Actual source code: geo.c
petsc-3.7.1 2016-05-15
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      1: /*
      2:  GAMG geometric-algebric multiogrid PC - Mark Adams 2011
      3:  */

      5: #include <../src/ksp/pc/impls/gamg/gamg.h>        /*I "petscpc.h" I*/
      6: #include <petsc/private/kspimpl.h>

      8: #if defined(PETSC_HAVE_TRIANGLE)
      9: #define REAL PetscReal
     10: #include <triangle.h>
     11: #endif

     13: #include <petscblaslapack.h>

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

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

     26: /* -------------------------------------------------------------------------- */
     27: /*
     28:    PCSetCoordinates_GEO

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

     45:   MatGetBlockSize(Amat, &bs);

     47:   MatGetOwnershipRange(Amat, &my0, &Iend);
     48:   nloc = (Iend-my0)/bs;

     50:   if (nloc!=a_nloc) SETERRQ2(PetscObjectComm((PetscObject)Amat),PETSC_ERR_ARG_WRONG, "Stokes not supported nloc = %d %d.",a_nloc,nloc);
     51:   if ((Iend-my0)%bs!=0) SETERRQ1(PetscObjectComm((PetscObject)Amat),PETSC_ERR_ARG_WRONG, "Bad local size %d.",nloc);

     53:   pc_gamg->data_cell_rows = 1;
     54:   if (!coords && nloc > 0) SETERRQ(PetscObjectComm((PetscObject)Amat),PETSC_ERR_ARG_WRONG, "Need coordinates for pc_gamg_type 'geo'.");
     55:   pc_gamg->data_cell_cols = ndm; /* coordinates */

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

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

     77: /* -------------------------------------------------------------------------- */
     78: /*
     79:    PCSetData_GEO

     81:   Input Parameter:
     82:    . pc -
     83: */
     86: PetscErrorCode PCSetData_GEO(PC pc, Mat m)
     87: {
     89:   SETERRQ(PetscObjectComm((PetscObject)pc),PETSC_ERR_PLIB,"GEO MG needs coordinates");
     90: }

     92: /* -------------------------------------------------------------------------- */
     93: /*
     94:    PCSetFromOptions_GEO

     96:   Input Parameter:
     97:    . pc -
     98: */
    101: PetscErrorCode PCSetFromOptions_GEO(PetscOptionItems *PetscOptionsObject,PC pc)
    102: {

    106:   PetscOptionsHead(PetscOptionsObject,"GAMG-GEO options");
    107:   {
    108:     /* -pc_gamg_sa_nsmooths */
    109:     /* pc_gamg_sa->smooths = 0; */
    110:     /* PetscOptionsInt("-pc_gamg_agg_nsmooths", */
    111:     /*                        "smoothing steps for smoothed aggregation, usually 1 (0)", */
    112:     /*                        "PCGAMGSetNSmooths_AGG", */
    113:     /*                        pc_gamg_sa->smooths, */
    114:     /*                        &pc_gamg_sa->smooths, */
    115:     /*                        &flag);  */
    116:     /*  */
    117:   }
    118:   PetscOptionsTail();
    119:   return(0);
    120: }

    122: /* -------------------------------------------------------------------------- */
    123: /*
    124:  triangulateAndFormProl

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

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

    178:   for (kk=0,sid=0; kk<nselected_2; kk++,sid += 2) {
    179:     PetscInt lid = selected_idx_2[kk];
    180:     in.pointlist[sid]   = coords[lid];
    181:     in.pointlist[sid+1] = coords[data_stride + lid];
    182:     if (lid>=nFineLoc) nPlotPts++;
    183:   }
    184:   if (sid != 2*nselected_2) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"sid %D != 2*nselected_2 %D",sid,nselected_2);

    186:   in.numberofsegments      = 0;
    187:   in.numberofedges         = 0;
    188:   in.numberofholes         = 0;
    189:   in.numberofregions       = 0;
    190:   in.trianglelist          = 0;
    191:   in.segmentmarkerlist     = 0;
    192:   in.pointattributelist    = 0;
    193:   in.pointmarkerlist       = 0;
    194:   in.triangleattributelist = 0;
    195:   in.trianglearealist      = 0;
    196:   in.segmentlist           = 0;
    197:   in.holelist              = 0;
    198:   in.regionlist            = 0;
    199:   in.edgelist              = 0;
    200:   in.edgemarkerlist        = 0;
    201:   in.normlist              = 0;

    203:   /* triangulate */
    204:   mid.pointlist = 0;            /* Not needed if -N switch used. */
    205:   /* Not needed if -N switch used or number of point attributes is zero: */
    206:   mid.pointattributelist = 0;
    207:   mid.pointmarkerlist    = 0; /* Not needed if -N or -B switch used. */
    208:   mid.trianglelist       = 0;    /* Not needed if -E switch used. */
    209:   /* Not needed if -E switch used or number of triangle attributes is zero: */
    210:   mid.triangleattributelist = 0;
    211:   mid.neighborlist          = 0; /* Needed only if -n switch used. */
    212:   /* Needed only if segments are output (-p or -c) and -P not used: */
    213:   mid.segmentlist = 0;
    214:   /* Needed only if segments are output (-p or -c) and -P and -B not used: */
    215:   mid.segmentmarkerlist = 0;
    216:   mid.edgelist          = 0;    /* Needed only if -e switch used. */
    217:   mid.edgemarkerlist    = 0; /* Needed if -e used and -B not used. */
    218:   mid.numberoftriangles = 0;

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

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

    250:       /* elems */
    251:       sprintf(fname,"C%d_%d.ele",level,rank); file = fopen(fname, "w");
    252:       /* First line: <# of triangles> <nodes per triangle> <# of attributes> */
    253:       fprintf(file, "%d %d %d\n",mid.numberoftriangles,3,0);
    254:       /* Remaining lines: <triangle #> <node> <node> <node> ... [attributes] */
    255:       for (kk=0,sid=0; kk<mid.numberoftriangles; kk++,sid += 3) {
    256:         fprintf(file, "%d %d %d %d\n",kk,mid.trianglelist[sid],mid.trianglelist[sid+1],mid.trianglelist[sid+2]);
    257:       }
    258:       fclose(file);

    260:       sprintf(fname,"C%d_%d.node",level,rank); file = fopen(fname, "w");
    261:       /* First line: <# of vertices> <dimension (must be 2)> <# of attributes> <# of boundary markers (0 or 1)> */
    262:       /* fprintf(file, "%d  %d  %d  %d\n",in.numberofpoints,2,0,0); */
    263:       fprintf(file, "%d  %d  %d  %d\n",nPlotPts,2,0,0);
    264:       /*Following lines: <vertex #> <x> <y> */
    265:       for (kk=0,sid=0; kk<in.numberofpoints; kk++,sid+=2) {
    266:         fprintf(file, "%d %e %e\n",kk,in.pointlist[sid],in.pointlist[sid+1]);
    267:       }

    269:       sid /= 2;
    270:       for (jj=0; jj<nFineLoc; jj++) {
    271:         PetscBool sel = PETSC_TRUE;
    272:         for (kk=0; kk<nselected_2 && sel; kk++) {
    273:           PetscInt lid = selected_idx_2[kk];
    274:           if (lid == jj) sel = PETSC_FALSE;
    275:         }
    276:         if (sel) fprintf(file, "%d %e %e\n",sid++,coords[jj],coords[data_stride + jj]);
    277:       }
    278:       fclose(file);
    279:       if (sid != nPlotPts) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"sid %D != nPlotPts %D",sid,nPlotPts);
    280:       level++;
    281:     }
    282:   }
    283: #if defined PETSC_GAMG_USE_LOG
    284:   PetscLogEventBegin(petsc_gamg_setup_events[FIND_V],0,0,0,0);
    285: #endif
    286:   { /* form P - setup some maps */
    287:     PetscInt clid,mm,*nTri,*node_tri;

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

    291:     /* need list of triangles on node */
    292:     for (kk=0; kk<nselected_2; kk++) nTri[kk] = 0;
    293:     for (tid=0,kk=0; tid<mid.numberoftriangles; tid++) {
    294:       for (jj=0; jj<3; jj++) {
    295:         PetscInt cid = mid.trianglelist[kk++];
    296:         if (nTri[cid] == 0) node_tri[cid] = tid;
    297:         nTri[cid]++;
    298:       }
    299:     }
    300: #define EPS 1.e-12
    301:     /* find points and set prolongation */
    302:     for (mm = clid = 0; mm < nFineLoc; mm++) {
    303:       PetscBool ise;
    304:       PetscCDEmptyAt(agg_lists_1,mm,&ise);
    305:       if (!ise) {
    306:         const PetscInt lid = mm;
    307:         /* for (clid_iterator=0;clid_iterator<nselected_1;clid_iterator++) { */
    308:         PetscScalar  AA[3][3];
    309:         PetscBLASInt N=3,NRHS=1,LDA=3,IPIV[3],LDB=3,INFO;
    310:         PetscCDPos   pos;
    311:         PetscCDGetHeadPos(agg_lists_1,lid,&pos);
    312:         while (pos) {
    313:           PetscInt flid;
    314:           PetscLLNGetID(pos, &flid);
    315:           PetscCDGetNextPos(agg_lists_1,lid,&pos);

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

    324:             /* look for it */
    325:             for (tid = node_tri[clid], jj=0;
    326:                  jj < 5 && !haveit && tid != -1;
    327:                  jj++) {
    328:               for (tt=0; tt<3; tt++) {
    329:                 PetscInt cid2 = mid.trianglelist[3*tid + tt];
    330:                 PetscInt lid2 = selected_idx_2[cid2];
    331:                 AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0;
    332:                 clids[tt] = cid2; /* store for interp */
    333:               }

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

    337:               /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */
    338:               PetscStackCallBLAS("LAPACKgesv",LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO));
    339:               {
    340:                 PetscBool have=PETSC_TRUE;  PetscReal lowest=1.e10;
    341:                 for (tt = 0, idx = 0; tt < 3; tt++) {
    342:                   if (PetscRealPart(alpha[tt]) > (1.0+EPS) || PetscRealPart(alpha[tt]) < -EPS) have = PETSC_FALSE;
    343:                   if (PetscRealPart(alpha[tt]) < lowest) {
    344:                     lowest = PetscRealPart(alpha[tt]);
    345:                     idx    = tt;
    346:                   }
    347:                 }
    348:                 haveit = have;
    349:               }
    350:               tid = mid.neighborlist[3*tid + idx];
    351:             }

    353:             if (!haveit) {
    354:               /* brute force */
    355:               for (tid=0; tid<mid.numberoftriangles && !haveit; tid++) {
    356:                 for (tt=0; tt<3; tt++) {
    357:                   PetscInt cid2 = mid.trianglelist[3*tid + tt];
    358:                   PetscInt lid2 = selected_idx_2[cid2];
    359:                   AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0;
    360:                   clids[tt] = cid2; /* store for interp */
    361:                 }
    362:                 for (tt=0; tt<3; tt++) alpha[tt] = fcoord[tt];
    363:                 /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */
    364:                 PetscStackCallBLAS("LAPACKgesv",LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO));
    365:                 {
    366:                   PetscBool have=PETSC_TRUE;  PetscReal worst=0.0, v;
    367:                   for (tt=0; tt<3 && have; tt++) {
    368:                     if (PetscRealPart(alpha[tt]) > 1.0+EPS || PetscRealPart(alpha[tt]) < -EPS) have=PETSC_FALSE;
    369:                     if ((v=PetscAbs(PetscRealPart(alpha[tt])-0.5)) > worst) worst = v;
    370:                   }
    371:                   if (worst < best_alpha) {
    372:                     best_alpha = worst; bestTID = tid;
    373:                   }
    374:                   haveit = have;
    375:                 }
    376:               }
    377:             }
    378:             if (!haveit) {
    379:               if (best_alpha > *a_worst_best) *a_worst_best = best_alpha;
    380:               /* use best one */
    381:               for (tt=0; tt<3; tt++) {
    382:                 PetscInt cid2 = mid.trianglelist[3*bestTID + tt];
    383:                 PetscInt lid2 = selected_idx_2[cid2];
    384:                 AA[tt][0] = coords[lid2]; AA[tt][1] = coords[data_stride + lid2]; AA[tt][2] = 1.0;
    385:                 clids[tt] = cid2; /* store for interp */
    386:               }
    387:               for (tt=0; tt<3; tt++) alpha[tt] = fcoord[tt];
    388:               /* SUBROUTINE DGESV(N, NRHS, A, LDA, IPIV, B, LDB, INFO) */
    389:               PetscStackCallBLAS("LAPACKgesv",LAPACKgesv_(&N, &NRHS, (PetscScalar*)AA, &LDA, IPIV, alpha, &LDB, &INFO));
    390:             }

    392:             /* put in row of P */
    393:             for (idx=0; idx<3; idx++) {
    394:               PetscScalar shp = alpha[idx];
    395:               if (PetscAbs(PetscRealPart(shp)) > 1.e-6) {
    396:                 PetscInt cgid = crsGID[clids[idx]];
    397:                 PetscInt jj   = cgid*bs, ii = fgid*bs; /* need to gloalize */
    398:                 for (tt=0; tt < bs; tt++, ii++, jj++) {
    399:                   MatSetValues(a_Prol,1,&ii,1,&jj,&shp,INSERT_VALUES);
    400:                 }
    401:               }
    402:             }
    403:           }
    404:         } /* aggregates iterations */
    405:         clid++;
    406:       } /* a coarse agg */
    407:     } /* for all fine nodes */

    409:     ISRestoreIndices(selected_2, &selected_idx_2);
    410:     MatAssemblyBegin(a_Prol,MAT_FINAL_ASSEMBLY);
    411:     MatAssemblyEnd(a_Prol,MAT_FINAL_ASSEMBLY);

    413:     PetscFree2(node_tri,nTri);
    414:   }
    415: #if defined PETSC_GAMG_USE_LOG
    416:   PetscLogEventEnd(petsc_gamg_setup_events[FIND_V],0,0,0,0);
    417: #endif
    418:   free(mid.trianglelist);
    419:   free(mid.neighborlist);
    420:   PetscFree(in.pointlist);
    421:   return(0);
    422: #else
    423:   SETERRQ(PetscObjectComm((PetscObject)a_Prol),PETSC_ERR_PLIB,"configure with TRIANGLE to use geometric MG");
    424: #endif
    425: }
    426: /* -------------------------------------------------------------------------- */
    427: /*
    428:    getGIDsOnSquareGraph - square graph, get

    430:    Input Parameter:
    431:    . nselected_1 - selected local indices (includes ghosts in input Gmat1)
    432:    . clid_lid_1 - [nselected_1] lids of selected nodes
    433:    . Gmat1 - graph that goes with 'selected_1'
    434:    Output Parameter:
    435:    . a_selected_2 - selected local indices (includes ghosts in output a_Gmat_2)
    436:    . a_Gmat_2 - graph that is squared of 'Gmat_1'
    437:    . a_crsGID[a_selected_2.size()] - map of global IDs of coarse grid nodes
    438: */
    441: 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)
    442: {
    444:   PetscMPIInt    size;
    445:   PetscInt       *crsGID, kk,my0,Iend,nloc;
    446:   MPI_Comm       comm;

    449:   PetscObjectGetComm((PetscObject)Gmat1,&comm);
    450:   MPI_Comm_size(comm,&size);
    451:   MatGetOwnershipRange(Gmat1,&my0,&Iend); /* AIJ */
    452:   nloc = Iend - my0; /* this does not change */

    454:   if (size == 1) { /* not much to do in serial */
    455:     PetscMalloc1(nselected_1, &crsGID);
    456:     for (kk=0; kk<nselected_1; kk++) crsGID[kk] = kk;
    457:     *a_Gmat_2 = 0;
    458:     ISCreateGeneral(PETSC_COMM_SELF,nselected_1,clid_lid_1,PETSC_COPY_VALUES,a_selected_2);
    459:   } else {
    460:     PetscInt    idx,num_fine_ghosts,num_crs_ghost,myCrs0;
    461:     Mat_MPIAIJ  *mpimat2;
    462:     Mat         Gmat2;
    463:     Vec         locState;
    464:     PetscScalar *cpcol_state;

    466:     /* scan my coarse zero gid, set 'lid_state' with coarse GID */
    467:     kk = nselected_1;
    468:     MPI_Scan(&kk, &myCrs0, 1, MPIU_INT, MPI_SUM, comm);
    469:     myCrs0 -= nselected_1;

    471:     if (a_Gmat_2) { /* output */
    472:       /* grow graph to get wider set of selected vertices to cover fine grid, invalidates 'llist' */
    473:       MatTransposeMatMult(Gmat1, Gmat1, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &Gmat2);
    474:       *a_Gmat_2 = Gmat2; /* output */
    475:     } else Gmat2 = Gmat1;  /* use local to get crsGIDs at least */
    476:     /* get coarse grid GIDS for selected (locals and ghosts) */
    477:     mpimat2 = (Mat_MPIAIJ*)Gmat2->data;
    478:     MatCreateVecs(Gmat2, &locState, 0);
    479:     VecSet(locState, (PetscScalar)(PetscReal)(-1)); /* set with UNKNOWN state */
    480:     for (kk=0; kk<nselected_1; kk++) {
    481:       PetscInt    fgid = clid_lid_1[kk] + my0;
    482:       PetscScalar v    = (PetscScalar)(kk+myCrs0);
    483:       VecSetValues(locState, 1, &fgid, &v, INSERT_VALUES); /* set with PID */
    484:     }
    485:     VecAssemblyBegin(locState);
    486:     VecAssemblyEnd(locState);
    487:     VecScatterBegin(mpimat2->Mvctx,locState,mpimat2->lvec,INSERT_VALUES,SCATTER_FORWARD);
    488:       VecScatterEnd(mpimat2->Mvctx,locState,mpimat2->lvec,INSERT_VALUES,SCATTER_FORWARD);
    489:     VecGetLocalSize(mpimat2->lvec, &num_fine_ghosts);
    490:     VecGetArray(mpimat2->lvec, &cpcol_state);
    491:     for (kk=0,num_crs_ghost=0; kk<num_fine_ghosts; kk++) {
    492:       if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) num_crs_ghost++;
    493:     }
    494:     PetscMalloc1(nselected_1+num_crs_ghost, &crsGID); /* output */
    495:     {
    496:       PetscInt *selected_set;
    497:       PetscMalloc1(nselected_1+num_crs_ghost, &selected_set);
    498:       /* do ghost of 'crsGID' */
    499:       for (kk=0,idx=nselected_1; kk<num_fine_ghosts; kk++) {
    500:         if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) {
    501:           PetscInt cgid = (PetscInt)PetscRealPart(cpcol_state[kk]);
    502:           selected_set[idx] = nloc + kk;
    503:           crsGID[idx++]     = cgid;
    504:         }
    505:       }
    506:       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);
    507:       VecRestoreArray(mpimat2->lvec, &cpcol_state);
    508:       /* do locals in 'crsGID' */
    509:       VecGetArray(locState, &cpcol_state);
    510:       for (kk=0,idx=0; kk<nloc; kk++) {
    511:         if ((PetscInt)PetscRealPart(cpcol_state[kk]) != -1) {
    512:           PetscInt cgid = (PetscInt)PetscRealPart(cpcol_state[kk]);
    513:           selected_set[idx] = kk;
    514:           crsGID[idx++]     = cgid;
    515:         }
    516:       }
    517:       if (idx != nselected_1) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"idx %D != nselected_1 %D",idx,nselected_1);
    518:       VecRestoreArray(locState, &cpcol_state);

    520:       if (a_selected_2 != 0) { /* output */
    521:         ISCreateGeneral(PETSC_COMM_SELF,(nselected_1+num_crs_ghost),selected_set,PETSC_OWN_POINTER,a_selected_2);
    522:       } else {
    523:         PetscFree(selected_set);
    524:       }
    525:     }
    526:     VecDestroy(&locState);
    527:   }
    528:   *a_crsGID = crsGID; /* output */
    529:   return(0);
    530: }

    532: /* -------------------------------------------------------------------------- */
    533: /*
    534:    PCGAMGGraph_GEO

    536:   Input Parameter:
    537:    . pc - this
    538:    . Amat - matrix on this fine level
    539:   Output Parameter:
    540:    . a_Gmat
    541: */
    544: PetscErrorCode PCGAMGGraph_GEO(PC pc,Mat Amat,Mat *a_Gmat)
    545: {
    546:   PetscErrorCode  ierr;
    547:   PC_MG           *mg      = (PC_MG*)pc->data;
    548:   PC_GAMG         *pc_gamg = (PC_GAMG*)mg->innerctx;
    549:   const PetscReal vfilter  = pc_gamg->threshold;
    550:   MPI_Comm        comm;
    551:   Mat             Gmat;
    552:   PetscBool       set,flg,symm;

    555:   PetscObjectGetComm((PetscObject)Amat,&comm);
    556:   PetscLogEventBegin(PC_GAMGGraph_GEO,0,0,0,0);

    558:   MatIsSymmetricKnown(Amat, &set, &flg);
    559:   symm = (PetscBool)!(set && flg);

    561:   PCGAMGCreateGraph(Amat, &Gmat);
    562:   PCGAMGFilterGraph(&Gmat, vfilter, symm);

    564:   *a_Gmat = Gmat;
    565:   PetscLogEventEnd(PC_GAMGGraph_GEO,0,0,0,0);
    566:   return(0);
    567: }

    569: /* -------------------------------------------------------------------------- */
    570: /*
    571:    PCGAMGCoarsen_GEO

    573:   Input Parameter:
    574:    . a_pc - this
    575:    . a_Gmat - graph
    576:   Output Parameter:
    577:    . a_llist_parent - linked list from selected indices for data locality only
    578: */
    581: PetscErrorCode PCGAMGCoarsen_GEO(PC a_pc,Mat *a_Gmat,PetscCoarsenData **a_llist_parent)
    582: {
    584:   PetscInt       Istart,Iend,nloc,kk,Ii,ncols;
    585:   IS             perm;
    586:   GAMGNode       *gnodes;
    587:   PetscInt       *permute;
    588:   Mat            Gmat  = *a_Gmat;
    589:   MPI_Comm       comm;
    590:   MatCoarsen     crs;

    593:   PetscObjectGetComm((PetscObject)a_pc,&comm);
    594:   PetscLogEventBegin(PC_GAMGCoarsen_GEO,0,0,0,0);
    595:   MatGetOwnershipRange(Gmat, &Istart, &Iend);
    596:   nloc = (Iend-Istart);

    598:   /* create random permutation with sort for geo-mg */
    599:   PetscMalloc1(nloc, &gnodes);
    600:   PetscMalloc1(nloc, &permute);

    602:   for (Ii=Istart; Ii<Iend; Ii++) { /* locals only? */
    603:     MatGetRow(Gmat,Ii,&ncols,0,0);
    604:     {
    605:       PetscInt lid = Ii - Istart;
    606:       gnodes[lid].lid    = lid;
    607:       gnodes[lid].degree = ncols;
    608:     }
    609:     MatRestoreRow(Gmat,Ii,&ncols,0,0);
    610:   }
    611:   if (PETSC_TRUE) {
    612:     PetscRandom  rand;
    613:     PetscBool    *bIndexSet;
    614:     PetscReal    rr;
    615:     PetscInt     iSwapIndex;

    617:     PetscRandomCreate(comm,&rand);
    618:     PetscCalloc1(nloc, &bIndexSet);
    619:     for (Ii = 0; Ii < nloc; Ii++) {
    620:       PetscRandomGetValueReal(rand,&rr);
    621:       iSwapIndex = (PetscInt) (rr*nloc);
    622:       if (!bIndexSet[iSwapIndex] && iSwapIndex != Ii) {
    623:         GAMGNode iTemp = gnodes[iSwapIndex];
    624:         gnodes[iSwapIndex]    = gnodes[Ii];
    625:         gnodes[Ii]            = iTemp;
    626:         bIndexSet[Ii]         = PETSC_TRUE;
    627:         bIndexSet[iSwapIndex] = PETSC_TRUE;
    628:       }
    629:     }
    630:     PetscRandomDestroy(&rand);
    631:     PetscFree(bIndexSet);
    632:   }
    633:   /* only sort locals */
    634:   qsort(gnodes, nloc, sizeof(GAMGNode), petsc_geo_mg_compare);
    635:   /* create IS of permutation */
    636:   for (kk=0; kk<nloc; kk++) permute[kk] = gnodes[kk].lid; /* locals only */
    637:   ISCreateGeneral(PETSC_COMM_SELF, nloc, permute, PETSC_OWN_POINTER, &perm);

    639:   PetscFree(gnodes);

    641:   /* get MIS aggs */

    643:   MatCoarsenCreate(comm, &crs);
    644:   MatCoarsenSetType(crs, MATCOARSENMIS);
    645:   MatCoarsenSetGreedyOrdering(crs, perm);
    646:   MatCoarsenSetAdjacency(crs, Gmat);
    647:   MatCoarsenSetStrictAggs(crs, PETSC_FALSE);
    648:   MatCoarsenApply(crs);
    649:   MatCoarsenGetData(crs, a_llist_parent);
    650:   MatCoarsenDestroy(&crs);

    652:   ISDestroy(&perm);
    653:   PetscLogEventEnd(PC_GAMGCoarsen_GEO,0,0,0,0);
    654:   return(0);
    655: }

    657: /* -------------------------------------------------------------------------- */
    658: /*
    659:  PCGAMGProlongator_GEO

    661:  Input Parameter:
    662:  . pc - this
    663:  . Amat - matrix on this fine level
    664:  . Graph - used to get ghost data for nodes in
    665:  . selected_1 - [nselected]
    666:  . agg_lists - [nselected]
    667:  Output Parameter:
    668:  . a_P_out - prolongation operator to the next level
    669:  */
    672: PetscErrorCode PCGAMGProlongator_GEO(PC pc,Mat Amat,Mat Gmat,PetscCoarsenData *agg_lists,Mat *a_P_out)
    673: {
    674:   PC_MG          *mg      = (PC_MG*)pc->data;
    675:   PC_GAMG        *pc_gamg = (PC_GAMG*)mg->innerctx;
    676:   const PetscInt dim      = pc_gamg->data_cell_cols, data_cols = pc_gamg->data_cell_cols;
    678:   PetscInt       Istart,Iend,nloc,my0,jj,kk,ncols,nLocalSelected,bs,*clid_flid;
    679:   Mat            Prol;
    680:   PetscMPIInt    rank, size;
    681:   MPI_Comm       comm;
    682:   IS             selected_2,selected_1;
    683:   const PetscInt *selected_idx;
    684:   MatType        mtype;

    687:   PetscObjectGetComm((PetscObject)Amat,&comm);
    688:   PetscLogEventBegin(PC_GAMGProlongator_GEO,0,0,0,0);
    689:   MPI_Comm_rank(comm,&rank);
    690:   MPI_Comm_size(comm,&size);
    691:   MatGetOwnershipRange(Amat, &Istart, &Iend);
    692:   MatGetBlockSize(Amat, &bs);
    693:   nloc = (Iend-Istart)/bs; my0 = Istart/bs;
    694:   if ((Iend-Istart) % bs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"(Iend %D - Istart %D) % bs %D",Iend,Istart,bs);

    696:   /* get 'nLocalSelected' */
    697:   PetscCDGetMIS(agg_lists, &selected_1);
    698:   ISGetSize(selected_1, &jj);
    699:   PetscMalloc1(jj, &clid_flid);
    700:   ISGetIndices(selected_1, &selected_idx);
    701:   for (kk=0,nLocalSelected=0; kk<jj; kk++) {
    702:     PetscInt lid = selected_idx[kk];
    703:     if (lid<nloc) {
    704:       MatGetRow(Gmat,lid+my0,&ncols,0,0);
    705:       if (ncols>1) clid_flid[nLocalSelected++] = lid; /* fiter out singletons */
    706:       MatRestoreRow(Gmat,lid+my0,&ncols,0,0);
    707:     }
    708:   }
    709:   ISRestoreIndices(selected_1, &selected_idx);
    710:   ISDestroy(&selected_1); /* this is selected_1 in serial */

    712:   /* create prolongator  matrix */
    713:   MatGetType(Amat,&mtype);
    714:   MatCreate(comm, &Prol);
    715:   MatSetSizes(Prol,nloc*bs,nLocalSelected*bs,PETSC_DETERMINE,PETSC_DETERMINE);
    716:   MatSetBlockSizes(Prol, bs, bs);
    717:   MatSetType(Prol, mtype);
    718:   MatSeqAIJSetPreallocation(Prol,3*data_cols,NULL);
    719:   MatMPIAIJSetPreallocation(Prol,3*data_cols,NULL,3*data_cols,NULL);

    721:   /* can get all points "removed" - but not on geomg */
    722:    MatGetSize(Prol, &kk, &jj);
    723:   if (!jj) {
    724:     PetscInfo(pc,"ERROE: no selected points on coarse grid\n");
    725:     PetscFree(clid_flid);
    726:     MatDestroy(&Prol);
    727:     *a_P_out = NULL;  /* out */
    728:     return(0);
    729:   }

    731:   {
    732:     PetscReal *coords;
    733:     PetscInt  data_stride;
    734:     PetscInt  *crsGID = NULL;
    735:     Mat       Gmat2;

    737:     if (dim != data_cols) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"dim %D != data_cols %D",dim,data_cols);
    738:     /* grow ghost data for better coarse grid cover of fine grid */
    739: #if defined PETSC_GAMG_USE_LOG
    740:     PetscLogEventBegin(petsc_gamg_setup_events[SET5],0,0,0,0);
    741: #endif
    742:     /* messy method, squares graph and gets some data */
    743:     getGIDsOnSquareGraph(nLocalSelected, clid_flid, Gmat, &selected_2, &Gmat2, &crsGID);
    744:     /* llist is now not valid wrt squared graph, but will work as iterator in 'triangulateAndFormProl' */
    745: #if defined PETSC_GAMG_USE_LOG
    746:     PetscLogEventEnd(petsc_gamg_setup_events[SET5],0,0,0,0);
    747: #endif
    748:     /* create global vector of coorindates in 'coords' */
    749:     if (size > 1) {
    750:       PCGAMGGetDataWithGhosts(Gmat2, dim, pc_gamg->data, &data_stride, &coords);
    751:     } else {
    752:       coords      = (PetscReal*)pc_gamg->data;
    753:       data_stride = pc_gamg->data_sz/pc_gamg->data_cell_cols;
    754:     }
    755:     MatDestroy(&Gmat2);

    757:     /* triangulate */
    758:     if (dim == 2) {
    759:       PetscReal metric,tm;
    760: #if defined PETSC_GAMG_USE_LOG
    761:       PetscLogEventBegin(petsc_gamg_setup_events[SET6],0,0,0,0);
    762: #endif
    763:       triangulateAndFormProl(selected_2, data_stride, coords,nLocalSelected, clid_flid, agg_lists, crsGID, bs, Prol, &metric);
    764: #if defined PETSC_GAMG_USE_LOG
    765:       PetscLogEventEnd(petsc_gamg_setup_events[SET6],0,0,0,0);
    766: #endif
    767:       PetscFree(crsGID);

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

    772:       MPIU_Allreduce(&metric, &tm, 1, MPIU_REAL, MPIU_MAX, comm);
    773:       if (tm > 1.) { /* needs to be globalized - should not happen */
    774:         PetscInfo1(pc," failed metric for coarse grid %e\n",(double)tm);
    775:         MatDestroy(&Prol);
    776:       } else if (metric > .0) {
    777:         PetscInfo1(pc,"worst metric for coarse grid = %e\n",(double)metric);
    778:       }
    779:     } else SETERRQ(comm,PETSC_ERR_PLIB,"3D not implemented for 'geo' AMG");
    780:     { /* create next coords - output */
    781:       PetscReal *crs_crds;
    782:       PetscMalloc1(dim*nLocalSelected, &crs_crds);
    783:       for (kk=0; kk<nLocalSelected; kk++) { /* grab local select nodes to promote - output */
    784:         PetscInt lid = clid_flid[kk];
    785:         for (jj=0; jj<dim; jj++) crs_crds[jj*nLocalSelected + kk] = pc_gamg->data[jj*nloc + lid];
    786:       }

    788:       PetscFree(pc_gamg->data);
    789:       pc_gamg->data    = crs_crds; /* out */
    790:       pc_gamg->data_sz = dim*nLocalSelected;
    791:     }
    792:     ISDestroy(&selected_2);
    793:   }

    795:   *a_P_out = Prol;  /* out */
    796:   PetscFree(clid_flid);
    797:   PetscLogEventEnd(PC_GAMGProlongator_GEO,0,0,0,0);
    798:   return(0);
    799: }

    803: static PetscErrorCode PCDestroy_GAMG_GEO(PC pc)
    804: {

    808:   PetscObjectComposeFunction((PetscObject)pc,"PCSetCoordinates_C",NULL);
    809:   return(0);
    810: }

    812: /* -------------------------------------------------------------------------- */
    813: /*
    814:  PCCreateGAMG_GEO

    816:   Input Parameter:
    817:    . pc -
    818: */
    821: PetscErrorCode  PCCreateGAMG_GEO(PC pc)
    822: {
    824:   PC_MG          *mg      = (PC_MG*)pc->data;
    825:   PC_GAMG        *pc_gamg = (PC_GAMG*)mg->innerctx;

    828:   pc_gamg->ops->setfromoptions = PCSetFromOptions_GEO;
    829:   pc_gamg->ops->destroy        = PCDestroy_GAMG_GEO;
    830:   /* reset does not do anything; setup not virtual */

    832:   /* set internal function pointers */
    833:   pc_gamg->ops->graph             = PCGAMGGraph_GEO;
    834:   pc_gamg->ops->coarsen           = PCGAMGCoarsen_GEO;
    835:   pc_gamg->ops->prolongator       = PCGAMGProlongator_GEO;
    836:   pc_gamg->ops->optprolongator    = NULL;
    837:   pc_gamg->ops->createdefaultdata = PCSetData_GEO;

    839:   PetscObjectComposeFunction((PetscObject)pc,"PCSetCoordinates_C",PCSetCoordinates_GEO);
    840:   return(0);
    841: }