
515:   *a_crsGID = crsGID; /* output */
516:   return 0;
517: }

519: /* -------------------------------------------------------------------------- */
520: /*
521:    PCGAMGGraph_GEO

523:   Input Parameter:
524:    . pc - this
525:    . Amat - matrix on this fine level
526:   Output Parameter:
527:    . a_Gmat
528: */
529: PetscErrorCode PCGAMGGraph_GEO(PC pc,Mat Amat,Mat *a_Gmat)
530: {
531:   PC_MG           *mg      = (PC_MG*)pc->data;
532:   PC_GAMG         *pc_gamg = (PC_GAMG*)mg->innerctx;
533:   const PetscReal vfilter  = pc_gamg->threshold[0];
534:   MPI_Comm        comm;
535:   Mat             Gmat;
536:   PetscBool       set,flg,symm;

538:   PetscObjectGetComm((PetscObject)Amat,&comm);
539:   PetscLogEventBegin(PC_GAMGGraph_GEO,0,0,0,0);

541:   MatIsSymmetricKnown(Amat, &set, &flg);
542:   symm = (PetscBool)!(set && flg);

544:   PCGAMGCreateGraph(Amat, &Gmat);
545:   PCGAMGFilterGraph(&Gmat, vfilter, symm);

547:   *a_Gmat = Gmat;
548:   PetscLogEventEnd(PC_GAMGGraph_GEO,0,0,0,0);
549:   return 0;
550: }

552: /* -------------------------------------------------------------------------- */
553: /*
554:    PCGAMGCoarsen_GEO

556:   Input Parameter:
557:    . a_pc - this
558:    . a_Gmat - graph
559:   Output Parameter:
560:    . a_llist_parent - linked list from selected indices for data locality only
561: */
562: PetscErrorCode PCGAMGCoarsen_GEO(PC a_pc,Mat *a_Gmat,PetscCoarsenData **a_llist_parent)
563: {
564:   PetscInt       Istart,Iend,nloc,kk,Ii,ncols;
565:   IS             perm;
566:   GAMGNode       *gnodes;
567:   PetscInt       *permute;
568:   Mat            Gmat  = *a_Gmat;
569:   MPI_Comm       comm;
570:   MatCoarsen     crs;

572:   PetscObjectGetComm((PetscObject)a_pc,&comm);
573:   PetscLogEventBegin(PC_GAMGCoarsen_GEO,0,0,0,0);
574:   MatGetOwnershipRange(Gmat, &Istart, &Iend);
575:   nloc = (Iend-Istart);

577:   /* create random permutation with sort for geo-mg */
578:   PetscMalloc1(nloc, &gnodes);
579:   PetscMalloc1(nloc, &permute);

581:   for (Ii=Istart; Ii<Iend; Ii++) { /* locals only? */
582:     MatGetRow(Gmat,Ii,&ncols,NULL,NULL);
583:     {
584:       PetscInt lid = Ii - Istart;
585:       gnodes[lid].lid    = lid;
586:       gnodes[lid].degree = ncols;
587:     }
588:     MatRestoreRow(Gmat,Ii,&ncols,NULL,NULL);
589:   }
590:   if (PETSC_TRUE) {
591:     PetscRandom  rand;
592:     PetscBool    *bIndexSet;
593:     PetscReal    rr;
594:     PetscInt     iSwapIndex;

596:     PetscRandomCreate(comm,&rand);
597:     PetscCalloc1(nloc, &bIndexSet);
598:     for (Ii = 0; Ii < nloc; Ii++) {
599:       PetscRandomGetValueReal(rand,&rr);
600:       iSwapIndex = (PetscInt) (rr*nloc);
601:       if (!bIndexSet[iSwapIndex] && iSwapIndex != Ii) {
602:         GAMGNode iTemp = gnodes[iSwapIndex];
603:         gnodes[iSwapIndex]    = gnodes[Ii];
604:         gnodes[Ii]            = iTemp;
605:         bIndexSet[Ii]         = PETSC_TRUE;
606:         bIndexSet[iSwapIndex] = PETSC_TRUE;
607:       }
608:     }
609:     PetscRandomDestroy(&rand);
610:     PetscFree(bIndexSet);
611:   }
612:   /* only sort locals */
613:   qsort(gnodes, nloc, sizeof(GAMGNode), petsc_geo_mg_compare);
614:   /* create IS of permutation */
615:   for (kk=0; kk<nloc; kk++) permute[kk] = gnodes[kk].lid; /* locals only */
616:   PetscFree(gnodes);
617:   ISCreateGeneral(PETSC_COMM_SELF, nloc, permute, PETSC_OWN_POINTER, &perm);

619:   /* get MIS aggs */

621:   MatCoarsenCreate(comm, &crs);
622:   MatCoarsenSetType(crs, MATCOARSENMIS);
623:   MatCoarsenSetGreedyOrdering(crs, perm);
624:   MatCoarsenSetAdjacency(crs, Gmat);
625:   MatCoarsenSetStrictAggs(crs, PETSC_FALSE);
626:   MatCoarsenApply(crs);
627:   MatCoarsenGetData(crs, a_llist_parent);
628:   MatCoarsenDestroy(&crs);

630:   ISDestroy(&perm);
631:   PetscLogEventEnd(PC_GAMGCoarsen_GEO,0,0,0,0);
632:   return 0;
633: }

635: /* -------------------------------------------------------------------------- */
636: /*
637:  PCGAMGProlongator_GEO

639:  Input Parameter:
640:  . pc - this
641:  . Amat - matrix on this fine level
642:  . Graph - used to get ghost data for nodes in
643:  . selected_1 - [nselected]
644:  . agg_lists - [nselected]
645:  Output Parameter:
646:  . a_P_out - prolongation operator to the next level
647:  */
648: PetscErrorCode PCGAMGProlongator_GEO(PC pc,Mat Amat,Mat Gmat,PetscCoarsenData *agg_lists,Mat *a_P_out)
649: {
650:   PC_MG          *mg      = (PC_MG*)pc->data;
651:   PC_GAMG        *pc_gamg = (PC_GAMG*)mg->innerctx;
652:   const PetscInt dim      = pc_gamg->data_cell_cols, data_cols = pc_gamg->data_cell_cols;
653:   PetscInt       Istart,Iend,nloc,my0,jj,kk,ncols,nLocalSelected,bs,*clid_flid;
654:   Mat            Prol;
655:   PetscMPIInt    rank, size;
656:   MPI_Comm       comm;
657:   IS             selected_2,selected_1;
658:   const PetscInt *selected_idx;
659:   MatType        mtype;

661:   PetscObjectGetComm((PetscObject)Amat,&comm);
662:   PetscLogEventBegin(PC_GAMGProlongator_GEO,0,0,0,0);
663:   MPI_Comm_rank(comm,&rank);
664:   MPI_Comm_size(comm,&size);
665:   MatGetOwnershipRange(Amat, &Istart, &Iend);
666:   MatGetBlockSize(Amat, &bs);
667:   nloc = (Iend-Istart)/bs; my0 = Istart/bs;

670:   /* get 'nLocalSelected' */
671:   PetscCDGetMIS(agg_lists, &selected_1);
672:   ISGetSize(selected_1, &jj);
673:   PetscMalloc1(jj, &clid_flid);
674:   ISGetIndices(selected_1, &selected_idx);
675:   for (kk=0,nLocalSelected=0; kk<jj; kk++) {
676:     PetscInt lid = selected_idx[kk];
677:     if (lid<nloc) {
678:       MatGetRow(Gmat,lid+my0,&ncols,NULL,NULL);
679:       if (ncols>1) clid_flid[nLocalSelected++] = lid; /* fiter out singletons */
680:       MatRestoreRow(Gmat,lid+my0,&ncols,NULL,NULL);
681:     }
682:   }
683:   ISRestoreIndices(selected_1, &selected_idx);
684:   ISDestroy(&selected_1); /* this is selected_1 in serial */

686:   /* create prolongator  matrix */
687:   MatGetType(Amat,&mtype);
688:   MatCreate(comm, &Prol);
689:   MatSetSizes(Prol,nloc*bs,nLocalSelected*bs,PETSC_DETERMINE,PETSC_DETERMINE);
690:   MatSetBlockSizes(Prol, bs, bs);
691:   MatSetType(Prol, mtype);
692:   MatSeqAIJSetPreallocation(Prol,3*data_cols,NULL);
693:   MatMPIAIJSetPreallocation(Prol,3*data_cols,NULL,3*data_cols,NULL);

695:   /* can get all points "removed" - but not on geomg */
696:   MatGetSize(Prol, &kk, &jj);
697:   if (!jj) {
698:     PetscInfo(pc,"ERROE: no selected points on coarse grid\n");
699:     PetscFree(clid_flid);
700:     MatDestroy(&Prol);
701:     *a_P_out = NULL;  /* out */
702:     return 0;
703:   }

705:   {
706:     PetscReal *coords;
707:     PetscInt  data_stride;
708:     PetscInt  *crsGID = NULL;
709:     Mat       Gmat2;

712:     /* grow ghost data for better coarse grid cover of fine grid */
713:     PetscLogEventBegin(petsc_gamg_setup_events[SET5],0,0,0,0);
714:     /* messy method, squares graph and gets some data */
715:     getGIDsOnSquareGraph(pc, nLocalSelected, clid_flid, Gmat, &selected_2, &Gmat2, &crsGID);
716:     /* llist is now not valid wrt squared graph, but will work as iterator in 'triangulateAndFormProl' */
717:     PetscLogEventEnd(petsc_gamg_setup_events[SET5],0,0,0,0);
718:     /* create global vector of coorindates in 'coords' */
719:     if (size > 1) {
720:       PCGAMGGetDataWithGhosts(Gmat2, dim, pc_gamg->data, &data_stride, &coords);
721:     } else {
722:       coords      = (PetscReal*)pc_gamg->data;
723:       data_stride = pc_gamg->data_sz/pc_gamg->data_cell_cols;
724:     }
725:     MatDestroy(&Gmat2);

727:     /* triangulate */
728:     if (dim == 2) {
729:       PetscReal metric,tm;
730:       PetscLogEventBegin(petsc_gamg_setup_events[SET6],0,0,0,0);
731:       triangulateAndFormProl(selected_2, data_stride, coords,nLocalSelected, clid_flid, agg_lists, crsGID, bs, Prol, &metric);
732:       PetscLogEventEnd(petsc_gamg_setup_events[SET6],0,0,0,0);
733:       PetscFree(crsGID);

735:       /* clean up and create coordinates for coarse grid (output) */
736:       if (size > 1) PetscFree(coords);

738:       MPIU_Allreduce(&metric, &tm, 1, MPIU_REAL, MPIU_MAX, comm);
739:       if (tm > 1.) { /* needs to be globalized - should not happen */
740:         PetscInfo(pc," failed metric for coarse grid %e\n",(double)tm);
741:         MatDestroy(&Prol);
742:       } else if (metric > .0) {
743:         PetscInfo(pc,"worst metric for coarse grid = %e\n",(double)metric);
744:       }
745:     } else SETERRQ(comm,PETSC_ERR_PLIB,"3D not implemented for 'geo' AMG");
746:     { /* create next coords - output */
747:       PetscReal *crs_crds;
748:       PetscMalloc1(dim*nLocalSelected, &crs_crds);
749:       for (kk=0; kk<nLocalSelected; kk++) { /* grab local select nodes to promote - output */
750:         PetscInt lid = clid_flid[kk];
751:         for (jj=0; jj<dim; jj++) crs_crds[jj*nLocalSelected + kk] = pc_gamg->data[jj*nloc + lid];
752:       }

754:       PetscFree(pc_gamg->data);
755:       pc_gamg->data    = crs_crds; /* out */
756:       pc_gamg->data_sz = dim*nLocalSelected;
757:     }
758:     ISDestroy(&selected_2);
759:   }

761:   *a_P_out = Prol;  /* out */
762:   PetscFree(clid_flid);
763:   PetscLogEventEnd(PC_GAMGProlongator_GEO,0,0,0,0);
764:   return 0;
765: }

767: static PetscErrorCode PCDestroy_GAMG_GEO(PC pc)
768: {
769:   PetscObjectComposeFunction((PetscObject)pc,"PCSetCoordinates_C",NULL);
770:   return 0;
771: }

773: /* -------------------------------------------------------------------------- */
774: /*
775:  PCCreateGAMG_GEO

777:   Input Parameter:
778:    . pc -
779: */
780: PetscErrorCode  PCCreateGAMG_GEO(PC pc)
781: {
782:   PC_MG          *mg      = (PC_MG*)pc->data;
783:   PC_GAMG        *pc_gamg = (PC_GAMG*)mg->innerctx;

785:   pc_gamg->ops->setfromoptions = PCSetFromOptions_GEO;
786:   pc_gamg->ops->destroy        = PCDestroy_GAMG_GEO;
787:   /* reset does not do anything; setup not virtual */

789:   /* set internal function pointers */
790:   pc_gamg->ops->graph             = PCGAMGGraph_GEO;
791:   pc_gamg->ops->coarsen           = PCGAMGCoarsen_GEO;
792:   pc_gamg->ops->prolongator       = PCGAMGProlongator_GEO;
793:   pc_gamg->ops->optprolongator    = NULL;
794:   pc_gamg->ops->createdefaultdata = PCSetData_GEO;

796:   PetscObjectComposeFunction((PetscObject)pc,"PCSetCoordinates_C",PCSetCoordinates_GEO);
797:   return 0;
798: }