Actual source code: mmsbaij.c
petsc-3.10.5 2019-03-28
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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,*indices,*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,size=sbaij->size;
     17:   PetscInt       *owners=sbaij->rangebs,*ec_owner,k;
     18:   const PetscInt *sowners;
     19:   PetscScalar    *ptr;

     22:   VecScatterDestroy(&sbaij->sMvctx);

     24:   /* For the first stab we make an array as long as the number of columns */
     25:   /* mark those columns that are in sbaij->B */
     26:   PetscCalloc1(Nbs,&indices);
     27:   for (i=0; i<mbs; i++) {
     28:     for (j=0; j<B->ilen[i]; j++) {
     29:       if (!indices[aj[B->i[i] + j]]) ec++;
     30:       indices[aj[B->i[i] + j]] = 1;
     31:     }
     32:   }

     34:   /* form arrays of columns we need */
     35:   PetscMalloc1(ec,&garray);
     36:   PetscMalloc2(2*ec,&sgarray,ec,&ec_owner);

     38:   ec = 0;
     39:   for (j=0; j<size; j++) {
     40:     for (i=owners[j]; i<owners[j+1]; i++) {
     41:       if (indices[i]) {
     42:         garray[ec]   = i;
     43:         ec_owner[ec] = j;
     44:         ec++;
     45:       }
     46:     }
     47:   }

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

     52:   /* compact out the extra columns in B */
     53:   for (i=0; i<mbs; i++) {
     54:     for (j=0; j<B->ilen[i]; j++) aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
     55:   }
     56:   B->nbs = ec;

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

     60:   PetscLayoutSetUp((sbaij->B->cmap));
     61:   PetscFree(indices);

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

     66:   /* create two temporary index sets for building scatter-gather */
     67:   PetscMalloc1(2*ec,&stmp);
     68:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,garray,PETSC_COPY_VALUES,&from);
     69:   for (i=0; i<ec; i++) stmp[i] = i;
     70:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,PETSC_COPY_VALUES,&to);

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

     78:   sbaij->garray = garray;

     80:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->Mvctx);
     81:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->lvec);
     82:   PetscLogObjectParent((PetscObject)mat,(PetscObject)from);
     83:   PetscLogObjectParent((PetscObject)mat,(PetscObject)to);

     85:   ISDestroy(&from);
     86:   ISDestroy(&to);

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

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

     96:   /* x index in the IS sfrom */
     97:   for (i=0; i<ec; i++) {
     98:     j          = ec_owner[i];
     99:     sgarray[i] = garray[i] + (sowners[j]/bs - owners[j]);
    100:   }
    101:   /* b index in the IS sfrom */
    102:   k = sowners[rank]/bs + mbs;
    103:   for (i=ec,j=0; i< 2*ec; i++,j++) sgarray[i] = k + j;
    104:   ISCreateBlock(PETSC_COMM_SELF,bs,2*ec,sgarray,PETSC_COPY_VALUES,&from);

    106:   /* x index in the IS sto */
    107:   k = sowners[rank]/bs + mbs;
    108:   for (i=0; i<ec; i++) stmp[i] = (k + i);
    109:   /* b index in the IS sto */
    110:   for (i=ec; i<2*ec; i++) stmp[i] = sgarray[i-ec];

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

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

    116:   VecGetLocalSize(sbaij->slvec1,&nt);
    117:   VecGetArray(sbaij->slvec1,&ptr);
    118:   VecCreateSeqWithArray(PETSC_COMM_SELF,1,bs*mbs,ptr,&sbaij->slvec1a);
    119:   VecCreateSeqWithArray(PETSC_COMM_SELF,1,nt-bs*mbs,ptr+bs*mbs,&sbaij->slvec1b);
    120:   VecRestoreArray(sbaij->slvec1,&ptr);

    122:   VecGetArray(sbaij->slvec0,&ptr);
    123:   VecCreateSeqWithArray(PETSC_COMM_SELF,1,nt-bs*mbs,ptr+bs*mbs,&sbaij->slvec0b);
    124:   VecRestoreArray(sbaij->slvec0,&ptr);

    126:   PetscFree(stmp);
    127:   MPI_Barrier(PetscObjectComm((PetscObject)mat));

    129:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->sMvctx);
    130:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->slvec0);
    131:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->slvec1);
    132:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->slvec0b);
    133:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->slvec1a);
    134:   PetscLogObjectParent((PetscObject)mat,(PetscObject)sbaij->slvec1b);
    135:   PetscLogObjectParent((PetscObject)mat,(PetscObject)from);
    136:   PetscLogObjectParent((PetscObject)mat,(PetscObject)to);

    138:   PetscLogObjectMemory((PetscObject)mat,(ec+1)*sizeof(PetscInt));
    139:   ISDestroy(&from);
    140:   ISDestroy(&to);
    141:   PetscFree2(sgarray,ec_owner);
    142:   return(0);
    143: }

    145: PetscErrorCode MatSetUpMultiply_MPISBAIJ_2comm(Mat mat)
    146: {
    147:   Mat_MPISBAIJ   *baij = (Mat_MPISBAIJ*)mat->data;
    148:   Mat_SeqBAIJ    *B    = (Mat_SeqBAIJ*)(baij->B->data);
    150:   PetscInt       i,j,*aj = B->j,ec = 0,*garray;
    151:   PetscInt       bs = mat->rmap->bs,*stmp;
    152:   IS             from,to;
    153:   Vec            gvec;
    154: #if defined(PETSC_USE_CTABLE)
    155:   PetscTable         gid1_lid1;
    156:   PetscTablePosition tpos;
    157:   PetscInt           gid,lid;
    158: #else
    159:   PetscInt Nbs = baij->Nbs,*indices;
    160: #endif

    163: #if defined(PETSC_USE_CTABLE)
    164:   /* use a table - Mark Adams */
    165:   PetscTableCreate(B->mbs,baij->Nbs+1,&gid1_lid1);
    166:   for (i=0; i<B->mbs; i++) {
    167:     for (j=0; j<B->ilen[i]; j++) {
    168:       PetscInt data,gid1 = aj[B->i[i]+j] + 1;
    169:       PetscTableFind(gid1_lid1,gid1,&data);
    170:       if (!data) {
    171:         /* one based table */
    172:         PetscTableAdd(gid1_lid1,gid1,++ec,INSERT_VALUES);
    173:       }
    174:     }
    175:   }
    176:   /* form array of columns we need */
    177:   PetscMalloc1(ec,&garray);
    178:   PetscTableGetHeadPosition(gid1_lid1,&tpos);
    179:   while (tpos) {
    180:     PetscTableGetNext(gid1_lid1,&tpos,&gid,&lid);
    181:     gid--; lid--;
    182:     garray[lid] = gid;
    183:   }
    184:   PetscSortInt(ec,garray);
    185:   PetscTableRemoveAll(gid1_lid1);
    186:   for (i=0; i<ec; i++) {
    187:     PetscTableAdd(gid1_lid1,garray[i]+1,i+1,INSERT_VALUES);
    188:   }
    189:   /* compact out the extra columns in B */
    190:   for (i=0; i<B->mbs; i++) {
    191:     for (j=0; j<B->ilen[i]; j++) {
    192:       PetscInt gid1 = aj[B->i[i] + j] + 1;
    193:       PetscTableFind(gid1_lid1,gid1,&lid);
    194:       lid--;
    195:       aj[B->i[i]+j] = lid;
    196:     }
    197:   }
    198:   B->nbs = ec;

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

    202:   PetscLayoutSetUp((baij->B->cmap));
    203:   PetscTableDestroy(&gid1_lid1);
    204: #else
    205:   /* For the first stab we make an array as long as the number of columns */
    206:   /* mark those columns that are in baij->B */
    207:   PetscCalloc1(Nbs,&indices);
    208:   for (i=0; i<B->mbs; i++) {
    209:     for (j=0; j<B->ilen[i]; j++) {
    210:       if (!indices[aj[B->i[i] + j]]) ec++;
    211:       indices[aj[B->i[i] + j]] = 1;
    212:     }
    213:   }

    215:   /* form array of columns we need */
    216:   PetscMalloc1(ec,&garray);
    217:   ec = 0;
    218:   for (i=0; i<Nbs; i++) {
    219:     if (indices[i]) {
    220:       garray[ec++] = i;
    221:     }
    222:   }

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

    227:   /* compact out the extra columns in B */
    228:   for (i=0; i<B->mbs; i++) {
    229:     for (j=0; j<B->ilen[i]; j++) {
    230:       aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
    231:     }
    232:   }
    233:   B->nbs = ec;

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

    237:   PetscFree(indices);
    238: #endif

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

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

    246:   PetscMalloc1(ec,&stmp);
    247:   for (i=0; i<ec; i++) stmp[i] = i;
    248:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,PETSC_OWN_POINTER,&to);

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

    255:   PetscLogObjectParent((PetscObject)mat,(PetscObject)baij->Mvctx);
    256:   PetscLogObjectParent((PetscObject)mat,(PetscObject)baij->lvec);
    257:   PetscLogObjectParent((PetscObject)mat,(PetscObject)from);
    258:   PetscLogObjectParent((PetscObject)mat,(PetscObject)to);

    260:   baij->garray = garray;

    262:   PetscLogObjectMemory((PetscObject)mat,(ec+1)*sizeof(PetscInt));
    263:   ISDestroy(&from);
    264:   ISDestroy(&to);
    265:   return(0);
    266: }

    268: /*
    269:      Takes the local part of an already assembled MPISBAIJ matrix
    270:    and disassembles it. This is to allow new nonzeros into the matrix
    271:    that require more communication in the matrix vector multiply.
    272:    Thus certain data-structures must be rebuilt.

    274:    Kind of slow! But that's what application programmers get when
    275:    they are sloppy.
    276: */
    277: PetscErrorCode MatDisAssemble_MPISBAIJ(Mat A)
    278: {
    279:   Mat_MPISBAIJ   *baij  = (Mat_MPISBAIJ*)A->data;
    280:   Mat            B      = baij->B,Bnew;
    281:   Mat_SeqBAIJ    *Bbaij = (Mat_SeqBAIJ*)B->data;
    283:   PetscInt       i,j,mbs=Bbaij->mbs,n = A->cmap->N,col,*garray=baij->garray;
    284:   PetscInt       k,bs=A->rmap->bs,bs2=baij->bs2,*rvals,*nz,ec,m=A->rmap->n;
    285:   MatScalar      *a = Bbaij->a;
    286:   PetscScalar    *atmp;
    287: #if defined(PETSC_USE_REAL_MAT_SINGLE)
    288:   PetscInt l;
    289: #endif

    292: #if defined(PETSC_USE_REAL_MAT_SINGLE)
    293:   PetscMalloc1(A->rmap->bs,&atmp);
    294: #endif
    295:   /* free stuff related to matrix-vec multiply */
    296:   VecGetSize(baij->lvec,&ec); /* needed for PetscLogObjectMemory below */
    297:   VecDestroy(&baij->lvec);
    298:   VecScatterDestroy(&baij->Mvctx);

    300:   VecDestroy(&baij->slvec0);
    301:   VecDestroy(&baij->slvec0b);
    302:   VecDestroy(&baij->slvec1);
    303:   VecDestroy(&baij->slvec1a);
    304:   VecDestroy(&baij->slvec1b);

    306:   if (baij->colmap) {
    307: #if defined(PETSC_USE_CTABLE)
    308:     PetscTableDestroy(&baij->colmap);
    309: #else
    310:     PetscFree(baij->colmap);
    311:     PetscLogObjectMemory((PetscObject)A,-Bbaij->nbs*sizeof(PetscInt));
    312: #endif
    313:   }

    315:   /* make sure that B is assembled so we can access its values */
    316:   MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
    317:   MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);

    319:   /* invent new B and copy stuff over */
    320:   PetscMalloc1(mbs,&nz);
    321:   for (i=0; i<mbs; i++) {
    322:     nz[i] = Bbaij->i[i+1]-Bbaij->i[i];
    323:   }
    324:   MatCreate(PETSC_COMM_SELF,&Bnew);
    325:   MatSetSizes(Bnew,m,n,m,n);
    326:   MatSetType(Bnew,((PetscObject)B)->type_name);
    327:   MatSeqBAIJSetPreallocation(Bnew,B->rmap->bs,0,nz);
    328:   PetscFree(nz);

    330:   if (Bbaij->nonew >= 0) { /* Inherit insertion error options (if positive). */
    331:     ((Mat_SeqSBAIJ*)Bnew->data)->nonew = Bbaij->nonew;
    332:   }

    334:   /*
    335:    Ensure that B's nonzerostate is monotonically increasing.
    336:    Or should this follow the MatSetValues() loop to preserve B's nonzerstate across a MatDisAssemble() call?
    337:    */
    338:   Bnew->nonzerostate = B->nonzerostate;
    339:   PetscMalloc1(bs,&rvals);
    340:   for (i=0; i<mbs; i++) {
    341:     rvals[0] = bs*i;
    342:     for (j=1; j<bs; j++) rvals[j] = rvals[j-1] + 1;
    343:     for (j=Bbaij->i[i]; j<Bbaij->i[i+1]; j++) {
    344:       col = garray[Bbaij->j[j]]*bs;
    345:       for (k=0; k<bs; k++) {
    346: #if defined(PETSC_USE_REAL_MAT_SINGLE)
    347:         for (l=0; l<bs; l++) atmp[l] = a[j*bs2+l];
    348: #else
    349:         atmp = a+j*bs2 + k*bs;
    350: #endif
    351:         MatSetValues_SeqSBAIJ(Bnew,bs,rvals,1,&col,atmp,B->insertmode);
    352:         col++;
    353:       }
    354:     }
    355:   }
    356: #if defined(PETSC_USE_REAL_MAT_SINGLE)
    357:   PetscFree(atmp);
    358: #endif
    359:   PetscFree(baij->garray);

    361:   baij->garray = 0;

    363:   PetscFree(rvals);
    364:   PetscLogObjectMemory((PetscObject)A,-ec*sizeof(PetscInt));
    365:   MatDestroy(&B);
    366:   PetscLogObjectParent((PetscObject)A,(PetscObject)Bnew);

    368:   baij->B = Bnew;

    370:   A->was_assembled = PETSC_FALSE;
    371:   return(0);
    372: }