Date: 2013-07-02T14:43:03+00:00

Actual source code: baijov.c
petsc-3.4.2 2013-07-02

      2: /*
      3:    Routines to compute overlapping regions of a parallel MPI matrix
      4:   and to find submatrices that were shared across processors.
      5: */
      6: #include <../src/mat/impls/baij/mpi/mpibaij.h>
      7: #include <petscbt.h>

      9: static PetscErrorCode MatIncreaseOverlap_MPIBAIJ_Local(Mat,PetscInt,char**,PetscInt*,PetscInt**);
     10: static PetscErrorCode MatIncreaseOverlap_MPIBAIJ_Receive(Mat,PetscInt,PetscInt**,PetscInt**,PetscInt*);
     11: extern PetscErrorCode MatGetRow_MPIBAIJ(Mat,PetscInt,PetscInt*,PetscInt**,PetscScalar**);
     12: extern PetscErrorCode MatRestoreRow_MPIBAIJ(Mat,PetscInt,PetscInt*,PetscInt**,PetscScalar**);

     16: PetscErrorCode MatIncreaseOverlap_MPIBAIJ(Mat C,PetscInt imax,IS is[],PetscInt ov)
     17: {
     19:   PetscInt       i,N=C->cmap->N, bs=C->rmap->bs;
     20:   IS             *is_new;

     23:   PetscMalloc(imax*sizeof(IS),&is_new);
     24:   /* Convert the indices into block format */
     25:   ISCompressIndicesGeneral(N,C->rmap->n,bs,imax,is,is_new);
     26:   if (ov < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Negative overlap specified\n");
     27:   for (i=0; i<ov; ++i) {
     28:     MatIncreaseOverlap_MPIBAIJ_Once(C,imax,is_new);
     29:   }
     30:   for (i=0; i<imax; i++) {ISDestroy(&is[i]);}
     31:   ISExpandIndicesGeneral(N,N,bs,imax,is_new,is);
     32:   for (i=0; i<imax; i++) {ISDestroy(&is_new[i]);}
     33:   PetscFree(is_new);
     34:   return(0);
     35: }

     37: /*
     38:   Sample message format:
     39:   If a processor A wants processor B to process some elements corresponding
     40:   to index sets is[1], is[5]
     41:   mesg [0] = 2   (no of index sets in the mesg)
     42:   -----------
     43:   mesg [1] = 1 => is[1]
     44:   mesg [2] = sizeof(is[1]);
     45:   -----------
     46:   mesg [5] = 5  => is[5]
     47:   mesg [6] = sizeof(is[5]);
     48:   -----------
     49:   mesg [7]
     50:   mesg [n]  data(is[1])
     51:   -----------
     52:   mesg[n+1]
     53:   mesg[m]  data(is[5])
     54:   -----------

     56:   Notes:
     57:   nrqs - no of requests sent (or to be sent out)
     58:   nrqr - no of requests recieved (which have to be or which have been processed
     59: */
     62: PetscErrorCode MatIncreaseOverlap_MPIBAIJ_Once(Mat C,PetscInt imax,IS is[])
     63: {
     64:   Mat_MPIBAIJ    *c = (Mat_MPIBAIJ*)C->data;
     65:   const PetscInt **idx,*idx_i;
     66:   PetscInt       *n,*w3,*w4,**data,len;
     68:   PetscMPIInt    size,rank,tag1,tag2,*w2,*w1,nrqr;
     69:   PetscInt       Mbs,i,j,k,**rbuf,row,proc=-1,nrqs,msz,**outdat,**ptr;
     70:   PetscInt       *ctr,*pa,*tmp,*isz,*isz1,**xdata,**rbuf2,*d_p;
     71:   PetscMPIInt    *onodes1,*olengths1,*onodes2,*olengths2;
     72:   PetscBT        *table;
     73:   MPI_Comm       comm;
     74:   MPI_Request    *s_waits1,*r_waits1,*s_waits2,*r_waits2;
     75:   MPI_Status     *s_status,*recv_status;
     76:   char           *t_p;

     79:   PetscObjectGetComm((PetscObject)C,&comm);
     80:   size = c->size;
     81:   rank = c->rank;
     82:   Mbs  = c->Mbs;

     84:   PetscObjectGetNewTag((PetscObject)C,&tag1);
     85:   PetscObjectGetNewTag((PetscObject)C,&tag2);

     87:   PetscMalloc2(imax+1,const PetscInt*,&idx,imax,PetscInt,&n);

     89:   for (i=0; i<imax; i++) {
     90:     ISGetIndices(is[i],&idx[i]);
     91:     ISGetLocalSize(is[i],&n[i]);
     92:   }

     94:   /* evaluate communication - mesg to who,length of mesg, and buffer space
     95:      required. Based on this, buffers are allocated, and data copied into them*/
     96:   PetscMalloc4(size,PetscMPIInt,&w1,size,PetscMPIInt,&w2,size,PetscInt,&w3,size,PetscInt,&w4);
     97:   PetscMemzero(w1,size*sizeof(PetscMPIInt));
     98:   PetscMemzero(w2,size*sizeof(PetscMPIInt));
     99:   PetscMemzero(w3,size*sizeof(PetscInt));
    100:   for (i=0; i<imax; i++) {
    101:     PetscMemzero(w4,size*sizeof(PetscInt)); /* initialise work vector*/
    102:     idx_i = idx[i];
    103:     len   = n[i];
    104:     for (j=0; j<len; j++) {
    105:       row = idx_i[j];
    106:       if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Index set cannot have negative entries");
    107:       PetscLayoutFindOwner(C->rmap,row*C->rmap->bs,&proc);
    108:       w4[proc]++;
    109:     }
    110:     for (j=0; j<size; j++) {
    111:       if (w4[j]) { w1[j] += w4[j]; w3[j]++;}
    112:     }
    113:   }

    115:   nrqs     = 0;              /* no of outgoing messages */
    116:   msz      = 0;              /* total mesg length (for all proc */
    117:   w1[rank] = 0;              /* no mesg sent to itself */
    118:   w3[rank] = 0;
    119:   for (i=0; i<size; i++) {
    120:     if (w1[i])  {w2[i] = 1; nrqs++;} /* there exists a message to proc i */
    121:   }
    122:   /* pa - is list of processors to communicate with */
    123:   PetscMalloc((nrqs+1)*sizeof(PetscInt),&pa);
    124:   for (i=0,j=0; i<size; i++) {
    125:     if (w1[i]) {pa[j] = i; j++;}
    126:   }

    128:   /* Each message would have a header = 1 + 2*(no of IS) + data */
    129:   for (i=0; i<nrqs; i++) {
    130:     j      = pa[i];
    131:     w1[j] += w2[j] + 2*w3[j];
    132:     msz   += w1[j];
    133:   }

    135:   /* Determine the number of messages to expect, their lengths, from from-ids */
    136:   PetscGatherNumberOfMessages(comm,w2,w1,&nrqr);
    137:   PetscGatherMessageLengths(comm,nrqs,nrqr,w1,&onodes1,&olengths1);

    139:   /* Now post the Irecvs corresponding to these messages */
    140:   PetscPostIrecvInt(comm,tag1,nrqr,onodes1,olengths1,&rbuf,&r_waits1);

    142:   /* Allocate Memory for outgoing messages */
    143:   PetscMalloc4(size,PetscInt*,&outdat,size,PetscInt*,&ptr,msz,PetscInt,&tmp,size,PetscInt,&ctr);
    144:   PetscMemzero(outdat,size*sizeof(PetscInt*));
    145:   PetscMemzero(ptr,size*sizeof(PetscInt*));
    146:   {
    147:     PetscInt *iptr = tmp,ict  = 0;
    148:     for (i=0; i<nrqs; i++) {
    149:       j         = pa[i];
    150:       iptr     +=  ict;
    151:       outdat[j] = iptr;
    152:       ict       = w1[j];
    153:     }
    154:   }

    156:   /* Form the outgoing messages */
    157:   /*plug in the headers*/
    158:   for (i=0; i<nrqs; i++) {
    159:     j            = pa[i];
    160:     outdat[j][0] = 0;
    161:     PetscMemzero(outdat[j]+1,2*w3[j]*sizeof(PetscInt));
    162:     ptr[j]       = outdat[j] + 2*w3[j] + 1;
    163:   }

    165:   /* Memory for doing local proc's work*/
    166:   {
    167:     PetscMalloc5(imax,PetscBT,&table, imax,PetscInt*,&data, imax,PetscInt,&isz,
    168:                         Mbs*imax,PetscInt,&d_p, (Mbs/PETSC_BITS_PER_BYTE+1)*imax,char,&t_p);
    169:     PetscMemzero(table,imax*sizeof(PetscBT));
    170:     PetscMemzero(data,imax*sizeof(PetscInt*));
    171:     PetscMemzero(isz,imax*sizeof(PetscInt));
    172:     PetscMemzero(d_p,Mbs*imax*sizeof(PetscInt));
    173:     PetscMemzero(t_p,(Mbs/PETSC_BITS_PER_BYTE+1)*imax*sizeof(char));

    175:     for (i=0; i<imax; i++) {
    176:       table[i] = t_p + (Mbs/PETSC_BITS_PER_BYTE+1)*i;
    177:       data[i]  = d_p + (Mbs)*i;
    178:     }
    179:   }

    181:   /* Parse the IS and update local tables and the outgoing buf with the data*/
    182:   {
    183:     PetscInt n_i,*data_i,isz_i,*outdat_j,ctr_j;
    184:     PetscBT  table_i;

    186:     for (i=0; i<imax; i++) {
    187:       PetscMemzero(ctr,size*sizeof(PetscInt));
    188:       n_i     = n[i];
    189:       table_i = table[i];
    190:       idx_i   = idx[i];
    191:       data_i  = data[i];
    192:       isz_i   = isz[i];
    193:       for (j=0; j<n_i; j++) {   /* parse the indices of each IS */
    194:         row  = idx_i[j];
    195:         PetscLayoutFindOwner(C->rmap,row*C->rmap->bs,&proc);
    196:         if (proc != rank) { /* copy to the outgoing buffer */
    197:           ctr[proc]++;
    198:           *ptr[proc] = row;
    199:           ptr[proc]++;
    200:         } else { /* Update the local table */
    201:           if (!PetscBTLookupSet(table_i,row)) data_i[isz_i++] = row;
    202:         }
    203:       }
    204:       /* Update the headers for the current IS */
    205:       for (j=0; j<size; j++) { /* Can Optimise this loop by using pa[] */
    206:         if ((ctr_j = ctr[j])) {
    207:           outdat_j        = outdat[j];
    208:           k               = ++outdat_j[0];
    209:           outdat_j[2*k]   = ctr_j;
    210:           outdat_j[2*k-1] = i;
    211:         }
    212:       }
    213:       isz[i] = isz_i;
    214:     }
    215:   }

    217:   /*  Now  post the sends */
    218:   PetscMalloc((nrqs+1)*sizeof(MPI_Request),&s_waits1);
    219:   for (i=0; i<nrqs; ++i) {
    220:     j    = pa[i];
    221:     MPI_Isend(outdat[j],w1[j],MPIU_INT,j,tag1,comm,s_waits1+i);
    222:   }

    224:   /* No longer need the original indices*/
    225:   for (i=0; i<imax; ++i) {
    226:     ISRestoreIndices(is[i],idx+i);
    227:   }
    228:   PetscFree2(idx,n);

    230:   for (i=0; i<imax; ++i) {
    231:     ISDestroy(&is[i]);
    232:   }

    234:   /* Do Local work*/
    235:   MatIncreaseOverlap_MPIBAIJ_Local(C,imax,table,isz,data);

    237:   /* Receive messages*/
    238:   PetscMalloc((nrqr+1)*sizeof(MPI_Status),&recv_status);
    239:   if (nrqr) {MPI_Waitall(nrqr,r_waits1,recv_status);}

    241:   PetscMalloc((nrqs+1)*sizeof(MPI_Status),&s_status);
    242:   if (nrqs) {MPI_Waitall(nrqs,s_waits1,s_status);}

    244:   /* Phase 1 sends are complete - deallocate buffers */
    245:   PetscFree4(outdat,ptr,tmp,ctr);
    246:   PetscFree4(w1,w2,w3,w4);

    248:   PetscMalloc((nrqr+1)*sizeof(PetscInt*),&xdata);
    249:   PetscMalloc((nrqr+1)*sizeof(PetscInt),&isz1);
    250:   MatIncreaseOverlap_MPIBAIJ_Receive(C,nrqr,rbuf,xdata,isz1);
    251:   PetscFree(rbuf[0]);
    252:   PetscFree(rbuf);

    254:   /* Send the data back*/
    255:   /* Do a global reduction to know the buffer space req for incoming messages*/
    256:   {
    257:     PetscMPIInt *rw1;

    259:     PetscMalloc(size*sizeof(PetscInt),&rw1);
    260:     PetscMemzero(rw1,size*sizeof(PetscInt));

    262:     for (i=0; i<nrqr; ++i) {
    263:       proc = recv_status[i].MPI_SOURCE;
    264:       if (proc != onodes1[i]) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"MPI_SOURCE mismatch");
    265:       rw1[proc] = isz1[i];
    266:     }

    268:     PetscFree(onodes1);
    269:     PetscFree(olengths1);

    271:     /* Determine the number of messages to expect, their lengths, from from-ids */
    272:     PetscGatherMessageLengths(comm,nrqr,nrqs,rw1,&onodes2,&olengths2);
    273:     PetscFree(rw1);
    274:   }
    275:   /* Now post the Irecvs corresponding to these messages */
    276:   PetscPostIrecvInt(comm,tag2,nrqs,onodes2,olengths2,&rbuf2,&r_waits2);

    278:   /*  Now  post the sends */
    279:   PetscMalloc((nrqr+1)*sizeof(MPI_Request),&s_waits2);
    280:   for (i=0; i<nrqr; ++i) {
    281:     j    = recv_status[i].MPI_SOURCE;
    282:     MPI_Isend(xdata[i],isz1[i],MPIU_INT,j,tag2,comm,s_waits2+i);
    283:   }

    285:   /* receive work done on other processors*/
    286:   {
    287:     PetscMPIInt idex;
    288:     PetscInt    is_no,ct1,max,*rbuf2_i,isz_i,*data_i,jmax;
    289:     PetscBT     table_i;
    290:     MPI_Status  *status2;

    292:     PetscMalloc((PetscMax(nrqr,nrqs)+1)*sizeof(MPI_Status),&status2);
    293:     for (i=0; i<nrqs; ++i) {
    294:       MPI_Waitany(nrqs,r_waits2,&idex,status2+i);
    295:       /* Process the message*/
    296:       rbuf2_i = rbuf2[idex];
    297:       ct1     = 2*rbuf2_i[0]+1;
    298:       jmax    = rbuf2[idex][0];
    299:       for (j=1; j<=jmax; j++) {
    300:         max     = rbuf2_i[2*j];
    301:         is_no   = rbuf2_i[2*j-1];
    302:         isz_i   = isz[is_no];
    303:         data_i  = data[is_no];
    304:         table_i = table[is_no];
    305:         for (k=0; k<max; k++,ct1++) {
    306:           row = rbuf2_i[ct1];
    307:           if (!PetscBTLookupSet(table_i,row)) data_i[isz_i++] = row;
    308:         }
    309:         isz[is_no] = isz_i;
    310:       }
    311:     }
    312:     if (nrqr) {MPI_Waitall(nrqr,s_waits2,status2);}
    313:     PetscFree(status2);
    314:   }

    316:   for (i=0; i<imax; ++i) {
    317:     ISCreateGeneral(PETSC_COMM_SELF,isz[i],data[i],PETSC_COPY_VALUES,is+i);
    318:   }

    321:   PetscFree(onodes2);
    322:   PetscFree(olengths2);

    324:   PetscFree(pa);
    325:   PetscFree(rbuf2[0]);
    326:   PetscFree(rbuf2);
    327:   PetscFree(s_waits1);
    328:   PetscFree(r_waits1);
    329:   PetscFree(s_waits2);
    330:   PetscFree(r_waits2);
    331:   PetscFree5(table,data,isz,d_p,t_p);
    332:   PetscFree(s_status);
    333:   PetscFree(recv_status);
    334:   PetscFree(xdata[0]);
    335:   PetscFree(xdata);
    336:   PetscFree(isz1);
    337:   return(0);
    338: }

    342: /*
    343:    MatIncreaseOverlap_MPIBAIJ_Local - Called by MatincreaseOverlap, to do
    344:        the work on the local processor.

    346:      Inputs:
    347:       C      - MAT_MPIBAIJ;
    348:       imax - total no of index sets processed at a time;
    349:       table  - an array of char - size = Mbs bits.

    351:      Output:
    352:       isz    - array containing the count of the solution elements corresponding
    353:                to each index set;
    354:       data   - pointer to the solutions
    355: */
    356: static PetscErrorCode MatIncreaseOverlap_MPIBAIJ_Local(Mat C,PetscInt imax,PetscBT *table,PetscInt *isz,PetscInt **data)
    357: {
    358:   Mat_MPIBAIJ *c = (Mat_MPIBAIJ*)C->data;
    359:   Mat         A  = c->A,B = c->B;
    360:   Mat_SeqBAIJ *a = (Mat_SeqBAIJ*)A->data,*b = (Mat_SeqBAIJ*)B->data;
    361:   PetscInt    start,end,val,max,rstart,cstart,*ai,*aj;
    362:   PetscInt    *bi,*bj,*garray,i,j,k,row,*data_i,isz_i;
    363:   PetscBT     table_i;

    366:   rstart = c->rstartbs;
    367:   cstart = c->cstartbs;
    368:   ai     = a->i;
    369:   aj     = a->j;
    370:   bi     = b->i;
    371:   bj     = b->j;
    372:   garray = c->garray;

    375:   for (i=0; i<imax; i++) {
    376:     data_i  = data[i];
    377:     table_i = table[i];
    378:     isz_i   = isz[i];
    379:     for (j=0,max=isz[i]; j<max; j++) {
    380:       row   = data_i[j] - rstart;
    381:       start = ai[row];
    382:       end   = ai[row+1];
    383:       for (k=start; k<end; k++) { /* Amat */
    384:         val = aj[k] + cstart;
    385:         if (!PetscBTLookupSet(table_i,val)) data_i[isz_i++] = val;
    386:       }
    387:       start = bi[row];
    388:       end   = bi[row+1];
    389:       for (k=start; k<end; k++) { /* Bmat */
    390:         val = garray[bj[k]];
    391:         if (!PetscBTLookupSet(table_i,val)) data_i[isz_i++] = val;
    392:       }
    393:     }
    394:     isz[i] = isz_i;
    395:   }
    396:   return(0);
    397: }
    400: /*
    401:       MatIncreaseOverlap_MPIBAIJ_Receive - Process the recieved messages,
    402:          and return the output

    404:          Input:
    405:            C    - the matrix
    406:            nrqr - no of messages being processed.
    407:            rbuf - an array of pointers to the recieved requests

    409:          Output:
    410:            xdata - array of messages to be sent back
    411:            isz1  - size of each message

    413:   For better efficiency perhaps we should malloc separately each xdata[i],
    414: then if a remalloc is required we need only copy the data for that one row
    415: rather than all previous rows as it is now where a single large chunck of
    416: memory is used.

    418: */
    419: static PetscErrorCode MatIncreaseOverlap_MPIBAIJ_Receive(Mat C,PetscInt nrqr,PetscInt **rbuf,PetscInt **xdata,PetscInt * isz1)
    420: {
    421:   Mat_MPIBAIJ    *c = (Mat_MPIBAIJ*)C->data;
    422:   Mat            A  = c->A,B = c->B;
    423:   Mat_SeqBAIJ    *a = (Mat_SeqBAIJ*)A->data,*b = (Mat_SeqBAIJ*)B->data;
    425:   PetscInt       rstart,cstart,*ai,*aj,*bi,*bj,*garray,i,j,k;
    426:   PetscInt       row,total_sz,ct,ct1,ct2,ct3,mem_estimate,oct2,l,start,end;
    427:   PetscInt       val,max1,max2,Mbs,no_malloc =0,*tmp,new_estimate,ctr;
    428:   PetscInt       *rbuf_i,kmax,rbuf_0;
    429:   PetscBT        xtable;

    432:   Mbs    = c->Mbs;
    433:   rstart = c->rstartbs;
    434:   cstart = c->cstartbs;
    435:   ai     = a->i;
    436:   aj     = a->j;
    437:   bi     = b->i;
    438:   bj     = b->j;
    439:   garray = c->garray;

    442:   for (i=0,ct=0,total_sz=0; i<nrqr; ++i) {
    443:     rbuf_i =  rbuf[i];
    444:     rbuf_0 =  rbuf_i[0];
    445:     ct    += rbuf_0;
    446:     for (j=1; j<=rbuf_0; j++) total_sz += rbuf_i[2*j];
    447:   }

    449:   if (c->Mbs) max1 = ct*(a->nz +b->nz)/c->Mbs;
    450:   else        max1 = 1;
    451:   mem_estimate = 3*((total_sz > max1 ? total_sz : max1)+1);
    452:   PetscMalloc(mem_estimate*sizeof(PetscInt),&xdata[0]);
    453:   ++no_malloc;
    454:   PetscBTCreate(Mbs,&xtable);
    455:   PetscMemzero(isz1,nrqr*sizeof(PetscInt));

    457:   ct3 = 0;
    458:   for (i=0; i<nrqr; i++) { /* for easch mesg from proc i */
    459:     rbuf_i =  rbuf[i];
    460:     rbuf_0 =  rbuf_i[0];
    461:     ct1    =  2*rbuf_0+1;
    462:     ct2    =  ct1;
    463:     ct3   += ct1;
    464:     for (j=1; j<=rbuf_0; j++) { /* for each IS from proc i*/
    465:       PetscBTMemzero(Mbs,xtable);
    466:       oct2 = ct2;
    467:       kmax = rbuf_i[2*j];
    468:       for (k=0; k<kmax; k++,ct1++) {
    469:         row = rbuf_i[ct1];
    470:         if (!PetscBTLookupSet(xtable,row)) {
    471:           if (!(ct3 < mem_estimate)) {
    472:             new_estimate = (PetscInt)(1.5*mem_estimate)+1;
    473:             PetscMalloc(new_estimate * sizeof(PetscInt),&tmp);
    474:             PetscMemcpy(tmp,xdata[0],mem_estimate*sizeof(PetscInt));
    475:             PetscFree(xdata[0]);
    476:             xdata[0]     = tmp;
    477:             mem_estimate = new_estimate; ++no_malloc;
    478:             for (ctr=1; ctr<=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1];
    479:           }
    480:           xdata[i][ct2++] = row;
    481:           ct3++;
    482:         }
    483:       }
    484:       for (k=oct2,max2=ct2; k<max2; k++)  {
    485:         row   = xdata[i][k] - rstart;
    486:         start = ai[row];
    487:         end   = ai[row+1];
    488:         for (l=start; l<end; l++) {
    489:           val = aj[l] + cstart;
    490:           if (!PetscBTLookupSet(xtable,val)) {
    491:             if (!(ct3 < mem_estimate)) {
    492:               new_estimate = (PetscInt)(1.5*mem_estimate)+1;
    493:               PetscMalloc(new_estimate * sizeof(PetscInt),&tmp);
    494:               PetscMemcpy(tmp,xdata[0],mem_estimate*sizeof(PetscInt));
    495:               PetscFree(xdata[0]);
    496:               xdata[0]     = tmp;
    497:               mem_estimate = new_estimate; ++no_malloc;
    498:               for (ctr=1; ctr<=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1];
    499:             }
    500:             xdata[i][ct2++] = val;
    501:             ct3++;
    502:           }
    503:         }
    504:         start = bi[row];
    505:         end   = bi[row+1];
    506:         for (l=start; l<end; l++) {
    507:           val = garray[bj[l]];
    508:           if (!PetscBTLookupSet(xtable,val)) {
    509:             if (!(ct3 < mem_estimate)) {
    510:               new_estimate = (PetscInt)(1.5*mem_estimate)+1;
    511:               PetscMalloc(new_estimate * sizeof(PetscInt),&tmp);
    512:               PetscMemcpy(tmp,xdata[0],mem_estimate*sizeof(PetscInt));
    513:               PetscFree(xdata[0]);
    514:               xdata[0]     = tmp;
    515:               mem_estimate = new_estimate; ++no_malloc;
    516:               for (ctr =1; ctr <=i; ctr++) xdata[ctr] = xdata[ctr-1] + isz1[ctr-1];
    517:             }
    518:             xdata[i][ct2++] = val;
    519:             ct3++;
    520:           }
    521:         }
    522:       }
    523:       /* Update the header*/
    524:       xdata[i][2*j]   = ct2 - oct2; /* Undo the vector isz1 and use only a var*/
    525:       xdata[i][2*j-1] = rbuf_i[2*j-1];
    526:     }
    527:     xdata[i][0] = rbuf_0;
    528:     xdata[i+1]  = xdata[i] + ct2;
    529:     isz1[i]     = ct2; /* size of each message */
    530:   }
    531:   PetscBTDestroy(&xtable);
    532:   PetscInfo3(C,"Allocated %D bytes, required %D, no of mallocs = %D\n",mem_estimate,ct3,no_malloc);
    533:   return(0);
    534: }

    538: PetscErrorCode MatGetSubMatrices_MPIBAIJ(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,Mat *submat[])
    539: {
    540:   IS             *isrow_new,*iscol_new;
    541:   Mat_MPIBAIJ    *c = (Mat_MPIBAIJ*)C->data;
    543:   PetscInt       nmax,nstages_local,nstages,i,pos,max_no,ncol,nrow,N=C->cmap->N,bs=C->rmap->bs;
    544:   PetscBool      colflag,*allcolumns,*allrows;

    547:   /* Currently, unsorted column indices will result in inverted column indices in the resulting submatrices. */
    548:   for (i = 0; i < ismax; ++i) {
    549:     PetscBool sorted;
    550:     ISSorted(iscol[i], &sorted);
    551:     if (!sorted) SETERRQ1(((PetscObject)iscol[i])->comm, PETSC_ERR_SUP, "Column index set %D not sorted", i);
    552:   }
    553:   /* The compression and expansion should be avoided. Doesn't point
    554:      out errors, might change the indices, hence buggey */
    555:   PetscMalloc2(ismax+1,IS,&isrow_new,ismax+1,IS,&iscol_new);
    556:   ISCompressIndicesGeneral(N,C->rmap->n,bs,ismax,isrow,isrow_new);
    557:   ISCompressIndicesGeneral(N,C->cmap->n,bs,ismax,iscol,iscol_new);

    559:   /* Check for special case: each processor gets entire matrix columns */
    560:   PetscMalloc2(ismax+1,PetscBool,&allcolumns,ismax+1,PetscBool,&allrows);
    561:   for (i=0; i<ismax; i++) {
    562:     ISIdentity(iscol[i],&colflag);
    563:     ISGetLocalSize(iscol[i],&ncol);
    564:     if (colflag && ncol == C->cmap->N) allcolumns[i] = PETSC_TRUE;
    565:     else allcolumns[i] = PETSC_FALSE;

    567:     ISIdentity(isrow[i],&colflag);
    568:     ISGetLocalSize(isrow[i],&nrow);
    569:     if (colflag && nrow == C->rmap->N) allrows[i] = PETSC_TRUE;
    570:     else allrows[i] = PETSC_FALSE;
    571:   }

    573:   /* Allocate memory to hold all the submatrices */
    574:   if (scall != MAT_REUSE_MATRIX) {
    575:     PetscMalloc((ismax+1)*sizeof(Mat),submat);
    576:   }
    577:   /* Determine the number of stages through which submatrices are done */
    578:   nmax = 20*1000000 / (c->Nbs * sizeof(PetscInt));
    579:   if (!nmax) nmax = 1;
    580:   nstages_local = ismax/nmax + ((ismax % nmax) ? 1 : 0);

    582:   /* Make sure every processor loops through the nstages */
    583:   MPI_Allreduce(&nstages_local,&nstages,1,MPIU_INT,MPI_MAX,PetscObjectComm((PetscObject)C));
    584:   for (i=0,pos=0; i<nstages; i++) {
    585:     if (pos+nmax <= ismax) max_no = nmax;
    586:     else if (pos == ismax) max_no = 0;
    587:     else                   max_no = ismax-pos;
    588:     MatGetSubMatrices_MPIBAIJ_local(C,max_no,isrow_new+pos,iscol_new+pos,scall,allrows+pos,allcolumns+pos,*submat+pos);
    589:     pos += max_no;
    590:   }

    592:   for (i=0; i<ismax; i++) {
    593:     ISDestroy(&isrow_new[i]);
    594:     ISDestroy(&iscol_new[i]);
    595:   }
    596:   PetscFree2(isrow_new,iscol_new);
    597:   PetscFree2(allcolumns,allrows);
    598:   return(0);
    599: }

    601: #if defined(PETSC_USE_CTABLE)
    604: PetscErrorCode PetscGetProc(const PetscInt row, const PetscMPIInt size, const PetscInt proc_gnode[], PetscMPIInt *rank)
    605: {
    606:   PetscInt       nGlobalNd = proc_gnode[size];
    607:   PetscMPIInt    fproc;

    611:   PetscMPIIntCast((PetscInt)(((float)row * (float)size / (float)nGlobalNd + 0.5)),&fproc);
    612:   if (fproc > size) fproc = size;
    613:   while (row < proc_gnode[fproc] || row >= proc_gnode[fproc+1]) {
    614:     if (row < proc_gnode[fproc]) fproc--;
    615:     else                         fproc++;
    616:   }
    617:   *rank = fproc;
    618:   return(0);
    619: }
    620: #endif

    622: /* -------------------------------------------------------------------------*/
    623: /* This code is used for BAIJ and SBAIJ matrices (unfortunate dependency) */
    626: PetscErrorCode MatGetSubMatrices_MPIBAIJ_local(Mat C,PetscInt ismax,const IS isrow[],const IS iscol[],MatReuse scall,PetscBool *allrows,PetscBool *allcolumns,Mat *submats)
    627: {
    628:   Mat_MPIBAIJ    *c = (Mat_MPIBAIJ*)C->data;
    629:   Mat            A  = c->A;
    630:   Mat_SeqBAIJ    *a = (Mat_SeqBAIJ*)A->data,*b = (Mat_SeqBAIJ*)c->B->data,*mat;
    631:   const PetscInt **irow,**icol,*irow_i;
    632:   PetscInt       *nrow,*ncol,*w3,*w4,start;
    634:   PetscMPIInt    size,tag0,tag1,tag2,tag3,*w1,*w2,nrqr,idex,end,proc;
    635:   PetscInt       **sbuf1,**sbuf2,rank,i,j,k,l,ct1,ct2,**rbuf1,row;
    636:   PetscInt       nrqs,msz,**ptr,*req_size,*ctr,*pa,*tmp,tcol;
    637:   PetscInt       **rbuf3,*req_source,**sbuf_aj,**rbuf2,max1,max2;
    638:   PetscInt       **lens,is_no,ncols,*cols,mat_i,*mat_j,tmp2,jmax;
    639:   PetscInt       ctr_j,*sbuf1_j,*sbuf_aj_i,*rbuf1_i,kmax,*lens_i;
    640:   PetscInt       bs     =C->rmap->bs,bs2=c->bs2,*a_j=a->j,*b_j=b->j,*cworkA,*cworkB;
    641:   PetscInt       cstart = c->cstartbs,nzA,nzB,*a_i=a->i,*b_i=b->i,imark;
    642:   PetscInt       *bmap  = c->garray,ctmp,rstart=c->rstartbs;
    643:   MPI_Request    *s_waits1,*r_waits1,*s_waits2,*r_waits2,*r_waits3,*s_waits3;
    644:   MPI_Status     *r_status1,*r_status2,*s_status1,*s_status3,*s_status2,*r_status3;
    645:   MPI_Comm       comm;
    646:   PetscBool      flag;
    647:   PetscMPIInt    *onodes1,*olengths1;
    648:   PetscBool      ijonly=c->ijonly; /* private flag indicates only matrix data structures are requested */

    650:   /* variables below are used for the matrix numerical values - case of !ijonly */
    651:   MPI_Request *r_waits4,*s_waits4;
    652:   MPI_Status  *r_status4,*s_status4;
    653:   MatScalar   **rbuf4,**sbuf_aa,*vals,*mat_a = NULL,*sbuf_aa_i,*vworkA = NULL,*vworkB = NULL;
    654:   MatScalar   *a_a=a->a,*b_a=b->a;

    656: #if defined(PETSC_USE_CTABLE)
    657:   PetscInt   tt;
    658:   PetscTable *rmap,*cmap,rmap_i,cmap_i=NULL;
    659: #else
    660:   PetscInt **cmap,*cmap_i=NULL,*rtable,*rmap_i,**rmap, Mbs = c->Mbs;
    661: #endif

    664:   PetscObjectGetComm((PetscObject)C,&comm);
    665:   tag0 = ((PetscObject)C)->tag;
    666:   size = c->size;
    667:   rank = c->rank;

    669:   /* Get some new tags to keep the communication clean */
    670:   PetscObjectGetNewTag((PetscObject)C,&tag1);
    671:   PetscObjectGetNewTag((PetscObject)C,&tag2);
    672:   PetscObjectGetNewTag((PetscObject)C,&tag3);

    674: #if defined(PETSC_USE_CTABLE)
    675:   PetscMalloc4(ismax,const PetscInt*,&irow,ismax,const PetscInt*,&icol,ismax,PetscInt,&nrow,ismax,PetscInt,&ncol);
    676: #else
    677:   PetscMalloc5(ismax,const PetscInt*,&irow,ismax,const PetscInt*,&icol,ismax,PetscInt,&nrow,ismax,PetscInt,&ncol,Mbs+1,PetscInt,&rtable);
    678:   /* Create hash table for the mapping :row -> proc*/
    679:   for (i=0,j=0; i<size; i++) {
    680:     jmax = C->rmap->range[i+1]/bs;
    681:     for (; j<jmax; j++) rtable[j] = i;
    682:   }
    683: #endif

    685:   for (i=0; i<ismax; i++) {
    686:     if (allrows[i]) {
    687:       irow[i] = NULL;
    688:       nrow[i] = C->rmap->N/bs;
    689:     } else {
    690:       ISGetIndices(isrow[i],&irow[i]);
    691:       ISGetLocalSize(isrow[i],&nrow[i]);
    692:     }

    694:     if (allcolumns[i]) {
    695:       icol[i] = NULL;
    696:       ncol[i] = C->cmap->N/bs;
    697:     } else {
    698:       ISGetIndices(iscol[i],&icol[i]);
    699:       ISGetLocalSize(iscol[i],&ncol[i]);
    700:     }
    701:   }

    703:   /* evaluate communication - mesg to who,length of mesg,and buffer space
    704:      required. Based on this, buffers are allocated, and data copied into them*/
    705:   PetscMalloc4(size,PetscMPIInt,&w1,size,PetscMPIInt,&w2,size,PetscInt,&w3,size,PetscInt,&w4);
    706:   PetscMemzero(w1,size*sizeof(PetscMPIInt));
    707:   PetscMemzero(w2,size*sizeof(PetscMPIInt));
    708:   PetscMemzero(w3,size*sizeof(PetscInt));
    709:   for (i=0; i<ismax; i++) {
    710:     PetscMemzero(w4,size*sizeof(PetscInt)); /* initialise work vector*/
    711:     jmax   = nrow[i];
    712:     irow_i = irow[i];
    713:     for (j=0; j<jmax; j++) {
    714:       if (allrows[i]) row = j;
    715:       else row = irow_i[j];

    717: #if defined(PETSC_USE_CTABLE)
    718:       PetscGetProc(row,size,c->rangebs,&proc);
    719: #else
    720:       proc = rtable[row];
    721: #endif
    722:       w4[proc]++;
    723:     }
    724:     for (j=0; j<size; j++) {
    725:       if (w4[j]) { w1[j] += w4[j];  w3[j]++;}
    726:     }
    727:   }

    729:   nrqs     = 0;              /* no of outgoing messages */
    730:   msz      = 0;              /* total mesg length for all proc */
    731:   w1[rank] = 0;              /* no mesg sent to intself */
    732:   w3[rank] = 0;
    733:   for (i=0; i<size; i++) {
    734:     if (w1[i])  { w2[i] = 1; nrqs++;} /* there exists a message to proc i */
    735:   }
    736:   PetscMalloc((nrqs+1)*sizeof(PetscInt),&pa); /*(proc -array)*/
    737:   for (i=0,j=0; i<size; i++) {
    738:     if (w1[i]) { pa[j] = i; j++; }
    739:   }

    741:   /* Each message would have a header = 1 + 2*(no of IS) + data */
    742:   for (i=0; i<nrqs; i++) {
    743:     j     = pa[i];
    744:     w1[j] += w2[j] + 2* w3[j];
    745:     msz   += w1[j];
    746:   }

    748:   /* Determine the number of messages to expect, their lengths, from from-ids */
    749:   PetscGatherNumberOfMessages(comm,w2,w1,&nrqr);
    750:   PetscGatherMessageLengths(comm,nrqs,nrqr,w1,&onodes1,&olengths1);

    752:   /* Now post the Irecvs corresponding to these messages */
    753:   PetscPostIrecvInt(comm,tag0,nrqr,onodes1,olengths1,&rbuf1,&r_waits1);

    755:   PetscFree(onodes1);
    756:   PetscFree(olengths1);

    758:   /* Allocate Memory for outgoing messages */
    759:   PetscMalloc4(size,PetscInt*,&sbuf1,size,PetscInt*,&ptr,2*msz,PetscInt,&tmp,size,PetscInt,&ctr);
    760:   PetscMemzero(sbuf1,size*sizeof(PetscInt*));
    761:   PetscMemzero(ptr,size*sizeof(PetscInt*));
    762:   {
    763:     PetscInt *iptr = tmp,ict = 0;
    764:     for (i=0; i<nrqs; i++) {
    765:       j        = pa[i];
    766:       iptr    += ict;
    767:       sbuf1[j] = iptr;
    768:       ict      = w1[j];
    769:     }
    770:   }

    772:   /* Form the outgoing messages */
    773:   /* Initialise the header space */
    774:   for (i=0; i<nrqs; i++) {
    775:     j           = pa[i];
    776:     sbuf1[j][0] = 0;
    777:     PetscMemzero(sbuf1[j]+1,2*w3[j]*sizeof(PetscInt));
    778:     ptr[j]      = sbuf1[j] + 2*w3[j] + 1;
    779:   }

    781:   /* Parse the isrow and copy data into outbuf */
    782:   for (i=0; i<ismax; i++) {
    783:     PetscMemzero(ctr,size*sizeof(PetscInt));
    784:     irow_i = irow[i];
    785:     jmax   = nrow[i];
    786:     for (j=0; j<jmax; j++) {  /* parse the indices of each IS */
    787:       if (allrows[i]) row = j;
    788:       else row = irow_i[j];

    790: #if defined(PETSC_USE_CTABLE)
    791:       PetscGetProc(row,size,c->rangebs,&proc);
    792: #else
    793:       proc = rtable[row];
    794: #endif
    795:       if (proc != rank) { /* copy to the outgoing buf*/
    796:         ctr[proc]++;
    797:         *ptr[proc] = row;
    798:         ptr[proc]++;
    799:       }
    800:     }
    801:     /* Update the headers for the current IS */
    802:     for (j=0; j<size; j++) { /* Can Optimise this loop too */
    803:       if ((ctr_j = ctr[j])) {
    804:         sbuf1_j        = sbuf1[j];
    805:         k              = ++sbuf1_j[0];
    806:         sbuf1_j[2*k]   = ctr_j;
    807:         sbuf1_j[2*k-1] = i;
    808:       }
    809:     }
    810:   }

    812:   /*  Now  post the sends */
    813:   PetscMalloc((nrqs+1)*sizeof(MPI_Request),&s_waits1);
    814:   for (i=0; i<nrqs; ++i) {
    815:     j    = pa[i];
    816:     MPI_Isend(sbuf1[j],w1[j],MPIU_INT,j,tag0,comm,s_waits1+i);
    817:   }

    819:   /* Post Recieves to capture the buffer size */
    820:   PetscMalloc((nrqs+1)*sizeof(MPI_Request),&r_waits2);
    821:   PetscMalloc((nrqs+1)*sizeof(PetscInt*),&rbuf2);
    822:   rbuf2[0] = tmp + msz;
    823:   for (i=1; i<nrqs; ++i) {
    824:     j        = pa[i];
    825:     rbuf2[i] = rbuf2[i-1]+w1[pa[i-1]];
    826:   }
    827:   for (i=0; i<nrqs; ++i) {
    828:     j    = pa[i];
    829:     MPI_Irecv(rbuf2[i],w1[j],MPIU_INT,j,tag1,comm,r_waits2+i);
    830:   }

    832:   /* Send to other procs the buf size they should allocate */

    834:   /* Receive messages*/
    835:   PetscMalloc((nrqr+1)*sizeof(MPI_Request),&s_waits2);
    836:   PetscMalloc((nrqr+1)*sizeof(MPI_Status),&r_status1);
    837:   PetscMalloc3(nrqr+1,PetscInt*,&sbuf2,nrqr,PetscInt,&req_size,nrqr,PetscInt,&req_source);
    838:   {
    839:     Mat_SeqBAIJ *sA  = (Mat_SeqBAIJ*)c->A->data,*sB = (Mat_SeqBAIJ*)c->B->data;
    840:     PetscInt    *sAi = sA->i,*sBi = sB->i,id,*sbuf2_i;

    842:     for (i=0; i<nrqr; ++i) {
    843:       MPI_Waitany(nrqr,r_waits1,&idex,r_status1+i);

    845:       req_size[idex] = 0;
    846:       rbuf1_i        = rbuf1[idex];
    847:       start          = 2*rbuf1_i[0] + 1;
    848:       MPI_Get_count(r_status1+i,MPIU_INT,&end);
    849:       PetscMalloc(end*sizeof(PetscInt),&sbuf2[idex]);
    850:       sbuf2_i        = sbuf2[idex];
    851:       for (j=start; j<end; j++) {
    852:         id              = rbuf1_i[j] - rstart;
    853:         ncols           = sAi[id+1] - sAi[id] + sBi[id+1] - sBi[id];
    854:         sbuf2_i[j]      = ncols;
    855:         req_size[idex] += ncols;
    856:       }
    857:       req_source[idex] = r_status1[i].MPI_SOURCE;
    858:       /* form the header */
    859:       sbuf2_i[0] = req_size[idex];
    860:       for (j=1; j<start; j++) sbuf2_i[j] = rbuf1_i[j];
    861:       MPI_Isend(sbuf2_i,end,MPIU_INT,req_source[idex],tag1,comm,s_waits2+i);
    862:     }
    863:   }
    864:   PetscFree(r_status1);
    865:   PetscFree(r_waits1);

    867:   /*  recv buffer sizes */
    868:   /* Receive messages*/
    869:   PetscMalloc((nrqs+1)*sizeof(PetscInt*),&rbuf3);
    870:   PetscMalloc((nrqs+1)*sizeof(MPI_Request),&r_waits3);
    871:   PetscMalloc((nrqs+1)*sizeof(MPI_Status),&r_status2);
    872:   if (!ijonly) {
    873:     PetscMalloc((nrqs+1)*sizeof(MatScalar*),&rbuf4);
    874:     PetscMalloc((nrqs+1)*sizeof(MPI_Request),&r_waits4);
    875:   }

    877:   for (i=0; i<nrqs; ++i) {
    878:     MPI_Waitany(nrqs,r_waits2,&idex,r_status2+i);
    879:     PetscMalloc(rbuf2[idex][0]*sizeof(PetscInt),&rbuf3[idex]);
    880:     MPI_Irecv(rbuf3[idex],rbuf2[idex][0],MPIU_INT,r_status2[i].MPI_SOURCE,tag2,comm,r_waits3+idex);
    881:     if (!ijonly) {
    882:       PetscMalloc(rbuf2[idex][0]*bs2*sizeof(MatScalar),&rbuf4[idex]);
    883:       MPI_Irecv(rbuf4[idex],rbuf2[idex][0]*bs2,MPIU_MATSCALAR,r_status2[i].MPI_SOURCE,tag3,comm,r_waits4+idex);
    884:     }
    885:   }
    886:   PetscFree(r_status2);
    887:   PetscFree(r_waits2);

    889:   /* Wait on sends1 and sends2 */
    890:   PetscMalloc((nrqs+1)*sizeof(MPI_Status),&s_status1);
    891:   PetscMalloc((nrqr+1)*sizeof(MPI_Status),&s_status2);

    893:   if (nrqs) {MPI_Waitall(nrqs,s_waits1,s_status1);}
    894:   if (nrqr) {MPI_Waitall(nrqr,s_waits2,s_status2);}
    895:   PetscFree(s_status1);
    896:   PetscFree(s_status2);
    897:   PetscFree(s_waits1);
    898:   PetscFree(s_waits2);

    900:   /* Now allocate buffers for a->j, and send them off */
    901:   PetscMalloc((nrqr+1)*sizeof(PetscInt*),&sbuf_aj);
    902:   for (i=0,j=0; i<nrqr; i++) j += req_size[i];
    903:   PetscMalloc((j+1)*sizeof(PetscInt),&sbuf_aj[0]);
    904:   for (i=1; i<nrqr; i++) sbuf_aj[i] = sbuf_aj[i-1] + req_size[i-1];

    906:   PetscMalloc((nrqr+1)*sizeof(MPI_Request),&s_waits3);
    907:   {
    908:     for (i=0; i<nrqr; i++) {
    909:       rbuf1_i   = rbuf1[i];
    910:       sbuf_aj_i = sbuf_aj[i];
    911:       ct1       = 2*rbuf1_i[0] + 1;
    912:       ct2       = 0;
    913:       for (j=1,max1=rbuf1_i[0]; j<=max1; j++) {
    914:         kmax = rbuf1[i][2*j];
    915:         for (k=0; k<kmax; k++,ct1++) {
    916:           row    = rbuf1_i[ct1] - rstart;
    917:           nzA    = a_i[row+1] - a_i[row];     nzB = b_i[row+1] - b_i[row];
    918:           ncols  = nzA + nzB;
    919:           cworkA = a_j + a_i[row]; cworkB = b_j + b_i[row];

    921:           /* load the column indices for this row into cols*/
    922:           cols = sbuf_aj_i + ct2;
    923:           for (l=0; l<nzB; l++) {
    924:             if ((ctmp = bmap[cworkB[l]]) < cstart) cols[l] = ctmp;
    925:             else break;
    926:           }
    927:           imark = l;
    928:           for (l=0; l<nzA; l++)   cols[imark+l] = cstart + cworkA[l];
    929:           for (l=imark; l<nzB; l++) cols[nzA+l] = bmap[cworkB[l]];
    930:           ct2 += ncols;
    931:         }
    932:       }
    933:       MPI_Isend(sbuf_aj_i,req_size[i],MPIU_INT,req_source[i],tag2,comm,s_waits3+i);
    934:     }
    935:   }
    936:   PetscMalloc((nrqs+1)*sizeof(MPI_Status),&r_status3);
    937:   PetscMalloc((nrqr+1)*sizeof(MPI_Status),&s_status3);

    939:   /* Allocate buffers for a->a, and send them off */
    940:   if (!ijonly) {
    941:     PetscMalloc((nrqr+1)*sizeof(MatScalar*),&sbuf_aa);
    942:     for (i=0,j=0; i<nrqr; i++) j += req_size[i];
    943:     PetscMalloc((j+1)*bs2*sizeof(MatScalar),&sbuf_aa[0]);
    944:     for (i=1; i<nrqr; i++) sbuf_aa[i] = sbuf_aa[i-1] + req_size[i-1]*bs2;

    946:     PetscMalloc((nrqr+1)*sizeof(MPI_Request),&s_waits4);
    947:     {
    948:       for (i=0; i<nrqr; i++) {
    949:         rbuf1_i   = rbuf1[i];
    950:         sbuf_aa_i = sbuf_aa[i];
    951:         ct1       = 2*rbuf1_i[0]+1;
    952:         ct2       = 0;
    953:         for (j=1,max1=rbuf1_i[0]; j<=max1; j++) {
    954:           kmax = rbuf1_i[2*j];
    955:           for (k=0; k<kmax; k++,ct1++) {
    956:             row    = rbuf1_i[ct1] - rstart;
    957:             nzA    = a_i[row+1] - a_i[row];     nzB = b_i[row+1] - b_i[row];
    958:             ncols  = nzA + nzB;
    959:             cworkA = a_j + a_i[row];     cworkB = b_j + b_i[row];
    960:             vworkA = a_a + a_i[row]*bs2; vworkB = b_a + b_i[row]*bs2;

    962:             /* load the column values for this row into vals*/
    963:             vals = sbuf_aa_i+ct2*bs2;
    964:             for (l=0; l<nzB; l++) {
    965:               if ((bmap[cworkB[l]]) < cstart) {
    966:                 PetscMemcpy(vals+l*bs2,vworkB+l*bs2,bs2*sizeof(MatScalar));
    967:               } else break;
    968:             }
    969:             imark = l;
    970:             for (l=0; l<nzA; l++) {
    971:               PetscMemcpy(vals+(imark+l)*bs2,vworkA+l*bs2,bs2*sizeof(MatScalar));
    972:             }
    973:             for (l=imark; l<nzB; l++) {
    974:               PetscMemcpy(vals+(nzA+l)*bs2,vworkB+l*bs2,bs2*sizeof(MatScalar));
    975:             }
    976:             ct2 += ncols;
    977:           }
    978:         }
    979:         MPI_Isend(sbuf_aa_i,req_size[i]*bs2,MPIU_MATSCALAR,req_source[i],tag3,comm,s_waits4+i);
    980:       }
    981:     }
    982:     PetscMalloc((nrqs+1)*sizeof(MPI_Status),&r_status4);
    983:     PetscMalloc((nrqr+1)*sizeof(MPI_Status),&s_status4);
    984:   }
    985:   PetscFree(rbuf1[0]);
    986:   PetscFree(rbuf1);

    988:   /* Form the matrix */
    989:   /* create col map: global col of C -> local col of submatrices */
    990:   {
    991:     const PetscInt *icol_i;
    992: #if defined(PETSC_USE_CTABLE)
    993:     PetscMalloc((1+ismax)*sizeof(PetscTable),&cmap);
    994:     for (i=0; i<ismax; i++) {
    995:       if (!allcolumns[i]) {
    996:         PetscTableCreate(ncol[i]+1,c->Nbs+1,&cmap[i]);
    997:         jmax   = ncol[i];
    998:         icol_i = icol[i];
    999:         cmap_i = cmap[i];
    1000:         for (j=0; j<jmax; j++) {
    1001:           PetscTableAdd(cmap_i,icol_i[j]+1,j+1,INSERT_VALUES);
    1002:         }
    1003:       } else {
    1004:         cmap[i] = NULL;
    1005:       }
    1006:     }
    1007: #else
    1008:     PetscMalloc(ismax*sizeof(PetscInt*),&cmap);
    1009:     for (i=0; i<ismax; i++) {
    1010:       if (!allcolumns[i]) {
    1011:         PetscMalloc(c->Nbs*sizeof(PetscInt),&cmap[i]);
    1012:         PetscMemzero(cmap[i],c->Nbs*sizeof(PetscInt));
    1013:         jmax   = ncol[i];
    1014:         icol_i = icol[i];
    1015:         cmap_i = cmap[i];
    1016:         for (j=0; j<jmax; j++) {
    1017:           cmap_i[icol_i[j]] = j+1;
    1018:         }
    1019:       } else { /* allcolumns[i] */
    1020:         cmap[i] = NULL;
    1021:       }
    1022:     }
    1023: #endif
    1024:   }

    1026:   /* Create lens which is required for MatCreate... */
    1027:   for (i=0,j=0; i<ismax; i++) j += nrow[i];
    1028:   PetscMalloc((1+ismax)*sizeof(PetscInt*)+ j*sizeof(PetscInt),&lens);
    1029:   lens[0] = (PetscInt*)(lens + ismax);
    1030:   PetscMemzero(lens[0],j*sizeof(PetscInt));
    1031:   for (i=1; i<ismax; i++) lens[i] = lens[i-1] + nrow[i-1];

    1033:   /* Update lens from local data */
    1034:   for (i=0; i<ismax; i++) {
    1035:     jmax = nrow[i];
    1036:     if (!allcolumns[i]) cmap_i = cmap[i];
    1037:     irow_i = irow[i];
    1038:     lens_i = lens[i];
    1039:     for (j=0; j<jmax; j++) {
    1040:       if (allrows[i]) row = j;
    1041:       else row = irow_i[j];

    1043: #if defined(PETSC_USE_CTABLE)
    1044:       PetscGetProc(row,size,c->rangebs,&proc);
    1045: #else
    1046:       proc = rtable[row];
    1047: #endif
    1048:       if (proc == rank) {
    1049:         /* Get indices from matA and then from matB */
    1050:         row    = row - rstart;
    1051:         nzA    = a_i[row+1] - a_i[row];     nzB = b_i[row+1] - b_i[row];
    1052:         cworkA =  a_j + a_i[row]; cworkB = b_j + b_i[row];
    1053:         if (!allcolumns[i]) {
    1054: #if defined(PETSC_USE_CTABLE)
    1055:           for (k=0; k<nzA; k++) {
    1056:             PetscTableFind(cmap_i,cstart+cworkA[k]+1,&tt);
    1057:             if (tt) lens_i[j]++;
    1058:           }
    1059:           for (k=0; k<nzB; k++) {
    1060:             PetscTableFind(cmap_i,bmap[cworkB[k]]+1,&tt);
    1061:             if (tt) lens_i[j]++;
    1062:           }

    1064: #else
    1065:           for (k=0; k<nzA; k++) {
    1066:             if (cmap_i[cstart + cworkA[k]]) lens_i[j]++;
    1067:           }
    1068:           for (k=0; k<nzB; k++) {
    1069:             if (cmap_i[bmap[cworkB[k]]]) lens_i[j]++;
    1070:           }
    1071: #endif
    1072:         } else { /* allcolumns */
    1073:           lens_i[j] = nzA + nzB;
    1074:         }
    1075:       }
    1076:     }
    1077:   }
    1078: #if defined(PETSC_USE_CTABLE)
    1079:   /* Create row map*/
    1080:   PetscMalloc((1+ismax)*sizeof(PetscTable),&rmap);
    1081:   for (i=0; i<ismax; i++) {
    1082:     PetscTableCreate(nrow[i]+1,c->Mbs+1,&rmap[i]);
    1083:   }
    1084: #else
    1085:   /* Create row map*/
    1086:   PetscMalloc((1+ismax)*sizeof(PetscInt*)+ ismax*Mbs*sizeof(PetscInt),&rmap);
    1087:   rmap[0] = (PetscInt*)(rmap + ismax);
    1088:   PetscMemzero(rmap[0],ismax*Mbs*sizeof(PetscInt));
    1089:   for (i=1; i<ismax; i++) rmap[i] = rmap[i-1] + Mbs;
    1090: #endif
    1091:   for (i=0; i<ismax; i++) {
    1092:     irow_i = irow[i];
    1093:     jmax   = nrow[i];
    1094: #if defined(PETSC_USE_CTABLE)
    1095:     rmap_i = rmap[i];
    1096:     for (j=0; j<jmax; j++) {
    1097:       if (allrows[i]) {
    1098:         PetscTableAdd(rmap_i,j+1,j+1,INSERT_VALUES);
    1099:       } else {
    1100:         PetscTableAdd(rmap_i,irow_i[j]+1,j+1,INSERT_VALUES);
    1101:       }
    1102:     }
    1103: #else
    1104:     rmap_i = rmap[i];
    1105:     for (j=0; j<jmax; j++) {
    1106:       if (allrows[i]) rmap_i[j] = j;
    1107:       else rmap_i[irow_i[j]] = j;
    1108:     }
    1109: #endif
    1110:   }

    1112:   /* Update lens from offproc data */
    1113:   {
    1114:     PetscInt    *rbuf2_i,*rbuf3_i,*sbuf1_i;
    1115:     PetscMPIInt ii;

    1117:     for (tmp2=0; tmp2<nrqs; tmp2++) {
    1118:       MPI_Waitany(nrqs,r_waits3,&ii,r_status3+tmp2);
    1119:       idex    = pa[ii];
    1120:       sbuf1_i = sbuf1[idex];
    1121:       jmax    = sbuf1_i[0];
    1122:       ct1     = 2*jmax+1;
    1123:       ct2     = 0;
    1124:       rbuf2_i = rbuf2[ii];
    1125:       rbuf3_i = rbuf3[ii];
    1126:       for (j=1; j<=jmax; j++) {
    1127:         is_no  = sbuf1_i[2*j-1];
    1128:         max1   = sbuf1_i[2*j];
    1129:         lens_i = lens[is_no];
    1130:         if (!allcolumns[is_no]) cmap_i = cmap[is_no];
    1131:         rmap_i = rmap[is_no];
    1132:         for (k=0; k<max1; k++,ct1++) {
    1133: #if defined(PETSC_USE_CTABLE)
    1134:           PetscTableFind(rmap_i,sbuf1_i[ct1]+1,&row);
    1135:           row--;
    1136:           if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"row not found in table");
    1137: #else
    1138:           row = rmap_i[sbuf1_i[ct1]];  /* the val in the new matrix to be */
    1139: #endif
    1140:           max2 = rbuf2_i[ct1];
    1141:           for (l=0; l<max2; l++,ct2++) {
    1142:             if (!allcolumns[is_no]) {
    1143: #if defined(PETSC_USE_CTABLE)
    1144:               PetscTableFind(cmap_i,rbuf3_i[ct2]+1,&tt);
    1145:               if (tt) lens_i[row]++;
    1146: #else
    1147:               if (cmap_i[rbuf3_i[ct2]]) lens_i[row]++;
    1148: #endif
    1149:             } else { /* allcolumns */
    1150:               lens_i[row]++;
    1151:             }
    1152:           }
    1153:         }
    1154:       }
    1155:     }
    1156:   }
    1157:   PetscFree(r_status3);
    1158:   PetscFree(r_waits3);
    1159:   if (nrqr) {MPI_Waitall(nrqr,s_waits3,s_status3);}
    1160:   PetscFree(s_status3);
    1161:   PetscFree(s_waits3);

    1163:   /* Create the submatrices */
    1164:   if (scall == MAT_REUSE_MATRIX) {
    1165:     if (ijonly) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP," MAT_REUSE_MATRIX and ijonly is not supported yet");
    1166:     /*
    1167:         Assumes new rows are same length as the old rows, hence bug!
    1168:     */
    1169:     for (i=0; i<ismax; i++) {
    1170:       mat = (Mat_SeqBAIJ*)(submats[i]->data);
    1171:       if ((mat->mbs != nrow[i]) || (mat->nbs != ncol[i] || C->rmap->bs != bs)) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Cannot reuse matrix. wrong size");
    1172:       PetscMemcmp(mat->ilen,lens[i],mat->mbs *sizeof(PetscInt),&flag);
    1173:       if (!flag) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_INCOMP,"Cannot reuse matrix. wrong no of nonzeros");
    1174:       /* Initial matrix as if empty */
    1175:       PetscMemzero(mat->ilen,mat->mbs*sizeof(PetscInt));

    1177:       submats[i]->factortype = C->factortype;
    1178:     }
    1179:   } else {
    1180:     PetscInt bs_tmp;
    1181:     if (ijonly) bs_tmp = 1;
    1182:     else        bs_tmp = bs;
    1183:     for (i=0; i<ismax; i++) {
    1184:       MatCreate(PETSC_COMM_SELF,submats+i);
    1185:       MatSetSizes(submats[i],nrow[i]*bs_tmp,ncol[i]*bs_tmp,nrow[i]*bs_tmp,ncol[i]*bs_tmp);
    1186:       MatSetType(submats[i],((PetscObject)A)->type_name);
    1187:       MatSeqBAIJSetPreallocation(submats[i],bs_tmp,0,lens[i]);
    1188:       MatSeqSBAIJSetPreallocation(submats[i],bs_tmp,0,lens[i]); /* this subroutine is used by SBAIJ routines */
    1189:     }
    1190:   }

    1192:   /* Assemble the matrices */
    1193:   /* First assemble the local rows */
    1194:   {
    1195:     PetscInt  ilen_row,*imat_ilen,*imat_j,*imat_i;
    1196:     MatScalar *imat_a = NULL;

    1198:     for (i=0; i<ismax; i++) {
    1199:       mat       = (Mat_SeqBAIJ*)submats[i]->data;
    1200:       imat_ilen = mat->ilen;
    1201:       imat_j    = mat->j;
    1202:       imat_i    = mat->i;
    1203:       if (!ijonly) imat_a = mat->a;
    1204:       if (!allcolumns[i]) cmap_i = cmap[i];
    1205:       rmap_i = rmap[i];
    1206:       irow_i = irow[i];
    1207:       jmax   = nrow[i];
    1208:       for (j=0; j<jmax; j++) {
    1209:         if (allrows[i]) row = j;
    1210:         else row = irow_i[j];

    1212: #if defined(PETSC_USE_CTABLE)
    1213:         PetscGetProc(row,size,c->rangebs,&proc);
    1214: #else
    1215:         proc = rtable[row];
    1216: #endif
    1217:         if (proc == rank) {
    1218:           row    = row - rstart;
    1219:           nzA    = a_i[row+1] - a_i[row];
    1220:           nzB    = b_i[row+1] - b_i[row];
    1221:           cworkA = a_j + a_i[row];
    1222:           cworkB = b_j + b_i[row];
    1223:           if (!ijonly) {
    1224:             vworkA = a_a + a_i[row]*bs2;
    1225:             vworkB = b_a + b_i[row]*bs2;
    1226:           }
    1227: #if defined(PETSC_USE_CTABLE)
    1228:           PetscTableFind(rmap_i,row+rstart+1,&row);
    1229:           row--;
    1230:           if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"row not found in table");
    1231: #else
    1232:           row = rmap_i[row + rstart];
    1233: #endif
    1234:           mat_i = imat_i[row];
    1235:           if (!ijonly) mat_a = imat_a + mat_i*bs2;
    1236:           mat_j    = imat_j + mat_i;
    1237:           ilen_row = imat_ilen[row];

    1239:           /* load the column indices for this row into cols*/
    1240:           if (!allcolumns[i]) {
    1241:             for (l=0; l<nzB; l++) {
    1242:               if ((ctmp = bmap[cworkB[l]]) < cstart) {
    1243: #if defined(PETSC_USE_CTABLE)
    1244:                 PetscTableFind(cmap_i,ctmp+1,&tcol);
    1245:                 if (tcol) {
    1246: #else
    1247:                 if ((tcol = cmap_i[ctmp])) {
    1248: #endif
    1249:                   *mat_j++ = tcol - 1;
    1250:                   PetscMemcpy(mat_a,vworkB+l*bs2,bs2*sizeof(MatScalar));
    1251:                   mat_a   += bs2;
    1252:                   ilen_row++;
    1253:                 }
    1254:               } else break;
    1255:             }
    1256:             imark = l;
    1257:             for (l=0; l<nzA; l++) {
    1258: #if defined(PETSC_USE_CTABLE)
    1259:               PetscTableFind(cmap_i,cstart+cworkA[l]+1,&tcol);
    1260:               if (tcol) {
    1261: #else
    1262:               if ((tcol = cmap_i[cstart + cworkA[l]])) {
    1263: #endif
    1264:                 *mat_j++ = tcol - 1;
    1265:                 if (!ijonly) {
    1266:                   PetscMemcpy(mat_a,vworkA+l*bs2,bs2*sizeof(MatScalar));
    1267:                   mat_a += bs2;
    1268:                 }
    1269:                 ilen_row++;
    1270:               }
    1271:             }
    1272:             for (l=imark; l<nzB; l++) {
    1273: #if defined(PETSC_USE_CTABLE)
    1274:               PetscTableFind(cmap_i,bmap[cworkB[l]]+1,&tcol);
    1275:               if (tcol) {
    1276: #else
    1277:               if ((tcol = cmap_i[bmap[cworkB[l]]])) {
    1278: #endif
    1279:                 *mat_j++ = tcol - 1;
    1280:                 if (!ijonly) {
    1281:                   PetscMemcpy(mat_a,vworkB+l*bs2,bs2*sizeof(MatScalar));
    1282:                   mat_a += bs2;
    1283:                 }
    1284:                 ilen_row++;
    1285:               }
    1286:             }
    1287:           } else { /* allcolumns */
    1288:             for (l=0; l<nzB; l++) {
    1289:               if ((ctmp = bmap[cworkB[l]]) < cstart) {
    1290:                 *mat_j++ = ctmp;
    1291:                 PetscMemcpy(mat_a,vworkB+l*bs2,bs2*sizeof(MatScalar));
    1292:                 mat_a   += bs2;
    1293:                 ilen_row++;
    1294:               } else break;
    1295:             }
    1296:             imark = l;
    1297:             for (l=0; l<nzA; l++) {
    1298:               *mat_j++ = cstart+cworkA[l];
    1299:               if (!ijonly) {
    1300:                 PetscMemcpy(mat_a,vworkA+l*bs2,bs2*sizeof(MatScalar));
    1301:                 mat_a += bs2;
    1302:               }
    1303:               ilen_row++;
    1304:             }
    1305:             for (l=imark; l<nzB; l++) {
    1306:               *mat_j++ = bmap[cworkB[l]];
    1307:               if (!ijonly) {
    1308:                 PetscMemcpy(mat_a,vworkB+l*bs2,bs2*sizeof(MatScalar));
    1309:                 mat_a += bs2;
    1310:               }
    1311:               ilen_row++;
    1312:             }
    1313:           }
    1314:           imat_ilen[row] = ilen_row;
    1315:         }
    1316:       }
    1317:     }
    1318:   }

    1320:   /*   Now assemble the off proc rows*/
    1321:   {
    1322:     PetscInt    *sbuf1_i,*rbuf2_i,*rbuf3_i,*imat_ilen,ilen;
    1323:     PetscInt    *imat_j,*imat_i;
    1324:     MatScalar   *imat_a = NULL,*rbuf4_i = NULL;
    1325:     PetscMPIInt ii;

    1327:     for (tmp2=0; tmp2<nrqs; tmp2++) {
    1328:       if (ijonly) ii = tmp2;
    1329:       else {
    1330:         MPI_Waitany(nrqs,r_waits4,&ii,r_status4+tmp2);
    1331:       }
    1332:       idex    = pa[ii];
    1333:       sbuf1_i = sbuf1[idex];
    1334:       jmax    = sbuf1_i[0];
    1335:       ct1     = 2*jmax + 1;
    1336:       ct2     = 0;
    1337:       rbuf2_i = rbuf2[ii];
    1338:       rbuf3_i = rbuf3[ii];
    1339:       if (!ijonly) rbuf4_i = rbuf4[ii];
    1340:       for (j=1; j<=jmax; j++) {
    1341:         is_no = sbuf1_i[2*j-1];
    1342:         if (!allcolumns[is_no]) cmap_i = cmap[is_no];
    1343:         rmap_i    = rmap[is_no];
    1344:         mat       = (Mat_SeqBAIJ*)submats[is_no]->data;
    1345:         imat_ilen = mat->ilen;
    1346:         imat_j    = mat->j;
    1347:         imat_i    = mat->i;
    1348:         if (!ijonly) imat_a = mat->a;
    1349:         max1 = sbuf1_i[2*j];
    1350:         for (k=0; k<max1; k++,ct1++) {
    1351:           row = sbuf1_i[ct1];
    1352: #if defined(PETSC_USE_CTABLE)
    1353:           PetscTableFind(rmap_i,row+1,&row);
    1354:           row--;
    1355:           if (row < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"row not found in table");
    1356: #else
    1357:           row = rmap_i[row];
    1358: #endif
    1359:           ilen  = imat_ilen[row];
    1360:           mat_i = imat_i[row];
    1361:           if (!ijonly) mat_a = imat_a + mat_i*bs2;
    1362:           mat_j = imat_j + mat_i;
    1363:           max2  = rbuf2_i[ct1];

    1365:           if (!allcolumns[is_no]) {
    1366:             for (l=0; l<max2; l++,ct2++) {
    1367: #if defined(PETSC_USE_CTABLE)
    1368:               PetscTableFind(cmap_i,rbuf3_i[ct2]+1,&tcol);
    1369:               if (tcol) {
    1370: #else
    1371:               if ((tcol = cmap_i[rbuf3_i[ct2]])) {
    1372: #endif
    1373:                 *mat_j++ = tcol - 1;
    1374:                 if (!ijonly) {
    1375:                   PetscMemcpy(mat_a,rbuf4_i+ct2*bs2,bs2*sizeof(MatScalar));
    1376:                   mat_a += bs2;
    1377:                 }
    1378:                 ilen++;
    1379:               }
    1380:             }
    1381:           } else { /* allcolumns */
    1382:             for (l=0; l<max2; l++,ct2++) {
    1383:               *mat_j++ = rbuf3_i[ct2];
    1384:               if (!ijonly) {
    1385:                 PetscMemcpy(mat_a,rbuf4_i+ct2*bs2,bs2*sizeof(MatScalar));
    1386:                 mat_a += bs2;
    1387:               }
    1388:               ilen++;
    1389:             }
    1390:           }
    1391:           imat_ilen[row] = ilen;
    1392:         }
    1393:       }
    1394:     }
    1395:   }
    1396:   if (!ijonly) {
    1397:     PetscFree(r_status4);
    1398:     PetscFree(r_waits4);
    1399:     if (nrqr) {MPI_Waitall(nrqr,s_waits4,s_status4);}
    1400:     PetscFree(s_waits4);
    1401:     PetscFree(s_status4);
    1402:   }

    1404:   /* Restore the indices */
    1405:   for (i=0; i<ismax; i++) {
    1406:     if (!allrows[i]) {
    1407:       ISRestoreIndices(isrow[i],irow+i);
    1408:     }
    1409:     if (!allcolumns[i]) {
    1410:       ISRestoreIndices(iscol[i],icol+i);
    1411:     }
    1412:   }

    1414:   /* Destroy allocated memory */
    1415: #if defined(PETSC_USE_CTABLE)
    1416:   PetscFree4(irow,icol,nrow,ncol);
    1417: #else
    1418:   PetscFree5(irow,icol,nrow,ncol,rtable);
    1419: #endif
    1420:   PetscFree4(w1,w2,w3,w4);
    1421:   PetscFree(pa);

    1423:   PetscFree4(sbuf1,ptr,tmp,ctr);
    1424:   PetscFree(sbuf1);
    1425:   PetscFree(rbuf2);
    1426:   for (i=0; i<nrqr; ++i) {
    1427:     PetscFree(sbuf2[i]);
    1428:   }
    1429:   for (i=0; i<nrqs; ++i) {
    1430:     PetscFree(rbuf3[i]);
    1431:   }
    1432:   PetscFree3(sbuf2,req_size,req_source);
    1433:   PetscFree(rbuf3);
    1434:   PetscFree(sbuf_aj[0]);
    1435:   PetscFree(sbuf_aj);
    1436:   if (!ijonly) {
    1437:     for (i=0; i<nrqs; ++i) {PetscFree(rbuf4[i]);}
    1438:     PetscFree(rbuf4);
    1439:     PetscFree(sbuf_aa[0]);
    1440:     PetscFree(sbuf_aa);
    1441:   }

    1443: #if defined(PETSC_USE_CTABLE)
    1444:   for (i=0; i<ismax; i++) {
    1445:     PetscTableDestroy((PetscTable*)&rmap[i]);
    1446:   }
    1447: #endif
    1448:   PetscFree(rmap);

    1450:   for (i=0; i<ismax; i++) {
    1451:     if (!allcolumns[i]) {
    1452: #if defined(PETSC_USE_CTABLE)
    1453:       PetscTableDestroy((PetscTable*)&cmap[i]);
    1454: #else
    1455:       PetscFree(cmap[i]);
    1456: #endif
    1457:     }
    1458:   }
    1459:   PetscFree(cmap);
    1460:   PetscFree(lens);

    1462:   for (i=0; i<ismax; i++) {
    1463:     MatAssemblyBegin(submats[i],MAT_FINAL_ASSEMBLY);
    1464:     MatAssemblyEnd(submats[i],MAT_FINAL_ASSEMBLY);
    1465:   }

    1467:   c->ijonly = PETSC_FALSE; /* set back to the default */
    1468:   return(0);
    1469: }