Actual source code: mmsbaij.c
petsc-3.13.6 2020-09-29
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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;
     57:   PetscLayoutDestroy(&sbaij->B->cmap);
     58:   PetscLayoutCreateFromSizes(PetscObjectComm((PetscObject)sbaij->B),ec*mat->rmap->bs,ec*mat->rmap->bs,mat->rmap->bs,&sbaij->B->cmap);
     59:   PetscFree(indices);

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

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

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

     76:   sbaij->garray = garray;

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

     83:   ISDestroy(&from);
     84:   ISDestroy(&to);

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

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

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

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

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

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

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

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

    124:   PetscFree(stmp);
    125:   MPI_Barrier(PetscObjectComm((PetscObject)mat));

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

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

    143: PetscErrorCode MatSetUpMultiply_MPISBAIJ_2comm(Mat mat)
    144: {
    145:   Mat_MPISBAIJ   *baij = (Mat_MPISBAIJ*)mat->data;
    146:   Mat_SeqBAIJ    *B    = (Mat_SeqBAIJ*)(baij->B->data);
    148:   PetscInt       i,j,*aj = B->j,ec = 0,*garray;
    149:   PetscInt       bs = mat->rmap->bs,*stmp;
    150:   IS             from,to;
    151:   Vec            gvec;
    152: #if defined(PETSC_USE_CTABLE)
    153:   PetscTable         gid1_lid1;
    154:   PetscTablePosition tpos;
    155:   PetscInt           gid,lid;
    156: #else
    157:   PetscInt Nbs = baij->Nbs,*indices;
    158: #endif

    161: #if defined(PETSC_USE_CTABLE)
    162:   /* use a table - Mark Adams */
    163:   PetscTableCreate(B->mbs,baij->Nbs+1,&gid1_lid1);
    164:   for (i=0; i<B->mbs; i++) {
    165:     for (j=0; j<B->ilen[i]; j++) {
    166:       PetscInt data,gid1 = aj[B->i[i]+j] + 1;
    167:       PetscTableFind(gid1_lid1,gid1,&data);
    168:       if (!data) {
    169:         /* one based table */
    170:         PetscTableAdd(gid1_lid1,gid1,++ec,INSERT_VALUES);
    171:       }
    172:     }
    173:   }
    174:   /* form array of columns we need */
    175:   PetscMalloc1(ec,&garray);
    176:   PetscTableGetHeadPosition(gid1_lid1,&tpos);
    177:   while (tpos) {
    178:     PetscTableGetNext(gid1_lid1,&tpos,&gid,&lid);
    179:     gid--; lid--;
    180:     garray[lid] = gid;
    181:   }
    182:   PetscSortInt(ec,garray);
    183:   PetscTableRemoveAll(gid1_lid1);
    184:   for (i=0; i<ec; i++) {
    185:     PetscTableAdd(gid1_lid1,garray[i]+1,i+1,INSERT_VALUES);
    186:   }
    187:   /* compact out the extra columns in B */
    188:   for (i=0; i<B->mbs; i++) {
    189:     for (j=0; j<B->ilen[i]; j++) {
    190:       PetscInt gid1 = aj[B->i[i] + j] + 1;
    191:       PetscTableFind(gid1_lid1,gid1,&lid);
    192:       lid--;
    193:       aj[B->i[i]+j] = lid;
    194:     }
    195:   }
    196:   B->nbs = ec;
    197:   PetscLayoutDestroy(&baij->B->cmap);
    198:   PetscLayoutCreateFromSizes(PetscObjectComm((PetscObject)baij->B),ec*mat->rmap->bs,ec*mat->rmap->bs,mat->rmap->bs,&baij->B->cmap);
    199:   PetscTableDestroy(&gid1_lid1);
    200: #else
    201:   /* For the first stab we make an array as long as the number of columns */
    202:   /* mark those columns that are in baij->B */
    203:   PetscCalloc1(Nbs,&indices);
    204:   for (i=0; i<B->mbs; i++) {
    205:     for (j=0; j<B->ilen[i]; j++) {
    206:       if (!indices[aj[B->i[i] + j]]) ec++;
    207:       indices[aj[B->i[i] + j]] = 1;
    208:     }
    209:   }

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

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

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

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

    233:   PetscFree(indices);
    234: #endif

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

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

    242:   PetscMalloc1(ec,&stmp);
    243:   for (i=0; i<ec; i++) stmp[i] = i;
    244:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,PETSC_OWN_POINTER,&to);

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

    251:   PetscLogObjectParent((PetscObject)mat,(PetscObject)baij->Mvctx);
    252:   PetscLogObjectParent((PetscObject)mat,(PetscObject)baij->lvec);
    253:   PetscLogObjectParent((PetscObject)mat,(PetscObject)from);
    254:   PetscLogObjectParent((PetscObject)mat,(PetscObject)to);

    256:   baij->garray = garray;

    258:   PetscLogObjectMemory((PetscObject)mat,(ec+1)*sizeof(PetscInt));
    259:   ISDestroy(&from);
    260:   ISDestroy(&to);
    261:   return(0);
    262: }

    264: /*
    265:      Takes the local part of an already assembled MPISBAIJ matrix
    266:    and disassembles it. This is to allow new nonzeros into the matrix
    267:    that require more communication in the matrix vector multiply.
    268:    Thus certain data-structures must be rebuilt.

    270:    Kind of slow! But that's what Section 1.5 Writing Application Codes with PETSc programmers get when
    271:    they are sloppy.
    272: */
    273: PetscErrorCode MatDisAssemble_MPISBAIJ(Mat A)
    274: {
    275:   Mat_MPISBAIJ   *baij  = (Mat_MPISBAIJ*)A->data;
    276:   Mat            B      = baij->B,Bnew;
    277:   Mat_SeqBAIJ    *Bbaij = (Mat_SeqBAIJ*)B->data;
    279:   PetscInt       i,j,mbs=Bbaij->mbs,n = A->cmap->N,col,*garray=baij->garray;
    280:   PetscInt       k,bs=A->rmap->bs,bs2=baij->bs2,*rvals,*nz,ec,m=A->rmap->n;
    281:   MatScalar      *a = Bbaij->a;
    282:   PetscScalar    *atmp;
    283: #if defined(PETSC_USE_REAL_MAT_SINGLE)
    284:   PetscInt l;
    285: #endif

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

    296:   VecDestroy(&baij->slvec0);
    297:   VecDestroy(&baij->slvec0b);
    298:   VecDestroy(&baij->slvec1);
    299:   VecDestroy(&baij->slvec1a);
    300:   VecDestroy(&baij->slvec1b);

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

    311:   /* make sure that B is assembled so we can access its values */
    312:   MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
    313:   MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);

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

    326:   if (Bbaij->nonew >= 0) { /* Inherit insertion error options (if positive). */
    327:     ((Mat_SeqSBAIJ*)Bnew->data)->nonew = Bbaij->nonew;
    328:   }

    330:   /*
    331:    Ensure that B's nonzerostate is monotonically increasing.
    332:    Or should this follow the MatSetValues() loop to preserve B's nonzerstate across a MatDisAssemble() call?
    333:    */
    334:   Bnew->nonzerostate = B->nonzerostate;
    335:   PetscMalloc1(bs,&rvals);
    336:   for (i=0; i<mbs; i++) {
    337:     rvals[0] = bs*i;
    338:     for (j=1; j<bs; j++) rvals[j] = rvals[j-1] + 1;
    339:     for (j=Bbaij->i[i]; j<Bbaij->i[i+1]; j++) {
    340:       col = garray[Bbaij->j[j]]*bs;
    341:       for (k=0; k<bs; k++) {
    342: #if defined(PETSC_USE_REAL_MAT_SINGLE)
    343:         for (l=0; l<bs; l++) atmp[l] = a[j*bs2+l];
    344: #else
    345:         atmp = a+j*bs2 + k*bs;
    346: #endif
    347:         MatSetValues_SeqSBAIJ(Bnew,bs,rvals,1,&col,atmp,B->insertmode);
    348:         col++;
    349:       }
    350:     }
    351:   }
    352: #if defined(PETSC_USE_REAL_MAT_SINGLE)
    353:   PetscFree(atmp);
    354: #endif
    355:   PetscFree(baij->garray);

    357:   baij->garray = 0;

    359:   PetscFree(rvals);
    360:   PetscLogObjectMemory((PetscObject)A,-ec*sizeof(PetscInt));
    361:   MatDestroy(&B);
    362:   PetscLogObjectParent((PetscObject)A,(PetscObject)Bnew);

    364:   baij->B = Bnew;

    366:   A->was_assembled = PETSC_FALSE;
    367:   return(0);
    368: }