Actual source code: agg.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: #include <petscblaslapack.h>

     10: typedef struct {
     11:   PetscInt  nsmooths;
     12:   PetscBool sym_graph;
     13:   PetscInt square_graph;
     14: } PC_GAMG_AGG;

     18: /*@
     19:    PCGAMGSetNSmooths - Set number of smoothing steps (1 is typical)

     21:    Not Collective on PC

     23:    Input Parameters:
     24: .  pc - the preconditioner context

     26:    Options Database Key:
     27: .  -pc_gamg_agg_nsmooths

     29:    Level: intermediate

     31:    Concepts: Aggregation AMG preconditioner

     33: .seealso: ()
     34: @*/
     35: PetscErrorCode PCGAMGSetNSmooths(PC pc, PetscInt n)
     36: {

     41:   PetscTryMethod(pc,"PCGAMGSetNSmooths_C",(PC,PetscInt),(pc,n));
     42:   return(0);
     43: }

     47: static PetscErrorCode PCGAMGSetNSmooths_AGG(PC pc, PetscInt n)
     48: {
     49:   PC_MG       *mg          = (PC_MG*)pc->data;
     50:   PC_GAMG     *pc_gamg     = (PC_GAMG*)mg->innerctx;
     51:   PC_GAMG_AGG *pc_gamg_agg = (PC_GAMG_AGG*)pc_gamg->subctx;

     54:   pc_gamg_agg->nsmooths = n;
     55:   return(0);
     56: }

     60: /*@
     61:    PCGAMGSetSymGraph -

     63:    Not Collective on PC

     65:    Input Parameters:
     66: .  pc - the preconditioner context

     68:    Options Database Key:
     69: .  -pc_gamg_sym_graph

     71:    Level: intermediate

     73:    Concepts: Aggregation AMG preconditioner

     75: .seealso: ()
     76: @*/
     77: PetscErrorCode PCGAMGSetSymGraph(PC pc, PetscBool n)
     78: {

     83:   PetscTryMethod(pc,"PCGAMGSetSymGraph_C",(PC,PetscBool),(pc,n));
     84:   return(0);
     85: }

     89: static PetscErrorCode PCGAMGSetSymGraph_AGG(PC pc, PetscBool n)
     90: {
     91:   PC_MG       *mg          = (PC_MG*)pc->data;
     92:   PC_GAMG     *pc_gamg     = (PC_GAMG*)mg->innerctx;
     93:   PC_GAMG_AGG *pc_gamg_agg = (PC_GAMG_AGG*)pc_gamg->subctx;

     96:   pc_gamg_agg->sym_graph = n;
     97:   return(0);
     98: }

    102: /*@
    103:    PCGAMGSetSquareGraph -

    105:    Not Collective on PC

    107:    Input Parameters:
    108: .  pc - the preconditioner context

    110:    Options Database Key:
    111: .  -pc_gamg_square_graph

    113:    Level: intermediate

    115:    Concepts: Aggregation AMG preconditioner

    117: .seealso: ()
    118: @*/
    119: PetscErrorCode PCGAMGSetSquareGraph(PC pc, PetscInt n)
    120: {

    125:   PetscTryMethod(pc,"PCGAMGSetSquareGraph_C",(PC,PetscInt),(pc,n));
    126:   return(0);
    127: }

    131: static PetscErrorCode PCGAMGSetSquareGraph_AGG(PC pc, PetscInt n)
    132: {
    133:   PC_MG       *mg          = (PC_MG*)pc->data;
    134:   PC_GAMG     *pc_gamg     = (PC_GAMG*)mg->innerctx;
    135:   PC_GAMG_AGG *pc_gamg_agg = (PC_GAMG_AGG*)pc_gamg->subctx;

    138:   pc_gamg_agg->square_graph = n;
    139:   return(0);
    140: }

    142: /* -------------------------------------------------------------------------- */
    143: /*
    144:    PCSetFromOptions_GAMG_AGG

    146:   Input Parameter:
    147:    . pc -
    148: */
    151: static PetscErrorCode PCSetFromOptions_GAMG_AGG(PetscOptionItems *PetscOptionsObject,PC pc)
    152: {
    154:   PC_MG          *mg          = (PC_MG*)pc->data;
    155:   PC_GAMG        *pc_gamg     = (PC_GAMG*)mg->innerctx;
    156:   PC_GAMG_AGG    *pc_gamg_agg = (PC_GAMG_AGG*)pc_gamg->subctx;

    159:   PetscOptionsHead(PetscOptionsObject,"GAMG-AGG options");
    160:   {
    161:     /* -pc_gamg_agg_nsmooths */
    162:     pc_gamg_agg->nsmooths = 1;

    164:     PetscOptionsInt("-pc_gamg_agg_nsmooths","smoothing steps for smoothed aggregation, usually 1","PCGAMGSetNSmooths",pc_gamg_agg->nsmooths,&pc_gamg_agg->nsmooths,NULL);

    166:     /* -pc_gamg_sym_graph */
    167:     pc_gamg_agg->sym_graph = PETSC_FALSE;

    169:     PetscOptionsBool("-pc_gamg_sym_graph","Set for asymmetric matrices","PCGAMGSetSymGraph",pc_gamg_agg->sym_graph,&pc_gamg_agg->sym_graph,NULL);

    171:     /* -pc_gamg_square_graph */
    172:     pc_gamg_agg->square_graph = 1;

    174:     PetscOptionsInt("-pc_gamg_square_graph","Number of levels to square graph for faster coarsening and lower coarse grid complexity","PCGAMGSetSquareGraph",pc_gamg_agg->square_graph,&pc_gamg_agg->square_graph,NULL);
    175:   }
    176:   PetscOptionsTail();
    177:   return(0);
    178: }

    180: /* -------------------------------------------------------------------------- */
    181: /*
    182:    PCDestroy_AGG

    184:   Input Parameter:
    185:    . pc -
    186: */
    189: static PetscErrorCode PCDestroy_GAMG_AGG(PC pc)
    190: {
    192:   PC_MG          *mg          = (PC_MG*)pc->data;
    193:   PC_GAMG        *pc_gamg     = (PC_GAMG*)mg->innerctx;

    196:   PetscFree(pc_gamg->subctx);
    197:   PetscObjectComposeFunction((PetscObject)pc,"PCSetCoordinates_C",NULL);
    198:   return(0);
    199: }

    201: /* -------------------------------------------------------------------------- */
    202: /*
    203:    PCSetCoordinates_AGG
    204:      - collective

    206:    Input Parameter:
    207:    . pc - the preconditioner context
    208:    . ndm - dimesion of data (used for dof/vertex for Stokes)
    209:    . a_nloc - number of vertices local
    210:    . coords - [a_nloc][ndm] - interleaved coordinate data: {x_0, y_0, z_0, x_1, y_1, ...}
    211: */

    215: static PetscErrorCode PCSetCoordinates_AGG(PC pc, PetscInt ndm, PetscInt a_nloc, PetscReal *coords)
    216: {
    217:   PC_MG          *mg      = (PC_MG*)pc->data;
    218:   PC_GAMG        *pc_gamg = (PC_GAMG*)mg->innerctx;
    220:   PetscInt       arrsz,kk,ii,jj,nloc,ndatarows,ndf;
    221:   Mat            mat = pc->pmat;

    226:   nloc = a_nloc;

    228:   /* SA: null space vectors */
    229:   MatGetBlockSize(mat, &ndf); /* this does not work for Stokes */
    230:   if (coords && ndf==1) pc_gamg->data_cell_cols = 1; /* scalar w/ coords and SA (not needed) */
    231:   else if (coords) {
    232:     if (ndm > ndf) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"degrees of motion %d > block size %d",ndm,ndf);
    233:     pc_gamg->data_cell_cols = (ndm==2 ? 3 : 6); /* displacement elasticity */
    234:     if (ndm != ndf) {
    235:       if (pc_gamg->data_cell_cols != ndf) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Don't know how to create null space for ndm=%d, ndf=%d.  Use MatSetNearNullSpace.",ndm,ndf);
    236:     }
    237:   } else pc_gamg->data_cell_cols = ndf; /* no data, force SA with constant null space vectors */
    238:   pc_gamg->data_cell_rows = ndatarows = ndf;
    239:   if (pc_gamg->data_cell_cols <= 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"pc_gamg->data_cell_cols %D <= 0",pc_gamg->data_cell_cols);
    240:   arrsz = nloc*pc_gamg->data_cell_rows*pc_gamg->data_cell_cols;

    242:   /* create data - syntactic sugar that should be refactored at some point */
    243:   if (!pc_gamg->data || (pc_gamg->data_sz != arrsz)) {
    244:     PetscFree(pc_gamg->data);
    245:     PetscMalloc1(arrsz+1, &pc_gamg->data);
    246:   }
    247:   /* copy data in - column oriented */
    248:   for (kk=0; kk<nloc; kk++) {
    249:     const PetscInt M     = nloc*pc_gamg->data_cell_rows; /* stride into data */
    250:     PetscReal      *data = &pc_gamg->data[kk*ndatarows]; /* start of cell */
    251:     if (pc_gamg->data_cell_cols==1) *data = 1.0;
    252:     else {
    253:       /* translational modes */
    254:       for (ii=0;ii<ndatarows;ii++) {
    255:         for (jj=0;jj<ndatarows;jj++) {
    256:           if (ii==jj)data[ii*M + jj] = 1.0;
    257:           else data[ii*M + jj] = 0.0;
    258:         }
    259:       }

    261:       /* rotational modes */
    262:       if (coords) {
    263:         if (ndm == 2) {
    264:           data   += 2*M;
    265:           data[0] = -coords[2*kk+1];
    266:           data[1] =  coords[2*kk];
    267:         } else {
    268:           data   += 3*M;
    269:           data[0] = 0.0;             data[M+0] =  coords[3*kk+2]; data[2*M+0] = -coords[3*kk+1];
    270:           data[1] = -coords[3*kk+2]; data[M+1] = 0.0;             data[2*M+1] =  coords[3*kk];
    271:           data[2] =  coords[3*kk+1]; data[M+2] = -coords[3*kk];   data[2*M+2] = 0.0;
    272:         }
    273:       }
    274:     }
    275:   }

    277:   pc_gamg->data_sz = arrsz;
    278:   return(0);
    279: }

    281: typedef PetscInt NState;
    282: static const NState NOT_DONE=-2;
    283: static const NState DELETED =-1;
    284: static const NState REMOVED =-3;
    285: #define IS_SELECTED(s) (s!=DELETED && s!=NOT_DONE && s!=REMOVED)

    287: /* -------------------------------------------------------------------------- */
    288: /*
    289:    smoothAggs - greedy grab of with G1 (unsquared graph) -- AIJ specific
    290:      - AGG-MG specific: clears singletons out of 'selected_2'

    292:    Input Parameter:
    293:    . Gmat_2 - glabal matrix of graph (data not defined)   base (squared) graph
    294:    . Gmat_1 - base graph to grab with                 base graph
    295:    Input/Output Parameter:
    296:    . aggs_2 - linked list of aggs with gids)
    297: */
    300: static PetscErrorCode smoothAggs(Mat Gmat_2, Mat Gmat_1,PetscCoarsenData *aggs_2)
    301: {
    303:   PetscBool      isMPI;
    304:   Mat_SeqAIJ     *matA_1, *matB_1=0, *matA_2, *matB_2=0;
    305:   MPI_Comm       comm;
    306:   PetscInt       lid,*ii,*idx,ix,Iend,my0,kk,n,j;
    307:   Mat_MPIAIJ     *mpimat_2 = 0, *mpimat_1=0;
    308:   const PetscInt nloc      = Gmat_2->rmap->n;
    309:   PetscScalar    *cpcol_1_state,*cpcol_2_state,*cpcol_2_par_orig,*lid_parent_gid;
    310:   PetscInt       *lid_cprowID_1;
    311:   NState         *lid_state;
    312:   Vec            ghost_par_orig2;

    315:   PetscObjectGetComm((PetscObject)Gmat_2,&comm);
    316:   MatGetOwnershipRange(Gmat_1,&my0,&Iend);

    318:   if (PETSC_FALSE) {
    319:     PetscViewer viewer; char fname[32]; static int llev=0;
    320:     sprintf(fname,"Gmat2_%d.m",llev++);
    321:     PetscViewerASCIIOpen(comm,fname,&viewer);
    322:     PetscViewerPushFormat(viewer, PETSC_VIEWER_ASCII_MATLAB);
    323:     MatView(Gmat_2, viewer);
    324:     PetscViewerPopFormat(viewer);
    325:     PetscViewerDestroy(&viewer);
    326:   }

    328:   /* get submatrices */
    329:   PetscObjectTypeCompare((PetscObject)Gmat_1, MATMPIAIJ, &isMPI);
    330:   if (isMPI) {
    331:     /* grab matrix objects */
    332:     mpimat_2 = (Mat_MPIAIJ*)Gmat_2->data;
    333:     mpimat_1 = (Mat_MPIAIJ*)Gmat_1->data;
    334:     matA_1   = (Mat_SeqAIJ*)mpimat_1->A->data;
    335:     matB_1   = (Mat_SeqAIJ*)mpimat_1->B->data;
    336:     matA_2   = (Mat_SeqAIJ*)mpimat_2->A->data;
    337:     matB_2   = (Mat_SeqAIJ*)mpimat_2->B->data;

    339:     /* force compressed row storage for B matrix in AuxMat */
    340:     MatCheckCompressedRow(mpimat_1->B,matB_1->nonzerorowcnt,&matB_1->compressedrow,matB_1->i,Gmat_1->rmap->n,-1.0);

    342:     PetscMalloc1(nloc, &lid_cprowID_1);
    343:     for (lid = 0; lid < nloc; lid++) lid_cprowID_1[lid] = -1;
    344:     for (ix=0; ix<matB_1->compressedrow.nrows; ix++) {
    345:       PetscInt lid = matB_1->compressedrow.rindex[ix];
    346:       lid_cprowID_1[lid] = ix;
    347:     }
    348:   } else {
    349:     matA_1        = (Mat_SeqAIJ*)Gmat_1->data;
    350:     matA_2        = (Mat_SeqAIJ*)Gmat_2->data;
    351:     lid_cprowID_1 = NULL;
    352:   }
    353:   if (nloc>0) {
    354:     if (!(matA_1 && !matA_1->compressedrow.use)) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"!(matA_1 && !matA_1->compressedrow.use)");
    355:     if (!(!matB_1 || matB_1->compressedrow.use)) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"!(matB_1==0 || matB_1->compressedrow.use)");
    356:     if (!(matA_2 && !matA_2->compressedrow.use)) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"!(matA_2 && !matA_2->compressedrow.use)");
    357:     if (!(!matB_2 || matB_2->compressedrow.use)) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"!(matB_2==0 || matB_2->compressedrow.use)");
    358:   }
    359:   /* get state of locals and selected gid for deleted */
    360:   PetscMalloc2(nloc, &lid_state,nloc, &lid_parent_gid);
    361:   for (lid = 0; lid < nloc; lid++) {
    362:     lid_parent_gid[lid] = -1.0;
    363:     lid_state[lid]      = DELETED;
    364:   }

    366:   /* set lid_state */
    367:   for (lid = 0; lid < nloc; lid++) {
    368:     PetscCDPos pos;
    369:     PetscCDGetHeadPos(aggs_2,lid,&pos);
    370:     if (pos) {
    371:       PetscInt gid1;

    373:       PetscLLNGetID(pos, &gid1);
    374:       if (gid1 != lid+my0) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"gid1 %D != lid %D + my0 %D",gid1,lid,my0);
    375:       lid_state[lid] = gid1;
    376:     }
    377:   }

    379:   /* map local to selected local, DELETED means a ghost owns it */
    380:   for (lid=kk=0; lid<nloc; lid++) {
    381:     NState state = lid_state[lid];
    382:     if (IS_SELECTED(state)) {
    383:       PetscCDPos pos;
    384:       PetscCDGetHeadPos(aggs_2,lid,&pos);
    385:       while (pos) {
    386:         PetscInt gid1;
    387:         PetscLLNGetID(pos, &gid1);
    388:         PetscCDGetNextPos(aggs_2,lid,&pos);

    390:         if (gid1 >= my0 && gid1 < Iend) lid_parent_gid[gid1-my0] = (PetscScalar)(lid + my0);
    391:       }
    392:     }
    393:   }
    394:   /* get 'cpcol_1/2_state' & cpcol_2_par_orig - uses mpimat_1/2->lvec for temp space */
    395:   if (isMPI) {
    396:     Vec tempVec;
    397:     /* get 'cpcol_1_state' */
    398:     MatCreateVecs(Gmat_1, &tempVec, 0);
    399:     for (kk=0,j=my0; kk<nloc; kk++,j++) {
    400:       PetscScalar v = (PetscScalar)lid_state[kk];
    401:       VecSetValues(tempVec, 1, &j, &v, INSERT_VALUES);
    402:     }
    403:     VecAssemblyBegin(tempVec);
    404:     VecAssemblyEnd(tempVec);
    405:     VecScatterBegin(mpimat_1->Mvctx,tempVec, mpimat_1->lvec,INSERT_VALUES,SCATTER_FORWARD);
    406:     VecScatterEnd(mpimat_1->Mvctx,tempVec, mpimat_1->lvec,INSERT_VALUES,SCATTER_FORWARD);
    407:     VecGetArray(mpimat_1->lvec, &cpcol_1_state);
    408:     /* get 'cpcol_2_state' */
    409:     VecScatterBegin(mpimat_2->Mvctx,tempVec, mpimat_2->lvec,INSERT_VALUES,SCATTER_FORWARD);
    410:       VecScatterEnd(mpimat_2->Mvctx,tempVec, mpimat_2->lvec,INSERT_VALUES,SCATTER_FORWARD);
    411:     VecGetArray(mpimat_2->lvec, &cpcol_2_state);
    412:     /* get 'cpcol_2_par_orig' */
    413:     for (kk=0,j=my0; kk<nloc; kk++,j++) {
    414:       PetscScalar v = (PetscScalar)lid_parent_gid[kk];
    415:       VecSetValues(tempVec, 1, &j, &v, INSERT_VALUES);
    416:     }
    417:     VecAssemblyBegin(tempVec);
    418:     VecAssemblyEnd(tempVec);
    419:     VecDuplicate(mpimat_2->lvec, &ghost_par_orig2);
    420:     VecScatterBegin(mpimat_2->Mvctx,tempVec, ghost_par_orig2,INSERT_VALUES,SCATTER_FORWARD);
    421:     VecScatterEnd(mpimat_2->Mvctx,tempVec, ghost_par_orig2,INSERT_VALUES,SCATTER_FORWARD);
    422:     VecGetArray(ghost_par_orig2, &cpcol_2_par_orig);

    424:     VecDestroy(&tempVec);
    425:   } /* ismpi */

    427:   /* doit */
    428:   for (lid=0; lid<nloc; lid++) {
    429:     NState state = lid_state[lid];
    430:     if (IS_SELECTED(state)) {
    431:       /* steal locals */
    432:       ii  = matA_1->i; n = ii[lid+1] - ii[lid];
    433:       idx = matA_1->j + ii[lid];
    434:       for (j=0; j<n; j++) {
    435:         PetscInt lidj   = idx[j], sgid;
    436:         NState   statej = lid_state[lidj];
    437:         if (statej==DELETED && (sgid=(PetscInt)PetscRealPart(lid_parent_gid[lidj])) != lid+my0) { /* steal local */
    438:           lid_parent_gid[lidj] = (PetscScalar)(lid+my0); /* send this if sgid is not local */
    439:           if (sgid >= my0 && sgid < Iend) {       /* I'm stealing this local from a local sgid */
    440:             PetscInt   hav=0,slid=sgid-my0,gidj=lidj+my0;
    441:             PetscCDPos pos,last=NULL;
    442:             /* looking for local from local so id_llist_2 works */
    443:             PetscCDGetHeadPos(aggs_2,slid,&pos);
    444:             while (pos) {
    445:               PetscInt gid;
    446:               PetscLLNGetID(pos, &gid);
    447:               if (gid == gidj) {
    448:                 if (!last) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"last cannot be null");
    449:                 PetscCDRemoveNextNode(aggs_2, slid, last);
    450:                 PetscCDAppendNode(aggs_2, lid, pos);
    451:                 hav  = 1;
    452:                 break;
    453:               } else last = pos;

    455:               PetscCDGetNextPos(aggs_2,slid,&pos);
    456:             }
    457:             if (hav!=1) {
    458:               if (!hav) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"failed to find adj in 'selected' lists - structurally unsymmetric matrix");
    459:               SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"found node %d times???",hav);
    460:             }
    461:           } else {            /* I'm stealing this local, owned by a ghost */
    462:             if (sgid != -1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Have un-symmetric graph (apparently). Use '-pc_gamg_sym_graph true' to symetrize the graph or '-pc_gamg_threshold -1.0' if the matrix is structurally symmetric.");
    463:             PetscCDAppendID(aggs_2, lid, lidj+my0);
    464:           }
    465:         }
    466:       } /* local neighbors */
    467:     } else if (state == DELETED && lid_cprowID_1) {
    468:       PetscInt sgidold = (PetscInt)PetscRealPart(lid_parent_gid[lid]);
    469:       /* see if I have a selected ghost neighbor that will steal me */
    470:       if ((ix=lid_cprowID_1[lid]) != -1) {
    471:         ii  = matB_1->compressedrow.i; n = ii[ix+1] - ii[ix];
    472:         idx = matB_1->j + ii[ix];
    473:         for (j=0; j<n; j++) {
    474:           PetscInt cpid   = idx[j];
    475:           NState   statej = (NState)PetscRealPart(cpcol_1_state[cpid]);
    476:           if (IS_SELECTED(statej) && sgidold != (PetscInt)statej) { /* ghost will steal this, remove from my list */
    477:             lid_parent_gid[lid] = (PetscScalar)statej; /* send who selected */
    478:             if (sgidold>=my0 && sgidold<Iend) { /* this was mine */
    479:               PetscInt   hav=0,oldslidj=sgidold-my0;
    480:               PetscCDPos pos,last=NULL;
    481:               /* remove from 'oldslidj' list */
    482:               PetscCDGetHeadPos(aggs_2,oldslidj,&pos);
    483:               while (pos) {
    484:                 PetscInt gid;
    485:                 PetscLLNGetID(pos, &gid);
    486:                 if (lid+my0 == gid) {
    487:                   /* id_llist_2[lastid] = id_llist_2[flid];   /\* remove lid from oldslidj list *\/ */
    488:                   if (!last) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"last cannot be null");
    489:                   PetscCDRemoveNextNode(aggs_2, oldslidj, last);
    490:                   /* ghost (PetscScalar)statej will add this later */
    491:                   hav = 1;
    492:                   break;
    493:                 } else last = pos;

    495:                 PetscCDGetNextPos(aggs_2,oldslidj,&pos);
    496:               }
    497:               if (hav!=1) {
    498:                 if (!hav) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"failed to find adj in 'selected' lists - structurally unsymmetric matrix");
    499:                 SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"found node %d times???",hav);
    500:               }
    501:             } else {
    502:               /* ghosts remove this later */
    503:             }
    504:           }
    505:         }
    506:       }
    507:     } /* selected/deleted */
    508:   } /* node loop */

    510:   if (isMPI) {
    511:     PetscScalar   *cpcol_2_parent,*cpcol_2_gid;
    512:     Vec           tempVec,ghostgids2,ghostparents2;
    513:     PetscInt      cpid,nghost_2;
    514:     GAMGHashTable gid_cpid;

    516:     VecGetSize(mpimat_2->lvec, &nghost_2);
    517:     MatCreateVecs(Gmat_2, &tempVec, 0);

    519:     /* get 'cpcol_2_parent' */
    520:     for (kk=0,j=my0; kk<nloc; kk++,j++) {
    521:       VecSetValues(tempVec, 1, &j, &lid_parent_gid[kk], INSERT_VALUES);
    522:     }
    523:     VecAssemblyBegin(tempVec);
    524:     VecAssemblyEnd(tempVec);
    525:     VecDuplicate(mpimat_2->lvec, &ghostparents2);
    526:     VecScatterBegin(mpimat_2->Mvctx,tempVec, ghostparents2,INSERT_VALUES,SCATTER_FORWARD);
    527:     VecScatterEnd(mpimat_2->Mvctx,tempVec, ghostparents2,INSERT_VALUES,SCATTER_FORWARD);
    528:     VecGetArray(ghostparents2, &cpcol_2_parent);

    530:     /* get 'cpcol_2_gid' */
    531:     for (kk=0,j=my0; kk<nloc; kk++,j++) {
    532:       PetscScalar v = (PetscScalar)j;
    533:       VecSetValues(tempVec, 1, &j, &v, INSERT_VALUES);
    534:     }
    535:     VecAssemblyBegin(tempVec);
    536:     VecAssemblyEnd(tempVec);
    537:     VecDuplicate(mpimat_2->lvec, &ghostgids2);
    538:     VecScatterBegin(mpimat_2->Mvctx,tempVec, ghostgids2,INSERT_VALUES,SCATTER_FORWARD);
    539:     VecScatterEnd(mpimat_2->Mvctx,tempVec, ghostgids2,INSERT_VALUES,SCATTER_FORWARD);
    540:     VecGetArray(ghostgids2, &cpcol_2_gid);

    542:     VecDestroy(&tempVec);

    544:     /* look for deleted ghosts and add to table */
    545:     GAMGTableCreate(2*nghost_2+1, &gid_cpid);
    546:     for (cpid = 0; cpid < nghost_2; cpid++) {
    547:       NState state = (NState)PetscRealPart(cpcol_2_state[cpid]);
    548:       if (state==DELETED) {
    549:         PetscInt sgid_new = (PetscInt)PetscRealPart(cpcol_2_parent[cpid]);
    550:         PetscInt sgid_old = (PetscInt)PetscRealPart(cpcol_2_par_orig[cpid]);
    551:         if (sgid_old == -1 && sgid_new != -1) {
    552:           PetscInt gid = (PetscInt)PetscRealPart(cpcol_2_gid[cpid]);
    553:           GAMGTableAdd(&gid_cpid, gid, cpid);
    554:         }
    555:       }
    556:     }

    558:     /* look for deleted ghosts and see if they moved - remove it */
    559:     for (lid=0; lid<nloc; lid++) {
    560:       NState state = lid_state[lid];
    561:       if (IS_SELECTED(state)) {
    562:         PetscCDPos pos,last=NULL;
    563:         /* look for deleted ghosts and see if they moved */
    564:         PetscCDGetHeadPos(aggs_2,lid,&pos);
    565:         while (pos) {
    566:           PetscInt gid;
    567:           PetscLLNGetID(pos, &gid);

    569:           if (gid < my0 || gid >= Iend) {
    570:             GAMGTableFind(&gid_cpid, gid, &cpid);
    571:             if (cpid != -1) {
    572:               /* a moved ghost - */
    573:               /* id_llist_2[lastid] = id_llist_2[flid];    /\* remove 'flid' from list *\/ */
    574:               PetscCDRemoveNextNode(aggs_2, lid, last);
    575:             } else last = pos;
    576:           } else last = pos;

    578:           PetscCDGetNextPos(aggs_2,lid,&pos);
    579:         } /* loop over list of deleted */
    580:       } /* selected */
    581:     }
    582:     GAMGTableDestroy(&gid_cpid);

    584:     /* look at ghosts, see if they changed - and it */
    585:     for (cpid = 0; cpid < nghost_2; cpid++) {
    586:       PetscInt sgid_new = (PetscInt)PetscRealPart(cpcol_2_parent[cpid]);
    587:       if (sgid_new >= my0 && sgid_new < Iend) { /* this is mine */
    588:         PetscInt   gid     = (PetscInt)PetscRealPart(cpcol_2_gid[cpid]);
    589:         PetscInt   slid_new=sgid_new-my0,hav=0;
    590:         PetscCDPos pos;
    591:         /* search for this gid to see if I have it */
    592:         PetscCDGetHeadPos(aggs_2,slid_new,&pos);
    593:         while (pos) {
    594:           PetscInt gidj;
    595:           PetscLLNGetID(pos, &gidj);
    596:           PetscCDGetNextPos(aggs_2,slid_new,&pos);

    598:           if (gidj == gid) { hav = 1; break; }
    599:         }
    600:         if (hav != 1) {
    601:           /* insert 'flidj' into head of llist */
    602:           PetscCDAppendID(aggs_2, slid_new, gid);
    603:         }
    604:       }
    605:     }

    607:     VecRestoreArray(mpimat_1->lvec, &cpcol_1_state);
    608:     VecRestoreArray(mpimat_2->lvec, &cpcol_2_state);
    609:     VecRestoreArray(ghostparents2, &cpcol_2_parent);
    610:     VecRestoreArray(ghostgids2, &cpcol_2_gid);
    611:     PetscFree(lid_cprowID_1);
    612:     VecDestroy(&ghostgids2);
    613:     VecDestroy(&ghostparents2);
    614:     VecDestroy(&ghost_par_orig2);
    615:   }

    617:   PetscFree2(lid_state,lid_parent_gid);
    618:   return(0);
    619: }

    621: /* -------------------------------------------------------------------------- */
    622: /*
    623:    PCSetData_AGG - called if data is not set with PCSetCoordinates.
    624:       Looks in Mat for near null space.
    625:       Does not work for Stokes

    627:   Input Parameter:
    628:    . pc -
    629:    . a_A - matrix to get (near) null space out of.
    630: */
    633: static PetscErrorCode PCSetData_AGG(PC pc, Mat a_A)
    634: {
    636:   PC_MG          *mg      = (PC_MG*)pc->data;
    637:   PC_GAMG        *pc_gamg = (PC_GAMG*)mg->innerctx;
    638:   MatNullSpace   mnull;

    641:   MatGetNearNullSpace(a_A, &mnull);
    642:   if (!mnull) {
    643:     PetscInt bs,NN,MM;
    644:     MatGetBlockSize(a_A, &bs);
    645:     MatGetLocalSize(a_A, &MM, &NN);
    646:     if (MM % bs) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"MM %D must be divisible by bs %D",MM,bs);
    647:     PCSetCoordinates_AGG(pc, bs, MM/bs, NULL);
    648:   } else {
    649:     PetscReal *nullvec;
    650:     PetscBool has_const;
    651:     PetscInt  i,j,mlocal,nvec,bs;
    652:     const Vec *vecs; const PetscScalar *v;
    653:     MatGetLocalSize(a_A,&mlocal,NULL);
    654:     MatNullSpaceGetVecs(mnull, &has_const, &nvec, &vecs);
    655:     pc_gamg->data_sz = (nvec+!!has_const)*mlocal;
    656:     PetscMalloc1((nvec+!!has_const)*mlocal,&nullvec);
    657:     if (has_const) for (i=0; i<mlocal; i++) nullvec[i] = 1.0;
    658:     for (i=0; i<nvec; i++) {
    659:       VecGetArrayRead(vecs[i],&v);
    660:       for (j=0; j<mlocal; j++) nullvec[(i+!!has_const)*mlocal + j] = PetscRealPart(v[j]);
    661:       VecRestoreArrayRead(vecs[i],&v);
    662:     }
    663:     pc_gamg->data           = nullvec;
    664:     pc_gamg->data_cell_cols = (nvec+!!has_const);

    666:     MatGetBlockSize(a_A, &bs);

    668:     pc_gamg->data_cell_rows = bs;
    669:   }
    670:   return(0);
    671: }

    673: /* -------------------------------------------------------------------------- */
    674: /*
    675:  formProl0

    677:    Input Parameter:
    678:    . agg_llists - list of arrays with aggregates -- list from selected vertices of aggregate unselected vertices
    679:    . bs - row block size
    680:    . nSAvec - column bs of new P
    681:    . my0crs - global index of start of locals
    682:    . data_stride - bs*(nloc nodes + ghost nodes) [data_stride][nSAvec]
    683:    . data_in[data_stride*nSAvec] - local data on fine grid
    684:    . flid_fgid[data_stride/bs] - make local to global IDs, includes ghosts in 'locals_llist'
    685:   Output Parameter:
    686:    . a_data_out - in with fine grid data (w/ghosts), out with coarse grid data
    687:    . a_Prol - prolongation operator
    688: */
    691: static PetscErrorCode formProl0(PetscCoarsenData *agg_llists,PetscInt bs,PetscInt nSAvec,PetscInt my0crs,PetscInt data_stride,PetscReal data_in[],const PetscInt flid_fgid[],PetscReal **a_data_out,Mat a_Prol)
    692: {
    694:   PetscInt       Istart,my0,Iend,nloc,clid,flid = 0,aggID,kk,jj,ii,mm,ndone,nSelected,minsz,nghosts,out_data_stride;
    695:   MPI_Comm       comm;
    696:   PetscMPIInt    rank;
    697:   PetscReal      *out_data;
    698:   PetscCDPos     pos;
    699:   GAMGHashTable  fgid_flid;

    701: /* #define OUT_AGGS */
    702: #if defined(OUT_AGGS)
    703:   static PetscInt llev = 0; char fname[32]; FILE *file = NULL; PetscInt pM;
    704: #endif

    707:   PetscObjectGetComm((PetscObject)a_Prol,&comm);
    708:   MPI_Comm_rank(comm,&rank);
    709:   MatGetOwnershipRange(a_Prol, &Istart, &Iend);
    710:   nloc = (Iend-Istart)/bs; my0 = Istart/bs;
    711:   if ((Iend-Istart) % bs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Iend %D - Istart %d must be divisible by bs %D",Iend,Istart,bs);
    712:   Iend   /= bs;
    713:   nghosts = data_stride/bs - nloc;

    715:   GAMGTableCreate(2*nghosts+1, &fgid_flid);
    716:   for (kk=0; kk<nghosts; kk++) {
    717:     GAMGTableAdd(&fgid_flid, flid_fgid[nloc+kk], nloc+kk);
    718:   }

    720: #if defined(OUT_AGGS)
    721:   sprintf(fname,"aggs_%d_%d.m",llev++,rank);
    722:   if (llev==1) file = fopen(fname,"w");
    723:   MatGetSize(a_Prol, &pM, &jj);
    724: #endif

    726:   /* count selected -- same as number of cols of P */
    727:   for (nSelected=mm=0; mm<nloc; mm++) {
    728:     PetscBool ise;
    729:     PetscCDEmptyAt(agg_llists, mm, &ise);
    730:     if (!ise) nSelected++;
    731:   }
    732:   MatGetOwnershipRangeColumn(a_Prol, &ii, &jj);
    733:   if ((ii/nSAvec) != my0crs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"ii %D /nSAvec %D  != my0crs %D",ii,nSAvec,my0crs);
    734:   if (nSelected != (jj-ii)/nSAvec) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_PLIB,"nSelected %D != (jj %D - ii %D)/nSAvec %D",nSelected,jj,ii,nSAvec);

    736:   /* aloc space for coarse point data (output) */
    737:   out_data_stride = nSelected*nSAvec;

    739:   PetscMalloc1(out_data_stride*nSAvec, &out_data);
    740:   for (ii=0;ii<out_data_stride*nSAvec;ii++) out_data[ii]=PETSC_MAX_REAL;
    741:   *a_data_out = out_data; /* output - stride nSelected*nSAvec */

    743:   /* find points and set prolongation */
    744:   minsz = 100;
    745:   ndone = 0;
    746:   for (mm = clid = 0; mm < nloc; mm++) {
    747:     PetscCDSizeAt(agg_llists, mm, &jj);
    748:     if (jj > 0) {
    749:       const PetscInt lid = mm, cgid = my0crs + clid;
    750:       PetscInt       cids[100]; /* max bs */
    751:       PetscBLASInt   asz  =jj,M=asz*bs,N=nSAvec,INFO;
    752:       PetscBLASInt   Mdata=M+((N-M>0) ? N-M : 0),LDA=Mdata,LWORK=N*bs;
    753:       PetscScalar    *qqc,*qqr,*TAU,*WORK;
    754:       PetscInt       *fids;
    755:       PetscReal      *data;
    756:       /* count agg */
    757:       if (asz<minsz) minsz = asz;

    759:       /* get block */
    760:       PetscMalloc5(Mdata*N, &qqc,M*N, &qqr,N, &TAU,LWORK, &WORK,M, &fids);

    762:       aggID = 0;
    763:       PetscCDGetHeadPos(agg_llists,lid,&pos);
    764:       while (pos) {
    765:         PetscInt gid1;
    766:         PetscLLNGetID(pos, &gid1);
    767:         PetscCDGetNextPos(agg_llists,lid,&pos);

    769:         if (gid1 >= my0 && gid1 < Iend) flid = gid1 - my0;
    770:         else {
    771:           GAMGTableFind(&fgid_flid, gid1, &flid);
    772:           if (flid < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Cannot find gid1 in table");
    773:         }
    774:         /* copy in B_i matrix - column oriented */
    775:         data = &data_in[flid*bs];
    776:         for (ii = 0; ii < bs; ii++) {
    777:           for (jj = 0; jj < N; jj++) {
    778:             PetscReal d = data[jj*data_stride + ii];
    779:             qqc[jj*Mdata + aggID*bs + ii] = d;
    780:           }
    781:         }
    782: #if defined(OUT_AGGS)
    783:         if (llev==1) {
    784:           char     str[] = "plot(%e,%e,'r*'), hold on,\n", col[] = "rgbkmc", sim[] = "*os+h>d<vx^";
    785:           PetscInt MM,pi,pj;
    786:           str[12] = col[(clid+17*rank)%6]; str[13] = sim[(clid+17*rank)%11];
    787:           MM      = (PetscInt)(PetscSqrtReal((PetscReal)pM));
    788:           pj      = gid1/MM; pi = gid1%MM;
    789:           fprintf(file,str,(double)pi,(double)pj);
    790:           /* fprintf(file,str,data[2*data_stride+1],-data[2*data_stride]); */
    791:         }
    792: #endif
    793:         /* set fine IDs */
    794:         for (kk=0; kk<bs; kk++) fids[aggID*bs + kk] = flid_fgid[flid]*bs + kk;

    796:         aggID++;
    797:       }

    799:       /* pad with zeros */
    800:       for (ii = asz*bs; ii < Mdata; ii++) {
    801:         for (jj = 0; jj < N; jj++, kk++) {
    802:           qqc[jj*Mdata + ii] = .0;
    803:         }
    804:       }

    806:       ndone += aggID;
    807:       /* QR */
    808:       PetscFPTrapPush(PETSC_FP_TRAP_OFF);
    809:       PetscStackCallBLAS("LAPACKgeqrf",LAPACKgeqrf_(&Mdata, &N, qqc, &LDA, TAU, WORK, &LWORK, &INFO));
    810:       PetscFPTrapPop();
    811:       if (INFO != 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"xGEQRF error");
    812:       /* get R - column oriented - output B_{i+1} */
    813:       {
    814:         PetscReal *data = &out_data[clid*nSAvec];
    815:         for (jj = 0; jj < nSAvec; jj++) {
    816:           for (ii = 0; ii < nSAvec; ii++) {
    817:             if (data[jj*out_data_stride + ii] != PETSC_MAX_REAL) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"data[jj*out_data_stride + ii] != %e",PETSC_MAX_REAL);
    818:            if (ii <= jj) data[jj*out_data_stride + ii] = PetscRealPart(qqc[jj*Mdata + ii]);
    819:            else data[jj*out_data_stride + ii] = 0.;
    820:           }
    821:         }
    822:       }

    824:       /* get Q - row oriented */
    825:       PetscStackCallBLAS("LAPACKungqr",LAPACKungqr_(&Mdata, &N, &N, qqc, &LDA, TAU, WORK, &LWORK, &INFO));
    826:       if (INFO != 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"xORGQR error arg %d",-INFO);

    828:       for (ii = 0; ii < M; ii++) {
    829:         for (jj = 0; jj < N; jj++) {
    830:           qqr[N*ii + jj] = qqc[jj*Mdata + ii];
    831:         }
    832:       }

    834:       /* add diagonal block of P0 */
    835:       for (kk=0; kk<N; kk++) {
    836:         cids[kk] = N*cgid + kk; /* global col IDs in P0 */
    837:       }
    838:       MatSetValues(a_Prol,M,fids,N,cids,qqr,INSERT_VALUES);

    840:       PetscFree5(qqc,qqr,TAU,WORK,fids);
    841:       clid++;
    842:     } /* coarse agg */
    843:   } /* for all fine nodes */
    844:   MatAssemblyBegin(a_Prol,MAT_FINAL_ASSEMBLY);
    845:   MatAssemblyEnd(a_Prol,MAT_FINAL_ASSEMBLY);

    847: /* MPIU_Allreduce(&ndone, &ii, 1, MPIU_INT, MPIU_SUM, comm); */
    848: /* MatGetSize(a_Prol, &kk, &jj); */
    849: /* MPIU_Allreduce(&minsz, &jj, 1, MPIU_INT, MPIU_MIN, comm); */
    850: /* PetscPrintf(comm," **** [%d]%s %d total done, %d nodes (%d local done), min agg. size = %d\n",rank,__FUNCT__,ii,kk/bs,ndone,jj); */

    852: #if defined(OUT_AGGS)
    853:   if (llev==1) fclose(file);
    854: #endif
    855:   GAMGTableDestroy(&fgid_flid);
    856:   return(0);
    857: }

    861: static PetscErrorCode PCView_GAMG_AGG(PC pc,PetscViewer viewer)
    862: {
    864:   PC_MG          *mg      = (PC_MG*)pc->data;
    865:   PC_GAMG        *pc_gamg = (PC_GAMG*)mg->innerctx;
    866:   PC_GAMG_AGG    *pc_gamg_agg = (PC_GAMG_AGG*)pc_gamg->subctx;

    869:   PetscViewerASCIIPrintf(viewer,"      AGG specific options\n");
    870:   PetscViewerASCIIPrintf(viewer,"        Symmetric graph %s\n",pc_gamg_agg->sym_graph ? "true" : "false");
    871:   return(0);
    872: }

    874: /* -------------------------------------------------------------------------- */
    875: /*
    876:    PCGAMGGraph_AGG

    878:   Input Parameter:
    879:    . pc - this
    880:    . Amat - matrix on this fine level
    881:   Output Parameter:
    882:    . a_Gmat -
    883: */
    886: static PetscErrorCode PCGAMGGraph_AGG(PC pc,Mat Amat,Mat *a_Gmat)
    887: {
    888:   PetscErrorCode            ierr;
    889:   PC_MG                     *mg          = (PC_MG*)pc->data;
    890:   PC_GAMG                   *pc_gamg     = (PC_GAMG*)mg->innerctx;
    891:   const PetscReal           vfilter      = pc_gamg->threshold;
    892:   PC_GAMG_AGG               *pc_gamg_agg = (PC_GAMG_AGG*)pc_gamg->subctx;
    893:   Mat                       Gmat;
    894:   MPI_Comm                  comm;
    895:   PetscBool /* set,flg , */ symm;

    898:   PetscObjectGetComm((PetscObject)Amat,&comm);
    899:   PetscLogEventBegin(PC_GAMGGraph_AGG,0,0,0,0);

    901:   /* MatIsSymmetricKnown(Amat, &set, &flg); || !(set && flg) -- this causes lot of symm calls */
    902:   symm = (PetscBool)(pc_gamg_agg->sym_graph); /* && !pc_gamg_agg->square_graph; */

    904:   PCGAMGCreateGraph(Amat, &Gmat);
    905:   PCGAMGFilterGraph(&Gmat, vfilter, symm);

    907:   *a_Gmat = Gmat;

    909:   PetscLogEventEnd(PC_GAMGGraph_AGG,0,0,0,0);
    910:   return(0);
    911: }

    913: /* -------------------------------------------------------------------------- */
    914: /*
    915:    PCGAMGCoarsen_AGG

    917:   Input Parameter:
    918:    . a_pc - this
    919:   Input/Output Parameter:
    920:    . a_Gmat1 - graph on this fine level - coarsening can change this (squares it)
    921:   Output Parameter:
    922:    . agg_lists - list of aggregates
    923: */
    926: static PetscErrorCode PCGAMGCoarsen_AGG(PC a_pc,Mat *a_Gmat1,PetscCoarsenData **agg_lists)
    927: {
    929:   PC_MG          *mg          = (PC_MG*)a_pc->data;
    930:   PC_GAMG        *pc_gamg     = (PC_GAMG*)mg->innerctx;
    931:   PC_GAMG_AGG    *pc_gamg_agg = (PC_GAMG_AGG*)pc_gamg->subctx;
    932:   Mat            mat,Gmat2, Gmat1 = *a_Gmat1;  /* squared graph */
    933:   IS             perm;
    934:   PetscInt       Istart,Iend,Ii,nloc,bs,n,m;
    935:   PetscInt       *permute;
    936:   PetscBool      *bIndexSet;
    937:   MatCoarsen     crs;
    938:   MPI_Comm       comm;
    939:   PetscMPIInt    rank;
    940:   PetscReal      rr;
    941:   PetscInt       iSwapIndex;

    944:   PetscLogEventBegin(PC_GAMGCoarsen_AGG,0,0,0,0);
    945:   PetscObjectGetComm((PetscObject)Gmat1,&comm);
    946:   MPI_Comm_rank(comm, &rank);
    947:   MatGetLocalSize(Gmat1, &n, &m);
    948:   MatGetBlockSize(Gmat1, &bs);
    949:   if (bs != 1) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_PLIB,"bs %D must be 1",bs);
    950:   nloc = n/bs;

    952:   if (pc_gamg->current_level < pc_gamg_agg->square_graph) {
    953:     PetscInfo2(a_pc,"Square Graph on level %d of %d to square\n",pc_gamg->current_level+1,pc_gamg_agg->square_graph);
    954:     MatTransposeMatMult(Gmat1, Gmat1, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &Gmat2);
    955:   } else Gmat2 = Gmat1;

    957:   /* get MIS aggs - randomize */
    958:   PetscMalloc1(nloc, &permute);
    959:   PetscCalloc1(nloc, &bIndexSet);
    960:   for (Ii = 0; Ii < nloc; Ii++) {
    961:     permute[Ii]   = Ii;
    962:   }
    963:   MatGetOwnershipRange(Gmat1, &Istart, &Iend);
    964:   for (Ii = 0; Ii < nloc; Ii++) {
    965:     PetscRandomGetValueReal(pc_gamg->random,&rr);
    966:     iSwapIndex = (PetscInt) (rr*nloc);
    967:     if (!bIndexSet[iSwapIndex] && iSwapIndex != Ii) {
    968:       PetscInt iTemp = permute[iSwapIndex];
    969:       permute[iSwapIndex]   = permute[Ii];
    970:       permute[Ii]           = iTemp;
    971:       bIndexSet[iSwapIndex] = PETSC_TRUE;
    972:     }
    973:   }
    974:   PetscFree(bIndexSet);

    976:   ISCreateGeneral(PETSC_COMM_SELF, nloc, permute, PETSC_USE_POINTER, &perm);
    977: #if defined PETSC_GAMG_USE_LOG
    978:   PetscLogEventBegin(petsc_gamg_setup_events[SET4],0,0,0,0);
    979: #endif
    980:   MatCoarsenCreate(comm, &crs);
    981:   MatCoarsenSetFromOptions(crs);
    982:   MatCoarsenSetGreedyOrdering(crs, perm);
    983:   MatCoarsenSetAdjacency(crs, Gmat2);
    984:   MatCoarsenSetStrictAggs(crs, PETSC_TRUE);
    985:   MatCoarsenApply(crs);
    986:   MatCoarsenGetData(crs, agg_lists); /* output */
    987:   MatCoarsenDestroy(&crs);

    989:   ISDestroy(&perm);
    990:   PetscFree(permute);
    991: #if defined PETSC_GAMG_USE_LOG
    992:   PetscLogEventEnd(petsc_gamg_setup_events[SET4],0,0,0,0);
    993: #endif

    995:   /* smooth aggs */
    996:   if (Gmat2 != Gmat1) {
    997:     const PetscCoarsenData *llist = *agg_lists;
    998:     smoothAggs(Gmat2, Gmat1, *agg_lists);
    999:     MatDestroy(&Gmat1);
    1000:     *a_Gmat1 = Gmat2; /* output */
    1001:     PetscCDGetMat(llist, &mat);
    1002:     if (mat) SETERRQ(comm,PETSC_ERR_ARG_WRONG, "Auxilary matrix with squared graph????");
    1003:   } else {
    1004:     const PetscCoarsenData *llist = *agg_lists;
    1005:     /* see if we have a matrix that takes precedence (returned from MatCoarsenApply) */
    1006:     PetscCDGetMat(llist, &mat);
    1007:     if (mat) {
    1008:       MatDestroy(&Gmat1);
    1009:       *a_Gmat1 = mat; /* output */
    1010:     }
    1011:   }
    1012:   PetscLogEventEnd(PC_GAMGCoarsen_AGG,0,0,0,0);
    1013:   return(0);
    1014: }

    1016: /* -------------------------------------------------------------------------- */
    1017: /*
    1018:  PCGAMGProlongator_AGG

    1020:  Input Parameter:
    1021:  . pc - this
    1022:  . Amat - matrix on this fine level
    1023:  . Graph - used to get ghost data for nodes in
    1024:  . agg_lists - list of aggregates
    1025:  Output Parameter:
    1026:  . a_P_out - prolongation operator to the next level
    1027:  */
    1030: static PetscErrorCode PCGAMGProlongator_AGG(PC pc,Mat Amat,Mat Gmat,PetscCoarsenData *agg_lists,Mat *a_P_out)
    1031: {
    1032:   PC_MG          *mg       = (PC_MG*)pc->data;
    1033:   PC_GAMG        *pc_gamg  = (PC_GAMG*)mg->innerctx;
    1034:   const PetscInt data_cols = pc_gamg->data_cell_cols;
    1036:   PetscInt       Istart,Iend,nloc,ii,jj,kk,my0,nLocalSelected,bs;
    1037:   Mat            Prol;
    1038:   PetscMPIInt    rank, size;
    1039:   MPI_Comm       comm;
    1040:   const PetscInt col_bs = data_cols;
    1041:   PetscReal      *data_w_ghost;
    1042:   PetscInt       myCrs0, nbnodes=0, *flid_fgid;
    1043:   MatType        mtype;

    1046:   PetscObjectGetComm((PetscObject)Amat,&comm);
    1047:   PetscLogEventBegin(PC_GAMGProlongator_AGG,0,0,0,0);
    1048:   MPI_Comm_rank(comm, &rank);
    1049:   MPI_Comm_size(comm, &size);
    1050:   MatGetOwnershipRange(Amat, &Istart, &Iend);
    1051:   MatGetBlockSize(Amat, &bs);
    1052:   nloc = (Iend-Istart)/bs; my0 = Istart/bs;
    1053:   if ((Iend-Istart) % bs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"(Iend %D - Istart %D) not divisible by bs %D",Iend,Istart,bs);

    1055:   /* get 'nLocalSelected' */
    1056:   for (ii=0, nLocalSelected = 0; ii < nloc; ii++) {
    1057:     PetscBool ise;
    1058:     /* filter out singletons 0 or 1? */
    1059:     PetscCDEmptyAt(agg_lists, ii, &ise);
    1060:     if (!ise) nLocalSelected++;
    1061:   }

    1063:   /* create prolongator, create P matrix */
    1064:   MatGetType(Amat,&mtype);
    1065:   MatCreate(comm, &Prol);
    1066:   MatSetSizes(Prol,nloc*bs,nLocalSelected*col_bs,PETSC_DETERMINE,PETSC_DETERMINE);
    1067:   MatSetBlockSizes(Prol, bs, col_bs);
    1068:   MatSetType(Prol, mtype);
    1069:   MatSeqAIJSetPreallocation(Prol, data_cols, NULL);
    1070:   MatMPIAIJSetPreallocation(Prol,data_cols, NULL,data_cols, NULL);
    1071:   /* nloc*bs, nLocalSelected*col_bs, */
    1072:   /* PETSC_DETERMINE, PETSC_DETERMINE, */
    1073:   /* data_cols, NULL, data_cols, NULL, */
    1074:   /* &Prol); */

    1076:   /* can get all points "removed" */
    1077:    MatGetSize(Prol, &kk, &ii);
    1078:   if (!ii) {
    1079:     PetscInfo(pc,"No selected points on coarse grid\n");
    1080:     MatDestroy(&Prol);
    1081:     *a_P_out = NULL;  /* out */
    1082:     return(0);
    1083:   }
    1084:   PetscInfo1(pc,"New grid %D nodes\n",ii/col_bs);
    1085:   MatGetOwnershipRangeColumn(Prol, &myCrs0, &kk);

    1087:   if ((kk-myCrs0) % col_bs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"(kk %D -myCrs0 %D) not divisible by col_bs %D",kk,myCrs0,col_bs);
    1088:   myCrs0 = myCrs0/col_bs;
    1089:   if ((kk/col_bs-myCrs0) != nLocalSelected) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_PLIB,"(kk %D/col_bs %D - myCrs0 %D) != nLocalSelected %D)",kk,col_bs,myCrs0,nLocalSelected);

    1091:   /* create global vector of data in 'data_w_ghost' */
    1092: #if defined PETSC_GAMG_USE_LOG
    1093:   PetscLogEventBegin(petsc_gamg_setup_events[SET7],0,0,0,0);
    1094: #endif
    1095:   if (size > 1) { /*  */
    1096:     PetscReal *tmp_gdata,*tmp_ldata,*tp2;
    1097:     PetscMalloc1(nloc, &tmp_ldata);
    1098:     for (jj = 0; jj < data_cols; jj++) {
    1099:       for (kk = 0; kk < bs; kk++) {
    1100:         PetscInt        ii,stride;
    1101:         const PetscReal *tp = pc_gamg->data + jj*bs*nloc + kk;
    1102:         for (ii = 0; ii < nloc; ii++, tp += bs) tmp_ldata[ii] = *tp;

    1104:         PCGAMGGetDataWithGhosts(Gmat, 1, tmp_ldata, &stride, &tmp_gdata);

    1106:         if (!jj && !kk) { /* now I know how many todal nodes - allocate */
    1107:           PetscMalloc1(stride*bs*data_cols, &data_w_ghost);
    1108:           nbnodes = bs*stride;
    1109:         }
    1110:         tp2 = data_w_ghost + jj*bs*stride + kk;
    1111:         for (ii = 0; ii < stride; ii++, tp2 += bs) *tp2 = tmp_gdata[ii];
    1112:         PetscFree(tmp_gdata);
    1113:       }
    1114:     }
    1115:     PetscFree(tmp_ldata);
    1116:   } else {
    1117:     nbnodes      = bs*nloc;
    1118:     data_w_ghost = (PetscReal*)pc_gamg->data;
    1119:   }

    1121:   /* get P0 */
    1122:   if (size > 1) {
    1123:     PetscReal *fid_glid_loc,*fiddata;
    1124:     PetscInt  stride;

    1126:     PetscMalloc1(nloc, &fid_glid_loc);
    1127:     for (kk=0; kk<nloc; kk++) fid_glid_loc[kk] = (PetscReal)(my0+kk);
    1128:     PCGAMGGetDataWithGhosts(Gmat, 1, fid_glid_loc, &stride, &fiddata);
    1129:     PetscMalloc1(stride, &flid_fgid);
    1130:     for (kk=0; kk<stride; kk++) flid_fgid[kk] = (PetscInt)fiddata[kk];
    1131:     PetscFree(fiddata);

    1133:     if (stride != nbnodes/bs) SETERRQ3(PETSC_COMM_SELF,PETSC_ERR_PLIB,"stride %D != nbnodes %D/bs %D",stride,nbnodes,bs);
    1134:     PetscFree(fid_glid_loc);
    1135:   } else {
    1136:     PetscMalloc1(nloc, &flid_fgid);
    1137:     for (kk=0; kk<nloc; kk++) flid_fgid[kk] = my0 + kk;
    1138:   }
    1139: #if defined PETSC_GAMG_USE_LOG
    1140:   PetscLogEventEnd(petsc_gamg_setup_events[SET7],0,0,0,0);
    1141:   PetscLogEventBegin(petsc_gamg_setup_events[SET8],0,0,0,0);
    1142: #endif
    1143:   {
    1144:     PetscReal *data_out = NULL;
    1145:     formProl0(agg_lists, bs, data_cols, myCrs0, nbnodes,data_w_ghost, flid_fgid, &data_out, Prol);
    1146:     PetscFree(pc_gamg->data);

    1148:     pc_gamg->data           = data_out;
    1149:     pc_gamg->data_cell_rows = data_cols;
    1150:     pc_gamg->data_sz        = data_cols*data_cols*nLocalSelected;
    1151:   }
    1152: #if defined PETSC_GAMG_USE_LOG
    1153:   PetscLogEventEnd(petsc_gamg_setup_events[SET8],0,0,0,0);
    1154: #endif
    1155:   if (size > 1) {PetscFree(data_w_ghost);}
    1156:   PetscFree(flid_fgid);

    1158:   *a_P_out = Prol;  /* out */

    1160:   PetscLogEventEnd(PC_GAMGProlongator_AGG,0,0,0,0);
    1161:   return(0);
    1162: }

    1164: /* -------------------------------------------------------------------------- */
    1165: /*
    1166:    PCGAMGOptProlongator_AGG

    1168:   Input Parameter:
    1169:    . pc - this
    1170:    . Amat - matrix on this fine level
    1171:  In/Output Parameter:
    1172:    . a_P_out - prolongation operator to the next level
    1173: */
    1176: static PetscErrorCode PCGAMGOptProlongator_AGG(PC pc,Mat Amat,Mat *a_P)
    1177: {
    1179:   PC_MG          *mg          = (PC_MG*)pc->data;
    1180:   PC_GAMG        *pc_gamg     = (PC_GAMG*)mg->innerctx;
    1181:   PC_GAMG_AGG    *pc_gamg_agg = (PC_GAMG_AGG*)pc_gamg->subctx;
    1182:   PetscInt       jj;
    1183:   Mat            Prol  = *a_P;
    1184:   MPI_Comm       comm;

    1187:   PetscObjectGetComm((PetscObject)Amat,&comm);
    1188:   PetscLogEventBegin(PC_GAMGOptProlongator_AGG,0,0,0,0);

    1190:   /* smooth P0 */
    1191:   for (jj = 0; jj < pc_gamg_agg->nsmooths; jj++) {
    1192:     Mat       tMat;
    1193:     Vec       diag;
    1194:     PetscReal alpha, emax, emin;
    1195: #if defined PETSC_GAMG_USE_LOG
    1196:     PetscLogEventBegin(petsc_gamg_setup_events[SET9],0,0,0,0);
    1197: #endif
    1198:     if (!jj) {
    1199:       KSP         eksp;
    1200:       Vec         bb, xx;
    1201:       PC          epc;

    1203:       MatCreateVecs(Amat, &bb, 0);
    1204:       MatCreateVecs(Amat, &xx, 0);

    1206:       VecSetRandom(bb,pc_gamg->random);

    1208:       KSPCreate(comm,&eksp);
    1209:       KSPSetErrorIfNotConverged(eksp,pc->erroriffailure);
    1210:       KSPSetTolerances(eksp,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,10);
    1211:       KSPSetNormType(eksp, KSP_NORM_NONE);
    1212:       KSPSetOptionsPrefix(eksp,((PetscObject)pc)->prefix);
    1213:       KSPAppendOptionsPrefix(eksp, "gamg_est_");
    1214:       KSPSetFromOptions(eksp);

    1216:       KSPSetInitialGuessNonzero(eksp, PETSC_FALSE);
    1217:       KSPSetOperators(eksp, Amat, Amat);
    1218:       KSPSetComputeSingularValues(eksp,PETSC_TRUE);

    1220:       KSPGetPC(eksp, &epc);
    1221:       PCSetType(epc, PCJACOBI);  /* smoother in smoothed agg. */

    1223:       /* solve - keep stuff out of logging */
    1224:       PetscLogEventDeactivate(KSP_Solve);
    1225:       PetscLogEventDeactivate(PC_Apply);
    1226:       KSPSolve(eksp, bb, xx);
    1227:       PetscLogEventActivate(KSP_Solve);
    1228:       PetscLogEventActivate(PC_Apply);

    1230:       KSPComputeExtremeSingularValues(eksp, &emax, &emin);
    1231:       PetscInfo3(pc,"Smooth P0: max eigen=%e min=%e PC=%s\n",emax,emin,PCJACOBI);
    1232:       VecDestroy(&xx);
    1233:       VecDestroy(&bb);
    1234:       KSPDestroy(&eksp);
    1235:     }

    1237:     /* smooth P1 := (I - omega/lam D^{-1}A)P0 */
    1238:     MatMatMult(Amat, Prol, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &tMat);
    1239:     MatCreateVecs(Amat, &diag, 0);
    1240:     MatGetDiagonal(Amat, diag); /* effectively PCJACOBI */
    1241:     VecReciprocal(diag);
    1242:     MatDiagonalScale(tMat, diag, 0);
    1243:     VecDestroy(&diag);
    1244:     alpha = -1.4/emax;
    1245:     MatAYPX(tMat, alpha, Prol, SUBSET_NONZERO_PATTERN);
    1246:     MatDestroy(&Prol);
    1247:     Prol  = tMat;
    1248: #if defined PETSC_GAMG_USE_LOG
    1249:     PetscLogEventEnd(petsc_gamg_setup_events[SET9],0,0,0,0);
    1250: #endif
    1251:   }
    1252:   PetscLogEventEnd(PC_GAMGOptProlongator_AGG,0,0,0,0);
    1253:   *a_P = Prol;
    1254:   return(0);
    1255: }

    1257: /* -------------------------------------------------------------------------- */
    1258: /*
    1259:    PCCreateGAMG_AGG

    1261:   Input Parameter:
    1262:    . pc -
    1263: */
    1266: PetscErrorCode  PCCreateGAMG_AGG(PC pc)
    1267: {
    1269:   PC_MG          *mg      = (PC_MG*)pc->data;
    1270:   PC_GAMG        *pc_gamg = (PC_GAMG*)mg->innerctx;
    1271:   PC_GAMG_AGG    *pc_gamg_agg;

    1274:   /* create sub context for SA */
    1275:   PetscNewLog(pc,&pc_gamg_agg);
    1276:   pc_gamg->subctx = pc_gamg_agg;

    1278:   pc_gamg->ops->setfromoptions = PCSetFromOptions_GAMG_AGG;
    1279:   pc_gamg->ops->destroy        = PCDestroy_GAMG_AGG;
    1280:   /* reset does not do anything; setup not virtual */

    1282:   /* set internal function pointers */
    1283:   pc_gamg->ops->graph             = PCGAMGGraph_AGG;
    1284:   pc_gamg->ops->coarsen           = PCGAMGCoarsen_AGG;
    1285:   pc_gamg->ops->prolongator       = PCGAMGProlongator_AGG;
    1286:   pc_gamg->ops->optprolongator    = PCGAMGOptProlongator_AGG;
    1287:   pc_gamg->ops->createdefaultdata = PCSetData_AGG;
    1288:   pc_gamg->ops->view              = PCView_GAMG_AGG;

    1290:   PetscObjectComposeFunction((PetscObject)pc,"PCGAMGSetNSmooths_C",PCGAMGSetNSmooths_AGG);
    1291:   PetscObjectComposeFunction((PetscObject)pc,"PCGAMGSetSymGraph_C",PCGAMGSetSymGraph_AGG);
    1292:   PetscObjectComposeFunction((PetscObject)pc,"PCGAMGSetSquareGraph_C",PCGAMGSetSquareGraph_AGG);
    1293:   PetscObjectComposeFunction((PetscObject)pc,"PCSetCoordinates_C",PCSetCoordinates_AGG);
    1294:   return(0);
    1295: }