Date: 2015-10-02T22:05:18+00:00

Actual source code: mmdense.c
petsc-3.6.2 2015-10-02
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      2: /*
      3:    Support for the parallel dense matrix vector multiply
      4: */
      5: #include <../src/mat/impls/dense/mpi/mpidense.h>
      6: #include <petscblaslapack.h>

     10: PetscErrorCode MatSetUpMultiply_MPIDense(Mat mat)
     11: {
     12:   Mat_MPIDense   *mdn = (Mat_MPIDense*)mat->data;
     14:   IS             from,to;
     15:   Vec            gvec;

     18:   /* Create local vector that is used to scatter into */
     19:   VecCreateSeq(PETSC_COMM_SELF,mat->cmap->N,&mdn->lvec);

     21:   /* Create temporary index set for building scatter gather */
     22:   ISCreateStride(PetscObjectComm((PetscObject)mat),mat->cmap->N,0,1,&from);
     23:   ISCreateStride(PETSC_COMM_SELF,mat->cmap->N,0,1,&to);

     25:   /* Create temporary global vector to generate scatter context */
     26:   /* n    = mdn->cowners[mdn->rank+1] - mdn->cowners[mdn->rank]; */

     28:   VecCreateMPIWithArray(PetscObjectComm((PetscObject)mat),1,mdn->nvec,mat->cmap->N,NULL,&gvec);

     30:   /* Generate the scatter context */
     31:   VecScatterCreate(gvec,from,mdn->lvec,to,&mdn->Mvctx);
     32:   PetscLogObjectParent((PetscObject)mat,(PetscObject)mdn->Mvctx);
     33:   PetscLogObjectParent((PetscObject)mat,(PetscObject)mdn->lvec);
     34:   PetscLogObjectParent((PetscObject)mat,(PetscObject)from);
     35:   PetscLogObjectParent((PetscObject)mat,(PetscObject)to);
     36:   PetscLogObjectParent((PetscObject)mat,(PetscObject)gvec);

     38:   ISDestroy(&to);
     39:   ISDestroy(&from);
     40:   VecDestroy(&gvec);
     41:   return(0);
     42: }

     44: extern PetscErrorCode MatGetSubMatrices_MPIDense_Local(Mat,PetscInt,const IS[],const IS[],MatReuse,Mat*);
     47: PetscErrorCode MatGetSubMatrices_MPIDense(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[])
     48: {
     50:   PetscInt       nmax,nstages_local,nstages,i,pos,max_no;

     53:   /* Allocate memory to hold all the submatrices */
     54:   if (scall != MAT_REUSE_MATRIX) {
     55:     PetscMalloc1(ismax+1,submat);
     56:   }
     57:   /* Determine the number of stages through which submatrices are done */
     58:   nmax = 20*1000000 / (C->cmap->N * sizeof(PetscInt));
     59:   if (!nmax) nmax = 1;
     60:   nstages_local = ismax/nmax + ((ismax % nmax) ? 1 : 0);

     62:   /* Make sure every processor loops through the nstages */
     63:   MPI_Allreduce(&nstages_local,&nstages,1,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)C));

     66:   for (i=0,pos=0; i<nstages; i++) {
     67:     if (pos+nmax <= ismax) max_no = nmax;
     68:     else if (pos == ismax) max_no = 0;
     69:     else                   max_no = ismax-pos;
     70:     MatGetSubMatrices_MPIDense_Local(C,max_no,isrow+pos,iscol+pos,scall,*submat+pos);
     71:     pos += max_no;
     72:   }
     73:   return(0);
     74: }
     75: /* -------------------------------------------------------------------------*/
     78: PetscErrorCode MatGetSubMatrices_MPIDense_Local(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submats)
     79: {
     80:   Mat_MPIDense   *c = (Mat_MPIDense*)C->data;
     81:   Mat            A  = c->A;
     82:   Mat_SeqDense   *a = (Mat_SeqDense*)A->data,*mat;
     84:   PetscMPIInt    rank,size,tag0,tag1,idex,end,i;
     85:   PetscInt       N = C->cmap->N,rstart = C->rmap->rstart,count;
     86:   const PetscInt **irow,**icol,*irow_i;
     87:   PetscInt       *nrow,*ncol,*w1,*w3,*w4,*rtable,start;
     88:   PetscInt       **sbuf1,m,j,k,l,ct1,**rbuf1,row,proc;
     89:   PetscInt       nrqs,msz,**ptr,*ctr,*pa,*tmp,bsz,nrqr;
     90:   PetscInt       is_no,jmax,**rmap,*rmap_i;
     91:   PetscInt       ctr_j,*sbuf1_j,*rbuf1_i;
     92:   MPI_Request    *s_waits1,*r_waits1,*s_waits2,*r_waits2;
     93:   MPI_Status     *r_status1,*r_status2,*s_status1,*s_status2;
     94:   MPI_Comm       comm;
     95:   PetscScalar    **rbuf2,**sbuf2;
     96:   PetscBool      sorted;

     99:   PetscObjectGetComm((PetscObject)C,&comm);
    100:   tag0 = ((PetscObject)C)->tag;
    101:   size = c->size;
    102:   rank = c->rank;
    103:   m    = C->rmap->N;

    105:   /* Get some new tags to keep the communication clean */
    106:   PetscObjectGetNewTag((PetscObject)C,&tag1);

    108:   /* Check if the col indices are sorted */
    109:   for (i=0; i<ismax; i++) {
    110:     ISSorted(isrow[i],&sorted);
    111:     if (!sorted) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"ISrow is not sorted");
    112:     ISSorted(iscol[i],&sorted);
    113:     if (!sorted) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"IScol is not sorted");
    114:   }

    116:   PetscMalloc5(ismax,&irow,ismax,&icol,ismax,&nrow,ismax,&ncol,m,&rtable);
    117:   for (i=0; i<ismax; i++) {
    118:     ISGetIndices(isrow[i],&irow[i]);
    119:     ISGetIndices(iscol[i],&icol[i]);
    120:     ISGetLocalSize(isrow[i],&nrow[i]);
    121:     ISGetLocalSize(iscol[i],&ncol[i]);
    122:   }

    124:   /* Create hash table for the mapping :row -> proc*/
    125:   for (i=0,j=0; i<size; i++) {
    126:     jmax = C->rmap->range[i+1];
    127:     for (; j<jmax; j++) rtable[j] = i;
    128:   }

    130:   /* evaluate communication - mesg to who,length of mesg, and buffer space
    131:      required. Based on this, buffers are allocated, and data copied into them*/
    132:   PetscMalloc3(2*size,&w1,size,&w3,size,&w4);
    133:   PetscMemzero(w1,size*2*sizeof(PetscInt)); /* initialize work vector*/
    134:   PetscMemzero(w3,size*sizeof(PetscInt)); /* initialize work vector*/
    135:   for (i=0; i<ismax; i++) {
    136:     PetscMemzero(w4,size*sizeof(PetscInt)); /* initialize work vector*/
    137:     jmax   = nrow[i];
    138:     irow_i = irow[i];
    139:     for (j=0; j<jmax; j++) {
    140:       row  = irow_i[j];
    141:       proc = rtable[row];
    142:       w4[proc]++;
    143:     }
    144:     for (j=0; j<size; j++) {
    145:       if (w4[j]) { w1[2*j] += w4[j];  w3[j]++;}
    146:     }
    147:   }

    149:   nrqs       = 0;              /* no of outgoing messages */
    150:   msz        = 0;              /* total mesg length (for all procs) */
    151:   w1[2*rank] = 0;              /* no mesg sent to self */
    152:   w3[rank]   = 0;
    153:   for (i=0; i<size; i++) {
    154:     if (w1[2*i])  { w1[2*i+1] = 1; nrqs++;} /* there exists a message to proc i */
    155:   }
    156:   PetscMalloc1(nrqs+1,&pa); /*(proc -array)*/
    157:   for (i=0,j=0; i<size; i++) {
    158:     if (w1[2*i]) { pa[j] = i; j++; }
    159:   }

    161:   /* Each message would have a header = 1 + 2*(no of IS) + data */
    162:   for (i=0; i<nrqs; i++) {
    163:     j        = pa[i];
    164:     w1[2*j] += w1[2*j+1] + 2* w3[j];
    165:     msz     += w1[2*j];
    166:   }
    167:   /* Do a global reduction to determine how many messages to expect*/
    168:   PetscMaxSum(comm,w1,&bsz,&nrqr);

    170:   /* Allocate memory for recv buffers . Make sure rbuf1[0] exists by adding 1 to the buffer length */
    171:   PetscMalloc1(nrqr+1,&rbuf1);
    172:   PetscMalloc1(nrqr*bsz,&rbuf1[0]);
    173:   for (i=1; i<nrqr; ++i) rbuf1[i] = rbuf1[i-1] + bsz;

    175:   /* Post the receives */
    176:   PetscMalloc1(nrqr+1,&r_waits1);
    177:   for (i=0; i<nrqr; ++i) {
    178:     MPI_Irecv(rbuf1[i],bsz,MPIU_INT,MPI_ANY_SOURCE,tag0,comm,r_waits1+i);
    179:   }

    181:   /* Allocate Memory for outgoing messages */
    182:   PetscMalloc4(size,&sbuf1,size,&ptr,2*msz,&tmp,size,&ctr);
    183:   PetscMemzero(sbuf1,size*sizeof(PetscInt*));
    184:   PetscMemzero(ptr,size*sizeof(PetscInt*));
    185:   {
    186:     PetscInt *iptr = tmp,ict = 0;
    187:     for (i=0; i<nrqs; i++) {
    188:       j        = pa[i];
    189:       iptr    += ict;
    190:       sbuf1[j] = iptr;
    191:       ict      = w1[2*j];
    192:     }
    193:   }

    195:   /* Form the outgoing messages */
    196:   /* Initialize the header space */
    197:   for (i=0; i<nrqs; i++) {
    198:     j           = pa[i];
    199:     sbuf1[j][0] = 0;
    200:     PetscMemzero(sbuf1[j]+1,2*w3[j]*sizeof(PetscInt));
    201:     ptr[j]      = sbuf1[j] + 2*w3[j] + 1;
    202:   }

    204:   /* Parse the isrow and copy data into outbuf */
    205:   for (i=0; i<ismax; i++) {
    206:     PetscMemzero(ctr,size*sizeof(PetscInt));
    207:     irow_i = irow[i];
    208:     jmax   = nrow[i];
    209:     for (j=0; j<jmax; j++) {  /* parse the indices of each IS */
    210:       row  = irow_i[j];
    211:       proc = rtable[row];
    212:       if (proc != rank) { /* copy to the outgoing buf*/
    213:         ctr[proc]++;
    214:         *ptr[proc] = row;
    215:         ptr[proc]++;
    216:       }
    217:     }
    218:     /* Update the headers for the current IS */
    219:     for (j=0; j<size; j++) { /* Can Optimise this loop too */
    220:       if ((ctr_j = ctr[j])) {
    221:         sbuf1_j        = sbuf1[j];
    222:         k              = ++sbuf1_j[0];
    223:         sbuf1_j[2*k]   = ctr_j;
    224:         sbuf1_j[2*k-1] = i;
    225:       }
    226:     }
    227:   }

    229:   /*  Now  post the sends */
    230:   PetscMalloc1(nrqs+1,&s_waits1);
    231:   for (i=0; i<nrqs; ++i) {
    232:     j    = pa[i];
    233:     MPI_Isend(sbuf1[j],w1[2*j],MPIU_INT,j,tag0,comm,s_waits1+i);
    234:   }

    236:   /* Post recieves to capture the row_data from other procs */
    237:   PetscMalloc1(nrqs+1,&r_waits2);
    238:   PetscMalloc1(nrqs+1,&rbuf2);
    239:   for (i=0; i<nrqs; i++) {
    240:     j     = pa[i];
    241:     count = (w1[2*j] - (2*sbuf1[j][0] + 1))*N;
    242:     PetscMalloc1(count+1,&rbuf2[i]);
    243:     MPI_Irecv(rbuf2[i],count,MPIU_SCALAR,j,tag1,comm,r_waits2+i);
    244:   }

    246:   /* Receive messages(row_nos) and then, pack and send off the rowvalues
    247:      to the correct processors */

    249:   PetscMalloc1(nrqr+1,&s_waits2);
    250:   PetscMalloc1(nrqr+1,&r_status1);
    251:   PetscMalloc1(nrqr+1,&sbuf2);

    253:   {
    254:     PetscScalar *sbuf2_i,*v_start;
    255:     PetscInt    s_proc;
    256:     for (i=0; i<nrqr; ++i) {
    257:       MPI_Waitany(nrqr,r_waits1,&idex,r_status1+i);
    258:       s_proc  = r_status1[i].MPI_SOURCE;         /* send processor */
    259:       rbuf1_i = rbuf1[idex];         /* Actual message from s_proc */
    260:       /* no of rows = end - start; since start is array idex[], 0idex, whel end
    261:          is length of the buffer - which is 1idex */
    262:       start = 2*rbuf1_i[0] + 1;
    263:       MPI_Get_count(r_status1+i,MPIU_INT,&end);
    264:       /* allocate memory sufficinet to hold all the row values */
    265:       PetscMalloc1((end-start)*N,&sbuf2[idex]);
    266:       sbuf2_i = sbuf2[idex];
    267:       /* Now pack the data */
    268:       for (j=start; j<end; j++) {
    269:         row     = rbuf1_i[j] - rstart;
    270:         v_start = a->v + row;
    271:         for (k=0; k<N; k++) {
    272:           sbuf2_i[0] = v_start[0];
    273:           sbuf2_i++;
    274:           v_start += C->rmap->n;
    275:         }
    276:       }
    277:       /* Now send off the data */
    278:       MPI_Isend(sbuf2[idex],(end-start)*N,MPIU_SCALAR,s_proc,tag1,comm,s_waits2+i);
    279:     }
    280:   }
    281:   /* End Send-Recv of IS + row_numbers */
    282:   PetscFree(r_status1);
    283:   PetscFree(r_waits1);
    284:   PetscMalloc1(nrqs+1,&s_status1);
    285:   if (nrqs) {MPI_Waitall(nrqs,s_waits1,s_status1);}
    286:   PetscFree(s_status1);
    287:   PetscFree(s_waits1);

    289:   /* Create the submatrices */
    290:   if (scall == MAT_REUSE_MATRIX) {
    291:     for (i=0; i<ismax; i++) {
    292:       mat = (Mat_SeqDense*)(submats[i]->data);
    293:       if ((submats[i]->rmap->n != nrow[i]) || (submats[i]->cmap->n != ncol[i])) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Cannot reuse matrix. wrong size");
    294:       PetscMemzero(mat->v,submats[i]->rmap->n*submats[i]->cmap->n*sizeof(PetscScalar));

    296:       submats[i]->factortype = C->factortype;
    297:     }
    298:   } else {
    299:     for (i=0; i<ismax; i++) {
    300:       MatCreate(PETSC_COMM_SELF,submats+i);
    301:       MatSetSizes(submats[i],nrow[i],ncol[i],nrow[i],ncol[i]);
    302:       MatSetType(submats[i],((PetscObject)A)->type_name);
    303:       MatSeqDenseSetPreallocation(submats[i],NULL);
    304:     }
    305:   }

    307:   /* Assemble the matrices */
    308:   {
    309:     PetscInt    col;
    310:     PetscScalar *imat_v,*mat_v,*imat_vi,*mat_vi;

    312:     for (i=0; i<ismax; i++) {
    313:       mat    = (Mat_SeqDense*)submats[i]->data;
    314:       mat_v  = a->v;
    315:       imat_v = mat->v;
    316:       irow_i = irow[i];
    317:       m      = nrow[i];
    318:       for (j=0; j<m; j++) {
    319:         row  = irow_i[j];
    320:         proc = rtable[row];
    321:         if (proc == rank) {
    322:           row     = row - rstart;
    323:           mat_vi  = mat_v + row;
    324:           imat_vi = imat_v + j;
    325:           for (k=0; k<ncol[i]; k++) {
    326:             col          = icol[i][k];
    327:             imat_vi[k*m] = mat_vi[col*C->rmap->n];
    328:           }
    329:         }
    330:       }
    331:     }
    332:   }

    334:   /* Create row map-> This maps c->row to submat->row for each submat*/
    335:   /* this is a very expensive operation wrt memory usage */
    336:   PetscMalloc1(ismax,&rmap);
    337:   PetscMalloc1(ismax*C->rmap->N,&rmap[0]);
    338:   PetscMemzero(rmap[0],ismax*C->rmap->N*sizeof(PetscInt));
    339:   for (i=1; i<ismax; i++) rmap[i] = rmap[i-1] + C->rmap->N;
    340:   for (i=0; i<ismax; i++) {
    341:     rmap_i = rmap[i];
    342:     irow_i = irow[i];
    343:     jmax   = nrow[i];
    344:     for (j=0; j<jmax; j++) {
    345:       rmap_i[irow_i[j]] = j;
    346:     }
    347:   }

    349:   /* Now Receive the row_values and assemble the rest of the matrix */
    350:   PetscMalloc1(nrqs+1,&r_status2);
    351:   {
    352:     PetscInt    is_max,tmp1,col,*sbuf1_i,is_sz;
    353:     PetscScalar *rbuf2_i,*imat_v,*imat_vi;

    355:     for (tmp1=0; tmp1<nrqs; tmp1++) { /* For each message */
    356:       MPI_Waitany(nrqs,r_waits2,&i,r_status2+tmp1);
    357:       /* Now dig out the corresponding sbuf1, which contains the IS data_structure */
    358:       sbuf1_i = sbuf1[pa[i]];
    359:       is_max  = sbuf1_i[0];
    360:       ct1     = 2*is_max+1;
    361:       rbuf2_i = rbuf2[i];
    362:       for (j=1; j<=is_max; j++) { /* For each IS belonging to the message */
    363:         is_no  = sbuf1_i[2*j-1];
    364:         is_sz  = sbuf1_i[2*j];
    365:         mat    = (Mat_SeqDense*)submats[is_no]->data;
    366:         imat_v = mat->v;
    367:         rmap_i = rmap[is_no];
    368:         m      = nrow[is_no];
    369:         for (k=0; k<is_sz; k++,rbuf2_i+=N) {  /* For each row */
    370:           row     = sbuf1_i[ct1]; ct1++;
    371:           row     = rmap_i[row];
    372:           imat_vi = imat_v + row;
    373:           for (l=0; l<ncol[is_no]; l++) { /* For each col */
    374:             col          = icol[is_no][l];
    375:             imat_vi[l*m] = rbuf2_i[col];
    376:           }
    377:         }
    378:       }
    379:     }
    380:   }
    381:   /* End Send-Recv of row_values */
    382:   PetscFree(r_status2);
    383:   PetscFree(r_waits2);
    384:   PetscMalloc1(nrqr+1,&s_status2);
    385:   if (nrqr) {MPI_Waitall(nrqr,s_waits2,s_status2);}
    386:   PetscFree(s_status2);
    387:   PetscFree(s_waits2);

    389:   /* Restore the indices */
    390:   for (i=0; i<ismax; i++) {
    391:     ISRestoreIndices(isrow[i],irow+i);
    392:     ISRestoreIndices(iscol[i],icol+i);
    393:   }

    395:   /* Destroy allocated memory */
    396:   PetscFree5(irow,icol,nrow,ncol,rtable);
    397:   PetscFree3(w1,w3,w4);
    398:   PetscFree(pa);

    400:   for (i=0; i<nrqs; ++i) {
    401:     PetscFree(rbuf2[i]);
    402:   }
    403:   PetscFree(rbuf2);
    404:   PetscFree4(sbuf1,ptr,tmp,ctr);
    405:   PetscFree(rbuf1[0]);
    406:   PetscFree(rbuf1);

    408:   for (i=0; i<nrqr; ++i) {
    409:     PetscFree(sbuf2[i]);
    410:   }

    412:   PetscFree(sbuf2);
    413:   PetscFree(rmap[0]);
    414:   PetscFree(rmap);

    416:   for (i=0; i<ismax; i++) {
    417:     MatAssemblyBegin(submats[i],MAT_FINAL_ASSEMBLY);
    418:     MatAssemblyEnd(submats[i],MAT_FINAL_ASSEMBLY);
    419:   }
    420:   return(0);
    421: }

    425: PetscErrorCode MatScale_MPIDense(Mat inA,PetscScalar alpha)
    426: {
    427:   Mat_MPIDense   *A     = (Mat_MPIDense*)inA->data;
    428:   Mat_SeqDense   *a     = (Mat_SeqDense*)A->A->data;
    429:   PetscScalar    oalpha = alpha;
    431:   PetscBLASInt   one = 1,nz;

    434:   PetscBLASIntCast(inA->rmap->n*inA->cmap->N,&nz);
    435:   PetscStackCallBLAS("BLASscal",BLASscal_(&nz,&oalpha,a->v,&one));
    436:   PetscLogFlops(nz);
    437:   return(0);
    438: }