Date: 2013-07-02T14:43:38+00:00

Actual source code: mmsbaij.c
petsc-3.4.2 2013-07-02

      2: /*
      3:    Support for the parallel SBAIJ matrix vector multiply
      4: */
      5: #include <../src/mat/impls/sbaij/mpi/mpisbaij.h>

      7: extern PetscErrorCode MatSetValues_SeqSBAIJ(Mat,PetscInt,const PetscInt [],PetscInt,const PetscInt [],const PetscScalar [],InsertMode);

     12: PetscErrorCode MatSetUpMultiply_MPISBAIJ(Mat mat)
     13: {
     14:   Mat_MPISBAIJ   *sbaij = (Mat_MPISBAIJ*)mat->data;
     15:   Mat_SeqBAIJ    *B     = (Mat_SeqBAIJ*)(sbaij->B->data);
     17:   PetscInt       Nbs = sbaij->Nbs,i,j,*indices,*aj = B->j,ec = 0,*garray,*sgarray;
     18:   PetscInt       bs  = mat->rmap->bs,*stmp,mbs=sbaij->mbs, vec_size,nt;
     19:   IS             from,to;
     20:   Vec            gvec;
     21:   PetscMPIInt    rank   =sbaij->rank,lsize,size=sbaij->size;
     22:   PetscInt       *owners=sbaij->rangebs,*ec_owner,k;
     23:   const PetscInt *sowners;
     24:   PetscScalar    *ptr;

     27:   VecScatterDestroy(&sbaij->sMvctx);

     29:   /* For the first stab we make an array as long as the number of columns */
     30:   /* mark those columns that are in sbaij->B */
     31:   PetscMalloc(Nbs*sizeof(PetscInt),&indices);
     32:   PetscMemzero(indices,Nbs*sizeof(PetscInt));
     33:   for (i=0; i<mbs; i++) {
     34:     for (j=0; j<B->ilen[i]; j++) {
     35:       if (!indices[aj[B->i[i] + j]]) ec++;
     36:       indices[aj[B->i[i] + j]] = 1;
     37:     }
     38:   }

     40:   /* form arrays of columns we need */
     41:   PetscMalloc(ec*sizeof(PetscInt),&garray);
     42:   PetscMalloc2(2*ec,PetscInt,&sgarray,ec,PetscInt,&ec_owner);

     44:   ec = 0;
     45:   for (j=0; j<size; j++) {
     46:     for (i=owners[j]; i<owners[j+1]; i++) {
     47:       if (indices[i]) {
     48:         garray[ec]   = i;
     49:         ec_owner[ec] = j;
     50:         ec++;
     51:       }
     52:     }
     53:   }

     55:   /* make indices now point into garray */
     56:   for (i=0; i<ec; i++) indices[garray[i]] = i;

     58:   /* compact out the extra columns in B */
     59:   for (i=0; i<mbs; i++) {
     60:     for (j=0; j<B->ilen[i]; j++) aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
     61:   }
     62:   B->nbs = ec;

     64:   sbaij->B->cmap->n = sbaij->B->cmap->N = ec*mat->rmap->bs;

     66:   PetscLayoutSetUp((sbaij->B->cmap));
     67:   PetscFree(indices);

     69:   /* create local vector that is used to scatter into */
     70:   VecCreateSeq(PETSC_COMM_SELF,ec*bs,&sbaij->lvec);

     72:   /* create two temporary index sets for building scatter-gather */
     73:   PetscMalloc(2*ec*sizeof(PetscInt),&stmp);
     74:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,garray,PETSC_COPY_VALUES,&from);
     75:   for (i=0; i<ec; i++) stmp[i] = i;
     76:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,PETSC_COPY_VALUES,&to);

     78:   /* generate the scatter context
     79:      -- Mvctx and lvec are not used by MatMult_MPISBAIJ(), but usefule for some applications */
     80:   VecCreateMPIWithArray(PetscObjectComm((PetscObject)mat),1,mat->cmap->n,mat->cmap->N,NULL,&gvec);
     81:   VecScatterCreate(gvec,from,sbaij->lvec,to,&sbaij->Mvctx);
     82:   VecDestroy(&gvec);

     84:   sbaij->garray = garray;

     86:   PetscLogObjectParent(mat,sbaij->Mvctx);
     87:   PetscLogObjectParent(mat,sbaij->lvec);
     88:   PetscLogObjectParent(mat,from);
     89:   PetscLogObjectParent(mat,to);

     91:   ISDestroy(&from);
     92:   ISDestroy(&to);

     94:   /* create parallel vector that is used by SBAIJ matrix to scatter from/into */
     95:   lsize = (mbs + ec)*bs;
     96:   VecCreateMPI(PetscObjectComm((PetscObject)mat),lsize,PETSC_DETERMINE,&sbaij->slvec0);
     97:   VecDuplicate(sbaij->slvec0,&sbaij->slvec1);
     98:   VecGetSize(sbaij->slvec0,&vec_size);

    100:   VecGetOwnershipRanges(sbaij->slvec0,&sowners);

    102:   /* x index in the IS sfrom */
    103:   for (i=0; i<ec; i++) {
    104:     j          = ec_owner[i];
    105:     sgarray[i] = garray[i] + (sowners[j]/bs - owners[j]);
    106:   }
    107:   /* b index in the IS sfrom */
    108:   k = sowners[rank]/bs + mbs;
    109:   for (i=ec,j=0; i< 2*ec; i++,j++) sgarray[i] = k + j;
    110:   ISCreateBlock(PETSC_COMM_SELF,bs,2*ec,sgarray,PETSC_COPY_VALUES,&from);

    112:   /* x index in the IS sto */
    113:   k = sowners[rank]/bs + mbs;
    114:   for (i=0; i<ec; i++) stmp[i] = (k + i);
    115:   /* b index in the IS sto */
    116:   for (i=ec; i<2*ec; i++) stmp[i] = sgarray[i-ec];

    118:   ISCreateBlock(PETSC_COMM_SELF,bs,2*ec,stmp,PETSC_COPY_VALUES,&to);

    120:   VecScatterCreate(sbaij->slvec0,from,sbaij->slvec1,to,&sbaij->sMvctx);

    122:   VecGetLocalSize(sbaij->slvec1,&nt);
    123:   VecGetArray(sbaij->slvec1,&ptr);
    124:   VecCreateSeqWithArray(PETSC_COMM_SELF,1,bs*mbs,ptr,&sbaij->slvec1a);
    125:   VecCreateSeqWithArray(PETSC_COMM_SELF,1,nt-bs*mbs,ptr+bs*mbs,&sbaij->slvec1b);
    126:   VecRestoreArray(sbaij->slvec1,&ptr);

    128:   VecGetArray(sbaij->slvec0,&ptr);
    129:   VecCreateSeqWithArray(PETSC_COMM_SELF,1,nt-bs*mbs,ptr+bs*mbs,&sbaij->slvec0b);
    130:   VecRestoreArray(sbaij->slvec0,&ptr);

    132:   PetscFree(stmp);
    133:   MPI_Barrier(PetscObjectComm((PetscObject)mat));

    135:   PetscLogObjectParent(mat,sbaij->sMvctx);
    136:   PetscLogObjectParent(mat,sbaij->slvec0);
    137:   PetscLogObjectParent(mat,sbaij->slvec1);
    138:   PetscLogObjectParent(mat,sbaij->slvec0b);
    139:   PetscLogObjectParent(mat,sbaij->slvec1a);
    140:   PetscLogObjectParent(mat,sbaij->slvec1b);
    141:   PetscLogObjectParent(mat,from);
    142:   PetscLogObjectParent(mat,to);

    144:   PetscLogObjectMemory(mat,(ec+1)*sizeof(PetscInt));
    145:   ISDestroy(&from);
    146:   ISDestroy(&to);
    147:   PetscFree2(sgarray,ec_owner);
    148:   return(0);
    149: }

    153: PetscErrorCode MatSetUpMultiply_MPISBAIJ_2comm(Mat mat)
    154: {
    155:   Mat_MPISBAIJ   *baij = (Mat_MPISBAIJ*)mat->data;
    156:   Mat_SeqBAIJ    *B    = (Mat_SeqBAIJ*)(baij->B->data);
    158:   PetscInt       i,j,*aj = B->j,ec = 0,*garray;
    159:   PetscInt       bs = mat->rmap->bs,*stmp;
    160:   IS             from,to;
    161:   Vec            gvec;
    162: #if defined(PETSC_USE_CTABLE)
    163:   PetscTable         gid1_lid1;
    164:   PetscTablePosition tpos;
    165:   PetscInt           gid,lid;
    166: #else
    167:   PetscInt Nbs = baij->Nbs,*indices;
    168: #endif

    171: #if defined(PETSC_USE_CTABLE)
    172:   /* use a table - Mark Adams */
    173:   PetscTableCreate(B->mbs,baij->Nbs+1,&gid1_lid1);
    174:   for (i=0; i<B->mbs; i++) {
    175:     for (j=0; j<B->ilen[i]; j++) {
    176:       PetscInt data,gid1 = aj[B->i[i]+j] + 1;
    177:       PetscTableFind(gid1_lid1,gid1,&data);
    178:       if (!data) {
    179:         /* one based table */
    180:         PetscTableAdd(gid1_lid1,gid1,++ec,INSERT_VALUES);
    181:       }
    182:     }
    183:   }
    184:   /* form array of columns we need */
    185:   PetscMalloc(ec*sizeof(PetscInt),&garray);
    186:   PetscTableGetHeadPosition(gid1_lid1,&tpos);
    187:   while (tpos) {
    188:     PetscTableGetNext(gid1_lid1,&tpos,&gid,&lid);
    189:     gid--; lid--;
    190:     garray[lid] = gid;
    191:   }
    192:   PetscSortInt(ec,garray);
    193:   PetscTableRemoveAll(gid1_lid1);
    194:   for (i=0; i<ec; i++) {
    195:     PetscTableAdd(gid1_lid1,garray[i]+1,i+1,INSERT_VALUES);
    196:   }
    197:   /* compact out the extra columns in B */
    198:   for (i=0; i<B->mbs; i++) {
    199:     for (j=0; j<B->ilen[i]; j++) {
    200:       PetscInt gid1 = aj[B->i[i] + j] + 1;
    201:       PetscTableFind(gid1_lid1,gid1,&lid);
    202:       lid--;
    203:       aj[B->i[i]+j] = lid;
    204:     }
    205:   }
    206:   B->nbs = ec;

    208:   baij->B->cmap->n = baij->B->cmap->N = ec*mat->rmap->bs;

    210:   PetscLayoutSetUp((baij->B->cmap));
    211:   PetscTableDestroy(&gid1_lid1);
    212: #else
    213:   /* For the first stab we make an array as long as the number of columns */
    214:   /* mark those columns that are in baij->B */
    215:   PetscMalloc(Nbs*sizeof(PetscInt),&indices);
    216:   PetscMemzero(indices,Nbs*sizeof(PetscInt));
    217:   for (i=0; i<B->mbs; i++) {
    218:     for (j=0; j<B->ilen[i]; j++) {
    219:       if (!indices[aj[B->i[i] + j]]) ec++;
    220:       indices[aj[B->i[i] + j]] = 1;
    221:     }
    222:   }

    224:   /* form array of columns we need */
    225:   PetscMalloc(ec*sizeof(PetscInt),&garray);
    226:   ec = 0;
    227:   for (i=0; i<Nbs; i++) {
    228:     if (indices[i]) {
    229:       garray[ec++] = i;
    230:     }
    231:   }

    233:   /* make indices now point into garray */
    234:   for (i=0; i<ec; i++) indices[garray[i]] = i;

    236:   /* compact out the extra columns in B */
    237:   for (i=0; i<B->mbs; i++) {
    238:     for (j=0; j<B->ilen[i]; j++) {
    239:       aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
    240:     }
    241:   }
    242:   B->nbs = ec;

    244:   baij->B->cmap->n = ec*mat->rmap->bs;

    246:   PetscFree(indices);
    247: #endif

    249:   /* create local vector that is used to scatter into */
    250:   VecCreateSeq(PETSC_COMM_SELF,ec*bs,&baij->lvec);

    252:   /* create two temporary index sets for building scatter-gather */
    253:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,garray,PETSC_COPY_VALUES,&from);

    255:   PetscMalloc(ec*sizeof(PetscInt),&stmp);
    256:   for (i=0; i<ec; i++) stmp[i] = i;
    257:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,PETSC_OWN_POINTER,&to);

    259:   /* create temporary global vector to generate scatter context */
    260:   VecCreateMPIWithArray(PetscObjectComm((PetscObject)mat),1,mat->cmap->n,mat->cmap->N,NULL,&gvec);
    261:   VecScatterCreate(gvec,from,baij->lvec,to,&baij->Mvctx);
    262:   VecDestroy(&gvec);

    264:   PetscLogObjectParent(mat,baij->Mvctx);
    265:   PetscLogObjectParent(mat,baij->lvec);
    266:   PetscLogObjectParent(mat,from);
    267:   PetscLogObjectParent(mat,to);

    269:   baij->garray = garray;

    271:   PetscLogObjectMemory(mat,(ec+1)*sizeof(PetscInt));
    272:   ISDestroy(&from);
    273:   ISDestroy(&to);
    274:   return(0);
    275: }

    277: /*
    278:      Takes the local part of an already assembled MPISBAIJ matrix
    279:    and disassembles it. This is to allow new nonzeros into the matrix
    280:    that require more communication in the matrix vector multiply.
    281:    Thus certain data-structures must be rebuilt.

    283:    Kind of slow! But that's what application programmers get when
    284:    they are sloppy.
    285: */
    288: PetscErrorCode MatDisAssemble_MPISBAIJ(Mat A)
    289: {
    290:   Mat_MPISBAIJ   *baij  = (Mat_MPISBAIJ*)A->data;
    291:   Mat            B      = baij->B,Bnew;
    292:   Mat_SeqBAIJ    *Bbaij = (Mat_SeqBAIJ*)B->data;
    294:   PetscInt       i,j,mbs=Bbaij->mbs,n = A->cmap->N,col,*garray=baij->garray;
    295:   PetscInt       k,bs=A->rmap->bs,bs2=baij->bs2,*rvals,*nz,ec,m=A->rmap->n;
    296:   MatScalar      *a = Bbaij->a;
    297:   PetscScalar    *atmp;
    298: #if defined(PETSC_USE_REAL_MAT_SINGLE)
    299:   PetscInt l;
    300: #endif

    303: #if defined(PETSC_USE_REAL_MAT_SINGLE)
    304:   PetscMalloc(A->rmap->bs*sizeof(PetscScalar),&atmp);
    305: #endif
    306:   /* free stuff related to matrix-vec multiply */
    307:   VecGetSize(baij->lvec,&ec); /* needed for PetscLogObjectMemory below */
    308:   VecDestroy(&baij->lvec);
    309:   VecScatterDestroy(&baij->Mvctx);

    311:   VecDestroy(&baij->slvec0);
    312:   VecDestroy(&baij->slvec0b);
    313:   VecDestroy(&baij->slvec1);
    314:   VecDestroy(&baij->slvec1a);
    315:   VecDestroy(&baij->slvec1b);

    317:   if (baij->colmap) {
    318: #if defined(PETSC_USE_CTABLE)
    319:     PetscTableDestroy(&baij->colmap);
    320: #else
    321:     PetscFree(baij->colmap);
    322:     PetscLogObjectMemory(A,-Bbaij->nbs*sizeof(PetscInt));
    323: #endif
    324:   }

    326:   /* make sure that B is assembled so we can access its values */
    327:   MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
    328:   MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);

    330:   /* invent new B and copy stuff over */
    331:   PetscMalloc(mbs*sizeof(PetscInt),&nz);
    332:   for (i=0; i<mbs; i++) {
    333:     nz[i] = Bbaij->i[i+1]-Bbaij->i[i];
    334:   }
    335:   MatCreate(PETSC_COMM_SELF,&Bnew);
    336:   MatSetSizes(Bnew,m,n,m,n);
    337:   MatSetType(Bnew,((PetscObject)B)->type_name);
    338:   MatSeqBAIJSetPreallocation(Bnew,B->rmap->bs,0,nz);

    340:   ((Mat_SeqSBAIJ*)Bnew->data)->nonew = Bbaij->nonew; /* Inherit insertion error options. */

    342:   PetscFree(nz);

    344:   PetscMalloc(bs*sizeof(PetscInt),&rvals);
    345:   for (i=0; i<mbs; i++) {
    346:     rvals[0] = bs*i;
    347:     for (j=1; j<bs; j++) rvals[j] = rvals[j-1] + 1;
    348:     for (j=Bbaij->i[i]; j<Bbaij->i[i+1]; j++) {
    349:       col = garray[Bbaij->j[j]]*bs;
    350:       for (k=0; k<bs; k++) {
    351: #if defined(PETSC_USE_REAL_MAT_SINGLE)
    352:         for (l=0; l<bs; l++) atmp[l] = a[j*bs2+l];
    353: #else
    354:         atmp = a+j*bs2 + k*bs;
    355: #endif
    356:         MatSetValues_SeqSBAIJ(Bnew,bs,rvals,1,&col,atmp,B->insertmode);
    357:         col++;
    358:       }
    359:     }
    360:   }
    361: #if defined(PETSC_USE_REAL_MAT_SINGLE)
    362:   PetscFree(atmp);
    363: #endif
    364:   PetscFree(baij->garray);

    366:   baij->garray = 0;

    368:   PetscFree(rvals);
    369:   PetscLogObjectMemory(A,-ec*sizeof(PetscInt));
    370:   MatDestroy(&B);
    371:   PetscLogObjectParent(A,Bnew);

    373:   baij->B = Bnew;

    375:   A->was_assembled = PETSC_FALSE;
    376:   return(0);
    377: }