Date: 2016-07-24T16:55:37+00:00

Actual source code: mmbaij.c
petsc-3.7.3 2016-07-24
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      2: /*
      3:    Support for the parallel BAIJ matrix vector multiply
      4: */
      5: #include <../src/mat/impls/baij/mpi/mpibaij.h>
      6: #include <petsc/private/isimpl.h>    /* needed because accesses data structure of ISLocalToGlobalMapping directly */

      8: extern PetscErrorCode MatSetValuesBlocked_SeqBAIJ(Mat,PetscInt,const PetscInt[],PetscInt,const PetscInt[],const PetscScalar[],InsertMode);

     12: PetscErrorCode MatSetUpMultiply_MPIBAIJ(Mat mat)
     13: {
     14:   Mat_MPIBAIJ    *baij = (Mat_MPIBAIJ*)mat->data;
     15:   Mat_SeqBAIJ    *B    = (Mat_SeqBAIJ*)(baij->B->data);
     17:   PetscInt       i,j,*aj = B->j,ec = 0,*garray;
     18:   PetscInt       bs = mat->rmap->bs,*stmp;
     19:   IS             from,to;
     20:   Vec            gvec;
     21: #if defined(PETSC_USE_CTABLE)
     22:   PetscTable         gid1_lid1;
     23:   PetscTablePosition tpos;
     24:   PetscInt           gid,lid;
     25: #else
     26:   PetscInt Nbs = baij->Nbs,*indices;
     27: #endif

     30: #if defined(PETSC_USE_CTABLE)
     31:   /* use a table - Mark Adams */
     32:   PetscTableCreate(B->mbs,baij->Nbs+1,&gid1_lid1);
     33:   for (i=0; i<B->mbs; i++) {
     34:     for (j=0; j<B->ilen[i]; j++) {
     35:       PetscInt data,gid1 = aj[B->i[i]+j] + 1;
     36:       PetscTableFind(gid1_lid1,gid1,&data);
     37:       if (!data) {
     38:         /* one based table */
     39:         PetscTableAdd(gid1_lid1,gid1,++ec,INSERT_VALUES);
     40:       }
     41:     }
     42:   }
     43:   /* form array of columns we need */
     44:   PetscMalloc1(ec+1,&garray);
     45:   PetscTableGetHeadPosition(gid1_lid1,&tpos);
     46:   while (tpos) {
     47:     PetscTableGetNext(gid1_lid1,&tpos,&gid,&lid);
     48:     gid--; lid--;
     49:     garray[lid] = gid;
     50:   }
     51:   PetscSortInt(ec,garray);
     52:   PetscTableRemoveAll(gid1_lid1);
     53:   for (i=0; i<ec; i++) {
     54:     PetscTableAdd(gid1_lid1,garray[i]+1,i+1,INSERT_VALUES);
     55:   }
     56:   /* compact out the extra columns in B */
     57:   for (i=0; i<B->mbs; i++) {
     58:     for (j=0; j<B->ilen[i]; j++) {
     59:       PetscInt gid1 = aj[B->i[i] + j] + 1;
     60:       PetscTableFind(gid1_lid1,gid1,&lid);
     61:       lid--;
     62:       aj[B->i[i]+j] = lid;
     63:     }
     64:   }
     65:   B->nbs           = ec;
     66:   baij->B->cmap->n = baij->B->cmap->N = ec*mat->rmap->bs;

     68:   PetscLayoutSetUp((baij->B->cmap));
     69:   PetscTableDestroy(&gid1_lid1);
     70: #else
     71:   /* Make an array as long as the number of columns */
     72:   /* mark those columns that are in baij->B */
     73:   PetscCalloc1(Nbs+1,&indices);
     74:   for (i=0; i<B->mbs; i++) {
     75:     for (j=0; j<B->ilen[i]; j++) {
     76:       if (!indices[aj[B->i[i] + j]]) ec++;
     77:       indices[aj[B->i[i] + j]] = 1;
     78:     }
     79:   }

     81:   /* form array of columns we need */
     82:   PetscMalloc1(ec+1,&garray);
     83:   ec   = 0;
     84:   for (i=0; i<Nbs; i++) {
     85:     if (indices[i]) {
     86:       garray[ec++] = i;
     87:     }
     88:   }

     90:   /* make indices now point into garray */
     91:   for (i=0; i<ec; i++) {
     92:     indices[garray[i]] = i;
     93:   }

     95:   /* compact out the extra columns in B */
     96:   for (i=0; i<B->mbs; i++) {
     97:     for (j=0; j<B->ilen[i]; j++) {
     98:       aj[B->i[i] + j] = indices[aj[B->i[i] + j]];
     99:     }
    100:   }
    101:   B->nbs           = ec;
    102:   baij->B->cmap->n = baij->B->cmap->N  = ec*mat->rmap->bs;

    104:   PetscLayoutSetUp((baij->B->cmap));
    105:   PetscFree(indices);
    106: #endif

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

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

    114:   PetscMalloc1(ec+1,&stmp);
    115:   for (i=0; i<ec; i++) stmp[i] = i;
    116:   ISCreateBlock(PETSC_COMM_SELF,bs,ec,stmp,PETSC_OWN_POINTER,&to);

    118:   /* create temporary global vector to generate scatter context */
    119:   VecCreateMPIWithArray(PetscObjectComm((PetscObject)mat),1,mat->cmap->n,mat->cmap->N,NULL,&gvec);

    121:   VecScatterCreate(gvec,from,baij->lvec,to,&baij->Mvctx);

    123:   PetscLogObjectParent((PetscObject)mat,(PetscObject)baij->Mvctx);
    124:   PetscLogObjectParent((PetscObject)mat,(PetscObject)baij->lvec);
    125:   PetscLogObjectParent((PetscObject)mat,(PetscObject)from);
    126:   PetscLogObjectParent((PetscObject)mat,(PetscObject)to);

    128:   baij->garray = garray;

    130:   PetscLogObjectMemory((PetscObject)mat,(ec+1)*sizeof(PetscInt));
    131:   ISDestroy(&from);
    132:   ISDestroy(&to);
    133:   VecDestroy(&gvec);
    134:   return(0);
    135: }

    137: /*
    138:      Takes the local part of an already assembled MPIBAIJ matrix
    139:    and disassembles it. This is to allow new nonzeros into the matrix
    140:    that require more communication in the matrix vector multiply.
    141:    Thus certain data-structures must be rebuilt.

    143:    Kind of slow! But that's what application programmers get when
    144:    they are sloppy.
    145: */
    148: PetscErrorCode MatDisAssemble_MPIBAIJ(Mat A)
    149: {
    150:   Mat_MPIBAIJ    *baij  = (Mat_MPIBAIJ*)A->data;
    151:   Mat            B      = baij->B,Bnew;
    152:   Mat_SeqBAIJ    *Bbaij = (Mat_SeqBAIJ*)B->data;
    154:   PetscInt       i,j,mbs=Bbaij->mbs,n = A->cmap->N,col,*garray=baij->garray;
    155:   PetscInt       bs2 = baij->bs2,*nz,ec,m = A->rmap->n;
    156:   MatScalar      *a  = Bbaij->a;
    157:   MatScalar      *atmp;

    161:   /* free stuff related to matrix-vec multiply */
    162:   VecGetSize(baij->lvec,&ec); /* needed for PetscLogObjectMemory below */
    163:   VecDestroy(&baij->lvec); baij->lvec = 0;
    164:   VecScatterDestroy(&baij->Mvctx); baij->Mvctx = 0;
    165:   if (baij->colmap) {
    166: #if defined(PETSC_USE_CTABLE)
    167:     PetscTableDestroy(&baij->colmap);
    168: #else
    169:     PetscFree(baij->colmap);
    170:     PetscLogObjectMemory((PetscObject)A,-Bbaij->nbs*sizeof(PetscInt));
    171: #endif
    172:   }

    174:   /* make sure that B is assembled so we can access its values */
    175:   MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);
    176:   MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);

    178:   /* invent new B and copy stuff over */
    179:   PetscMalloc1(mbs,&nz);
    180:   for (i=0; i<mbs; i++) {
    181:     nz[i] = Bbaij->i[i+1]-Bbaij->i[i];
    182:   }
    183:   MatCreate(PetscObjectComm((PetscObject)B),&Bnew);
    184:   MatSetSizes(Bnew,m,n,m,n);
    185:   MatSetType(Bnew,((PetscObject)B)->type_name);
    186:   MatSeqBAIJSetPreallocation(Bnew,B->rmap->bs,0,nz);

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

    190:   MatSetOption(Bnew,MAT_ROW_ORIENTED,PETSC_FALSE);
    191:   /*
    192:    Ensure that B's nonzerostate is monotonically increasing.
    193:    Or should this follow the MatSetValuesBlocked() loop to preserve B's nonzerstate across a MatDisAssemble() call?
    194:    */
    195:   Bnew->nonzerostate = B->nonzerostate;

    197:   for (i=0; i<mbs; i++) {
    198:     for (j=Bbaij->i[i]; j<Bbaij->i[i+1]; j++) {
    199:       col  = garray[Bbaij->j[j]];
    200:       atmp = a + j*bs2;
    201:       MatSetValuesBlocked_SeqBAIJ(Bnew,1,&i,1,&col,atmp,B->insertmode);
    202:     }
    203:   }
    204:   MatSetOption(Bnew,MAT_ROW_ORIENTED,PETSC_TRUE);

    206:   PetscFree(nz);
    207:   PetscFree(baij->garray);
    208:   PetscLogObjectMemory((PetscObject)A,-ec*sizeof(PetscInt));
    209:   MatDestroy(&B);
    210:   PetscLogObjectParent((PetscObject)A,(PetscObject)Bnew);

    212:   baij->B          = Bnew;
    213:   A->was_assembled = PETSC_FALSE;
    214:   A->assembled     = PETSC_FALSE;
    215:   return(0);
    216: }

    218: /*      ugly stuff added for Glenn someday we should fix this up */

    220: static PetscInt *uglyrmapd = 0,*uglyrmapo = 0;  /* mapping from the local ordering to the "diagonal" and "off-diagonal" parts of the local matrix */
    221: static Vec      uglydd     = 0,uglyoo     = 0;  /* work vectors used to scale the two parts of the local matrix */

    226: PetscErrorCode MatMPIBAIJDiagonalScaleLocalSetUp(Mat inA,Vec scale)
    227: {
    228:   Mat_MPIBAIJ    *ina = (Mat_MPIBAIJ*) inA->data; /*access private part of matrix */
    229:   Mat_SeqBAIJ    *B   = (Mat_SeqBAIJ*)ina->B->data;
    231:   PetscInt       bs = inA->rmap->bs,i,n,nt,j,cstart,cend,no,*garray = ina->garray,*lindices;
    232:   PetscInt       *r_rmapd,*r_rmapo;

    235:   MatGetOwnershipRange(inA,&cstart,&cend);
    236:   MatGetSize(ina->A,NULL,&n);
    237:   PetscCalloc1(inA->rmap->mapping->n+1,&r_rmapd);
    238:   nt   = 0;
    239:   for (i=0; i<inA->rmap->mapping->n; i++) {
    240:     if (inA->rmap->mapping->indices[i]*bs >= cstart && inA->rmap->mapping->indices[i]*bs < cend) {
    241:       nt++;
    242:       r_rmapd[i] = inA->rmap->mapping->indices[i] + 1;
    243:     }
    244:   }
    245:   if (nt*bs != n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Hmm nt*bs %D n %D",nt*bs,n);
    246:   PetscMalloc1(n+1,&uglyrmapd);
    247:   for (i=0; i<inA->rmap->mapping->n; i++) {
    248:     if (r_rmapd[i]) {
    249:       for (j=0; j<bs; j++) {
    250:         uglyrmapd[(r_rmapd[i]-1)*bs+j-cstart] = i*bs + j;
    251:       }
    252:     }
    253:   }
    254:   PetscFree(r_rmapd);
    255:   VecCreateSeq(PETSC_COMM_SELF,n,&uglydd);

    257:   PetscCalloc1(ina->Nbs+1,&lindices);
    258:   for (i=0; i<B->nbs; i++) {
    259:     lindices[garray[i]] = i+1;
    260:   }
    261:   no   = inA->rmap->mapping->n - nt;
    262:   PetscCalloc1(inA->rmap->mapping->n+1,&r_rmapo);
    263:   nt   = 0;
    264:   for (i=0; i<inA->rmap->mapping->n; i++) {
    265:     if (lindices[inA->rmap->mapping->indices[i]]) {
    266:       nt++;
    267:       r_rmapo[i] = lindices[inA->rmap->mapping->indices[i]];
    268:     }
    269:   }
    270:   if (nt > no) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Hmm nt %D no %D",nt,n);
    271:   PetscFree(lindices);
    272:   PetscMalloc1(nt*bs+1,&uglyrmapo);
    273:   for (i=0; i<inA->rmap->mapping->n; i++) {
    274:     if (r_rmapo[i]) {
    275:       for (j=0; j<bs; j++) {
    276:         uglyrmapo[(r_rmapo[i]-1)*bs+j] = i*bs + j;
    277:       }
    278:     }
    279:   }
    280:   PetscFree(r_rmapo);
    281:   VecCreateSeq(PETSC_COMM_SELF,nt*bs,&uglyoo);
    282:   return(0);
    283: }

    287: PetscErrorCode  MatMPIBAIJDiagonalScaleLocal(Mat A,Vec scale)
    288: {
    289:   /* This routine should really be abandoned as it duplicates MatDiagonalScaleLocal */

    293:   PetscTryMethod(A,"MatDiagonalScaleLocal_C",(Mat,Vec),(A,scale));
    294:   return(0);
    295: }

    299: PetscErrorCode  MatDiagonalScaleLocal_MPIBAIJ(Mat A,Vec scale)
    300: {
    301:   Mat_MPIBAIJ    *a = (Mat_MPIBAIJ*) A->data; /*access private part of matrix */
    303:   PetscInt       n,i;
    304:   PetscScalar    *d,*o,*s;

    307:   if (!uglyrmapd) {
    308:     MatMPIBAIJDiagonalScaleLocalSetUp(A,scale);
    309:   }

    311:   VecGetArray(scale,&s);

    313:   VecGetLocalSize(uglydd,&n);
    314:   VecGetArray(uglydd,&d);
    315:   for (i=0; i<n; i++) {
    316:     d[i] = s[uglyrmapd[i]]; /* copy "diagonal" (true local) portion of scale into dd vector */
    317:   }
    318:   VecRestoreArray(uglydd,&d);
    319:   /* column scale "diagonal" portion of local matrix */
    320:   MatDiagonalScale(a->A,NULL,uglydd);

    322:   VecGetLocalSize(uglyoo,&n);
    323:   VecGetArray(uglyoo,&o);
    324:   for (i=0; i<n; i++) {
    325:     o[i] = s[uglyrmapo[i]]; /* copy "off-diagonal" portion of scale into oo vector */
    326:   }
    327:   VecRestoreArray(scale,&s);
    328:   VecRestoreArray(uglyoo,&o);
    329:   /* column scale "off-diagonal" portion of local matrix */
    330:   MatDiagonalScale(a->B,NULL,uglyoo);
    331:   return(0);
    332: }