Date: 2021-03-03T22:26:21+00:00

Actual source code: mmsbaij.c
petsc-3.14.5 2021-03-03
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      2: /*
      3:    Support for the parallel SBAIJ matrix vector multiply
      4: */
      5: #include <../src/mat/impls/sbaij/mpi/mpisbaij.h>

      7: PetscErrorCode MatSetUpMultiply_MPISBAIJ(Mat mat)
      8: {
      9:   Mat_MPISBAIJ   *sbaij = (Mat_MPISBAIJ*)mat->data;
     10:   Mat_SeqBAIJ    *B     = (Mat_SeqBAIJ*)(sbaij->B->data);
     12:   PetscInt       Nbs = sbaij->Nbs,i,j,*aj = B->j,ec = 0,*garray,*sgarray;
     13:   PetscInt       bs  = mat->rmap->bs,*stmp,mbs=sbaij->mbs, vec_size,nt;
     14:   IS             from,to;
     15:   Vec            gvec;
     16:   PetscMPIInt    rank = sbaij->rank,lsize;
     17:   PetscInt       *owners = sbaij->rangebs,*ec_owner,k;
     18:   const PetscInt *sowners;
     19:   PetscScalar    *ptr;
     20: #if defined(PETSC_USE_CTABLE)
     21:   PetscTable         gid1_lid1; /* one-based gid to lid table */
     22:   PetscTablePosition tpos;
     23:   PetscInt           gid,lid;
     24: #else
     25:   PetscInt           *indices;
     26: #endif

     29: #if defined(PETSC_USE_CTABLE)
     30:   PetscTableCreate(mbs,Nbs+1,&gid1_lid1);
     31:   for (i=0; i<B->mbs; i++) {
     32:     for (j=0; j<B->ilen[i]; j++) {
     33:       PetscInt data,gid1 = aj[B->i[i]+j] + 1;
     34:       PetscTableFind(gid1_lid1,gid1,&data);
     35:       if (!data) {PetscTableAdd(gid1_lid1,gid1,++ec,INSERT_VALUES);}
     36:     }
     37:   }
     38:   /* form array of columns we need */
     39:   PetscMalloc1(ec,&garray);
     40:   PetscTableGetHeadPosition(gid1_lid1,&tpos);
     41:   while (tpos) {
     42:     PetscTableGetNext(gid1_lid1,&tpos,&gid,&lid);
     43:     gid--; lid--;
     44:     garray[lid] = gid;
     45:   }
     46:   PetscSortInt(ec,garray);
     47:   PetscTableRemoveAll(gid1_lid1);
     48:   for (i=0; i<ec; i++) {PetscTableAdd(gid1_lid1,garray[i]+1,i+1,INSERT_VALUES);}
     49:   /* compact out the extra columns in B */
     50:   for (i=0; i<B->mbs; i++) {
     51:     for (j=0; j<B->ilen[i]; j++) {
     52:       PetscInt gid1 = aj[B->i[i] + j] + 1;
     53:       PetscTableFind(gid1_lid1,gid1,&lid);
     54:       lid--;
     55:       aj[B->i[i]+j] = lid;
     56:     }
     57:   }
     58:   PetscTableDestroy(&gid1_lid1);
     59:   PetscMalloc2(2*ec,&sgarray,ec,&ec_owner);
     60:   for (i=j=0; i<ec; i++) {
     61:     while (garray[i]>=owners[j+1]) j++;
     62:     ec_owner[i] = j;
     63:   }
     64: #else
     65:   /* For the first stab we make an array as long as the number of columns */
     66:   /* mark those columns that are in sbaij->B */
     67:   PetscCalloc1(Nbs,&indices);
     68:   for (i=0; i<mbs; i++) {
     69:     for (j=0; j<B->ilen[i]; j++) {
     70:       if (!indices[aj[B->i[i] + j]]) ec++;
     71:       indices[aj[B->i[i] + j]] = 1;
     72:     }
     73:   }

     75:   /* form arrays of columns we need */
     76:   PetscMalloc1(ec,&garray);
     77:   PetscMalloc2(2*ec,&sgarray,ec,&ec_owner);

     79:   ec = 0;
     80:   for (j=0; j<sbaij->size; j++) {
     81:     for (i=owners[j]; i<owners[j+1]; i++) {
     82:       if (indices[i]) {
     83:         garray[ec]   = i;
     84:         ec_owner[ec] = j;
     85:         ec++;
     86:       }
     87:     }
     88:   }

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

     93:   /* compact out the extra columns in B */
     94:   for (i=0; i<mbs; i++) {
     95:     for (j=0; j<B->ilen[i]; j++) aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
     96:   }
     97:   PetscFree(indices);
     98: #endif
     99:   B->nbs = ec;
    100:   PetscLayoutDestroy(&sbaij->B->cmap);
    101:   PetscLayoutCreateFromSizes(PetscObjectComm((PetscObject)sbaij->B),ec*mat->rmap->bs,ec*mat->rmap->bs,mat->rmap->bs,&sbaij->B->cmap);

    103:   VecScatterDestroy(&sbaij->sMvctx);
    104:   /* create local vector that is used to scatter into */
    105:   VecCreateSeq(PETSC_COMM_SELF,ec*bs,&sbaij->lvec);

    107:   /* create two temporary index sets for building scatter-gather */
    108:   PetscMalloc1(2*ec,&stmp);
    109:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,garray,PETSC_COPY_VALUES,&from);
    110:   for (i=0; i<ec; i++) stmp[i] = i;
    111:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,PETSC_COPY_VALUES,&to);

    113:   /* generate the scatter context
    114:      -- Mvctx and lvec are not used by MatMult_MPISBAIJ(), but have other uses, such as in MatDiagonalScale_MPISBAIJ */
    115:   VecCreateMPIWithArray(PetscObjectComm((PetscObject)mat),1,mat->cmap->n,mat->cmap->N,NULL,&gvec);
    116:   VecScatterCreate(gvec,from,sbaij->lvec,to,&sbaij->Mvctx);
    117:   VecDestroy(&gvec);

    119:   sbaij->garray = garray;

    121:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->Mvctx);
    122:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->lvec);
    123:   PetscLogObjectParent((PetscObject)mat,(PetscObject)from);
    124:   PetscLogObjectParent((PetscObject)mat,(PetscObject)to);

    126:   ISDestroy(&from);
    127:   ISDestroy(&to);

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

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

    137:   /* x index in the IS sfrom */
    138:   for (i=0; i<ec; i++) {
    139:     j          = ec_owner[i];
    140:     sgarray[i] = garray[i] + (sowners[j]/bs - owners[j]);
    141:   }
    142:   /* b index in the IS sfrom */
    143:   k = sowners[rank]/bs + mbs;
    144:   for (i=ec,j=0; i< 2*ec; i++,j++) sgarray[i] = k + j;
    145:   ISCreateBlock(PETSC_COMM_SELF,bs,2*ec,sgarray,PETSC_COPY_VALUES,&from);

    147:   /* x index in the IS sto */
    148:   k = sowners[rank]/bs + mbs;
    149:   for (i=0; i<ec; i++) stmp[i] = (k + i);
    150:   /* b index in the IS sto */
    151:   for (i=ec; i<2*ec; i++) stmp[i] = sgarray[i-ec];

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

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

    157:   VecGetLocalSize(sbaij->slvec1,&nt);
    158:   VecGetArray(sbaij->slvec1,&ptr);
    159:   VecCreateSeqWithArray(PETSC_COMM_SELF,1,bs*mbs,ptr,&sbaij->slvec1a);
    160:   VecCreateSeqWithArray(PETSC_COMM_SELF,1,nt-bs*mbs,ptr+bs*mbs,&sbaij->slvec1b);
    161:   VecRestoreArray(sbaij->slvec1,&ptr);

    163:   VecGetArray(sbaij->slvec0,&ptr);
    164:   VecCreateSeqWithArray(PETSC_COMM_SELF,1,nt-bs*mbs,ptr+bs*mbs,&sbaij->slvec0b);
    165:   VecRestoreArray(sbaij->slvec0,&ptr);

    167:   PetscFree(stmp);
    168:   MPI_Barrier(PetscObjectComm((PetscObject)mat));

    170:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->sMvctx);
    171:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->slvec0);
    172:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->slvec1);
    173:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->slvec0b);
    174:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->slvec1a);
    175:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->slvec1b);
    176:   PetscLogObjectParent((PetscObject)mat,(PetscObject)from);
    177:   PetscLogObjectParent((PetscObject)mat,(PetscObject)to);

    179:   PetscLogObjectMemory((PetscObject)mat,(ec+1)*sizeof(PetscInt));
    180:   ISDestroy(&from);
    181:   ISDestroy(&to);
    182:   PetscFree2(sgarray,ec_owner);
    183:   return(0);
    184: }

    186: /*
    187:      Takes the local part of an already assembled MPISBAIJ matrix
    188:    and disassembles it. This is to allow new nonzeros into the matrix
    189:    that require more communication in the matrix vector multiply.
    190:    Thus certain data-structures must be rebuilt.

    192:    Kind of slow! But that's what application programmers get when
    193:    they are sloppy.
    194: */
    195: PetscErrorCode MatDisAssemble_MPISBAIJ(Mat A)
    196: {
    197:   Mat_MPISBAIJ   *baij  = (Mat_MPISBAIJ*)A->data;
    198:   Mat            B      = baij->B,Bnew;
    199:   Mat_SeqBAIJ    *Bbaij = (Mat_SeqBAIJ*)B->data;
    201:   PetscInt       i,j,mbs=Bbaij->mbs,n = A->cmap->N,col,*garray=baij->garray;
    202:   PetscInt       k,bs=A->rmap->bs,bs2=baij->bs2,*rvals,*nz,ec,m=A->rmap->n;
    203:   MatScalar      *a = Bbaij->a;
    204:   PetscScalar    *atmp;
    205: #if defined(PETSC_USE_REAL_MAT_SINGLE)
    206:   PetscInt l;
    207: #endif

    210: #if defined(PETSC_USE_REAL_MAT_SINGLE)
    211:   PetscMalloc1(A->rmap->bs,&atmp);
    212: #endif
    213:   /* free stuff related to matrix-vec multiply */
    214:   VecGetSize(baij->lvec,&ec); /* needed for PetscLogObjectMemory below */
    215:   VecDestroy(&baij->lvec);
    216:   VecScatterDestroy(&baij->Mvctx);

    218:   VecDestroy(&baij->slvec0);
    219:   VecDestroy(&baij->slvec0b);
    220:   VecDestroy(&baij->slvec1);
    221:   VecDestroy(&baij->slvec1a);
    222:   VecDestroy(&baij->slvec1b);

    224:   if (baij->colmap) {
    225: #if defined(PETSC_USE_CTABLE)
    226:     PetscTableDestroy(&baij->colmap);
    227: #else
    228:     PetscFree(baij->colmap);
    229:     PetscLogObjectMemory((PetscObject)A,-Bbaij->nbs*sizeof(PetscInt));
    230: #endif
    231:   }

    233:   /* make sure that B is assembled so we can access its values */
    234:   MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
    235:   MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);

    237:   /* invent new B and copy stuff over */
    238:   PetscMalloc1(mbs,&nz);
    239:   for (i=0; i<mbs; i++) {
    240:     nz[i] = Bbaij->i[i+1]-Bbaij->i[i];
    241:   }
    242:   MatCreate(PETSC_COMM_SELF,&Bnew);
    243:   MatSetSizes(Bnew,m,n,m,n);
    244:   MatSetType(Bnew,((PetscObject)B)->type_name);
    245:   MatSeqBAIJSetPreallocation(Bnew,B->rmap->bs,0,nz);
    246:   PetscFree(nz);

    248:   if (Bbaij->nonew >= 0) { /* Inherit insertion error options (if positive). */
    249:     ((Mat_SeqSBAIJ*)Bnew->data)->nonew = Bbaij->nonew;
    250:   }

    252:   /*
    253:    Ensure that B's nonzerostate is monotonically increasing.
    254:    Or should this follow the MatSetValues() loop to preserve B's nonzerstate across a MatDisAssemble() call?
    255:    */
    256:   Bnew->nonzerostate = B->nonzerostate;
    257:   PetscMalloc1(bs,&rvals);
    258:   for (i=0; i<mbs; i++) {
    259:     rvals[0] = bs*i;
    260:     for (j=1; j<bs; j++) rvals[j] = rvals[j-1] + 1;
    261:     for (j=Bbaij->i[i]; j<Bbaij->i[i+1]; j++) {
    262:       col = garray[Bbaij->j[j]]*bs;
    263:       for (k=0; k<bs; k++) {
    264: #if defined(PETSC_USE_REAL_MAT_SINGLE)
    265:         for (l=0; l<bs; l++) atmp[l] = a[j*bs2+l];
    266: #else
    267:         atmp = a+j*bs2 + k*bs;
    268: #endif
    269:         MatSetValues_SeqSBAIJ(Bnew,bs,rvals,1,&col,atmp,B->insertmode);
    270:         col++;
    271:       }
    272:     }
    273:   }
    274: #if defined(PETSC_USE_REAL_MAT_SINGLE)
    275:   PetscFree(atmp);
    276: #endif
    277:   PetscFree(baij->garray);

    279:   baij->garray = NULL;

    281:   PetscFree(rvals);
    282:   PetscLogObjectMemory((PetscObject)A,-ec*sizeof(PetscInt));
    283:   MatDestroy(&B);
    284:   PetscLogObjectParent((PetscObject)A,(PetscObject)Bnew);

    286:   baij->B = Bnew;

    288:   A->was_assembled = PETSC_FALSE;
    289:   return(0);
    290: }