Actual source code: mmsbaij.c

      1: #define PETSCMAT_DLL

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

      8: EXTERN PetscErrorCode MatSetValues_SeqSBAIJ(Mat,PetscInt,const PetscInt [],PetscInt,const PetscInt [],const PetscScalar [],InsertMode);

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

     28:   if (sbaij->lvec) {
     29:     VecDestroy(sbaij->lvec);
     30:     sbaij->lvec = 0;
     31:   }
     32:   if (sbaij->Mvctx) {
     33:     VecScatterDestroy(sbaij->Mvctx);
     34:     sbaij->Mvctx = 0;
     35:   }

     37:   /* For the first stab we make an array as long as the number of columns */
     38:   /* mark those columns that are in sbaij->B */
     39:   PetscMalloc((Nbs+1)*sizeof(PetscInt),&indices);
     40:   PetscMemzero(indices,Nbs*sizeof(PetscInt));
     41:   for (i=0; i<mbs; i++) {
     42:     for (j=0; j<B->ilen[i]; j++) {
     43:       if (!indices[aj[B->i[i] + j]]) ec++;
     44:       indices[aj[B->i[i] + j] ] = 1;
     45:     }
     46:   }

     48:   /* form arrays of columns we need */
     49:   PetscMalloc((ec+1)*sizeof(PetscInt),&garray);
     50:   PetscMalloc((3*ec+1)*sizeof(PetscInt),&sgarray);
     51:   ec_owner = sgarray + 2*ec;
     52:
     53:   ec = 0;
     54:   for (j=0; j<size; j++){
     55:     for (i=owners[j]; i<owners[j+1]; i++){
     56:       if (indices[i]) {
     57:         garray[ec]   = i;
     58:         ec_owner[ec] = j;
     59:         ec++;
     60:       }
     61:     }
     62:   }

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

     67:   /* compact out the extra columns in B */
     68:   for (i=0; i<mbs; i++) {
     69:     for (j=0; j<B->ilen[i]; j++) aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
     70:   }
     71:   B->nbs      = ec;
     72:   sbaij->B->n = ec*mat->bs;
     73:   PetscFree(indices);

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

     78:   /* create two temporary index sets for building scatter-gather */
     79:   PetscMalloc((2*ec+1)*sizeof(PetscInt),&stmp);
     80:   for (i=0; i<ec; i++) stmp[i] = bs*garray[i];
     81:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,&from);
     82:
     83:   for (i=0; i<ec; i++) { stmp[i] = bs*i; }
     84:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,&to);

     86:   /* generate the scatter context
     87:      -- Mvctx and lvec are not used by MatMult_MPISBAIJ(), but usefule for some applications */
     88:   VecCreateMPI(mat->comm,mat->n,mat->N,&gvec);
     89:   VecScatterCreate(gvec,from,sbaij->lvec,to,&sbaij->Mvctx);
     90:   VecScatterPostRecvs(gvec,sbaij->lvec,INSERT_VALUES,SCATTER_FORWARD,sbaij->Mvctx);

     92:   sbaij->garray = garray;
     93:   PetscLogObjectParent(mat,sbaij->Mvctx);
     94:   PetscLogObjectParent(mat,sbaij->lvec);
     95:   PetscLogObjectParent(mat,from);
     96:   PetscLogObjectParent(mat,to);

     98:   ISDestroy(from);
     99:   ISDestroy(to);

    101:   /* create parallel vector that is used by SBAIJ matrix to scatter from/into */
    102:   lsize = (mbs + ec)*bs;
    103:   VecCreateMPI(mat->comm,lsize,PETSC_DETERMINE,&sbaij->slvec0);
    104:   VecDuplicate(sbaij->slvec0,&sbaij->slvec1);
    105:   VecGetSize(sbaij->slvec0,&vec_size);

    107:   VecGetPetscMap(sbaij->slvec0,&vecmap);
    108:   PetscMapGetGlobalRange(vecmap,&sowners);
    109:
    110:   /* x index in the IS sfrom */
    111:   for (i=0; i<ec; i++) {
    112:     j = ec_owner[i];
    113:     sgarray[i]  = garray[i] + (sowners[j]/bs - owners[j]);
    114:   }
    115:   /* b index in the IS sfrom */
    116:   k = sowners[rank]/bs + mbs;
    117:   for (i=ec,j=0; i< 2*ec; i++,j++) sgarray[i] = k + j;
    118:
    119:   for (i=0; i<2*ec; i++) stmp[i] = bs*sgarray[i];
    120:   ISCreateBlock(PETSC_COMM_SELF,bs,2*ec,stmp,&from);
    121:
    122:   /* x index in the IS sto */
    123:   k = sowners[rank]/bs + mbs;
    124:   for (i=0; i<ec; i++) stmp[i] = bs*(k + i);
    125:   /* b index in the IS sto */
    126:   for (i=ec; i<2*ec; i++) stmp[i] = bs*sgarray[i-ec];

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

    130:   /* gnerate the SBAIJ scatter context */
    131:   VecScatterCreate(sbaij->slvec0,from,sbaij->slvec1,to,&sbaij->sMvctx);
    132:
    133:    /*
    134:       Post the receives for the first matrix vector product. We sync-chronize after
    135:     this on the chance that the user immediately calls MatMult() after assemblying
    136:     the matrix.
    137:   */
    138:   VecScatterPostRecvs(sbaij->slvec0,sbaij->slvec1,INSERT_VALUES,SCATTER_FORWARD,sbaij->sMvctx);

    140:   VecGetLocalSize(sbaij->slvec1,&nt);
    141:   VecGetArray(sbaij->slvec1,&ptr);
    142:   VecCreateSeqWithArray(PETSC_COMM_SELF,bs*mbs,ptr,&sbaij->slvec1a);
    143:   VecCreateSeqWithArray(PETSC_COMM_SELF,nt-bs*mbs,ptr+bs*mbs,&sbaij->slvec1b);
    144:   VecRestoreArray(sbaij->slvec1,&ptr);

    146:   VecGetArray(sbaij->slvec0,&ptr);
    147:   VecCreateSeqWithArray(PETSC_COMM_SELF,nt-bs*mbs,ptr+bs*mbs,&sbaij->slvec0b);
    148:   VecRestoreArray(sbaij->slvec0,&ptr);

    150:   PetscFree(stmp);
    151:   MPI_Barrier(mat->comm);
    152:
    153:   PetscLogObjectParent(mat,sbaij->sMvctx);
    154:   PetscLogObjectParent(mat,sbaij->slvec0);
    155:   PetscLogObjectParent(mat,sbaij->slvec1);
    156:   PetscLogObjectParent(mat,sbaij->slvec0b);
    157:   PetscLogObjectParent(mat,sbaij->slvec1a);
    158:   PetscLogObjectParent(mat,sbaij->slvec1b);
    159:   PetscLogObjectParent(mat,from);
    160:   PetscLogObjectParent(mat,to);
    161:
    162:   PetscLogObjectMemory(mat,(ec+1)*sizeof(PetscInt));
    163:   ISDestroy(from);
    164:   ISDestroy(to);
    165:   VecDestroy(gvec);
    166:   PetscFree(sgarray);

    168:   return(0);
    169: }

    173: PetscErrorCode MatSetUpMultiply_MPISBAIJ_2comm(Mat mat)
    174: {
    175:   Mat_MPISBAIJ       *baij = (Mat_MPISBAIJ*)mat->data;
    176:   Mat_SeqBAIJ        *B = (Mat_SeqBAIJ*)(baij->B->data);
    177:   PetscErrorCode     ierr;
    178:   PetscInt           i,j,*aj = B->j,ec = 0,*garray;
    179:   PetscInt           bs = mat->bs,*stmp;
    180:   IS                 from,to;
    181:   Vec                gvec;
    182: #if defined (PETSC_USE_CTABLE)
    183:   PetscTable         gid1_lid1;
    184:   PetscTablePosition tpos;
    185:   PetscInt           gid,lid;
    186: #else
    187:   PetscInt           Nbs = baij->Nbs,*indices;
    188: #endif

    192: #if defined (PETSC_USE_CTABLE)
    193:   /* use a table - Mark Adams */
    194:   PetscTableCreate(B->mbs,&gid1_lid1);
    195:   for (i=0; i<B->mbs; i++) {
    196:     for (j=0; j<B->ilen[i]; j++) {
    197:       PetscInt data,gid1 = aj[B->i[i]+j] + 1;
    198:       PetscTableFind(gid1_lid1,gid1,&data);
    199:       if (!data) {
    200:         /* one based table */
    201:         PetscTableAdd(gid1_lid1,gid1,++ec);
    202:       }
    203:     }
    204:   }
    205:   /* form array of columns we need */
    206:   PetscMalloc((ec+1)*sizeof(PetscInt),&garray);
    207:   PetscTableGetHeadPosition(gid1_lid1,&tpos);
    208:   while (tpos) {
    209:     PetscTableGetNext(gid1_lid1,&tpos,&gid,&lid);
    210:     gid--; lid--;
    211:     garray[lid] = gid;
    212:   }
    213:   PetscSortInt(ec,garray);
    214:   PetscTableRemoveAll(gid1_lid1);
    215:   for (i=0; i<ec; i++) {
    216:     PetscTableAdd(gid1_lid1,garray[i]+1,i+1);
    217:   }
    218:   /* compact out the extra columns in B */
    219:   for (i=0; i<B->mbs; i++) {
    220:     for (j=0; j<B->ilen[i]; j++) {
    221:       PetscInt gid1 = aj[B->i[i] + j] + 1;
    222:       PetscTableFind(gid1_lid1,gid1,&lid);
    223:       lid --;
    224:       aj[B->i[i]+j] = lid;
    225:     }
    226:   }
    227:   B->nbs     = ec;
    228:   baij->B->n = ec*mat->bs;
    229:   PetscTableDelete(gid1_lid1);
    230:   /* Mark Adams */
    231: #else
    232:   /* For the first stab we make an array as long as the number of columns */
    233:   /* mark those columns that are in baij->B */
    234:   PetscMalloc((Nbs+1)*sizeof(PetscInt),&indices);
    235:   PetscMemzero(indices,Nbs*sizeof(PetscInt));
    236:   for (i=0; i<B->mbs; i++) {
    237:     for (j=0; j<B->ilen[i]; j++) {
    238:       if (!indices[aj[B->i[i] + j]]) ec++;
    239:       indices[aj[B->i[i] + j] ] = 1;
    240:     }
    241:   }

    243:   /* form array of columns we need */
    244:   PetscMalloc((ec+1)*sizeof(PetscInt),&garray);
    245:   ec = 0;
    246:   for (i=0; i<Nbs; i++) {
    247:     if (indices[i]) {
    248:       garray[ec++] = i;
    249:     }
    250:   }

    252:   /* make indices now point into garray */
    253:   for (i=0; i<ec; i++) {
    254:     indices[garray[i]] = i;
    255:   }

    257:   /* compact out the extra columns in B */
    258:   for (i=0; i<B->mbs; i++) {
    259:     for (j=0; j<B->ilen[i]; j++) {
    260:       aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
    261:     }
    262:   }
    263:   B->nbs       = ec;
    264:   baij->B->n   = ec*mat->bs;
    265:   PetscFree(indices);
    266: #endif
    267:
    268:   /* create local vector that is used to scatter into */
    269:   VecCreateSeq(PETSC_COMM_SELF,ec*bs,&baij->lvec);

    271:   /* create two temporary index sets for building scatter-gather */
    272:   for (i=0; i<ec; i++) {
    273:     garray[i] = bs*garray[i];
    274:   }
    275:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,garray,&from);
    276:   for (i=0; i<ec; i++) {
    277:     garray[i] = garray[i]/bs;
    278:   }

    280:   PetscMalloc((ec+1)*sizeof(PetscInt),&stmp);
    281:   for (i=0; i<ec; i++) { stmp[i] = bs*i; }
    282:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,&to);
    283:   PetscFree(stmp);

    285:   /* create temporary global vector to generate scatter context */
    286:   /* this is inefficient, but otherwise we must do either
    287:      1) save garray until the first actual scatter when the vector is known or
    288:      2) have another way of generating a scatter context without a vector.*/
    289:   VecCreateMPI(mat->comm,mat->n,mat->N,&gvec);

    291:   /* gnerate the scatter context */
    292:   VecScatterCreate(gvec,from,baij->lvec,to,&baij->Mvctx);

    294:   /*
    295:       Post the receives for the first matrix vector product. We sync-chronize after
    296:     this on the chance that the user immediately calls MatMult() after assemblying
    297:     the matrix.
    298:   */
    299:   VecScatterPostRecvs(gvec,baij->lvec,INSERT_VALUES,SCATTER_FORWARD,baij->Mvctx);
    300:   MPI_Barrier(mat->comm);

    302:   PetscLogObjectParent(mat,baij->Mvctx);
    303:   PetscLogObjectParent(mat,baij->lvec);
    304:   PetscLogObjectParent(mat,from);
    305:   PetscLogObjectParent(mat,to);
    306:   baij->garray = garray;
    307:   PetscLogObjectMemory(mat,(ec+1)*sizeof(PetscInt));
    308:   ISDestroy(from);
    309:   ISDestroy(to);
    310:   VecDestroy(gvec);
    311:   return(0);
    312: }

    315: /*
    316:      Takes the local part of an already assembled MPIBAIJ matrix
    317:    and disassembles it. This is to allow new nonzeros into the matrix
    318:    that require more communication in the matrix vector multiply.
    319:    Thus certain data-structures must be rebuilt.

    321:    Kind of slow! But that's what application programmers get when
    322:    they are sloppy.
    323: */
    326: PetscErrorCode DisAssemble_MPISBAIJ(Mat A)
    327: {
    328:   Mat_MPISBAIJ   *baij = (Mat_MPISBAIJ*)A->data;
    329:   Mat           B = baij->B,Bnew;
    330:   Mat_SeqBAIJ   *Bbaij = (Mat_SeqBAIJ*)B->data;
    332:   PetscInt i,j,mbs=Bbaij->mbs,n = A->N,col,*garray=baij->garray;
    333:   PetscInt           k,bs=A->bs,bs2=baij->bs2,*rvals,*nz,ec,m=A->m;
    334:   MatScalar     *a = Bbaij->a;
    335:   PetscScalar   *atmp;
    336: #if defined(PETSC_USE_MAT_SINGLE)
    337:   PetscInt           l;
    338: #endif

    341: #if defined(PETSC_USE_MAT_SINGLE)
    342:   PetscMalloc(A->bs*sizeof(PetscScalar),&atmp);
    343: #endif
    344:   /* free stuff related to matrix-vec multiply */
    345:   VecGetSize(baij->lvec,&ec); /* needed for PetscLogObjectMemory below */
    346:   VecDestroy(baij->lvec); baij->lvec = 0;
    347:   VecScatterDestroy(baij->Mvctx); baij->Mvctx = 0;
    348:   if (baij->colmap) {
    349: #if defined (PETSC_USE_CTABLE)
    350:     PetscTableDelete(baij->colmap); baij->colmap = 0;
    351: #else
    352:     PetscFree(baij->colmap);
    353:     baij->colmap = 0;
    354:     PetscLogObjectMemory(A,-Bbaij->nbs*sizeof(PetscInt));
    355: #endif
    356:   }

    358:   /* make sure that B is assembled so we can access its values */
    359:   MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
    360:   MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);

    362:   /* invent new B and copy stuff over */
    363:   PetscMalloc(mbs*sizeof(PetscInt),&nz);
    364:   for (i=0; i<mbs; i++) {
    365:     nz[i] = Bbaij->i[i+1]-Bbaij->i[i];
    366:   }
    367:   MatCreate(PETSC_COMM_SELF,&Bnew);
    368:   MatSetSizes(Bnew,m,n,m,n);
    369:   MatSetType(Bnew,B->type_name);
    370:   MatSeqBAIJSetPreallocation(Bnew,B->bs,0,nz);
    371:   PetscFree(nz);
    372:
    373:   PetscMalloc(bs*sizeof(PetscInt),&rvals);
    374:   for (i=0; i<mbs; i++) {
    375:     rvals[0] = bs*i;
    376:     for (j=1; j<bs; j++) { rvals[j] = rvals[j-1] + 1; }
    377:     for (j=Bbaij->i[i]; j<Bbaij->i[i+1]; j++) {
    378:       col = garray[Bbaij->j[j]]*bs;
    379:       for (k=0; k<bs; k++) {
    380: #if defined(PETSC_USE_MAT_SINGLE)
    381:         for (l=0; l<bs; l++) atmp[l] = a[j*bs2+l];
    382: #else
    383:         atmp = a+j*bs2 + k*bs;
    384: #endif
    385:         MatSetValues_SeqSBAIJ(Bnew,bs,rvals,1,&col,atmp,B->insertmode);
    386:         col++;
    387:       }
    388:     }
    389:   }
    390: #if defined(PETSC_USE_MAT_SINGLE)
    391:   PetscFree(atmp);
    392: #endif
    393:   PetscFree(baij->garray);
    394:   baij->garray = 0;
    395:   PetscFree(rvals);
    396:   PetscLogObjectMemory(A,-ec*sizeof(PetscInt));
    397:   MatDestroy(B);
    398:   PetscLogObjectParent(A,Bnew);
    399:   baij->B = Bnew;
    400:   A->was_assembled = PETSC_FALSE;
    401:   return(0);
    402: }